Achieving agile, efficient, and robust locomotion in bipedal robots remains a grand challenge of robotics. Traditional model-based control methods are theoretically grounded but are often sensitive to model mismatch and state-estimation uncertainty, limiting their adaptability to real-world environments. Conversely, data-driven approaches such as reinforcement learning produce remarkable behaviors but often lack interpretability, require non-trivial reward shaping, and raise safety concerns.
\r\n\r\nThis thesis bridges these two paradigms through a unified framework that begins with model-based behavior synthesis and culminates in data-driven adaptation. The first part focuses on constructing walking behaviors and controllers using reduced-order models of locomotion. A hierarchy of planners and controllers is developed to enable robust walking for flat-footed and multi-domain gaits, as well as safety-critical locomotion over constrained footholds such as stairs and stepping stones. Additionally, this work introduces RoMoCo, a modular open-source architecture, a modular open-source architecture designed to unify reduced-order planning, output synthesis, and whole-body control across multiple bipedal platforms.
\r\n\r\nBuilding on this foundation, the second part introduces data-driven mechanisms that enable robots to improve and personalize their behaviors through various forms of data. Episodic data collected during repeated executions are used to correct modeling errors and reduce constraint violations. Human preference data facilitates automatic gain tuning through interactive feedback. Online robot data enables adaptation of reduced-order models by learning step-to-step dynamics directly from real executions. Finally, large-scale simulation data support a reinforcement-learning framework designed for hardware deployment, where model-guided rewards enable efficient training and introduce perception inputs, yielding policies capable of dynamic stepping-stone traversal on real robots.
\r\n\r\nTogether, these contributions form a progression from theoretically grounded model-based control to data-enabled adaptation, demonstrating that reduced-order models and data-driven learning are complementary. Their integration enables bipedal robots such as Cassie and G1 to walk safely, robustly, and efficiently across diverse terrains, marking a step toward human-level agility in legged locomotion.
", "doi": "10.7907/e1sk-7771", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18519", "collection": "thesis", "collection_id": "18519", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04282026-200138296", "type": "thesis", "title": "Synthetic Control of the Biological Central Dogma", "author": [ { "family_name": "Gerber", "given_name": "Bryan Michael", "orcid": "0000-0002-3979-1095", "clpid": "Gerber-Bryan-Michael" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Kaihang", "orcid": "0000-0001-7657-8755", "clpid": "Wang-Kaihang" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Wang", "given_name": "Kaihang", "orcid": "0000-0001-7657-8755", "clpid": "Wang-Kaihang" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The Central Dogma of biology dictates the flow of information within all living organisms. By focusing on the construction of synthetic DNA, the transcription of target RNA, and the translation of select proteins, we can improve the synthetic control of engineered organisms. Prioritizing the mis-connection rate present when attaching two DNA molecules, I propose two conceptual improvements to DNA assembly technologies. The high efficiency of the first technique, called Sidewinder, is demonstrated through the construction of a GFP mutation library from DNA oligos, whose diversity is confirmed by high-fidelity sequencing and functional phenotypic analysis. The second DNA assembly technique, High Temperature (HighT) assembly, is demonstrated by high efficiency plasmid ligation, direct integration into bacterial genomes by two independent recombinase HighT assembly-to-integration systems, and the construction of multiple eukaryotic genes including MAPT, VEGFA, BRCA1 and the Sonic Hedgehog embryonic development gene 10-kB genomic DNA segment from the functionally extinct Northern White Rhino. Applications of synthetic DNA are then explored through the import of orthogonal transcription and translation molecular machinery into cells, where they directly regulate protein production. On the transcription level, variations in inducible split-T7 polymerase systems are used to create an orthogonal signaling pathway for low leak and tunable transcriptional control of target genes. Unnatural amino acid incorporation is used to translationally regulate genomically modified essential genes, where exposure to this molecule is demonstrated to enable translation of select essential genes. Through the lens of the Central Dogma, in this thesis I will explore various frameworks to build and fine tune the cells we may aspire to create.", "doi": "10.7907/1t51-1e91", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17647", "collection": "thesis", "collection_id": "17647", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08252025-232825764", "primary_object_url": { "basename": "Manisha_Kapasiawala_Caltech_PhD_Thesis.pdf", "content": "final", "filesize": 35470940, "license": "other", "mime_type": "application/pdf", "url": "/17647/1/Manisha_Kapasiawala_Caltech_PhD_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Design Considerations for Synthetic Cells", "author": [ { "family_name": "Kapasiawala", "given_name": "Manisha Kaushik", "orcid": "0000-0002-0302-2921", "clpid": "Kapasiawala-Manisha-Kaushik" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Voorhees", "given_name": "Rebecca M.", "orcid": "0000-0003-1640-2293", "clpid": "Voorhees-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Efforts to understand life as we know it and life as it can be have culminated in the field of synthetic cell research, which aims to build life from the bottom up using individual biological components. Recent progress in the field has enabled the reconstitution of many functions of living cells in synthetic cells, from cell-cell communication to membrane protein expression and function. However, future progress in the field is limited by many challenges, including irreproducibility, lack of predictability, difficulties in integrating existing synthetic cell modules (or subsystems), and the need for autonomous functionalities.
\r\n\r\nIn this work, I describe my efforts towards addressing these challenges. In Chapter 2, I describe sources of variability in transcription-translation (TX-TL) systems, the biological machinery used to implement biomolecular programs in synthetic cells. In Chapter 3, I describe a novel methodology for readily building more predictive models of TX-TL performance. In Chapter 4, I present a design for a proof-of-concept for integrating an energy regeneration subsystem and a motility subsystem to achieve autonomous programmable motility and highlight some early successes towards achieving that goal. Throughout this work, I highlight many design principles for building synthetic cells reproducibly, more predictably, and with novel functionalities.
", "doi": "10.7907/zfhy-bk03", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17643", "collection": "thesis", "collection_id": "17643", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08212025-191338101", "primary_object_url": { "basename": "olson_blade_2026_thesis.pdf", "content": "final", "filesize": 8714374, "license": "other", "mime_type": "application/pdf", "url": "/17643/6/olson_blade_2026_thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Synthetic Antigen-Presenting Vesicles for Selective Immunomodulation", "author": [ { "family_name": "Olson", "given_name": "Blade A.", "orcid": "0000-0002-1526-1399", "clpid": "Olson-Blade-A" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The rapid advancement of generative artificial intelligence has enabled unprecedented progress for the field of computational protein design. A forthcoming challenge for generative protein design algorithms is the immunocompatibility of these de novo designed molecules with organism physiology, namely humans. A separate, but related, aspirational goal for synthetic biology is to perform cellular reprogramming in vivo so that cell-based therapies and biologics are generated endogenously by patients rather than being externally manufactured or expanded before delivery, as is the case with biologics, T cell therapies, and stem cell therapies; again, a major hurdle for the in vivo production of these therapies and in vivo cellular reprogramming is immunogenicity.
\r\n\r\nTo address these challenges, we first demonstrate a cell-like, cell-free approach for in vivo cellular reprogramming with the induced release of pMHCI and pMHCII-loaded synthetic antigen-presenting vesicles that are secreted from non-immune cells by DNA and mRNA transfection to facilitate the selective expansion or silencing of immune responses. Next, we show initial results for the use of human tonsil organoids as a quantitative assay for adenoviral vector immunogenicity, enabling future directed evolution approaches for immunogenicity reduction as well as generation of an immunogenicity dataset to tailor modern computational protein design algorithms for human immunocompatibility. Together, these projects represent complementary methods to control protein immunogenicity, either through rationally engineered or directedly evolved modifications identified by physiologically-relevant in vitro models, or with an administered mRNA therapeutic that selectively modifies the immune response to a protein that cannot be computationally redesigned.
", "doi": "10.7907/fxzx-yn04", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17771", "collection": "thesis", "collection_id": "17771", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11242025-191228061", "type": "thesis", "title": "Naturally-Inspired Circuits for Microbial Composition Control and Biosensing", "author": [ { "family_name": "Kratz", "given_name": "Matthieu Francois", "clpid": "Kratz-Matthieu-Francois" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Demirer", "given_name": "G\u00f6zde S.", "orcid": "0000-0002-3007-1489", "clpid": "Demirer-G\u00f6zde-S" }, { "family_name": "Hay", "given_name": "Bruce A.", "orcid": "0000-0002-5486-0482", "clpid": "Hay-B-A" }, { "family_name": "Bois", "given_name": "Justin S.", "orcid": "0000-0001-7137-8746", "clpid": "Bois-J-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "When considering the design of gene circuits, there are many possible sources of inspiration. Many early synthetic gene circuits used nature as an inspiration, seeking to recreate biological behaviors with non-native components. As the field grew, alternative approaches sourcing designs from adjacent engineering fields and computational approaches emerged and grew in prominence. Despite this shift, there remains a great deal of naturally-inspired circuits that provide useful functions for biotechnology. Indeed nature has often been uniquely capable of exploiting typically undesirable phenomena, e.g. noise to create biologically useful function. This thesis presents two projects directly inspired by natural systems. Each project aims to replicate a behavior or circuit topology found in nature, leveraging its unique dynamics to address key challenges in biotechnology. Chapters 2 and 3 will cover the development of a circuit emulating the microbial behavior of phase variation, whereby individual cells reversibly and stochastically transition between distinct phenotypes. We recreate this behavior using serine recombinases and demonstrate how it can enable stable, bulk control of phenotype composition\u2014a task of great relevance to biotechnology. Chapter 4 lays the groundwork for applying the biologically-relevant feed-forward loop topology to the problem of spurious biosensor activation. We realize this topology in a modular manner using small transcription activating RNAs (STARs) and provide a preliminary characterization of its dynamical properties. Finally, we discuss alternative implementations that may provide more directly applicable properties than the current STAR implementation", "doi": "10.7907/d42b-jh46", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17682", "collection": "thesis", "collection_id": "17682", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09162025-184128136", "primary_object_url": { "basename": "Subramanian_Arjuna_thesis_vFINAL.pdf", "content": "final", "filesize": 98788613, "license": "other", "mime_type": "application/pdf", "url": "/17682/1/Subramanian_Arjuna_thesis_vFINAL.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Rewriting the Sequence and Structure Rules of Deep Protein Space", "author": [ { "family_name": "Subramanian", "given_name": "Arjuna Michael", "orcid": "0009-0004-2790-0209", "clpid": "Subramanian-Arjuna-Michael" } ], "thesis_advisor": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "With a 20-letter alphabet, conceivable protein sequence-space is enormous; sparks of structure and function are vanishingly rare. Despite massive advances in AI-guided protein design, we remain largely ignorant of the sequences and structures that populate the depths of protein space more than a handful of mutations away from what nature has tried. In this work, we leverage the potential of one specific class of AI protein model \u2014 the protein language model, or PLM \u2014 to internalize the essential features of the protein sequence-structure map while retaining the capacity to explore its extremes. Guided by a \"novelty first, fitness next\" mentality, we harness this balance towards systematic discovery of new-to-nature sequences and structures throughout deep protein space.
\r\n\r\nIn the first section, we dissect the ability of PLMs to explore natural and novel regimes of sequence and structure during free generation. We find that while these models readily emit novel sequences encoding artificial proteins that appear biophysically feasible in silico, they fail to completely or representatively capture the known distribution of natural protein structures. We expose a fundamental tradeoff between the ability of a PLM to generate with sequence novelty or structural coverage but not both simultaneously; prioritizing sampling of far-from-natural sequences triggers a collapse to a handful of simple structural motifs and disordered regions.
\r\n\r\nTurning this sequence novelty vs. structural breadth tradeoff to our advantage, the second section is devoted to the development of \"foldtuning\" \u2014 a structure-preserving, sequence-remodeling engine for navigating the far corners of sequence-space with PLM-based probes. We successfully scale and deploy foldtuning for >700 targets, pushing artificial sequences past the point of detectable homology to any real protein documented in nature, discovering novel sequence-level semantics and grammar for mimicking known protein folds, and accessing potential reservoirs of downstream structural and functional innovation. Experimental validation of select targets reveals that foldtuning produces realizable and functional binders in contexts including a toxin/antitoxin system and peptide hormone signaling.
\r\n\r\nShifting to focus on structural novelty, the final section introduces two PLM-driven methods for the discovery of new-to-nature structures. We show that with appropriate steering functions, PLMs readily yield well-structured domains (featuring diverse secondary and supersecondary elements) outside the several thousand such families cataloged from among known proteins. Overall, this work makes substantial inroads towards the challenge of locating viable far-from-natural regions of protein density across the global sequence-structure map, and revises our notions of the physical constraints on sequence and structure in valid proteins. Moreover, it sets the stage for future assembly of synthetic biological systems composed fully of new-to-nature parts and ultimately for modeling efforts that close the design loop from sequence all the way to complex phenotype.
", "doi": "10.7907/p4st-m614", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17747", "collection": "thesis", "collection_id": "17747", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11032025-192332480", "primary_object_url": { "basename": "phd_thesis_submission.pdf", "content": "final", "filesize": 32786900, "license": "other", "mime_type": "application/pdf", "url": "/17747/1/phd_thesis_submission.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Leveraging Aerial Transformation for Enhanced Air\u2013Ground Robotic Mobility", "author": [ { "family_name": "Mandralis", "given_name": "Ioannis M.", "orcid": "0000-0001-5270-0672", "clpid": "Mandralis-Ioannis-M" } ], "thesis_advisor": [ { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Ground-aerial robots can extend endurance, versatility, and robustness by combining wheeled motion with flight, yet many flying-rolling robot designs add actuators that increase weight and reduce efficiency. Morphobots mitigate this by using multi-purpose actuators and body shape change to switch modes on the ground, but unpredictable vehicle-ground interactions can be an obstacle to robust operation. This dissertation develops the Aerially Transforming Morphobot (ATMO), a quadcopter that reconfigures in flight to land on wheels, enabling reliable air-ground transitions, mode switching without the hindrances of ground-morphing, and improved agility. We present ATMO\u2019s design and performance characterization, analyze its dynamics\u2013revealing transformation-induced couplings incompatible with standard quadcopter control\u2013and introduce a model-predictive control framework that stabilizes ATMO through aerial transformation to execute dynamic transitions. We then compare this approach with a learning-based controller that uses deep reinforcement learning for end-to-end morpho-transition, validating both experimentally. Finally, we revisit ATMO\u2019s design using aerodynamic principles to expand morphing flight through wake vectoring, showing that passive structures in the rotor wake substantially increase available thrust authority. Overall, we demonstrate that aerial shape change improves agility and reliability, highlighting a new direction for research in ground-aerial robotics.", "doi": "10.7907/srg8-sx98", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18770", "collection": "thesis", "collection_id": "18770", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022026-081334128", "type": "thesis", "title": "Tokens, Topologies, Taxa: Towards Declarative Biology and Bioengineering", "author": [ { "family_name": "Martinez", "given_name": "Zachary A.", "orcid": "0000-0002-7830-3162", "clpid": "Martinez-Zachary-A" } ], "thesis_advisor": [ { "family_name": "Thomson", "given_name": "Matthew W.", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" }, { "family_name": "Wang", "given_name": "Kaihang", "orcid": "0000-0001-7657-8755", "clpid": "Wang-Kaihang" }, { "family_name": "Bois", "given_name": "Justin", "orcid": "0000-0001-7137-8746", "clpid": "Bois-Justin" }, { "family_name": "Thomson", "given_name": "Matthew W.", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Contemporary deep-learning models for the life-sciences have outpaced the tooling that lets experimentalists compose them. Three contributions are presented in response, a software platform, exemplary tasks built on it, and a predicted structural proteome of a defined gut microbiome. The underlying argument is that for experimentalists who use rather than build deep-learning methods, difficulties with composition and usability now outpace availability.
\r\n\r\nTRILL, a platform for AI-based protein engineering and analysis, is open-source, runs locally, and wraps models/methods behind a uniform vocabulary of thirteen top-level commands. Furthermore, TRILL is scalable, ranging from parallel fine-tuning of large models on a supercomputer to democratized, parameter off-loading in compute-limited scenarios. Models can be swapped with a one-argument change rather than a pipeline rewrite, and fast predictions can be paired with physics-based validation where overconfidence costs most.
\r\n\r\nProtein language models were fine-tuned using a homology-aware strategy, decreasing data leakage when evaluating generated proteins. Classifiers for cellulase, antimicrobial, and toxin activity were trained and applied to a scan of over two hundred million proteins from the NCBI non-redundant catalogue. An end-to-end pipeline carried seventeen predicted toxins of unknown function through structure prediction, binder design, and molecular dynamics on nearly nine hundred designed complexes.
\r\n\r\nThe third contribution targets hCom2, a defined synthetic gut consortium. We present a structural resource, where roughly four hundred thousand structures of its proteome were predicted using TRILL, segmented into eight hundred thousand domains, and assigned CATH designations. A case study demonstrating the utility of this structural database identifies nineteen carriers of the Helicobacter pylori virulence-factor TIPalpha fold across fourteen strains where sequence-only annotation fails.
", "doi": "10.7907/b5ye-jy33", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17182", "collection": "thesis", "collection_id": "17182", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292025-041809434", "primary_object_url": { "basename": "fzl_thesis_final.pdf", "content": "final", "filesize": 29018197, "license": "other", "mime_type": "application/pdf", "url": "/17182/1/fzl_thesis_final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Evaluation of the Generalizability of Machine Learning-Assisted Protein Engineering Methods", "author": [ { "family_name": "Li", "given_name": "Francesca-Zhoufan", "orcid": "0000-0002-5710-9512", "clpid": "Li-Francesca-Zhoufan" } ], "thesis_advisor": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Yang", "given_name": "Kevin K.", "orcid": "0000-0001-9045-6826", "clpid": "Yang-Kevin-K" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Engineered proteins can carry out a vast array of functions and have become indispensable across numerous industrial applications. To accelerate wet-lab protein engineering efforts, machine learning-based methods have advanced rapidly. However, a gap remains between state-of-the-art machine learning methods and their practical adoption. A key factor contributing to this disconnect is the lack of application-relevant benchmarking and generalizable insights across protein engineering tasks. This thesis evaluates machine learning-assisted protein engineering approaches to identify generalizable strategies. The central problem considered is learning the mapping from protein sequence to function\u2014known as the fitness landscape\u2014to enable the prediction of unseen variant fitness. Chapter 1 introduces the background and context for machine learning-assisted protein engineering and highlights the practical constraint of limited experimental budgets. Chapter 2 investigates transfer learning, which leverages models pretrained on large protein sequence databases to generate informative representations for modeling task specific sequence-function relationships. Evaluation across ten diverse tasks shows that while transfer learning is effective in structure prediction, it underperforms in variant fitness prediction\u2014a key objective in protein engineering. Chapter 3 evaluates alternative strategies with a focus on combinatorial fitness landscapes, a common setting in protein engineering. Across 16 diverse landscapes, focused training improves the performance of various machine learning approaches by strategically selecting training variants using zero-shot predictors, which estimate variant fitness from auxiliary information without relying on experimental data. Building on these insights, Chapter 4 addresses the specific challenge of engineering enzymes\u2014proteins that convert substrates into products\u2014for novel chemistries. While six general zero-shot predictors without substrate information can predict enzyme activity on non-native substrates, they fail on more out-of-distribution, new-to-nature chemistries. Incorporating substrate information into zero-shot predictors leads to more generalizable performance across all tested chemistries, spanning 22 substrates. Overall, this thesis identifies generalizable strategies for machine learning-assisted protein engineering by systematically evaluating and improving how sequence-to-function relationships are modeled across diverse tasks.", "doi": "10.7907/yzb2-cb66", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17425", "collection": "thesis", "collection_id": "17425", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06092025-020707222", "type": "thesis", "title": "Perception-Driven Autonomy and Learning Control for Ground Vehicles", "author": [ { "family_name": "Lupu", "given_name": "Elena Sorina", "orcid": "0000-0002-3968-2630", "clpid": "Lupu-Elena-Sorina" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Hadaegh", "given_name": "Fred", "orcid": "0000-0002-0992-6323", "clpid": "Fred-Hadaegh" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Autonomous robots are widely recognized as highly valuable and are expected to become increasingly prevalent. They will play a critical role across a wide range of terrestrial applications in complex, unstructured environments, as well as in space, supporting infrastructure and exploration on various bodies throughout the solar system and beyond. Looking ahead, autonomous robots will play a crucial role in the search for extraterrestrial life by enabling exploration of remote and extreme environments beyond Earth.\r\nAs robots need to approach more complex tasks, the ability to rapidly perceive, understand, make real-time decisions, and operate at speed requires advances in perception-driven controls, improved predictability, and robustness to disturbances. \r\nTo enable these capabilities, the first part of this thesis proposes an innovative approach to enhancing ground vehicle mobility by integrating a vision-based control algorithm that adapts to changes in real-time. \r\nOur approach improves the vehicle's ability to assess and respond to complex terrains in real-time by leveraging visual information through visual foundation models and meta-learning.\r\nOur controller has provable guarantees of exponential stability and was validated on board two ground vehicles.\r\nNext, an extension of the previously mentioned method applied to detecting objects in space using a visual foundation model is presented. Our method was successfully demonstrated in space in early 2025 aboard the EdgeNode Lite spacecraft.\r\nEfficient operation comes from the synergy of suitable autonomy and control with a suitable robot body.\r\nFollowing this consideration, the second part of the thesis presents the design and control of multi-degrees of freedom robots designed for mobility in complex environments.\r\nIt presents a nonlinear tracking controller with adaptation to improve the walking performance of walking-flying robots. This is illustrated by our implementation on Leonardo, the first robot to combine walking with flying to create a new type of locomotion, which we showcase in complex acrobatic movements such as slacklining and skateboarding.\r\nIn a second case study, we aim to further understand and improve biped walking by introducing a bipedal robot designed to be lightweight, easily manufactured, and easily repaired, serving as a platform for testing learning-based controllers.\r\nWe introduce and demonstrate the performance of two controllers: a model-based and a learning-based control.\r\nThis work highlights the importance of tightly integrated perception, control, and electromechanical design in achieving robust autonomy: on Earth, in orbit, and beyond.", "doi": "10.7907/79tk-eg16", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17345", "collection": "thesis", "collection_id": "17345", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012025-210705210", "type": "thesis", "title": "Domestication of Environmental Bacteria for Biosensing Applications", "author": [ { "family_name": "Larsson", "given_name": "Elin Maria", "orcid": "0000-0003-1341-5937", "clpid": "Larsson-Elin-Maria" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Hay", "given_name": "Bruce A.", "orcid": "0000-0002-5486-0482", "clpid": "Hay-B-A" }, { "family_name": "Cao", "given_name": "Mengyi", "orcid": "0000-0002-3117-3401", "clpid": "Cao-Mengyi" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The field of synthetic biology has made impressive progress in the past 25 years, but is still lacking when it comes to our capability to predictably engineer organisms outside of a small group of lab model organisms. In this thesis, I present the efforts to domesticate two soil bacteria important in agriculture for biosensing. The first, Pseudomonas synxantha, a wheat-colonizing bacterium that helps fight off fungal disease, was engineered into a bioreporter for phosphorus limitation. We also made cell-free extract from this organism, to enable rapid characterization of genetic elements. For the second, Xenorhabdus griffiniae, we asked the question of whether this bacterium can sense the presence of its entomopathogenic nematode host Steinernema hermaphroditum. We learned that X. griffiniae is able to sense its host and we were able to build an early variant of a nematode reporter by first characterizing genetic elements in X. griffiniae.", "doi": "10.7907/m077-7633", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17024", "collection": "thesis", "collection_id": "17024", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02252025-021704066", "primary_object_url": { "basename": "_Thesis Final Final Draft.pdf", "content": "final", "filesize": 52470568, "license": "other", "mime_type": "application/pdf", "url": "/17024/1/_Thesis Final Final Draft.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Planning for an Uncertain Future: Tree-Based Methods for Real-Time Fault Estimation, Collision Avoidance, and Multi-Agent Reconfiguration", "author": [ { "family_name": "Ragan", "given_name": "James Francis, III", "orcid": "0009-0005-5680-9794", "clpid": "Ragan-James-Francis-III" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Watkins", "given_name": "Michael M.", "clpid": "Watkins-M-M" }, { "family_name": "Hadaegh", "given_name": "Fred Y.", "orcid": "0000-0002-0992-6323", "clpid": "Hadaegh-F-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "Autonomous Robotics and Control Lab" }, { "literal": "div_eng" } ], "abstract": "Autonomous spacecraft making independent high-level decisions present the promise of dramatically increased productivity in space for both exploration and economic activity. While autonomy has seen limited use in space to date owing to a lack of flight heritage, limited computational resources, and a traditionally risk adverse industry, the growing numbers of spacecraft and increasingly ambitious missions will soon render the current ground-intensive mode of space operation untenable.
\r\n \r\nIn this thesis, we develop two critical capabilities for an autonomous future in space. The first is proactive fault estimation, which seeks to rapidly and safely identify the root causes of onboard anomalies by planning sequences of test actions to gather information while probabilistically ensuring safety. The second is real-time reconfiguration to enable formations of spacecraft to respond quickly and effectively to changing environments or mission objectives.
\r\n\r\nWe achieve both goals using various forms of Monte-Carlo Tree Search planning. By formalizing each capability as sequential decision-making problems, and developing algorithms well suited to information gathering, we show that our algorithms provably converge to optimal solutions while maintaining the ability to run in real-time on robotic spacecraft simulators. We present several algorithmic innovations, including marginalized filtering, sampling-based chance constraint evaluation, and an array-based implementation of Monte-Carlo Tree Search. Through and numerical simulations and hardware experiments, we demonstrate that these modifications enable our algorithms to outperform existing tree search methods and achieve better scaling across system complexity, noise, and simulation depth.
", "doi": "10.7907/ptpk-d504", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17024", "collection": "thesis", "collection_id": "17024", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02252025-021704066", "primary_object_url": { "basename": "_Thesis Final Final Draft.pdf", "content": "final", "filesize": 52470568, "license": "other", "mime_type": "application/pdf", "url": "/17024/1/_Thesis Final Final Draft.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Planning for an Uncertain Future: Tree-Based Methods for Real-Time Fault Estimation, Collision Avoidance, and Multi-Agent Reconfiguration", "author": [ { "family_name": "Ragan", "given_name": "James Francis, III", "orcid": "0009-0005-5680-9794", "clpid": "Ragan-James-Francis-III" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Watkins", "given_name": "Michael M.", "clpid": "Watkins-M-M" }, { "family_name": "Hadaegh", "given_name": "Fred Y.", "orcid": "0000-0002-0992-6323", "clpid": "Hadaegh-F-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "Autonomous Robotics and Control Lab" }, { "literal": "div_eng" } ], "abstract": "Autonomous spacecraft making independent high-level decisions present the promise of dramatically increased productivity in space for both exploration and economic activity. While autonomy has seen limited use in space to date owing to a lack of flight heritage, limited computational resources, and a traditionally risk adverse industry, the growing numbers of spacecraft and increasingly ambitious missions will soon render the current ground-intensive mode of space operation untenable.
\r\n \r\nIn this thesis, we develop two critical capabilities for an autonomous future in space. The first is proactive fault estimation, which seeks to rapidly and safely identify the root causes of onboard anomalies by planning sequences of test actions to gather information while probabilistically ensuring safety. The second is real-time reconfiguration to enable formations of spacecraft to respond quickly and effectively to changing environments or mission objectives.
\r\n\r\nWe achieve both goals using various forms of Monte-Carlo Tree Search planning. By formalizing each capability as sequential decision-making problems, and developing algorithms well suited to information gathering, we show that our algorithms provably converge to optimal solutions while maintaining the ability to run in real-time on robotic spacecraft simulators. We present several algorithmic innovations, including marginalized filtering, sampling-based chance constraint evaluation, and an array-based implementation of Monte-Carlo Tree Search. Through and numerical simulations and hardware experiments, we demonstrate that these modifications enable our algorithms to outperform existing tree search methods and achieve better scaling across system complexity, noise, and simulation depth.
", "doi": "10.7907/ptpk-d504", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16465", "collection": "thesis", "collection_id": "16465", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022024-014038700", "primary_object_url": { "basename": "ApurvaBadithela_June2024.pdf", "content": "final", "filesize": 96248118, "license": "other", "mime_type": "application/pdf", "url": "/16465/9/ApurvaBadithela_June2024.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Test and Evaluation of Autonomous Systems: Reactive Test Synthesis and Task-Relevant Evaluation of Perception", "author": [ { "family_name": "Badithela", "given_name": "Apurva Srinivas", "orcid": "0000-0002-9788-2702", "clpid": "Apurva-Apurva-Srinivas" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Chandy", "given_name": "K. Mani", "orcid": "0000-0001-9190-1290", "clpid": "Chandy-K-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-Tichakorn" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Autonomous robotic systems have potential for profound impact on our society -- legged and wheeled robots for search and rescue missions, drones for wildfire management, self-driving cars for improving mobility, and robotic space missions for exploration and repair of spacecraft. The complexity of these systems implies that formal guarantees during the design phase alone is not sufficient; mainstream deployment of these systems requires principled frameworks for test and evaluation, and verification and validation. This thesis studies two such challenges to mainstream deployment of these systems.
\r\n\r\nFirst, we consider the problem of evaluating perception models in a manner relevant to the system-level specification and the downstream planner. Perception and planning modules are often designed under different computational and mathematical paradigms. This talk will focus on evaluating models for classification and detection tasks, and leverages confusion matrices which are popularly used in computer vision to evaluate object detection models to derive probabilistic guarantees at the system-level. However, not all perception errors are equally safety-critical, and traditional confusion matrices account for all objects equally. Thus, task-relevant metrics such as proposition labeled confusion matrices are introduced. These are constructed by identifying propositional formulas relevant to the downstream planning logic and the system-level specification, and result in less conservative system-level guarantees. Using this analysis, fundamental tradeoffs in perception models are reflected in the tradeoffs of probabilistic guarantees. This framework is illustrated on a car-pedestrian example in simulation, and the confusion matrices are constructed from state-of-the-art detection models evaluated on the nuScenes dataset.
\r\n\r\nSecond, we consider the problem of automatically synthesizing tests for autonomous robotic systems. These systems reason over both discrete (e.g., navigate left or right around an obstacle) and continuous variables (e.g., continuous trajectories). This talk presents a flow-based approach for test environment synthesis which handles discrete variables and is also reactive to the system under test. Reactivity is important to account for uncertainties in system modeling, and to adapt to system behavior without knowledge of the system controller. These tests are synthesized from high-level specifications of desired behavior. Though the problem is shown to be NP-hard, a flow-based mixed-integer linear program formulation is used that scales well to medium-sized examples (e.g., >10,000 integer variables). The test environment can consist of static and reactive obstacles as well as dynamic test agents, whose strategies are synthesized to match the solution of the flow-based optimization. The overview of the approach is as follows. First, principles of automata theory are used to translate the high-level system and test objectives, and the non-deterministic abstraction of the system into a network flow optimization. The solution of this optimization is then parsed into GR(1) formulas in linear temporal logic. This GR(1) formula is used to synthesize reactive strategies of a dynamic test agent in a counterexample-guided fashion. We provide guarantees that the synthesized test strategy will realize the desired test behavior under the assumption of a well-designed system, the test strategy is reactive and least-restrictive,. This framework is illustrated on several simulation and hardware experiments with quadrupeds, showing promise towards a layered approach to test and evaluation.
", "doi": "10.7907/e8qz-rd26", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16453", "collection": "thesis", "collection_id": "16453", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312024-094443866", "primary_object_url": { "basename": "JGraebener_thesis_1.pdf", "content": "final", "filesize": 26529382, "license": "other", "mime_type": "application/pdf", "url": "/16453/1/JGraebener_thesis_1.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Formal Methods for Test and Evaluation: Reasoning over Tests, Automated Test Synthesis, and System Diagnostics", "author": [ { "family_name": "Graebener", "given_name": "Josefine Berta Marie", "orcid": "0000-0002-1376-0741", "clpid": "Graebener-Josefine-Berta-Marie" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Meiron", "given_name": "Daniel I.", "orcid": "0000-0003-0397-3775", "clpid": "Meiron-D-I" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "With the integration of autonomous systems into our everyday lives edging closer to reality, ensuring the safety of these systems is paramount. Part of the safety verification process is a rigorous testing procedure, which currently does not exist for autonomous vehicles. In this thesis, we aim to provide approaches using formal methods to increase the efficiency of testing campaigns.\r\nFirst, we provide a framework based on assume-guarantee contracts to specify tests in the form of a test structure. Using these test structures, we then show how to combine, split, and compare tests. Additionally, we characterize when tests can be combined and when the resulting test requires temporal constraints. Next, we demonstrate the approach on examples and find a strategy for a test agent using winning sets and Monte Carlo tree search.
\r\n\r\nSecond, we present a framework to automatically synthesize a test environment, consisting of static and reactive obstacles, and dynamic test agents. We characterize the desired test behavior in a system and a test objective in the form of a linear temporal logic specification, consisting of sub-tasks commonly used for robotic missions. This test environment must ensure that the test is not impossible (i.e. a correct system can pass the test), but also that every test execution that satisfies the system objective also satisfies the test objective. We use tools from automata theory to construct the virtual product graph that represents all possible test executions, and the virtual system graph, which corresponds to the system's perspective.\r\nWe formulate this routing problem as a network flow optimization on the virtual product graph in the form of a mixed integer linear program for different test environments. We show that this routing problem is NP-hard. We propose a counterexample-guided search using GR(1) synthesis to find a strategy for a test agent. This framework is demonstrated in several examples in simulation and hardware.
\r\n\r\nLastly, we present a framework to diagnose a system-level fault by identifying the component responsible for the failure. We make use of assume-guarantee contracts and Pacti, a tool for compositional system analysis and design, to construct a diagnostics map, which allows us to trace a system-level guarantee to possible causes. We show that this framework can reduce the number of statements that need to be checked in the diagnostics process. We illustrate this framework on several abstract examples and two examples inspired by a real-world autonomous system.
", "doi": "10.7907/4xdc-b988", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16438", "collection": "thesis", "collection_id": "16438", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292024-221741183", "primary_object_url": { "basename": "Thesis_Rev_TaraChari.pdf", "content": "final", "filesize": 11821855, "license": "cc_by_nc_nd", "mime_type": "application/pdf", "url": "/16438/1/Thesis_Rev_TaraChari.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Perturbing the Genome: From Bench to Biophysics", "author": [ { "family_name": "Chari", "given_name": "Tara Varada", "orcid": "0000-0002-6953-4313", "clpid": "Chari-Tara-Varada" } ], "thesis_advisor": [ { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "thesis_committee": [ { "family_name": "Qian", "given_name": "Lulu", "orcid": "0000-0003-4115-2409", "clpid": "Qian-Lulu" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Anderson", "given_name": "David J.", "orcid": "0000-0001-6175-3872", "clpid": "Anderson-D-J" }, { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "In single-cell genomics, we can simultaneously assay hundreds of thousands of cells, their molecular contents, and how they respond to perturbation, from genetic knockouts to environmental changes. This thesis focuses on how to merge experimental and computational techniques to generate and analyze large-scale perturbation data for high-resolution systems biology. Beginning at the bench, we demonstrate how combining large-scale cell atlas surveys with multi-condition experimentation can illuminate the diversity of cell types across whole organisms and cellular strategies in response to environmental changes and perturbations. We then investigate the limitations of current practice in exploratory analysis, and strategies for determining preservation or distortion of biological insight by these data transformation and dimensionality reduction techniques. To address these limitations, we demonstrate how stochastic biophysical models can rewrite the way we interpret complex perturbation data, taking greater advantage of the diverse molecular measurements to develop biological hypotheses about DNA and RNA regulation in cellular function, development, and disease.
", "doi": "10.7907/5drv-ma07", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16430", "collection": "thesis", "collection_id": "16430", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282024-210649680", "type": "thesis", "title": "Scalar Vortex Coronagraphs for Imaging Habitable Exoplanets", "author": [ { "family_name": "Desai", "given_name": "Niyati K.", "orcid": "0000-0002-2843-8325", "clpid": "Desai-Niyati-K" } ], "thesis_advisor": [ { "family_name": "Mawet", "given_name": "Dimitri", "orcid": "0000-0002-8895-4735", "clpid": "Mawet-D" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Meiron", "given_name": "Daniel I.", "orcid": "0000-0003-0397-3775", "clpid": "Meiron-D-I" }, { "family_name": "Bailey", "given_name": "Vanessa", "orcid": "0000-0002-5407-2806", "clpid": "Bailey-Vanessa" }, { "family_name": "Mawet", "given_name": "Dimitri", "orcid": "0000-0002-8895-4735", "clpid": "Mawet-D" } ], "local_group": [ { "literal": "3MT Competition (Caltech)" }, { "literal": "div_eng" } ], "abstract": "Of the over 5,600 exoplanets detected to date, less than 2% have ever been directly imaged. Direct imaging is crucial for the study of habitable exoplanets around Sun-like stars because it offers the potential to characterize their atmospheres and detect biosignatures. However, the extreme contrast between star and planet light poses immense challenges which coronagraphs aim to address. Future telescopes, like NASA's upcoming Habitable Worlds Observatory, necessitate coronagraphs capable of suppressing starlight to contrast levels of 10-10 and operating in broadband light to directly image and characterize habitable planets. To meet these ambitious goals, innovations in focal plane mask technologies and wavefront sensing and control strategies are imperative.
\r\n\r\nThis thesis investigates the viability of scalar vortex coronagraphs for direct imaging of habitable exoplanets. The first part of this thesis focuses on simulation efforts for modeling various coronagraph mask topographies and laboratory testing. Analysis of current scalar vortex topographies found phase wrapping is favorable over classic vortex designs. The chromatic performance of one such design \u2014 the wrapped staircase scalar vortex coronagraph \u2014 is investigated and a laboratory demonstration is presented.
\r\n\r\nNext, this thesis explores the behavior of different wavefront sensing and control methods combined with the wrapped staircase scalar vortex coronagraph. Three techniques were implemented on a high contrast imaging testbed and competitive performance between model-free and model-based techniques was found, particularly with increasingly complex mask designs.
\r\n\r\nLastly, new scalar vortex mask designs which combine radially and azimuthally varying features are investigated. Specifically, the benefits of adding central phase dimples to scalar masks to improve broadband performance are explored. Hybrid designs incorporating phase dimples are found to suppress chromatic leakage and show substantial improvement in broadband contrast over current scalar vortex designs.
\r\n\r\nOverall, this thesis advances the understanding and development of scalar vortex coronagraphs for exoplanet direct imaging, explores their potential for future space telescopes and highlights avenues for further research and experimentation.
", "doi": "10.7907/wnma-x832", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16167", "collection": "thesis", "collection_id": "16167", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08282023-193415593", "type": "thesis", "title": "Adaptive Optoelectronic Systems: From Bio- Sensing to Free-Space Optical Communication", "author": [ { "family_name": "Aghlmand", "given_name": "Fatemeh", "orcid": "0000-0002-5103-9314", "clpid": "Aghlmand-Fatemeh" } ], "thesis_advisor": [ { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Scherer", "given_name": "Axel", "orcid": "0000-0002-2160-9064", "clpid": "Scherer-A" }, { "family_name": "Marandi", "given_name": "Alireza", "orcid": "0000-0002-0470-0050", "clpid": "Marandi-A" }, { "family_name": "Mirhosseini", "given_name": "Mohammad", "orcid": "0000-0002-9084-6880", "clpid": "Mirhosseini-M" }, { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" } ], "local_group": [ { "literal": "MICS Lab (Mixed Mode Integrated Circuits and Systems)" }, { "literal": "div_eng" } ], "abstract": "Portable and point-of-care medical devices are becoming an essential part of today\u2019s medical technology. An affordable personal device that can diagnose and monitor a medical condition in real-time will improve the patient\u2019s life quality in many ways. Additionally, by autonomously providing the suitable treatment, a universal healthcare device can be accessible to most of the population at a low cost. Despite considerable efforts and great outcomes, most of the prior arts in realizing these devices have limitations that hinder their widespread use in portable applications. On the other hand, comprehensive environmental sensing has drawn great attention in the last few years. Monitoring the quality of water, soil, air, and waste is of utmost importance to study their effect on human life and also to recognize the consequence of human actions on the planet.
\r\n\r\nThe most important factors in developing a compact and portable device for medical and environmental applications are their integration level, ease of use with biomarkers, and reliability of the results. Detecting a specific chemical in the biology world relies on a biochemical reaction with a transducer that can convert the resulting signal into a measurable signal in various modalities, such as electrical, magnetic, or optical. Hence, the biosensing device is often a multidisciplinary apparatus that is not readily integrable due to the need for miniaturizing otherwise bulky optical or magnetic components. The key requirement in device miniaturization, though, is to use standard technologies to avoid extra cost and processing time for the device\u2019s mass production. The path towards achieving such a device needs revisiting the existing solutions and the capabilities of the powerful yet affordable CMOS technologies to seamlessly integrate various device components, namely electronics, biology, and optics/magnetics. This dissertation provides an overview of integrated biosensors and presents novel designs in optics and electronics to implement a fully integrated and miniaturized device for medical and environmental applications.
\r\n\r\nFluorescence sensing is one of the most reliable and widespread detection methods with well- established tools in synthetic biology. Specifically, bacterial-based fluorescence sensors offer unsurpassed advantages to labeled detection since bacterial cells, when engineered, can respond to various elements in their surroundings at a low cost and quite efficiently. The use of live bacterial cells is also of great importance in establishing the bidirectional link with the CMOS device. By monitoring the dynamics of the cells\u2019 growth and their protein expression, a desired biology response can be initiated upon receiving the stimulating signal from the device. The conventional methods in fluorescence sensing involve an elaborate setup with many external optical components unsuitable for portable and in vivo applications. Hence, integrating silicon chips and live bacterial biosensors in a miniaturized \"Silicon-Cell\" system can enable a wide range of applications for both sensing and remediation. Such integrated systems need on-chip optical filtering in the wavelength range compatible with fluorescent proteins, which are widely used signal reporters for bacterial biosensors.
\r\n\r\nIn the first part of this dissertation, we introduce a fully integrated fluorescence sensor in 65nm standard CMOS process comprising on-chip bandpass optical filters, photodiodes, and processing circuitry. The metal/dielectric layers in CMOS are employed to implement low- loss cavity-type optical filters, achieving a bandpass response at 600/700nm range suitable to work with fluorescent proteins. The sensitivity of the sensor is further improved in the electrical domain by using a C-TIA with variable switched capacitor gain, a voltage- controlled current source (VCCS), and feedback-controlled low-leakage switches, resulting in a minimum measured current of 1.05fA with SNR >18dB. The sensor can measure the statics/dynamics of the fluorescence signal as well as the growth of living E. coli bacterial cells. Using a differential design and layout, the sensor can distinguish two biochemical signals by measuring two fluorescent proteins encoded in a single bacterial strain. Furthermore, a proof of concept is demonstrated to establish bidirectional communication between living cells and the CMOS chip, using a fluorescent protein regulated by an optogenetic control.
\r\n\r\nIn the second part of this dissertation, we describe a fully integrated high-bandwidth optical receiver for RF-over-free-space optics (RoFSO). This work is motivated by the availability of a wide, unregulated bandwidth at the optical frequencies and the lower cost and setup time due to using atmosphere instead of fiber optics as the communication channel. Nonetheless, the atmospheric link poses serious challenges, including severe beam intensity and phase distortions. Here we present novel solutions at the system and circuit level to make the receiver adaptive and resilient to the mentioned distortions. The chip is designed and implemented in a 28nm CMOS process, and it is shown to achieve a measured gain of 58dB and bandwidth of 18GHz. The link performance is assessed by exposing the system to more than 26dB of optical loss, equivalent to 3.5km of free space distance under moderate visibility conditions. For a proof-of-concept demonstration, an 8Gbps non-coherent DPSK signal with an RF bandwidth of 10GHz is transmitted, resulting in a BER of 1 \u00d7 10\u207b\u2074 for a minimum received power of -30dBm and while consuming 19.2mW power at the receiver.
", "doi": "10.7907/hj19-7516", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16137", "collection": "thesis", "collection_id": "16137", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07062023-214417026", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 3653001, "license": "other", "mime_type": "application/pdf", "url": "/16137/1/Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Distributed Control Theory for Biological and Cyberphysical Systems", "author": [ { "family_name": "Li", "given_name": "Jing Shuang (Lisa)", "orcid": "0000-0003-4931-8709", "clpid": "Li-Jing-Shuang-Lisa" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Anderson", "given_name": "James", "orcid": "0000-0001-8210-6527", "clpid": "Anderson-James" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In engineering, control theory plays a crucial role in the design and analysis of robust and efficient systems --- including robots, spacecraft, and power grids. In biology, control theory underlies sensorimotor and locomotion models of organisms. Distributed control is particularly useful for large-scale cyber-physical systems and also in biological systems, where communication is more limited than in engineered counterparts. In this thesis, I provide a number of theoretical advances in distributed control theory on the relationship between communication within controllers vs. closed-loop behavior in both the online and offline settings, on the application of distributed methods to robust control, and on necessarily information flow within controllers subject to communication constraints. I then discuss the applications of these theoretical advances to the primate cortex, as well as to sensorimotor models of drosophila locomotion. Overall, the contributions outlined in this thesis facilitate modeling techniques and insights that were previously unavailable.", "doi": "10.7907/p3k0-rv78", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16087", "collection": "thesis", "collection_id": "16087", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062023-021337351", "primary_object_url": { "basename": "Caltech_Thesis_Ayush_Pandey.pdf", "content": "final", "filesize": 15175323, "license": "other", "mime_type": "application/pdf", "url": "/16087/4/Caltech_Thesis_Ayush_Pandey.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Modeling Frameworks for Modular and Scalable Biological Circuit Design", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Del Vecchio", "given_name": "Domitilla", "orcid": "0000-0001-6472-8576", "clpid": "DelVecchio-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Synthetic biology is a rapidly evolving interdisciplinary field that combines principles from biology, bioengineering, biochemistry, and computational sciences to design and engineer new biological systems for various applications. This thesis focuses on addressing the challenges in engineering large and complex biological circuits. We develop modular modeling frameworks, formal theory, and computer-assisted design (CAD) tools for design and analysis of biological systems at a larger scale.
\r\n\r\nThis thesis introduces a new problem of robustness in structured model reduction of dynamical systems and provides bounds on a robustness distance metric for linear and nonlinear systems. With this theory, we show the discrimination and quantification of different mathematical models, considering resource loading effects in biological circuits.
\r\n\r\nUsing our proposed model reduction robustness theory and its associated software development, we build a modeling, analysis, and parameter identification pipeline. This pipeline is demonstrated through the characterization of DNA recombination enzymes in a cell-free protein expression system. This pipeline is a general approach to systematically develop mathematical models, infer parameters from experimental data, and guide experimental design choices.
\r\n\r\nIdentification of parameters in detailed mathematical models is a major challenge in synthetic biology where only sparse data is available. This prevents the application of our detail-driven modeling approach to larger biological systems. Hence, to address this limitation, we present a formal methods-based approach for specifying and synthesizing implementations for the design of biological circuits. We present a contract-based design framework for synthetic biology. We write formal description of design objectives at a higher level of abstraction without modeling the details of each component. This design framework facilitates the design and prediction of complex synthetic biological circuits at scale.
\r\n\r\nOverall, this thesis contributes to the advancement of synthetic biology by providing novel modeling frameworks, analysis methods, and design approaches. These contributions aim to enable the design and analysis of complex biological systems and foster the systematic engineering of biological circuits.
", "doi": "10.7907/qacp-dw76", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16368", "collection": "thesis", "collection_id": "16368", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05042024-011724418", "type": "thesis", "title": "Complexity of Transcriptomic Data Analysis and Implications for Biological Discovery", "author": [ { "family_name": "Luebbert", "given_name": "Laura", "orcid": "0000-0003-1379-2927", "clpid": "Luebbert-Laura" } ], "thesis_advisor": [ { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "thesis_committee": [ { "family_name": "Van Valen", "given_name": "David A.", "orcid": "0000-0001-7534-7621", "clpid": "Van-Valen-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "local_group": [ { "literal": "3MT Competition (Caltech)" }, { "literal": "div_bbe" } ], "abstract": "Over the past decade, the advancement of \u2018omics\u2019 technologies has ushered in a new era for the life sciences. Given the high-throughput nature of omics technologies, this era is characterized by unique computational challenges pertaining to data size and dimensionality, and technical and biological noise. Concurrently, it offers opportunities, as global, untargeted, and parallel measurement of large amounts of information often captures unexpected insights.
\r\n\r\nThis thesis describes challenges inherent to the omics era of life sciences, particularly highlighting the increasing importance of merging expertise in biology and computer science. It describes the development of multiple software tools designed to address several of these challenges, which were immediately adopted and widely implemented in transcriptomics and proteomics research. Additionally, it contains three chapters focused on unraveling previously unquantifiable information, including the interpretation of sequencing data from organisms with low-quality reference genome assemblies and workflows for identifying novel viruses using single-cell RNA sequencing data already massively generated in research, healthcare, and agriculture.
", "doi": "10.7907/xnw5-v914", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16324", "collection": "thesis", "collection_id": "16324", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03132024-155539035", "primary_object_url": { "basename": "JLee_Thesis_Final.pdf", "content": "final", "filesize": 14709267, "license": "other", "mime_type": "application/pdf", "url": "/16324/1/JLee_Thesis_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Ultrasound Control and Imaging of Cellular Immunotherapy", "author": [ { "family_name": "Lee", "given_name": "Justin", "orcid": "0000-0002-3657-4386", "clpid": "Lee-Justin" } ], "thesis_advisor": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "thesis_committee": [ { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wang", "given_name": "Kaihang", "orcid": "0000-0001-7657-8755", "clpid": "Wang-Kaihang" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Biomedical ultrasound-based therapeutics and diagnostics are becoming an increasingly important clinical tool. Techniques like focused ultrasound tissue heating and microbubble-enhanced ultrasound imaging have enabled new ways to noninvasively treat and detect diseases cost-effectively and safely. While these are great leaps forward in ultrasound technology, leveraging synthetic biology tools to engineer cells with the capabilities to interact with ultrasound in novel ways may enable even more avenues for ultrasound to address important clinical challenges.
\r\n\r\nIn this thesis, we explore the potential in engineering immune cells with various genetic elements which interact with either therapeutic or diagnostic ultrasound in novel ways. In Chapter 2, we engineer T-cells capable of sensing increases in temperature and responding by activating expression of therapeutic proteins to potentially increase safety of cell-based immunotherapies by controlling their spatiotemporal activation. In Chapters 3 and 4, we develop monocytes as ultrasound reporter cells for cancer detection by engineering them to express gas vesicles (GVs), a class of air-filled protein nanostructures natively found in certain aquatic microbes, which have been demonstrated to produce ultrasound contrast. We demonstrate the potential to confine GV expression to certain disease related signals to create ultrasound reporter cells. Together, these findings highlight the potential of engineering cells to activate in certain locations in response to ultrasound heating or serve as sentinel cells for disease detection.
", "doi": "10.7907/60sh-a389", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16313", "collection": "thesis", "collection_id": "16313", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03042024-201031352", "primary_object_url": { "basename": "swei_PH_D_Thesis_vf.pdf", "content": "final", "filesize": 9919168, "license": "other", "mime_type": "application/pdf", "url": "/16313/1/swei_PH_D_Thesis_vf.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Data-Driven Safety-Critical Autonomy in Unknown, Unstructured, and Dynamic Environments", "author": [ { "family_name": "Wei", "given_name": "Skylar Xueyao", "orcid": "000-0002-6336-9433", "clpid": "Wei-Skylar-Xueyao" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Brunton", "given_name": "Steven L.", "orcid": "0000-0002-6565-5118", "clpid": "Brunton-S-L" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis addresses the critical challenge of ensuring safety in autonomous exploration within unknown, unstructured, dynamic environments, a domain filled with various types of uncertainties. These include model uncertainties in system dynamics, localization uncertainties stemming from measurement noises, and the risks of collision in environments with dynamic obstacles. Traditional models for vehicle planning and control are often simplified for computational feasibility, but this simplification without careful analysis can compromise safety and system stability. My research introduces a novel, comprehensive framework to provide probabilistically safe planning and control for robot autonomy, structured around three components:
\r\n\r\n(1) Probabilistic Uncertainty Quantification for Model Mismatches:
\r\nThis segment focuses on identifying model discrepancies given closed-loop tracking data in an unstructured environment where a reduced-order robot model is used for planning and control. The disturbance is modeled as a scalar-valued stochastic process of a norm on the difference between the reduce-order robot model and actual system evolution. In an online and risk-aware framework, Gaussian Process Regression is employed to extract the probabilistic upper bound to such stochastic process, referred to as the Surface-at-Risk. Theoretical guarantees on the accuracy of the fitted discrepancy surface are analyzed and verified to the data sets collected during system operation.
\r\n\r\nIn an offline setting, conformal prediction, a statistical inference tool, is employed to obtain probabilistic upper bounds of matched and unmatched model disturbance in the system from data, without any assumption of the latent probability distribution governing these discrepancies. Building on these bounds, the robot's nominal ancillary controller is augmented for extending robustness and stability guarantees of the closed-loop system in the face of such discrepancies. Additionally, a maximum tracking error tube is constructed along the planned trajectory using the reduced-order model. Such error tubes describe the maximum permissible deviation in actual trajectory tracking under the augmented ancillary controller and the worst-case matched and unmatched model uncertainties, thereby delineating safe operational boundaries for the system.
\r\n\r\n(2) Data-Driven Unsafe Set Prediction for Dynamic Obstacles:
\r\nThis thesis topic develops an online, data-driven predictive model for dynamic obstacles, accounting for measurement noise and low-frequency data rates. \r\n First inspired by singular spectrum analysis (SSA), a time-series forecast technique, obstacle models characterized by linear recurrence relationships are extracted from real-time position observables. Using the statistical bootstrap technique, a set of predicted obstacle trajectories are constructed, which in turn are reformulated into deterministic distributionally robust obstacle avoidance constraints, reflecting a user-defined risk tolerance.
\r\nFurther refining the obstacle predictor for intention-unknown obstacles, a linear, time-varying model is learned from data using time-delay embedding of obstacle position observables. Additive process and measurement noises are anticipated in the learned model, where their intensities are estimated from data. For inferring prediction uncertainties, a companion data-driven Kalman Filter (DDKF) is constructed to forecast obstacle positions and uncertainties. This \"heuristic unsafe set\" from DDKF is then dynamically calibrated using adaptive conformal prediction, ensuring safety without relying on any distribution assumptions regarding the uncertainties or model accuracy. The calibrated sets, called conformal prediction sets, are then reformulated into convex state constraints.
\r\n\r\n(3) Safety-Critical Planning:
\r\nThe thesis proposes two methods for ensuring safety in planning and navigation: Probabilistic-Safe Model Predictive Control (MPC) and Probabilistic-Safe Model Predictive Path Integral (MPPI) given uncertainties arising from operating in unknown, unstructured, and dynamic environments. The MPC approach integrates the quantified obstacle avoidance constraints into a convex program to balance computational tractability while providing probabilistic safety guarantees. In contrast, the MPPI method, a sampling-based strategy, incorporating unsafe sets into a cost map derived from sensory data, optimizes reference tracking trajectory while guaranteeing collision avoidance up to a user-defined risk tolerance.
\r\n\r\nIn unknown and cluttered environments automatically, the proposed framework learns an upper bound on model residuals from data and systematically calculates the safety buffers needed to provide the desired probabilistic safe navigation of robotics systems. Additionally, in the presence of dynamic obstacles, the proposed data-driven predictor systematically extracts an obstacle model and makes obstacle-occupied unsafe set forecasts. These features largely eliminate the \"hand tuning\" of the underlying planner and controller that is normally required in heuristic-based algorithms. The efficacy of these proposed frameworks is empirically validated through Monte Carlo Simulations, alongside hardware validations on both ground and aerial vehicles, demonstrating their robustness, versatility, and applicability in real-world scenarios.
", "doi": "10.7907/qpbp-0x81", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16213", "collection": "thesis", "collection_id": "16213", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10232023-184021847", "primary_object_url": { "basename": "saladi-dissertation.pdf", "content": "final", "filesize": 327264663, "license": "other", "mime_type": "application/pdf", "url": "/16213/1/saladi-dissertation.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Some Computer Studies of Membrane Proteins, Molecular Chaperones, and Color", "author": [ { "family_name": "Saladi", "given_name": "Shyam Madhukar", "orcid": "0000-0001-9701-3059", "clpid": "Saladi-Shyam-Madhukar" } ], "thesis_advisor": [ { "family_name": "Clemons", "given_name": "William M.", "orcid": "0000-0002-0021-889X", "clpid": "Clemons-W-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Clemons", "given_name": "William M.", "orcid": "0000-0002-0021-889X", "clpid": "Clemons-W-M" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Hoelz", "given_name": "Andre", "orcid": "0000-0003-0923-3284", "clpid": "Hoelz-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis shares a series of stories on seemingly disparate topics united by my efforts and love of computers. Initially, I discuss how the challenge of membrane protein expression provided an initial impetus for research. I channeled efforts towards developing a predictive (machine-learning) model for heterologous overexpression in E. coli. While we made strides to extend this model to other systems (not discussed here), my time was refocused onto questions of more fundamental biochemical interest: the biogenesis of tail-anchored membrane proteins. I built structural, predictive, and phylogenetic models to better understand how the C-terminal domain of co-chaperone Sgt2 functioned, refined the definition of the wider Sti1 family which includes Sgt2-C, and extended our understanding of those features of tail-anchored proteins that determine successful targeting in Yeast and Human cells. I developed a deep phylogeny of Get3, a chaperone involved in tail-anchored protein biogenesis, and helped specifically place Get3 proteins of photosynthesising organisms into evolutionary context. Along the way, I developed a parallel and compelling theme around data visualization, specifically around the use of colormaps across the life sciences. In particular, I built an application to screen and notify preprint authors when their manuscript had poor colormap usage. This was the first time automated software has been used to help authors improve their work at the preprint stage, an area that has grown significantly since my initial work. Finally, I brought together structural biology and data visualization by making perceptually uniform colormaps available in popular molecular visualization software tools to advocate for more thoughtful color usage in the field.", "doi": "10.7907/40cw-kn70", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16481", "collection": "thesis", "collection_id": "16481", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-141219249", "primary_object_url": { "basename": "JuradoQuiroga_Zoila_2024_Submitted.pdf", "content": "final", "filesize": 79519830, "license": "other", "mime_type": "application/pdf", "url": "/16481/1/JuradoQuiroga_Zoila_2024_Submitted.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Towards a Synthetic Nucleus: Separating Transcription and Translation in Cell-Free Protein Expression Systems", "author": [ { "family_name": "Jurado Quiroga", "given_name": "Zoila Estefani", "orcid": "0000-0003-4160-5068", "clpid": "Jurado-Quiroga-Zoila-Estefani" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Voorhees", "given_name": "Rebecca M.", "orcid": "0000-0003-1640-2293", "clpid": "Voorhees-R-M" }, { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Synthetic cells represent the culmination of decades of research aimed at deciphering the intricacies of life at its most basic level. The result of the fusion of biology, chemistry, physics, and engineering, synthetic cells promise to revolutionize biotechnology, medicine, and beyond. This thesis focuses on the ramifications of incorporating a synthetic nucleus within a synthetic cell.
\r\n\r\nTo experimentally study transcription and translation, we use a commercially available cell-free protein expression system comprising all the purified proteins essential for protein production (PURE), along with a fluorescent RNA aptamer--malachite green aptamer (MGapt), and a green fluorescent protein (deGFP). We observed that the chemical composition of the PURE system significantly impacts MGapt fluorescence, leading to inaccurate RNA calculations. We identify the reducing agent, dithiothreitol (DTT), to address this challenge as a crucial chemical affecting MGapt fluorescence. We propose a model that can reliably model MGapt measurements in commercial PURE. This investigation illuminates the intricate dynamics of MGapt in PURE and emphasizes the necessity of accounting for environmental factors in RNA measurements employing aptamers.
\r\n\r\n\r\nSubsequently, to advance our understanding of a synthetic nucleus and analyze the effects of separating transcription and translation in a cell-free protein expression, we propose and validate a chemical reaction network model for transcription (TX) in PURE. Additionally, we used open-source software to expand an existing translation (TL) model for any arbitrary DNA sequence to create a nearly complete model of TX-TL in PURE. Leveraging this model, we investigate the effect of introducing a synthetic nucleus by modulating the RNA diffusion rate and resource allocation. This detailed model showcases our capability to comprehensively model protein expression in PURE, enabling insights into the efficacy of segregating transcription and translation processes within the artificial cell environment. Lastly, we provide a perspective on the future of synthetic cells with an artificial nucleus and propose further steps to develop the proposed synthetic nucleus model.
", "doi": "10.7907/kvq4-6132", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16465", "collection": "thesis", "collection_id": "16465", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022024-014038700", "primary_object_url": { "basename": "ApurvaBadithela_June2024.pdf", "content": "final", "filesize": 96248118, "license": "other", "mime_type": "application/pdf", "url": "/16465/9/ApurvaBadithela_June2024.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Test and Evaluation of Autonomous Systems: Reactive Test Synthesis and Task-Relevant Evaluation of Perception", "author": [ { "family_name": "Badithela", "given_name": "Apurva Srinivas", "orcid": "0000-0002-9788-2702", "clpid": "Apurva-Apurva-Srinivas" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Chandy", "given_name": "K. Mani", "orcid": "0000-0001-9190-1290", "clpid": "Chandy-K-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-Tichakorn" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Autonomous robotic systems have potential for profound impact on our society -- legged and wheeled robots for search and rescue missions, drones for wildfire management, self-driving cars for improving mobility, and robotic space missions for exploration and repair of spacecraft. The complexity of these systems implies that formal guarantees during the design phase alone is not sufficient; mainstream deployment of these systems requires principled frameworks for test and evaluation, and verification and validation. This thesis studies two such challenges to mainstream deployment of these systems.
\r\n\r\nFirst, we consider the problem of evaluating perception models in a manner relevant to the system-level specification and the downstream planner. Perception and planning modules are often designed under different computational and mathematical paradigms. This talk will focus on evaluating models for classification and detection tasks, and leverages confusion matrices which are popularly used in computer vision to evaluate object detection models to derive probabilistic guarantees at the system-level. However, not all perception errors are equally safety-critical, and traditional confusion matrices account for all objects equally. Thus, task-relevant metrics such as proposition labeled confusion matrices are introduced. These are constructed by identifying propositional formulas relevant to the downstream planning logic and the system-level specification, and result in less conservative system-level guarantees. Using this analysis, fundamental tradeoffs in perception models are reflected in the tradeoffs of probabilistic guarantees. This framework is illustrated on a car-pedestrian example in simulation, and the confusion matrices are constructed from state-of-the-art detection models evaluated on the nuScenes dataset.
\r\n\r\nSecond, we consider the problem of automatically synthesizing tests for autonomous robotic systems. These systems reason over both discrete (e.g., navigate left or right around an obstacle) and continuous variables (e.g., continuous trajectories). This talk presents a flow-based approach for test environment synthesis which handles discrete variables and is also reactive to the system under test. Reactivity is important to account for uncertainties in system modeling, and to adapt to system behavior without knowledge of the system controller. These tests are synthesized from high-level specifications of desired behavior. Though the problem is shown to be NP-hard, a flow-based mixed-integer linear program formulation is used that scales well to medium-sized examples (e.g., >10,000 integer variables). The test environment can consist of static and reactive obstacles as well as dynamic test agents, whose strategies are synthesized to match the solution of the flow-based optimization. The overview of the approach is as follows. First, principles of automata theory are used to translate the high-level system and test objectives, and the non-deterministic abstraction of the system into a network flow optimization. The solution of this optimization is then parsed into GR(1) formulas in linear temporal logic. This GR(1) formula is used to synthesize reactive strategies of a dynamic test agent in a counterexample-guided fashion. We provide guarantees that the synthesized test strategy will realize the desired test behavior under the assumption of a well-designed system, the test strategy is reactive and least-restrictive,. This framework is illustrated on several simulation and hardware experiments with quadrupeds, showing promise towards a layered approach to test and evaluation.
", "doi": "10.7907/e8qz-rd26", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16061", "collection": "thesis", "collection_id": "16061", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-192547723", "primary_object_url": { "basename": "ShengThesis_CaltechTHESIS.pdf", "content": "final", "filesize": 8747307, "license": "other", "mime_type": "application/pdf", "url": "/16061/1/ShengThesis_CaltechTHESIS.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Synthetic Circuits for Multicellular Spatial Patterning", "author": [ { "family_name": "Wang", "given_name": "Sheng", "orcid": "0000-0002-4070-7313", "clpid": "Wang-Sheng" } ], "thesis_advisor": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Meister", "given_name": "Markus", "orcid": "0000-0003-2136-6506", "clpid": "Meister-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Self-organized spatial periodic patterning mechanisms are responsible for the generation of repetitive structures, such as digits, vertebrae, and teeth, during multicellular development. Adopting a synthetic biology approach, we aim to unravel the core principles of multicellular spatial patterning by designing and reconstituting it in tissue-cultured cell lines.
\r\n\r\nThe reaction-diffusion mechanism, as an established paradigm, has successfully elucidated and forecasted pattern formation across varying scales and species. However, the potential for reconstituting synthetic reaction-diffusion patterns using unconventional reaction-diffusion elements within mammalian cell cultures has been insufficiently explored, thus leaving a gap in our comprehension of how spatial periodic patterns could be generated.
\r\n\r\nThe simplest reaction-diffusion systems are thought to necessitate a minimum of two morphogens to generate periodic patterns. In contrast, with the help of mathematical modeling, we illustrate that a simpler circuit, comprising only a single diffusible morphogen, can adequately produce long-range, spatially periodic patterns. These patterns propagate outward from transient initiating perturbations and remain stable after the disturbance is removed. Moreover, introducing an additional bistable intracellular feedback or operation on a growing cell lattice can enhance the robustness of the patterning against noise.
\r\n\r\nConcurrently, we reconstruct the Turing pattern in mammalian cell culture utilizing a bottom-up approach. We construct a synthetic circuit based on two signaling pathways. After validation of each circuit component, we exhibit the spatial pattern formation driven by a synthetic reaction-diffusion circuit within the mammalian cell line. This adaptable circuit facilitates us to adjust circuit parameters or implement various boundary conditions, thereby revealing the impact of these alterations on patterning dynamics.
\r\n\r\nCollectively, these findings lay the groundwork for the engineering of pattern formation in the nascent field of synthetic developmental biology.
", "doi": "10.7907/3rbk-g805", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15070", "collection": "thesis", "collection_id": "15070", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12022022-010002116", "type": "thesis", "title": "Engineering Conditional Guide RNAs for Cell-Selective Regulation of CRISPR/Cas9", "author": [ { "family_name": "Chen", "given_name": "Zhewei", "orcid": "0000-0002-7422-095X", "clpid": "Chen-Zhewei" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "orcid": "0000-0002-1653-3202", "clpid": "Rothemund-P-W-K" }, { "family_name": "Hay", "given_name": "Bruce A.", "orcid": "0000-0002-5486-0482", "clpid": "Hay-B-A" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_bbe" } ], "abstract": "CRISPR/Cas9 is a versatile platform for implementing diverse modes of genetic perturbation such as gene silencing, induction, deletion, or replacement. This technology is popularly used in developmental biology to probe genetic circuitry via constitutive gene knockdown. Global gene silencing could introduce artifacts in the study of developmental regulatory pathways, and this motivates the development of cell-selective gene editing. Our lab has recently created conditional guide RNAs (cgRNA) that enable CRISPR/Cas9 systems to silence a desired gene Y conditioned on the detection of an RNA transcript X inside of a cell. cgRNA systems were discovered via insertion and deletion mutations that systematically explored the structure function of the guide RNA. Nucleic acid engineering software (NUPACK) was used to generate orthogonal libraries of cgRNA molecules that executed both ON \u2192 OFF logic (conditional inactivation by an RNA trigger) and OFF \u2192 ON logic (conditional activation by an RNA trigger). A dCas9-based RFP silencing assay in bacteria was developed and used to show these cgRNA sequences were functional and could detect short exogenous trigger sequences in an orthogonal and doseresponsive manner. Subsequent studies on cgRNA structure and function enabled us to engineer next-generation systems that have fewer constraints on the trigger sequence or structure. These next-generation cgRNAs were tested against short synthetic mRNA transcripts, truncated sub-sequences of endogenous mRNAs, and full-length endogenous mRNAs. Synthetic mRNA transcripts were used to study the effect of protein translation on trigger RNA binding. cgRNAs were capable of detecting synthetic sequences embedded in the 3\u2032 UTR of fluorescent protein mRNAs. cgRNAs could also detect short synthetic mRNAs or truncated subsequences from endogenous mRNAs. However, the detection of native full-length endogenous mRNAs remained challenging because we cannot reliably predict the local structure of sub-sequences within a long RNA transcript. High-throughput cgRNAscreening may prove necessary for finding accessible binding sites onmRNA transcripts. Nevertheless, cgRNA functionalities could be useful in developmental biology by enabling precision perturbation of regulatory events, linking guide RNA activity to an RNA marker X correlated to a specific cell type or temporal expression pattern. This work opens the possibility for future applications such as cell-selective gene therapies.
", "doi": "10.7907/cajs-d417", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15225", "collection": "thesis", "collection_id": "15225", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292023-181810775", "primary_object_url": { "basename": "Marken_Thesis_Final.pdf", "content": "final", "filesize": 4502877, "license": "other", "mime_type": "application/pdf", "url": "/15225/1/Marken_Thesis_Final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Experimental and Theoretical Frameworks for Enabling Environmental Synthetic Biology", "author": [ { "family_name": "Marken", "given_name": "John Paul", "orcid": "0000-0001-9696-088X", "clpid": "Marken-John-Paul" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Hay", "given_name": "Bruce A.", "orcid": "0000-0002-5486-0482", "clpid": "Hay-B-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Although the field of synthetic biology has made great advances toward becoming a mature engineering discipline over its first quarter-century, the vast majority of these efforts have focused on improving the design and performance of genetic circuits intended to operate in well-controlled, laboratory settings. The goal of safely deploying engineered microbes to reliably perform their programmed functions in natural, uncontrolled environments begets its own set of foundational challenges that will require new frameworks that shift our existing mindsets about the way we engineer biological systems.
\r\n\r\nThese frameworks, because they focus on enabling system properties that were not priorities for conventional synthetic biology research, can constitute a new field of research which I refer to as environmental synthetic biology. The central priorities of environmental synthetic biology include (1) developing and characterizing effective ways to introduce engineered biological systems into natural environments, (2) ensuring that the performance of these systems can remain robust and predictable in the face of environmental variability, (3) developing and characterizing ways to control and monitor the behavior of an engineered system after deployment in an inaccessible environment, and (4) developing fundamental architectures to enable autonomous system operation and adaptation within environmental contexts.
\r\n\r\nIn this thesis, I present the initial steps towards the development of three frame- works that address these priorities of environmental synthetic biology. The first framework, described in Chapter 2, demonstrates the potential of using DNA as the substrate for addressable and adaptable intercellular communication in engineered populations. This enables the ability to one day create multicellular systems that can autonomously reconfigure their own architecture in the face of changing environmental conditions. The second framework, described in Chapters 3 and 4, presents a new mathematical representation of biomolecular reaction systems that enables geometric bounds on the space of possible behaviors under all possible configurations for a particular system architecture. The third, ongoing framework emphasizes the importance of explicitly incorporating the physiological state of the host cell into the assessment of a genetic circuit\u2019s behavior by exploring the impact of cellular growth arrest on transcriptional response curves. The preliminary results of this work are presented in Chapter 5.
", "doi": "10.7907/h50w-p058", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15163", "collection": "thesis", "collection_id": "15163", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05112023-130637882", "primary_object_url": { "basename": "Liaw_Eric_2023_Thesis.pdf", "content": "final", "filesize": 10234218, "license": "other", "mime_type": "application/pdf", "url": "/15163/2/Liaw_Eric_2023_Thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "A Novel, Rapid Phenotypic Assay for a Beta-Lactam Antibiotic Susceptibility and an Analysis of its Theoretical Limits", "author": [ { "family_name": "Liaw", "given_name": "Eric Jer-Jiun", "orcid": "0000-0003-2244-8335", "clpid": "Liaw-Eric-Jer-Jiun" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Current management of bacterial infections is limited by the slow turnaround time of culture-based antibiotic susceptibility testing (AST). Culture-free phenotypic AST methods, though faster, are limited not only by analytical sensitivity but also by the low number, density, and purity of live pathogens present in clinical specimens before culturing. Separating and concentrating pathogens from clinical specimen matrices and improving the analytic sensitivity of phenotypic measurement technologies remain active areas of research. However, to date, the literature lacks consensus over what is a reasonable goal for the minimum number of pathogens in a clinical specimen needed to accurately perform phenotypic AST.
\r\n\r\nI describe \"bulk filtration AST\" and \"digital filtration AST,\" two new filtration-based AST methods that improve an AST method previously published by others and myself. These methods use nucleic acid quantification to assess the activity of antibiotic classes (and only those classes) targeting peptidoglycan turnover, specifically the beta-lactams, which are the most frequently prescribed class of antibiotics. I use filtration AST to quantify the in vitro pharmacodynamics of beta-lactam antibiotics over time scales shorter than two hours, and I simultaneously validate the methods' accuracies on clinical isolates of Enterobacteriaceae. To analyze filtration AST results, either for fitting parameter values or for predicting susceptibility, I derive probabilistic models for the outcomes of each of the two filtration AST methods, then perform Bayesian parameter inference from my data.
\r\n\r\nI then propose a general mathematical framework for defining the concepts of the phenotypic assay and the ideal phenotypic assay. Within this framework, I calculate the ideal filtration AST performance as a function of the number of cells assayed, my fitted pharmacodynamic parameters, and other variables. Interestingly, the observed performance of my implementation of digital filtration AST is consistent with the implementation's approaching the ideal performance. I hope my demonstration of these new methods and my theoretical framework will help guide future research into rapid phenotypic AST.
", "doi": "10.7907/qhvg-7q92", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15149", "collection": "thesis", "collection_id": "15149", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292023-003436131", "type": "thesis", "title": "Enabling Robust and User-Customized Bipedal Locomotion on Lower-Body Assistive Devices via Hybrid System Theory and Preference-Based Learning", "author": [ { "family_name": "Tucker", "given_name": "Maegan Lindsay", "orcid": "0000-0001-7363-6809", "clpid": "Tucker-Maegan-Lindsay" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Practical robotic assistive devices have the potential to transform many aspects of our society, from enabling locomotive autonomy to facilitating rehabilitation. However, as is typically the case when having autonomous systems interact closely with humans, one must simultaneously solve multiple grand challenges. My work focuses specifically on 1) leveraging hybrid system theory to achieve stable and robust walking that generalizes well across various human models and environmental conditions, and 2) developing an online learning strategy to customize the experimental walking for individual user comfort. The presented methodology is grounded in realizing lower-body exoskeleton locomotion for subjects with motor complete paraplegia, with extensions to other robotic applications. The contributions are broken down as follows.
\r\n\r\nFirst, by leveraging tools from nonlinear control theory, I propose techniques for systematically addressing locomotive robustness. These techniques include: using saltation matrices to generate robust gaits with experimental demonstrations on the Atalante lower-body exoskeleton; and developing an input-to-state stability perspective to certify robustness to uncertain impact events. Importantly, these methods aim to better understand the mathematical conditions underlying robust locomotion -- a necessary step towards realizing safe locomotion across varying human models and environmental conditions. Second, I develop a preference-based learning framework to explicitly optimize user comfort during exoskeleton locomotion (achieved using the aforementioned nonlinear control methodology) by learning directly from subjective feedback. This framework is implemented in real-world settings, including the clinical realization of user-preferred locomotion for two subjects with motor complete paraplegia.Third, the extensibility of this framework is demonstrated through three general robotic applications: tuning constraints of the gait generation optimization problem with demonstrations on a planar biped; tuning Lyapunov-based controller gains on a 3D biped; and tuning control barrier function parameters for performant yet safe exploration on a quadrupedal platform. Lastly, I discuss other relevant clinical considerations for lower-body assistive devices including how exoskeleton locomotion influences metabolic cost of transport, the study of latent factors underlying user-preferred walking, and embedding musculoskeletal models directly in the gait generation process.
", "doi": "10.7907/j9hk-xa17", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15132", "collection": "thesis", "collection_id": "15132", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04132023-015900885", "primary_object_url": { "basename": "Ma_Yitong_2023.pdf", "content": "final", "filesize": 17632710, "license": "other", "mime_type": "application/pdf", "url": "/15132/1/Ma_Yitong_2023.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Multicellular Synthetic Biology in Mammalian Systems", "author": [ { "family_name": "Ma", "given_name": "Yitong", "orcid": "0000-0003-4446-7326", "clpid": "Ma-Yitong" } ], "thesis_advisor": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "In multicellular organisms, different types of cells use intercellular signals to communicate and regulate population dynamics, and further coordinate complex behaviors. This presents a rarely tapped into potential for mammalian synthetic biology, which was largely restricted to engineering a single cell type in the past to mimic and use similar multicellular designs to achieve more functionalities. However, with current synthetic biology tools and designs, there are several major challenges to achieve a multicellular circuit. Challenges include precise and tunable control over cell type switching, having an orthogonal cell-cell communication signal, and robust control of cell populations.
\r\n\r\nTo address these challenges, this thesis presents a system for tunable regulating of gene expression with DNA methylation, an auxin-based module for mammalian cell-cell communication, and a robust circuit for population control in mammalian cells. I further applied these work to engineering immune cells to show the potential of multicellular circuits in immunotherapies. Together, these works demonstrated the possibility of constructing multicellular circuits in mammalian systems, and that multicellular circuit can further extend the scope of synthetic biology to achieve more complex functions.
", "doi": "10.7907/w0q1-7s17", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15195", "collection": "thesis", "collection_id": "15195", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05192023-015643241", "primary_object_url": { "basename": "Palmer_Emily_2023_Thesis.pdf", "content": "final", "filesize": 90569338, "license": "other", "mime_type": "application/pdf", "url": "/15195/1/Palmer_Emily_2023_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Locomotory Control Algorithms and Their Neuronal Implementation in Drosophila melanogaster", "author": [ { "family_name": "Palmer", "given_name": "Emily Hope", "orcid": "0009-0006-8370-4709", "clpid": "Palmer-Emily-Hope" } ], "thesis_advisor": [ { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Scientists and engineers alike have long looked to animals in their pursuit of understanding the natural world and how best to interact with it. While researchers have looked across diverse classes, insects have been extensively studied for their rich diversity of life histories and abilities to perform at spatial and temporal scales difficult for engineered systems. Within insects, the fruit fly, Drosophila melanogaster, is a particularly well-studied organism because of its experimental tractability and status as a genetic model organism, providing both detailed descriptions of a broad suite of behaviors and access to and control over specific sets of tissue. In this work, we make use of these tools to study two behaviors in Drosophila, local search, the behavior in which walking flies will search the area around a food site in search of other food sources nearby, and the optomotor response, wherein they will stabilize in response to visual motion during flight. In these studies, we will use modern techniques from both biology and engineering, to exhaustively characterize and describe the observed behaviors and attempt to untangle the underlying algorithms and their neuronal implementation.
\r\n\r\nFirst, we explore the algorithmic structure of local search in fruit flies. When flies encounter a piece of food, they will often perform walking searches nearby; as food tends to be patchy in natural settings, searches may allow flies to locate other food sites in the area. We induce local search using optogenetic stimulation of sugar-sensing neurons and constrain the flies to a dark, annular arena. These experimental details result in a simplified behavior, as the fly has access to a limited sensory environment, so that the search can be interpreted as an example of idiothetic path integration, and the search itself is one-dimensionalized and therefore more easily analyzed. Our experiments, in tandem with complementary modeling using a state transition diagram formalization of the behaviors, generate two principle findings. First, flies can integrate their location in two dimensions--after the optogenetic activation is disabled and the flies can no longer receive the food stimulus, they will continue to search over the former food site even after completing a full revolution of the annular arena. Second, when multiple food sites are present, they search over a center of the food sites, rather than over one distinct food site. These results both provide insights into the algorithmic structure of local search and an experimental and descriptive paradigm for further inquiries into the behavior.
\r\n\r\nSecond, we investigate the role of a population of neurons, the DNg02s, in the optomotor response. In response to visual patterns of wide-field motion, such that the entire world is moving in the fly-centric reference frame, the animal will attempt to steer to cancel the visual motion, as the most parsimonious explanation of the motion is that the fly itself is moving in the global reference frame. We demonstrate that the DNg02 neurons are a required component in the neural circuitry underlying the optomotor response, but that they are insufficient to induce steering behaviors. We conclude with a set of models that fully recapitulate the collected dataset. With current techniques, distinguishing between the two possible models of the downstream connectivity from the DNg02s to the motor neurons associated with wing motor output is not possible. However, as new datasets become available, particularly complete connectomes of the Drosophila nervous system, the neuronal pathways from the DNg02s to the motor systems may be elucidated.
", "doi": "10.7907/yyjd-a554", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15104", "collection": "thesis", "collection_id": "15104", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02082023-223824752", "primary_object_url": { "basename": "Thesis_Anushri_Dixit.pdf", "content": "final", "filesize": 95636900, "license": "other", "mime_type": "application/pdf", "url": "/15104/1/Thesis_Anushri_Dixit.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Risk-Aware Planning and Control in Extreme Environments", "author": [ { "family_name": "Dixit", "given_name": "Anushri C.", "orcid": "0000-0002-9698-2189", "clpid": "Dixit-Anushri-C" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Mazumdar", "given_name": "Eric V.", "orcid": "0000-0002-1815-269X", "clpid": "Mazumdar-Eric" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Safety-critical control and planning for autonomous systems operating in unstructured environments is a challenging problem must be addressed as autonomous vehicles, surgical robots, and autonomous industrial robots become more pervasive. This thesis addresses some of the issues in safety critical autonomy by introducing new techniques for computationally tractable and efficient safety-critical control. The approach developed in this thesis arises from taking a deeper look at two questions: 1) How can we obtain better uncertainty quantification of the disturbances that affect autonomous systems either as a result of unmodeled changes in the environment or due to sensor imperfections? 2) Given richer uncertainty quantification techniques, how do incorporate the diverse uncertainty descriptions into the control and planning framework without sacrificing the tractability and efficiency of existing approaches?
\r\n\r\nI address the above two questions by developing risk-aware control and planning techniques for traversal of a mobile robot over static but extreme terrain and in the presence of dynamic obstacles. We first look at algorithms for risk-aware terrain assessment, and extensively test them on wheeled and legged robots that were deployed in subterranean tunnel, urban, and cave environments for search and rescue operations in the DARPA Subterranean Challenge. I then present a theory for risk-aware model predictive control in static environments and in the presence of dynamic obstacles. Coherent risk measures are applied to this planning and control framework in order to account for diverse uncertainty descriptions. Computationally tractable reformulations of the optimal control problem are realized through constraint tightening techniques.
\r\n \r\nI then investigate algorithms for uncertainty assessment and prediction of apriori unknown, dynamic obstacles using data-driven techniques. We use a technique from signal processing literature called Singular Spectrum Analysis for making linear predictions of dynamic obstacles. The obstacle motion predictions are equipped with error predictions to account for the uncertainty in the sensing heuristically using bootstrapping techniques. We use a statistical tool, Adaptive Conformal Inference, to further calibrate the heuristic error prediction online to obtain true uncertainty prediction while using nonstationary data to analyze the performance of the data-driven predictor. These techniques provide reactive, real-time, risk-aware obstacle avoidance in dynamic environments.
", "doi": "10.7907/xv2b-tj24", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15094", "collection": "thesis", "collection_id": "15094", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01302023-023806052", "primary_object_url": { "basename": "sjhan_thesis-2023-u.pdf", "content": "final", "filesize": 6220970, "license": "other", "mime_type": "application/pdf", "url": "/15094/4/sjhan_thesis-2023-u.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Control and State-Estimation of Jump Stochastic Systems by Learning Recurrent Spatiotemporal Patterns", "author": [ { "family_name": "Han", "given_name": "SooJean", "orcid": "0000-0003-1195-6465", "clpid": "Han-SooJean" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Wierman", "given_name": "Adam C.", "orcid": "0000-0002-5923-0199", "clpid": "Wierman-A-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis establishes control and estimation architectures that combine both model-based and model-free methods by theoretically characterizing several types of jump stochastic systems (JSSs), i.e., systems with random and repetitive jump phenomena. By expanding the capabilities of model-based stochastic control and estimation, there is potential for artificial intelligence to be implemented as a supplement to theory-influenced design instead of being used end-to-end. We begin by deriving sufficient conditions for stochastic incremental stability for nonlinear systems perturbed by two types of non-Gaussian noise: 1) shot noise processes represented as compound Poisson processes, and 2) finite-measure L\u00e9vy processes constructed as affine combinations of Gaussian white and Poisson shot noise processes. We then present a controller architecture based on a concept we call pattern-learning for prediction (PLP) for discrete-time/discrete-event systems, in which we can take advantage of the fact that the underlying jump process is a sequence of random variables that occurs as repeated patterns of interest. Finally, we demonstrate control and estimation for JSSs in three real-world applications. First, we consider the control of networks with dynamic topology (e.g., power grid with fault-tolerance to downed lines), for which PLP is integrated with variations of the novel system-level synthesis framework for disturbance-rejection. Second, we perform congestion control of vehicle traffic flow over metropolitan intersection networks, for which PLP is extended to pattern-learning with memory and prediction (PLMP) via the inclusion of episodic control, designed to reduce memory consumption by exploiting structural symmetries and temporal repetition in the network. Third, we perform estimation and forecasting (the dual problem to control) for epidemic spread throughout a population network under jump phenomena such as superspreader effects and the emergence of variant viruses. Our results indicate that learning patterns in the jump process makes controller/observer design efficient in data-consumption and computation time, which suggests that it can potentially be used for other JSSs in the real world.", "doi": "10.7907/gyae-jv94", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15194", "collection": "thesis", "collection_id": "15194", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05192023-001330664", "type": "thesis", "title": "Engineering of Second-Generation Acoustic Reporter Genes", "author": [ { "family_name": "Hurt", "given_name": "Robert Cooper", "orcid": "0000-0002-4347-6901", "clpid": "Hurt-Robert-Cooper" } ], "thesis_advisor": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "thesis_committee": [ { "family_name": "Lester", "given_name": "Henry A.", "orcid": "0000-0002-5470-5255", "clpid": "Lester-H-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "A major outstanding challenge in the fields of biological research, synthetic biology, and cell-based medicine is visualizing the functions of natural and engineered cells noninvasively inside opaque organisms. Ultrasound imaging has the potential to address this challenge as a widely available technique with a tissue penetration of several centimeters and spatial resolution below 100 \u00b5m. Recently, the first genetically encoded acoustic reporters were developed based on bacterial gas vesicles (GVs) to link ultrasound signals to molecular and cellular function. However, the properties of these first-generation acoustic reporter genes (ARGs) resulted in limited sensitivity and specificity for imaging gene expression in vivo.
\r\n\r\nThe goal of my thesis work has been to engineer second-generation ARGs with improved acoustic and expression phenotypes compared to the existing first-generation constructs. I took two complementary engineering approaches to developing these constructs: homolog screening and directed evolution, sometimes referred to as the \u201cnature and nurture\u201d of protein engineering. The resulting constructs offer major qualitative and quantitative improvements, including much stronger ultrasound contrast, the ability to produce nonlinear signals distinguishable from background tissue in vivo, stable long-term expression, and compatibility with in vitro multiplexed imaging. In collaboration with others in the lab, we demonstrate the capabilities of these next-generation ARGs by imaging in situ gene expression in mouse models of breast cancer and tumor-homing therapeutic bacteria, noninvasively revealing the unique spatial distributions of tumor growth and colonization by therapeutic cells in living subjects and providing real-time guidance for interventions such as needle biopsies.
\r\n\r\nThis thesis is organized as follows: in the first two chapters, I introduce the key background needed to understand both the importance and properties of ARGS, and how they have been and could be engineered. In the next two chapters, I detail specific efforts to engineer them\u2014one involving the construction of a high-throughput, semi-automated setup for acoustic phenotyping of cells and its application to ARG directed evolution, and another involving the screening of several GV cluster homologs to identify ones suitable for use as improved ARGs. Finally, I conclude with insights gleaned from these two ARG engineering projects and suggestions for future ones.
\r\n\r\nThe approaches, results, and ideas presented in this thesis represent the current state-of-the-art in ARG engineering and application. While recent technology development in this field has unlocked exciting new use cases for ARGs in noninvasive biological imaging, most of their potential for basic science and disease diagnosis and treatment has yet to be realized.
", "doi": "10.7907/qs6v-5d67", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14986", "collection": "thesis", "collection_id": "14986", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07252022-061122576", "primary_object_url": { "basename": "Thesis Ronghui Zhu.pdf", "content": "final", "filesize": 31903908, "license": "other", "mime_type": "application/pdf", "url": "/14986/1/Thesis Ronghui Zhu.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Multicellular Circuit Design in Mammalian Cells", "author": [ { "family_name": "Zhu", "given_name": "Ronghui", "orcid": "0000-0001-8171-482X", "clpid": "Zhu-Ronghui" } ], "thesis_advisor": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Hay", "given_name": "Bruce A.", "orcid": "0000-0002-5486-0482", "clpid": "Hay-B-A" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Multicellular circuits control the development of multicellular organisms, through programming processes such as cell proliferation, cell differentiation, cell movement, and cell signaling. A fundamental goal of biology is to understand the design principles of these multicellular circuits, and use these principles to design synthetic multicellular systems for therapeutic purposes. Top-down approaches, for example analyzing embryos bearing genetic mutations, have identified key genes in many multicellular circuits, but are challenging to study these circuits in an isolated context and in a quantitative and systematic manner. An alternative, complementary approach is to engineer or reconstitute multicellular circuits from bottom-up, which allows us to overcome the limitations of top-down approach and gain quantitative insights into multicellular circuit design. In this thesis, we use this bottom-up approach to explore the design principles of two multicellular circuits. In the first project, we took inspiration from two prevalent features from natural multistable circuits, namely competitive protein-protein interactions and positive autoregulation, to design a synthetic multistable circuit architecture called MultiFate. Both in the model and in the experiment, MultiFate circuits generate multiple cellular states, each stable for weeks, allow control over state-switching and state stability, and can be easily expanded to generate more states. In the second project, we use a gradient reconstitution system to systematically analyze a gradient modulation circuit consisting of BMP4 and its modulators, Chordin, Twsg and BMP-1. We found that the circuit can give rise to diverse gradient modulation capabilities. In particular, the full circuit is sufficient for active ligand shuttling and generation of non-monotonic displaced gradient. These multicellular circuits could provide a foundation for engineering synthetic multicellular systems in mammalian cells.
", "doi": "10.7907/p0fn-qa56", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15093", "collection": "thesis", "collection_id": "15093", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01272023-184413283", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 16608292, "license": "other", "mime_type": "application/pdf", "url": "/15093/1/Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Towards Integrated Molecular Machines: Structural, Mechanical, and Computational Motifs", "author": [ { "family_name": "Sarraf", "given_name": "Namita", "orcid": "0000-0001-8692-7429", "clpid": "Sarraf-Namita" } ], "thesis_advisor": [ { "family_name": "Qian", "given_name": "Lulu", "orcid": "0000-0003-4115-2409", "clpid": "Qian-Lulu" } ], "thesis_committee": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "orcid": "0000-0002-1653-3202", "clpid": "Rothemund-P-W-K" }, { "family_name": "Qian", "given_name": "Lulu", "orcid": "0000-0003-4115-2409", "clpid": "Qian-Lulu" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The programmability of DNA has made it well-suited for building molecular machines, performing nanoscale self-assembly, and computing via biochemical circuits. In the last few decades, great strides have been made in characterizing the interactions between DNA molecules such that they can be predicted and engineered.
\r\n\r\nThe development of frameworks for those interactions has enabled the construction of more complex molecular systems that can execute specified programs. Such programs have included mechanical tasks, like walking and sorting cargo; assembly and reconfiguration of 2D and 3D shapes; and computation, like Boolean logic and pattern recognition.
\r\n\r\nHowever, the continuing development of more complex molecular programs relies upon expanding the modules available for molecular systems to use to execute them. Expanded functionality of mechanical, structural, and computation modules are required in order to build compound systems that can interact with the physical world, reconfigure, and analyze signals in a variety of interesting ways. In this dissertation, we will discuss our contributions to this effort, which include exploring a motif for molecular robotic behavior, characterizing tile-tile interactions, and developing new capabilities for bimolecular circuits.
\r\n\r\nWithin the framework of a maze-solving molecular robot, we aim to implement walking behavior on DNA origami that introduces a surface modification via a four-way strand displacement reaction. Surprisingly, our experiments suggest that the walking behavior is at least two orders of magnitude slower than expected. To understand why, we quantitatively explore to what extent the speed and completion level of the robot can be modulated by design considerations such as toehold lengths, track redundancy, and strand purity. Another factor affecting the reaction rate is the number of tethering points, and we demonstrate an order of magnitude speed up in the four-way strand displacement reaction when we remove one tethering point. The characterization of a surface-modifying four-way strand displacement reaction is a useful tool for the continued development of molecular robots with more complex functionality.
\r\n\r\nFree-floating DNA origami tiles, called invaders here, can swap out DNA origami tiles within larger assemblies via a technique called tile displacement, which has previously been demonstrated using single tile and dimer invaders with 4- and 9-tile arrays. We introduce initial structures and invading assemblies with more complex shapes. We explore the robustness of this reaction by testing a variety of edge configurations and comparing their reaction rates. We demonstrate tunable growth of one of the invaders, which can grow into polymers of arbitrary length or close into 3D structures. By a tile displacement reaction, we reconfigure the 3D structures into 2D. The invaders with complex shapes are able to reconfigure the original tile assembly at rates comparable to simpler tile displacement reactions, and two reconfiguration events can take place sequentially or simultaneously.
\r\n\r\nFinally, we build two new modules for use with biochemical circuits. The first, a loser-take-all circuit, yields binary outputs indicating which analog signal is the smallest among all inputs. We implement a signal reversal function that converts the smallest input to the largest output, which can then be composed with a previously developed winner-take-all function to achieve loser-take-all. By making concentration adjustments, we can mitigate biases in the circuit that are a result of sequence-dependent different in reaction rates. We experimentally demonstrate a three-input loser-take-all circuit with nine input combinations. With further development, this circuit could be used to implement the activation function in neural networks that perform pattern classification according to which memory an input pattern is least similar to.
\r\n\r\nThe second circuit processes information using temporary memory. We design and implement a circuit that outputs distinct logic decisions based on relative timing information of a pair inputs and their logic values. We show that we can mitigate crosstalk in the circuit by utilizing mismatches and adjusting toehold lengths. The circuit is able to display clear ON-OFF separation at time intervals as short as one minute between the two inputs arriving.
", "doi": "10.7907/cdwp-c709", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15210", "collection": "thesis", "collection_id": "15210", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262023-141116640", "primary_object_url": { "basename": "HiroDissertation.pdf", "content": "final", "filesize": 18037879, "license": "other", "mime_type": "application/pdf", "url": "/15210/1/HiroDissertation.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Contraction Theory for Robust Learning-Based Control: Toward Aerospace and Robotic Autonomy", "author": [ { "family_name": "Tsukamoto", "given_name": "Hiroyasu", "orcid": "0000-0002-6337-266", "clpid": "Tsukamoto-Hiroyasu" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Pellegrino", "given_name": "Sergio", "orcid": "0000-0001-9373-3278", "clpid": "Pellegrino-S" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Watkins", "given_name": "Michael M.", "clpid": "Watkins-M-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Machine learning and AI have been used for achieving autonomy in various aerospace and robotic systems. In next-generation research tasks, which could involve highly nonlinear, complicated, and large-scale decision-making problems in safety-critical situations, however, the existing performance guarantees of black-box AI approaches may not be sufficiently powerful. This thesis gives a mathematical overview of contraction theory, with some practical examples drawn from joint projects with NASA JPL, for enjoying formal guarantees of nonlinear control theory even with the use of machine learning-based and data-driven methods. This is not to argue that these methods are always better than conventional approaches, but to provide formal tools to investigate their performance for further discussion, so we can design and operate truly autonomous aerospace and robotic systems safely, robustly, adaptively, and intelligently in real-time.
\r\n\r\nContraction theory is an analytical tool to study differential dynamics of a non-autonomous (i.e., time-varying) nonlinear system under a contraction metric defined with a uniformly positive definite matrix, the existence of which results in a necessary and sufficient characterization of incremental exponential stability of multiple solution trajectories with respect to each other. Its nonlinear stability analysis boils down to finding a suitable contraction metric that satisfies a stability condition expressed as a linear matrix inequality, resulting in many parallels drawn between linear systems theory and contraction theory for nonlinear systems. This yields much-needed safety and stability guarantees for neural network-based control and estimation schemes, without resorting to a more involved method of using uniform asymptotic stability for input-to-state stability. Such distinctive features permit the systematic construction of a contraction metric via convex optimization, thereby obtaining an explicit exponential bound on the distance between a time-varying target trajectory and solution trajectories perturbed externally due to disturbances and learning errors. The first two parts of this thesis are about a theoretical overview of contraction theory and its advantages, with an emphasis on deriving formal robustness and stability guarantees for deep learning-based 1) feedback control, 2) state estimation, 3) motion planning, 4) multi-agent collision avoidance and robust tracking augmentation, 5) adaptive control, 6) neural net-based system identification and control, for nonlinear systems perturbed externally by deterministic and stochastic disturbances. In particular, we provide a detailed review of techniques for finding contraction metrics and associated control and estimation laws using deep neural networks.
\r\n\r\nIn the third part of the thesis, we present several numerical simulations and empirical validation of our proposed approaches to assess the impact of our findings on realizing aerospace and robotic autonomy. We mainly focus on the two joint projects with NASA JPL: 1) Science-Infused Spacecraft Autonomy for Interstellar Object Exploration and 2) Constellation Autonomous Space Technology Demonstration of Orbital Reconfiguration (CASTOR), where we also perform hardware demonstrations of our methods using our thruster-based spacecraft simulators (M-STAR) and in high-conflict, distributed, intelligent UAV swarm reconfiguration with up to 20 UAVs (crazyflies).
", "doi": "10.7907/rznp-g568", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15275", "collection": "thesis", "collection_id": "15275", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-032907616", "primary_object_url": { "basename": "Taylor_Thesis_Submitted.pdf", "content": "final", "filesize": 31746445, "license": "other", "mime_type": "application/pdf", "url": "/15275/1/Taylor_Thesis_Submitted.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Robust Safety-Critical Control: A Lyapunov and Barrier Approach", "author": [ { "family_name": "Taylor", "given_name": "Andrew James", "orcid": "0000-0002-5990-590X", "clpid": "Taylor-Andrew-James" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Accompanying the technological advances of the past decade has been the promise for widespread growth of autonomous systems into nearly all domains of human society, including manufacturing, transportation, and healthcare. At the same time, there have been several tragic failures that reveal potential risks with the expansion of autonomous systems into everyday life, and indicate that it is vital for safety to be accounted for in the design of control systems.
\r\n\r\nThis thesis seeks to develop a theory of robust safety-critical control for autonomous systems. This theory will be built upon the foundational tools of Control Lyapunov Functions (CLFs) and Control Barrier Functions (CBFs), which provide a powerful paradigm for the design of model-based safety-critical controllers. The dependence of CLF and CBF-based controllers on a system model makes them susceptible to modeling inaccuracies, potentially resulting in unsafe behavior when deploying these controllers on real-world systems.
\r\n\r\nIn this thesis I present methods for resolving four classes of model inaccuracies referred to as model error, disturbances, measurement error, and input sampling, which are commonly faced challenges when designing controllers for robotic systems. The proposed methods are unified by their shared use of CLFs and CBFs to produce controllers possessing rigorous and robust safety guarantees that can be demonstrated in simulation or experimentally. A hallmark of these methods is a focus on enabling control synthesis through convex optimization, which ensures that controllers can be efficiently computed on real-world robotic hardware platforms.
\r\n\r\nIn addressing model error, I consider both data-driven learning approaches and adaptive control approaches. I present three episodic learning frameworks that iteratively augment existing CLF and CBF-based controllers specified via convex optimization problems to improve the stability and safety properties of a system, which I demonstrate in simulation and experimentally. I also establish a relationship between the degradation of stability and safety properties with the magnitude of residual learning error through the perspective of Input-to-State Stability (ISS) and Input-to-State Safety (ISSf). Lastly, I develop an adaptive safety-critical control framework for systems with parametric model error through the notion of adaptive CBFs.
\r\n\r\nIn addressing disturbances, I resolve challenges in balancing performance and robustness with ISSf-based controllers through the notion of Tunable Input-to-State Safety (TISSf), which permits prioritizing robustness to disturbances only when safety requirements are close to being violated. I demonstrate the capabilities of TISSf-based control design experimentally on an autonomous semi-trailer truck system that is subject to input disturbances due to complex unmodeled actuator dynamics. Lastly, I develop a framework for achieving ISSf-like finite-time safety guarantees for discrete-time systems subject to stochastic disturbances through the use of CBFs and convex optimization.
\r\n\r\nIn addressing measurement error, I develop the notion of Measurement-Robust CBFs (MR-CBFs), which permit control synthesis through convex optimization in the presence of imperfect measurements. I demonstrate the capability of MR-CBFs on an experimental Segway system using a vision-based measurement system, validating the tractability of using controllers specified through increasingly complex classes of convex optimization problems on real-world systems. Lastly, I present an application of Preference Based Learning (PBL) in tuning the robustness parameters of a CBF-based controller, demonstrating the first use of PBL with CBFs and providing a tool for tuning the safety and performance of the robust controllers proposed in this thesis.
\r\n\r\nIn addressing input sampling, I consider both sampled-data and event-triggered paradigms for modeling input sampling. I provide a method for synthesizing CLF-based controllers for sampled-data systems by integrating feedback linearization with approximate discrete-time models, leading to a significant improvement over continuous-time CLF-based controllers implemented with input sampling. I then develop a framework for achieving safety of sampled-data systems through approximate discrete-time models through the notion of practical safety and Sampled-Data CBFs (SD-CBFs), which I demonstrate with convex-optimization based controllers in simulation. Lastly, I develop a method for event-triggered safety-critical control that uses ISSf to achieve safety while satisfying the requirement of a minimum interevent time.
\r\n\r\nCollectively, these contributions constitute a significant advance in the theory of robust safety-critical control by establishing a framework, unified by the use of CLFs and CBFs in conjunction with convex optimization, that addresses a wide class of challenges faced in the design of safety-critical control systems.
", "doi": "10.7907/bpht-by81", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15262", "collection": "thesis", "collection_id": "15262", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012023-203113987", "type": "thesis", "title": "Distributed and Localized Model Predictive Control", "author": [ { "family_name": "Amo Alonso", "given_name": "Carmen", "orcid": "0000-0001-7593-5992", "clpid": "Amo-Alonso-Carmen" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Mazumdar", "given_name": "Eric V.", "orcid": "0000-0002-1815-269X", "clpid": "Mazumdar-Eric" }, { "family_name": "Matni", "given_name": "Nikolai", "orcid": "0000-0003-4936-3921", "clpid": "Matni-Nikolai" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The increasing presence of large-scale distributed systems highlights the need for scalable control strategies where only local communication is required. Moreover, in safety-critical systems it is imperative that such control strategies handle constraints in the presence of disturbances and enjoy theoretical and performance guarantees. In response to this need, we present the Distributed and Localized Model Predictive Control (DLMPC) algorithm for large-scale linear systems. DLMPC is a distributed closed-loop model predictive control (MPC) scheme wherein only local state and model information needs to be exchanged between subsystems for the computation and implementation of control actions. The resulting distributed algorithms tackle various types of additive disturbances and enjoy recursive feasibility and asymptotic stability guarantees that introduce minimal conservatism and can be computed in an offline fashion without adding to the computational burden. We also provide analysis and guarantees on the global performance of DLMPC, and demonstrate that in cases where the underlying topology of the system is sparse (as is the case in most large-scale networks), the inclusion of local communication constraints does not result in a suboptimal solution. Moreover, we show that when no noise is present, this algorithm can be extended to the purely data-driven case where all previous guarantees hold and the need for a model is fully replaced by past-trajectory data. We show that the amount of data needed for our synthesis problem is independent of the size of the global system. Lastly, we explore the potential of DLMPC for hardware accelerated implementation in GPU by exploiting the fact that the structure of the DLMPC problem captures some of the limitations of GPU computations. In all algorithmic and theoretical results presented in this thesis, only local information exchange is necessary, and computational complexity is independent of the global system size. DLMPC is the first MPC algorithm that allows for the scalable, efficient and data-driven computation and implementation of distributed closed-loop control policies and enjoys theoretical guarantees.", "doi": "10.7907/6pje-yd82", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15086", "collection": "thesis", "collection_id": "15086", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01172023-195222304", "type": "thesis", "title": "Applications of Dynamic Nucleic Acid Nanotechnology in Closed-Loop Genetic Circuits and Detection of Viral Pathogens", "author": [ { "family_name": "Huang", "given_name": "Jining", "orcid": "0000-0002-3798-4790", "clpid": "Huang-Jining" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Nucleic acid nanotechnologies have provided a platform where biologically relevant molecules can be engineered to perform programmable functions. Relative to proteins, complex nucleic acid-based systems can be designed more readily due to the countable nature of base-pairing interactions and readily available physical models. These features of nucleic acids enable us to design novel interaction pathways and functions by providing well-behaved molecular mechanisms. Two examples of these mechanisms are the conditional guide RNA (cgRNA) and the hybridization chain reaction (HCR). A cgRNA is a conditional programmable regulator where an expressed RNA trigger can conditionally turn on or off transcriptional regulation. HCR is a molecular mechanism for in vitro and in situ amplification of signals to spatially identify proteins, RNA, or DNA in a sample. This thesis will first demonstrate the use of these nucleic acid molecular mechanisms in closed-loop genetic circuits and infectious disease testing using cgRNAs and HCR, respectively, then provide updated tools for the nucleic acid design community to exploit the programmable nature of nucleic acids.
\r\n\r\nWe begin by demonstrating the use of conditional programmable cgRNAs in closed-loop genetic circuits. Synthetic genetic circuits allow scientists to engineer arbitrary molecular interactions in living organisms. Feedback circuits in particular are recurrently found in nature and enable useful functionalities. However, protein components of genetic circuits cannot be designed scalably, are often mined from preexisting genomes, and present difficulties in being biologically orthogonal to themselves or the host organism. We are motivated to address these limitations by using orthogonal nucleic acid circuits created de novo. One potential component of these circuits are conditional guide RNAs (cgRNAs). cgRNAs are switchable transcriptional regulators, and this allows gene expression to be modulated through the expression of a small RNA trigger. Here we assess cgRNAs as a component for feedback genetic circuits. As an initial demonstration of cgRNA synthetic circuits, we built and validated a simple threshold circuit and demonstrated its orthogonality and scalability by showing independent circuit functions of two switches in a single cell. We also created a larger toggle switch that is made from the same components as the previous switches. These experiments show the orthogonality and feedback capabilities of cgRNAs will position them as a composable component for scalable synthetic biology.
\r\n\r\nWe then used the hybridization chain reaction mechanism to develop an adaptable and sensitive test for the detection of SARS-CoV-2. The lateral flow assay format enables rapid, instrument-free, at-home testing for SARS-CoV-2. Due to the absence of signal amplification, this simplicity comes at a cost in sensitivity. Here, we enhance sensitivity by developing an amplified lateral flow assay that incorporates isothermal, enzyme-free signal amplification based on the mechanism of hybridization chain reaction (HCR). The simplicity of the user experience after the test begins is maintained by using a disposable 3-channel lateral flow device to automatically deliver reagents to the test region in three successive stages without user interaction. Prior to starting the test, a 15-minute heat step is required. Detecting gamma-irradiated SARS-CoV-2 virions in an extraction buffer, the current amplified HCR lateral flow assay achieves a limit of detection of 200 copies/\u00b5L using nucleic acid probes to target the SARS-CoV-2 RNA genome. By comparison, five commercial unamplified lateral flow assays that use proprietary antibodies to target the viral nucleocapsid protein exhibit limits of detection of 500 copies/\u00b5L, 1000 copies/\u00b5L, 2000 copies/\u00b5L, 2000 copies/\u00b5L, and 20,000 copies/\u00b5L. By swapping out nucleic acid probes to target different pathogens, amplified HCR lateral flow assays offer a platform for adaptable and sensitive at-home testing for emergent diseases.
\r\n\r\nComponents for the previous two projects are designed and analyzed with NUPACK. NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences. NUPACK algorithms are unique in treating complex and test tube ensembles containing arbitrary numbers of interacting strand species, providing crucial tools for capturing concentration effects essential to analyzing and designing the intermolecular interactions that are a hallmark of these fields. The all-new NUPACK web app (nupack.org) has been re-architected for the cloud, leveraging a cluster that scales dynamically in response to user demand to enable rapid job submission and result inspection even at times of peak user demand. The web app exploits the all-new NUPACK 4 scientific code base as its backend, offering enhanced physical models (coaxial and dangle stacking sub-ensembles), dramatic speedups (20-120\u00d7 for test tube analysis), and increased scalability for large complexes.
", "doi": "10.7907/54tw-ym95", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16114", "collection": "thesis", "collection_id": "16114", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06122023-232029846", "primary_object_url": { "basename": "Werner_Thesis.pdf", "content": "final", "filesize": 34782096, "license": "other", "mime_type": "application/pdf", "url": "/16114/2/Werner_Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Uncertainty and Decentralization: Two Themes in an Energy Transformation", "author": [ { "family_name": "Werner", "given_name": "Lucien Desloge", "orcid": "0000-0003-1613-1702", "clpid": "Werner-Lucien-Desloge" } ], "thesis_advisor": [ { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Wierman", "given_name": "Adam C.", "orcid": "0000-0002-5923-0199", "clpid": "Wierman-A-C" } ], "thesis_committee": [ { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Wierman", "given_name": "Adam C.", "orcid": "0000-0002-5923-0199", "clpid": "Wierman-A-C" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_eng" } ], "abstract": "Over the last two decades, the rapidly decreasing units costs of solar, wind, and energy storage technologies have launched a fundamental transformation in how electric power is produced, distributed, and consumed. Proliferation of these technologies has effected a shift towards a more decentralized, flexible, and sustainable energy system that can meet the growing demand for energy while reducing greenhouse gas emissions from fossil fuels. The work in this thesis studies two principal themes in this transformation: uncertainty and decentralization.
\r\n\r\nUncertainty is a key challenge in the modern grid resulting from the weather dependence of variable renewables and volatile loads like electric vehicles distributed throughout the grid. Electricity markets, whose function is to regulate the precise balance of supply and demand across the system, face a pressing need for dispatch mechanisms that account for uncertainty while providing participation incentives for generators and loads. We introduce a framework for multi-stage market dispatch and pricing under a general description of forecast uncertainty that enables system operators to explicitly incorporate uncertainty into market-clearing prices. In related work, we study mechanisms that guarantee feasibility of multi-interval dispatch under robust uncertainty and provide participation incentives for shiftable demand response in forward multi-interval markets.
\r\n\r\nThe trend towards a more decentralized energy system stems from the inherent modularity of distributed energy resources (DERs), such as solar and storage, as well as the persistent growth in end-use loads. This evolution presents significant challenges to system operators who typically lack the tools and processes for managing a complex, distributed power system. To fill this gap, we introduce and implement a Microgrid Operating System (OS), a software platform for monitoring, modeling, and optimizing microgrids and distribution systems. The Microgrid OS is a central layer that links DER hardware, such as batteries, solar, and flexible loads, to energy applications like cost minimization, emissions reduction, and wholesale market participation. The core functions it provides are data acquisition and processing, system modeling and learning, and optimization and control. We present key modules of the Microgrid OS in the context of several implementation projects in microgrids, commercial buildings, and distribution networks.
", "doi": "10.7907/scmm-p028", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16107", "collection": "thesis", "collection_id": "16107", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06122023-162907795", "primary_object_url": { "basename": "Akella_Prithvi_2023.pdf", "content": "final", "filesize": 20419417, "license": "other", "mime_type": "application/pdf", "url": "/16107/1/Akella_Prithvi_2023.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Reliable Controller Synthesis: Guarantees for Safety-Critical System Testing and Verification", "author": [ { "family_name": "Akella", "given_name": "Prithvi", "orcid": "0000-0003-4375-0015", "clpid": "Akella-Prithvi" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Chandy", "given_name": "K. Mani", "orcid": "0000-0001-9190-1290", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The well-known quote by George Box states that \"All models are wrong, but some are useful\", and the controls and robotics communities alike have followed a similar paradigm to make significant theoretical and practical advances in the study of controllable systems to date. However, recent robotic system requirements include formal considerations for system safety, especially as we engineer systems that are required to work alongside us in our daily lives. As such, current research directions require analyses that consider these inaccurate system models, our inaccurate understanding of the environments in which these systems operate, and their combined effects on safe, effective system operation, e.g. the canonical autonomous driving problem in exceedingly difficult-to-model urban environments. Recently, this has led to burgeoning efforts in a formal study of controller verification. Specifically, verification denotes the process of determining whether a controller steers its system to exhibit desired behaviors despite the variety of environments the system might face during operation, e.g. whether the autonomous car's controller successfully drives the car to a destination without crashing into obstacles or pedestrians along the way. However, formalization of such a verification pipeline has proved difficult to date, especially since both the models we use for controller synthesis and our understanding of system environments are typically inaccurate.
\r\n \r\nAs a result, this thesis describes our efforts in the development of a formal verification pipeline that addresses a few key challenges in traditional approaches to safety-critical system verification. The first contribution centers on difficult, reactive test synthesis. By test synthesis, we mean the construction of a (potentially difficult) environment in which we require the system under test to perform its objective, e.g. placement of parked cars around which an autonomous vehicle must park. Typically phrased as an optimization problem over the space of allowable environments, these tests are \"static\" insofar as they do not react to the system's choices made during the test. We posit that such reactivity could more accurately identify worst-case system behavior. As a result, we phrase reactive, maximally difficult test synthesis as a game-theoretic optimization problem, leveraging the same control theoretic tools that facilitate safety-critical controller synthesis - control barrier functions and signal temporal logic. We prove that our proposed synthesis technique is always solvable and always produces a realizable test environment. Finally, we showcase our results by synthesizing reactive tests for both single and multi-agent systems.
\r\n\r\nThe second set of contributions centers on our efforts in uncertainty quantification. Due to un-modeled system and environmental aspects affecting system evolution in unpredictable ways, real-life systems need not realize the same paths every time. As such, typical analyses phrase verification as an optimization problem minimizing the expected value of a function over system trajectories with the expectation taken over this path variability, the distribution for which is assumed to be known. However, we posit that such an analysis should be risk-aware, i.e. account for this variability in a more principled fashion than an expectation-specific analysis, and should not assume apriori knowledge of the distribution corresponding to path variability, as it will be unknown in practice. To that end, we develop methods to bound a subset of risk measures for random variables whose distributions are unknown. This subset includes both Value-at-Risk and other, coherent risk measures heavily utilized in the controls and robotics communities. Simultaneously, we note that the same procedure can be applied to a wide class of non-convex optimization problems. In doing so, we develop a percentile-based optimization approach that rapidly identifies percentile solutions to optimization problems, i.e. a 90-th percentile solution is as good as 90% of solutions in the considered decision space.
\r\n\r\nThe third set of contributions focuses on the application of the prior mathematical developments to facilitate both risk-aware safety-critical system verification and controller synthesis. We phrase risk-aware controller verification as a risk-measure identification problem and utilize the prior bounding results to provide an efficient, dimensionally-independent verification procedure. Then, we phrase risk-aware controller synthesis as an optimization problem maximizing the bound provided by our risk-aware verification method, and show that this problem is solvable by the percentile optimization methods mentioned prior. Finally, we lay the foundation for the utilization of the aforementioned mathematical developments in other aspects of controls and robotics and communities more broadly. We show how risk-measure bounding can augment models both offline and online to robustify safety-critical controllers, how percentile optimization can facilitate \"optimal\" input selection and guarantee generation for non-convex finite-time optimal controllers, and how multiple applications of the percentile approach can also bound the optimality gap of reported percentile solutions. We showcase all these results on hardware for multiple systems and highlight the data efficiency of our proposed approaches.
", "doi": "10.7907/jej3-4444", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15082", "collection": "thesis", "collection_id": "15082", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01072023-214003146", "primary_object_url": { "basename": "ProsTHESIS.pdf", "content": "final", "filesize": 19996579, "license": "other", "mime_type": "application/pdf", "url": "/15082/1/ProsTHESIS.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Model-Based Lower-Limb Powered Prosthesis Control: Developing and Realizing Nonlinear Subsystem Control Methods for Generalizable Prosthesis Control", "author": [ { "family_name": "Gehlhar", "given_name": "Rachel", "orcid": "0000-0002-4838-8839", "clpid": "Gehlhar-Rachel" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "While there are over 600,000 lower-limb amputees in the US, commercially available prostheses remain limited to mostly passive devices. People that walk with a passive prosthesis experience an increase in energy expenditure, a decrease in comfortable walking speed, and gait asymmetry which leads to degenerative conditions. To address these limitations, researchers have developed powered prostheses with the aim of replicating the net positive energy biological limbs supply to humans in walking. These active devices have been shown to decrease users' metabolic cost and increase their comfortable walking speed. However, the control methods to achieve these results typically require hours of heuristic tuning for every user and every behavior. This motivates developing more formal prosthesis control methods that generalize between users.
\r\n\r\nFormal nonlinear control methods have been developed to realize energy efficient, human-like walking on bipedal robots. These model-based approaches provide a systematic approach to generate and realize provably stable walking gaits. However, these methods cannot be directly applied to prostheses since they depend on a dynamic model of the entire system, and in the case of the prosthesis, the human dynamics are unknown.
\r\n\r\nTo address this challenge, we develop a theoretical framework to translate model-based bipedal control methods to prostheses with the aim of realizing a generalizable prosthesis control method. We separate the prosthesis subsystem from the remaining human portion of the system and model the human's impact on the prosthesis dynamics with a measure of the interaction forces between the human and the prosthesis. We theoretically prove that a model-based controller developed in this separable subsystem framework is equivalent to one developed with knowledge of the full-order human-prosthesis system. With control Lyapunov functions, we develop a wider class of subsystem controllers that solely depend on local information but provide full-order system guarantees, even in the presence of force estimate errors. This work bridges the gap between bipedal control methods and prostheses, allowing us to leverage the benefits of model-based approaches on prostheses.
\r\n\r\nWe demonstrated a controller of this class through an online optimization-based approach on a powered knee-ankle prosthesis, realizing the first model-dependent lower-limb prosthesis controller that accounts for the interaction force between the human and the prosthesis. For a first pass, a force-estimation method was used that yields improved tracking of the desired trajectories over model-independent prosthesis control methods. Then, we incorporated a load cell into the prosthesis platform at the human-prosthesis attachment point to measure the interaction forces, and an inertial measurement to measure the rotation and velocity of the human's thigh. These two sensors completed the prosthesis dynamics model. A pressure sensor incorporated into the prosthesis' shoe measured the ground reaction forces, enabling the prosthesis to respond to its real-world environment, proving robust to 4 different terrains. We extended this controller to a multi-domain hybrid system approach to model the changing contact points occurring in human heel-toe roll. By allowing the prosthesis to sense the human's large varying dynamic load and respond accordingly, this model-based prosthesis controller emulated subject-specific human kinematic trends on a knee-ankle prosthesis for two subjects with no tuning in between, suggesting this approach could yield a method that generalizes between users.
", "doi": "10.7907/6724-6e14", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15071", "collection": "thesis", "collection_id": "15071", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12022022-073109279", "primary_object_url": { "basename": "2022_12_05_JTM_Thesis_v037.pdf", "content": "final", "filesize": 8086854, "license": "other", "mime_type": "application/pdf", "url": "/15071/1/2022_12_05_JTM_Thesis_v037.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Engineering and Rapid Prototyping for Biology in Extreme Conditions", "author": [ { "family_name": "Meyerowitz", "given_name": "Joseph Toshiro", "orcid": "0000-0002-3426-0885", "clpid": "Meyerowitz-Joseph-Toshiro" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-3426-0885", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this thesis we show three projects in which biological systems are engineered for increased robustness to environmental stressors such as toxic small molecules. Several lignocellulose-derived growth inhibitors commonly found in industrial feedstocks for fermentation were used to grow a panel of yeast knockouts for several efflux pumps and detoxifying enzymes. Some specific knockout strains showed slowed growth on specific growth inhibitors, while other knockout strains showed the same growth rate as the wild-type. One efflux pump was identified for vanillin, YHK8, and was overexpressed in yeast. The overexpression strain did not show an improved tolerance to vanillin, and grew more slowly than the wild-type. To regulate the expression of the vanillin pump, a sensor for vanillin was created. The starting enzyme was the wild-type qacR transcription factor, and several variants were generated using computational protein design. The designs were synthesized and tested using in vitro transcription-translation (TX-TL) as part of a rapid prototyping process. This rapid prototyping considerably sped up the design-build-test process. Finally, four bacteria, Pseudomonas synxantha 2-79, Pseudomonas chlororaphis PCL1391, Pseudomonas aureofaciens 30-84, and E. coli are tested against the same lignocellulose growth inhibitors. The Pseudomonas spp. show an improved tolerance to the growth inhibitors. We then develop some ability to engineer and prototype in all three species. A panel of promoter parts were integrated into the P. synxantha genome to produce a collection of test strains. These same promoter parts were also used as DNA templates for TX-TL reactions. The in vivo measurements of promoter strength and in vitro measurements show similar relative strengths between the parts, showing the Pseudomonas-based TX-TL systems can be used for design-build-test activities in these non-model organisms. This alternate approach to developing tolerance, starting with a species that already has a working tolerance to the stressor in question, changes the problem to one of building engineering capabilities in the new chassis.", "doi": "10.7907/9gbb-n831", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16069", "collection": "thesis", "collection_id": "16069", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-235550987", "primary_object_url": { "basename": "Thesis_Kai_Matsuka.pdf", "content": "final", "filesize": 14316975, "license": "other", "mime_type": "application/pdf", "url": "/16069/1/Thesis_Kai_Matsuka.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Vision-Based Navigation and Large-Scale Estimation for Spacecraft Swarms", "author": [ { "family_name": "Matsuka", "given_name": "Kai", "orcid": "0000-0003-2116-9756", "clpid": "Matsuka-Kai" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Watkins", "given_name": "Michael M.", "clpid": "Watkins-M-M" }, { "family_name": "Hadaegh", "given_name": "Fred", "orcid": "0000-0002-0992-6323", "clpid": "Fred-Hadaegh" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "There has been dramatic growth in the space industry over the past 20 years. Around the same time, robotics and autonomy research has advanced significantly, resulting in a plethora of new mission concepts employing autonomy, such as on-orbit inspection, mission extension, space structure assembly, and orbital debris removal becoming within the realm of possibility. Two of the key autonomous technologies that are critical to the success of these missions are (1) advanced coordination of multi-agent systems and (2) robust vision-based navigation for on-orbit servicing in close proximity. However, there are challenges to simply applying the existing technology to space systems. First, there are domain-specific challenges that are unique to space, such as orbital mechanics and harsh lighting conditions. Second, even at a theoretical level, previous works in the controls and robotics literature are limited when applied to large-scale, locally coupled systems such as spacecraft swarms. To this end, this thesis develops novel algorithms for addressing these gaps.
\r\n\r\nIn the first part of the thesis, we present a decentralized, scalable algorithm for swarm localization, called the Decentralized Pose Estimation (DPE) algorithm. With the DPE algorithm, each spacecraft computes relative navigation estimates with respect to others in the swarm but achieves higher performance through the benefit of multi-agent coordination. The DPE algorithm considers both communication and relative sensing graphs and defines an observable local formation. Each spacecraft jointly localizes its local subset of spacecraft using direct and communicated measurements. Since the algorithm is local, the algorithm complexity does not grow with the number of spacecraft in the swarm. As part of the DPE, we present the Swarm Reference Frame Estimation (SRFE) algorithm, a distributed consensus algorithm to co-estimate a common Local-Vertical, Local-Horizontal frame. The DPE combined with the SRFE provides a scalable, fully-decentralized navigation solution that improves the estimation accuracy compared to when without multi-agent coordination. Numerical simulations and experiments using Caltech's robotic spacecraft simulators are presented to validate the effectiveness and scalability of the DPE algorithm. We show that DPE has much higher accuracy than the best possible estimate without any coordination, while simultaneously being scalable to an arbitrarily large number of agents.
\r\n\r\nIn the second part of the thesis, we propose a novel computer vision algorithm to track the pose of an unknown and uncooperative target using multiple decentralized observers. Vision-based pose determination of an unknown target is challenging due to factors such as lack of cooperative visual markers and harsh lighting conditions of space, and the problem is even harder for distributed observers. To address this challenge, we develop the algorithm called the Multi-Spacecraft Simultaneous Estimation of Pose and Shape algorithm or MSEPS. Within MSEPS, a team of chaser spacecraft, each equipped with a monocular camera, exchange information over a local network to jointly estimate the relative kinematic state of the target and its sparse shape landmarks. In this approach, each spacecraft processes its images and extracts its own set of visual keypoints in parallel. Then, the team uses the local network to jointly estimate the target pose and shape in a distributed fashion by applying the consensus algorithm over the inter-spacecraft communication links. To the best of the authors' knowledge, this is the first cooperative vision-based algorithm for estimating the pose and shape of a space object by means of an arbitrary number of spacecraft.\r\nWe validate our algorithm using simulations of relative orbits and observations captured by each chaser spacecraft and show the multiple observers successfully agree on a consistent estimate and track the target pose accurately.
\r\n\r\nIn the third part of the thesis, we develop some new simulation tools that bridge the gap between robotics and space technology. When developing robotics algorithms for on-orbit systems such as DPE and MSEPS, we identified a need for new simulation tools that tightly integrate robotics algorithms with high-fidelity models of space environments such as astrodynamics effects and visual conditions. To this end, we first develop a ROS2-compatible software interface for Basilisk, the open-source astrodynamics simulation software. This tool allows running Basilisk in parallel with ROS2 in real-time and translates messages between Basilisk modules and ROS2 modules, such that control algorithms implemented in ROS2 can interact with the high-fidelity dynamics within Basilisk in a closed-loop fashion. Second, we develop a ROS2-compatible camera simulation module that uses the Neural Radiance Fields (NeRF) to rapidly generate novel images. These synthetic images are used as inputs to validate the vision-based navigation algorithm in a closed-loop fashion. To validate these simulation tools, we also developed a set of autonomous algorithms for on-orbit inspection and use the simulated measurements as inputs to the algorithm. The real-time numerical simulations demonstrate that our tools can be integrated with autonomy algorithms implemented in ROS2 in a closed-loop fashion to validate the feasibility of the mission.
\r\n\r\nIn the process of addressing some lessons learned from DPE and MSEPS works, we identified that there is a gap in general frameworks for solving the optimal estimation problems for probabilistic inference of large-scale problems involving networked systems. This gap is not just applicable to spacecraft swarms, but also to a general class of large-scale, multi-agent problems in robotics and controls such as localization and mapping, wireless sensor networks, and electrical power grids. Therefore, in the fourth part of the thesis, we address this fundamental gap by developing novel algorithms for Distributed Factor Graph Optimization (DFGO) problems that arise in large-scale networked systems. We develop algorithms for both batch and real-time problems. First, for the batch DFGO problem, we derive a type of the Alternating Direction Method of Multipliers (ADMM) algorithm called the Local Consensus ADMM (LC-ADMM). LC-ADMM is fully localized; therefore, the computational effort, communication bandwidth, and memory for each agent scale like O(1) with respect to the network size. We establish two new theoretical results for LC-ADMM: (1) exponential convergence when the objective is strongly convex and has a Lipschitz continuous subdifferential, and (2) o(1/k) when the objective is convex and has a unique solution. We also show that LC-ADMM allows the use of non-quadratic loss functions, such as l1-norm and Huber loss. Second, we also develop the Incremental DFGO algorithm (iDFGO) for real-time problems by combining the ideas from LC-ADMM and the Bayes tree. To derive a time-scalable algorithm, we exploit the temporal sparsity of the real-time factor graph and the convergence of the augmented factors of LC-ADMM. The iDFGO algorithm incrementally recomputes estimates when new factors are added to the graph and is scalable with respect to both network size and time. We validate LC-ADMM and iDFGO in simulations with examples from multi-agent Simultaneous Localization and Mapping (SLAM) and power grids.
", "doi": "10.7907/spf8-8p84", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14394", "collection": "thesis", "collection_id": "14394", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10122021-213903517", "type": "thesis", "title": "Koopman-based Learning and Control of Agile Robotic Systems", "author": [ { "family_name": "Folkestad", "given_name": "Carl A. A.", "orcid": "0000-0002-3436-8247", "clpid": "Folkestad-Carl-A-A" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Learning methods to enable high performance control systems have recently shown promising results in selected environments and applications. These advances promote the next generation of autonomous robots capable of significantly improving efficiency, cost, and safety in their respective domains. Importantly, these systems are safety-critical and operate in proximity to humans in diverse and uncertain environments. As a result, operational failures may cause significant material and societal losses. Additionally, robot learning and control are further complicated by requiring fast controller update rates and operational constraint satisfaction.
\r\n\r\nTo address these challenges, this thesis presents multiple methods based on Koopman operator theory. The first approach develops algorithms to learn lifted-dimensional models of nonlinear systems and leverages the models in model predictive control (MPC) design. Koopman-based methods typically employ hand-crafted observable functions to \"lift\" the state variables to the higher dimensional space. For most systems, this leads to poor prediction performance and inefficient use of data and computational resources. Instead, I present methods that generate observable functions from data, both based on underlying theory and by incorporating the observable functions and model structure in a neural network model. This allows lower dimensional models, important for real-time control, and enables the nonlinearities of control-affine dynamics to be captured, crucial to describing many robotic systems. I use quadrotor drones to experimentally demonstrate that the learned models combined with MPC can achieve close to optimal behavior while respecting important operational constraints.
\r\n \r\nThe last part of the thesis is concerned with endowing systems with an arbitrary nominal control policy with safety guarantees. Control barrier functions (CBFs) are a powerful tool to achieve this, yet they rely on the computation of control invariant sets, which is notoriously difficult. To avoid this, a backup strategy can be used to implicitly define a control invariant set. However, this requires forward integration of the system dynamics under a backup controller, which is prohibitively expensive for realistic systems. I present a method that replaces the expensive integration using learned Koopman operators of the closed-loop dynamics. As a result, the online computation time required to evaluate the controller is drastically reduced, enabling real-time use. I also derive an error bound on the unmodeled dynamics in order to robustify the CBF controller and demonstrate the method on multi-agent collision avoidance for wheeled robots and quadrotors.
", "doi": "10.7907/2t6d-j206", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14467", "collection": "thesis", "collection_id": "14467", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01042022-184525578", "type": "thesis", "title": "Development and Scaling of Differentiation Circuit Architectures for Improving the Evolutionary Stability of Burdensome Functions in E. coli", "author": [ { "family_name": "Williams", "given_name": "Rory Logan", "orcid": "0000-0003-2605-5790", "clpid": "Williams-Rory-Logan" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Bois", "given_name": "Justin S.", "orcid": "0000-0001-7137-8746", "clpid": "Bois-J-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "With advances in the sequencing and synthesis of DNA, automation, and computation, we are increasingly able to rapidly and reliably program functions into cells. However, because the functions we engineer cells to perform are often both unnecessary for the cell\u2019s survival and burdensome to cell growth, mutation and natural selection can rapidly lead to loss of function. Though numerous strategies have made headway, improving the evolutionary stability of engineered functions remains a goal of the synthetic biology community. To address this problem generally, we developed a strategy relying on integrase-mediated recombination which allows non-producing progenitor cells to differentiate at a tunable rate, thereby continuously replenishing producer cells expressing the orthogonal T7 RNAP. While this strategy removes selective pressure for mutations inactivating the function of interest in the progenitor cell population, a strategy of terminal differentiation, in which the capacity of differentiated cells to grow is limited, was necessary to prevent the expansion of such mutations in the differentiated cell population. To experimentally implement terminal differentiation, we co-opted the R6K plasmid system, using differentiation to simultaneously activate expression of T7 RNAP, and inactivate expression of \u03c0 protein (an essential factor for R6K plasmid replication), thereby allowing limitation of differentiated cell growth through antibiotic selection. Critically, we demonstrated computationally that terminal differentiation endows the circuit with robustness to mutations which disrupt T7 RNAP driven expression, and to plasmid instability effects that result in decreased expression. Intuitively and computationally identifying the category of mutations which disrupt the differentiation process as the Achilles's heel of terminal differentiation, we developed a redundant architecture using a novel split-\u03c0 protein system which required 2 mutations to break the circuit. We experimentally demonstrated a trade-off between rate of production and duration of function as the differentiation rate is tuned, an increased benefit of terminal differentiation with higher-burden expression, and that redundancy improves the evolutionary stability of the terminal differentiation architecture. Specifically we achieve a maximum of ~2.8x (single-cassette terminal differentiation) and ~4.2x (redundant terminal differentiation) the total fluorescent protein production achieved from comparable high-burden naive expression in which all cells inducibly express T7 RNAP. We further demonstrate differentiation can enable the expression of even toxic functions, and develop a terminal differentiation circuit architecture which will allow the degree of redundancy and therefore the evolutionary stability of the architecture to be scaled to arbitrary degrees.
", "doi": "10.7907/5k67-b636", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14373", "collection": "thesis", "collection_id": "14373", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09262021-022402778", "primary_object_url": { "basename": "clamons_sam_2021.pdf", "content": "final", "filesize": 16274905, "license": "other", "mime_type": "application/pdf", "url": "/14373/1/clamons_sam_2021.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Three Problems in the Design and Specification of Biomolecular Circuits", "author": [ { "family_name": "Clamons", "given_name": "Samuel Eric", "orcid": "0000-0002-7993-2278", "clpid": "Clamons-Samuel-Eric" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "orcid": "0000-0002-1653-3202", "clpid": "Rothemund-P-W-K" }, { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Programming biological materials is a daunting challenge. Although part of this challenge is practical -- cloning is difficult, synthesizing DNA is expensive at scale, etc. -- a number of the challenges of bioengineering (and synthetic biology in particular) are problems of design and specification. If we could place arbitrary molecules on a surface with perfect precision, what should we place and where? If we could arbitrarily change the genetic content of a cell, even with perfect knowledge of the function and action of every component, what changes would actually enact the functions we want that cell to have? In this thesis, we explore three specific design and specification challenges at three different levels of abstraction, and demonstrate methods for overcoming them. On the level of design language, we use a specialized class of cellular automaton to probe what chemistry can do when restricted to a surface. On the level of \\textbf{part specification}, we use several models of CRISPR/Cas9-based transcriptional regulators to understand what dynamic functions those regulators can perform and why, and provide some some suggestions for how to engineer such regulators to more robustly perform those functions. On the level of module design, we consider an easy-to-encounter trap in when modeling a replicating DNA species in a CRN-based biocircuit simulation, for which we suggest a simple, flexible, biologically-plausible workaround.
", "doi": "10.7907/9b4h-8f95", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14637", "collection": "thesis", "collection_id": "14637", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272022-171138586", "primary_object_url": { "basename": "deposit_thesis.pdf", "content": "final", "filesize": 26224719, "license": "other", "mime_type": "application/pdf", "url": "/14637/1/deposit_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Autonomous Temporal Understanding and State Estimation during Robot-Assisted Surgery", "author": [ { "family_name": "Qin", "given_name": "Yidan", "orcid": "0000-0002-7766-1021", "clpid": "Qin-Yidan" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel W.", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Tai", "given_name": "Yu-Chong", "orcid": "0000-0001-8529-106X", "clpid": "Tai-Yu-Chong" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Robot-Assisted Surgery (RAS) has become increasingly important in modern surgical practice for its many benefits and advantages for both the patient and the healthcare professionals, as compared to traditional open surgeries and minimally invasive surgeries such as laparoscopy. Artificial intelligence applications during RAS and post-operative analysis can provide various surgeon-assisting functionalities and could potentially achieve a better surgery outcome. These applications, ranging from providing surgeons with advisory information during RAS and post-operative analysis to virtual fixture and supervised autonomous surgical tasks, share a necessary prerequisite of a comprehensive understanding of the current surgical scene. This understanding should include the knowledge of the current surgical task being performed, the surgeon's actions and gestures, the state of the patient, etc. Currently, there is yet to be a unified effort to achieve the autonomous temporal understanding and perception of an RAS at the high accuracy and efficiency required in the highly safety-critical field of medicine.
\r\n\r\nThis thesis develops novel modeling methodologies and deep learning-based models for the autonomous perception and temporal segmentation of the current surgical scene during an RAS. An RAS procedure is modeled as a hierarchical system consisting of discrete surgical states at multiple levels of temporal granularity. These surgical states take the form of surgical tasks, operational steps, fine-grained surgical actions, etc. A broad range of computational experiments were performed to develop methods that achieve an accurate, robust, and efficient estimation of these surgical states. Multiple novel deep learning-based models for feature extraction, noise elimination, and efficient training were proposed and tested. This thesis also shows the significant benefits of incorporating multiple types of data streams recorded by the surgical robotic system to a more accurate surgical state estimation effort.
\r\n\r\nTwo new RAS datasets that contains real-world RAS procedures and diverse experimental settings were collected and annotated--filling a gap in the data sets available for the development and testing of of robust surgical state estimation models. The performance and robustness of models in this thesis work were showcased with these highly complex and dynamic real-world RAS datasets and compared against state-of-the-art methods. A significant model performance improvement was observed in both surgical state estimation accuracy and efficiency. The modeling methodologies and deep learning-based models developed in this work have diverse potential applications to the development of a next-generation surgical robotic systems.
", "doi": "10.7907/n58k-tr61", "publication_date": "2022-06-10", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14652", "collection": "thesis", "collection_id": "14652", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302022-235732314", "primary_object_url": { "basename": "2022_XFZ_PhD_Thesis_final.pdf", "content": "final", "filesize": 24249102, "license": "other", "mime_type": "application/pdf", "url": "/14652/1/2022_XFZ_PhD_Thesis_final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Biocontrol of Biomolecular Systems: Polyhedral Constraints on Binding's Regulation of Catalysis from Biocircuits to Metabolism", "author": [ { "family_name": "Xiao", "given_name": "Fangzhou", "orcid": "0000-0002-5001-5644", "clpid": "Xiao-Fangzhou" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "One eventual goal of bioengineering is to build complex biological machines that fully realize the unique potential of biotechnology, namely adaptation, survival, growth, and dominance. In order to do so, not only do we need theoretical understanding and reliable manufacturing of biological parts and components, we also need a systems theory that captures fundamental structures to obtain insight about the space of all possible behaviors when parts are put together. This enables us to understand what can and cannot be achieved. Examples from other engineering disciplines are Turing machines for computers, information channels for communication networks, linear input output systems for electrical circuits, and thermodynamics for heat engines. This work is an attempt at developing a systems theory tailored to biomolecular systems in cells. The results form the following statements.
\r\n\r\nBiomolecular systems are binding and catalysis reactions. Catalysis determines the direction of change, while binding regulates how the catalysis rates vary with reactant concentrations. Given a binding reaction network, the full range of regulatory profiles can be captured by the reaction orders of catalysis, which in turn is constrained in polyhedral sets determined by the stoichiometry of binding. This constitute a rule, that since cells control catalysis by binding, cells control catalysis rates by regulating reaction orders constrained in polyhedral sets. This rule has ramifications in several directions. On metabolism, by incorporating the constraint that reaction orders of metabolic fluxes, not the fluxes themselves, are controlled, we can predict metabolism dynamics directly from network stoichiometry, e.g. glycolytic oscillations and growth arrests. This is a fully dynamic upgrade of flux balance analysis, a popular constraint-based method to model metabolism. On systems biology, this rule derives a method of biocircuit analysis based on the full range of values that reaction orders can take. This allows discovery of necessary and sufficient conditions for a circuit to achieve a certain function, thus revealing regimes hidden by traditional methods of analysis. It also promotes holistic comparisons of different circuit implementations, e.g. activating versus repressing, thur enabling biocircuit design where we know when a design will work, and when a design will fail. On dynamics and control of biocircuits, reaction order can work as a robust basis for stability, perfect adaptation, multistability, and oscillations. Lyapunov functions and dissipative control theory tailored for biomolecular systems are constructed based on reaction orders. On the mathematics of biology, it relates bioregulation to convex polyhedra, log derivative operator decompositions, and fundamental rules of calculus for positive variables.
", "doi": "10.7907/rtwq-v497", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14917", "collection": "thesis", "collection_id": "14917", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012022-061623441", "type": "thesis", "title": "Creating ARCHER: A 3D Hopping Robot with Flywheels for Attitude Control", "author": [ { "family_name": "Ambrose", "given_name": "Eric Ryan", "orcid": "0000-000194335650", "clpid": "Ambrose-Eric-Ryan" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Niemeyer", "given_name": "Gunter", "clpid": "Niemeyer-G" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The field of robotic hopping began over 40 years ago, when it was first shown that robust hopping could be achieved on real hardware. In the years since then, it's become clear that hopping requires high performance and precision from its actuation and planning, due to its extreme interactions with the environment occurring over periodic, yet very short durations of time. Despite being of lower dimensionality than many other legged robots, hoppers are very underactuated, which only adds to the difficulty of planning motions quickly for real-time needs.
\r\n\r\nThe studies of robotic hopping presented in this thesis start with a look into two different actuation styles for creating vertical periodic motion: a compress-release mechanism and a moving-mass mechanism. The dynamics of each were examined from the perspective of stability and robustness to uncertainties in the model and measurements. The compress-release hopper (CRH) was found to be very stable, simple to control, and robust to all uncertainties, but inherently had some inefficiencies due to the requirement of holding compression during portions of the aerial phase. The moving-mass hopper (MMH) required optimization to generate the proper cyclic motions as well as closed-loop control to make them stable. Furthermore, the original configuration of the MMH was also less energetically efficient and robust to uncertainty than the CRH.
\r\n\r\nIn an effort to improve the efficiency of the MMH, a second-generation robot was designed using the principle of parallel elasticity. This involved placing a second spring in parallel to the actuator which would naturally guide the motion of the moving-mass into an optimal path, eliminating a significant portion of actuation effort and improving the overall efficiency. An added benefit of this change was that the robot no longer required closed loop control to create stable hopping. This new robot was built and tested in the lab showing a dramatic improvement over the previous design. The principle of controlling the compliance in the actuator for efficient motion was then taken one step further by creating custom, nonlinear stiffness springs which would provide a more ideal trajectory of motion. This process utilized a design-in-the-loop optimization strategy that would both design these springs as well as the motions of the moving-mass to yield better actuation efficiency. A set of these springs was created and attached to the second-gen MMH, replacing the lower spring, and tested in the lab. These springs did slightly improve the efficiency of the robot, but were restricted by the material selection of the springs due to manufacturing limitations.
\r\n\r\nMoving into the realm of 3-Dimensional hopping, a final robot was designed and built: ARCHER. Unlike traditional hopping robots which use a torso with very large inertia to control the leg motion and balance, ARCHER uses a set of three flywheels. The goal of this robot was twofold: to study the feasibility of using flywheels alone to control attitude, and to take advantage of the principle of decoupled systems. By using strategically placed flywheels, the dynamics of the leg and the attitude subsystems were decoupled, meaning their actuation did not have a direct influence on each other. This allows for simpler motion planning and control. The culmination of this thesis was running experiments with this robot, showing its initial performance and ability to hop with separate controllers for each subsystem.
", "doi": "10.7907/gbts-va63", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14424", "collection": "thesis", "collection_id": "14424", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11102021-210013472", "type": "thesis", "title": "Compilation and Inference with Chemical Reaction Networks", "author": [ { "family_name": "Poole", "given_name": "William", "orcid": "0000-0002-2958-6776", "clpid": "Poole-William" } ], "thesis_advisor": [ { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The successful advancement and deployment of technologies in the field of synthetic biology will require sophisticated computational infrastructure coupled with new theoretical ideas in order to more effectively engineer and reverse engineer biochemical networks. This thesis argues that the field of machine learning can inform the development of these underlying principles and techniques. First, software for compiling diverse chemical reaction network models of biological circuits from simple specifications is described. Second, three chemical reaction network implementations of a powerful machine learning model called a Boltzmann machine are analyzed and compared. Third, the class of detailed balanced chemical reaction networks are proven to be capable of probabilistic inference and, when coupled to a driven chemical system, autonomous learning. Finally, the use of machine learning to interpret and understand biological systems is explored in an experimental case study modeling E. coli cell extract metabolism.
", "doi": "10.7907/x3qc-je74", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14436", "collection": "thesis", "collection_id": "14436", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11302021-224628633", "primary_object_url": { "basename": "zhan_eric_2022_thesis.pdf", "content": "final", "filesize": 8876717, "license": "other", "mime_type": "application/pdf", "url": "/14436/1/zhan_eric_2022_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "New Algorithms for Programmatic Deep Learning with Applications to Behavior Modeling", "author": [ { "family_name": "Zhan", "given_name": "Eric", "orcid": "0000-0003-0521-5329", "clpid": "Zhan-Eric" } ], "thesis_advisor": [ { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Chaudhuri", "given_name": "Swarat", "orcid": "0000-0002-6859-1391", "clpid": "Chaudhuri-Swarat" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Raw behavioral data is becoming increasingly more abundant and more easily obtainable in spatiotemporal domains such as sports, video games, navigation & driving, motion capture, and animal science. How can we best use this data to advance their respective domains forward? For instance, researchers for self-driving vehicles would like to identify the key features of the environment state that impact decision-making the most; game developers would like to populate their games with characters that have unique and diverse behaviors to create a more immersive gaming experience; and behavioral neuroscientists would like to uncover the underlying mechanisms that drive learning in animals. Machine learning, the science of developing models and algorithms to identify and leverage patterns in data, is well-equipped to aid in these endeavors. But how do we integrate machine learning with these spatiotemporal domains in a principled way? In this dissertation, we develop and introduce new algorithms in programmatic deep learning that tackle some of the new challenges encountered in behavior modeling.
\r\n\r\nOur work in programmatic deep learning comprises two main themes: in the first, we show how to use expert-written programs as sources of weak labels in domains where manually-annotated expert labels are scarce; in the second, we explore programs as a flexible function class with human-interpretable structure and show how to learn them via neurosymbolic program learning. Augmenting deep learning with programmatic structure allows domain experts to easily incorporate domain knowledge into machine learning models; we show that this results in significant improvements in many behavior modeling applications like imitation learning, controllable generation, counterfactual analysis, and unsupervised clustering.
", "doi": "10.7907/5n5q-x203", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14455", "collection": "thesis", "collection_id": "14455", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12212021-193826426", "primary_object_url": { "basename": "Shur-Andrey-2021-thesis-final.pdf", "content": "final", "filesize": 4080541, "license": "other", "mime_type": "application/pdf", "url": "/14455/3/Shur-Andrey-2021-thesis-final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Serine Integrase-Based Event Recording in E. coli", "author": [ { "family_name": "Shur", "given_name": "Andrey Sergeyvich", "orcid": "0000-0001-9372-6713", "clpid": "Shur-Andrey-Sergeyvich" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "DNA is a unique molecule that has evolved to serve as the genetic material for life. It seems straightforward to consider this molecule not only as a wonder of the natural world but as a tool for information storage and retrieval. Bacteria have evolved to conserve DNA, but bacteriophages have evolved to specifically integrate their genomes using integrases. In response to viruses, bacteria have evolved the RNA-guided nuclease Cas9 to destroy viral DNA before it can be integrated. The fruits of these evolutionary pressures prove useful to the researcher interested in easily editing DNA. In this work, we have engineered a genetic circuit that can enact specific and controlled genetic changes in response to changing small molecule concentrations. Known DNA sequences can be repeatedly integrated into a synthetic array such that their identity and order encodes information about past small molecule concentrations that the cell has experienced. To accomplish this, we use catalytically inactive CRISPR-Cas9 (dCas9) to bind to and block attachment sites for the integrase Bxb1. Through the co-expression of dCas9 and guide RNA, Bxb1 can be directed to integrate one of two engineered \"ink\" plasmids, which correspond to two orthogonal small molecule inducers whose presence or absence as a function of time can be recorded with this system. Integrase sites present on these plasmids are found to not participate in intramolecular \"deletion\" reactions if closer than 100 bp. Guide RNAs overlapping integrase attachment sites are found to effectively block integrase activity at those sites if the overlap is equal to 9 or 19 base pairs. Other overlap values, including forward or reverse binding result in ineffective integrase activity repression. We develop 8 orthogonal guide RNA sequences capable of binding to and repressing integrase activity at the attP site. Plasmid multimers are sequenced using Oxford Nanopore sequencing and found to follow population-level predictions of event record identity. Single DNA states are found insufficient for identifying past history of events; an ensemble of DNA states at the population level must be used. A modular modeling framework is developed (Global enumeration) to describe this system, and integrated with the existing chemical reaction network creation automation software BioCRNpyler. The modeling framework developed here automatically creates chemical reaction networks based on typical linear DNA-based synthetic biology \"genetic constructs\" and predicts transcripts and proteins produced based on simple transcription/translation rules. Integrase-based recombination events can also be predicted in a recursive way.
", "doi": "10.7907/x4q0-nx18", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14935", "collection": "thesis", "collection_id": "14935", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022022-064735213", "type": "thesis", "title": "Safe Input Regulation for Robotic Systems", "author": [ { "family_name": "Singletary", "given_name": "Andrew Wills", "orcid": "0000-0001-6635-4256", "clpid": "Singletary-Andrew-Wills" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Feron", "given_name": "Eric M.", "orcid": "0000-0001-7717-2159", "clpid": "Feron-E-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The safety of robotic systems is paramount to their continued emergence into our lives. From collaborative industrial manipulators to drone deliveries to autonomous vehicles, safety is the primary concern when it comes to the continued adoption of these technologies. While a number of techniques can be used to design safe controllers and planners that govern the actions of these robots, few are able to provide the type of safety guarantee needed to bring these technologies into reality.
\r\n\r\nThe goal of this thesis is to provide a framework for regulating, or filtering, existing control inputs before they are applied by the robot, in order to ensure that safety is upheld. To illustrate this, consider one of the primary applications for this method: human-operated robotic platforms. For vehicles, this framework would modify the throttle, braking, and steering commands from a human driver to prevent him from driving off the road or into other cars. However, when the human is operating the vehicle safely, his commands should go unaltered. This illustrates the idea of a minimally invasive safety regulator: one that only engages when absolutely necessary to ensure safety.
\r\n\r\nWithin the last decade, the mathematical framework that allows us to achieve this result, control barrier functions, was introduced. Its adoption among the nonlinear controls community has been rapid, and the method has been used to create controllers that guarantee safety on a large class of systems. Despite this, real-world implementations of control barrier functions are less common, since they require a very accurate model of the system, and they can be difficult to formulate properly. This work provides several major extensions, improvements, and modifications of control barrier functions that allow them to be utilized on a variety of real-world robotic systems.
\r\n\r\nThe first major contribution of this thesis is a set of formulations for safety regulators that do not depend on complete knowledge of the underlying dynamical systems. Three unique formulations are proposed, whose usages depend on the level of knowledge of the underlying system. The resulting performance and safety guarantees are analyzed in real-world applications of quadrotor collision avoidance and fast-food frying with industrial manipulators. The second major contribution is a set of two safety filtering frameworks that utilize knowledge of the full-order dynamics, but allow for guaranteed safety in the presence of input constraints on high-dimensional systems. Two formulations are given, with one designed for use on microcontrollers with minimal computational resources. Both formulations utilize the knowledge of an existing \"backup controller\" that attempts to take the system into a small, safe \"backup set\". This method is demonstrated in simulation on a robotic manipulator and a Segway robot, and on hardware for collision avoidance and geofencing of single and multi-agent racing drones. The third major contribution is a novel discrete-time formulation of control barrier functions that allow for safety regulation of discrete-time systems. We show how safety constraints can be encoded as temporal logic specifications that are enforced over discrete-time models of the systems and their environments. The fourth and final major contribution is a unified, multi-rate control framework that guarantees safety at both the high-level, in discrete-time, and the low-level, in continuous-time. A mid-level Model Predictive Controller (MPC) is used to generate reference signals based on the high-level planner which are tracked by the low-level controller.
\r\n\r\nTogether, these four major contributions result in safe input regulation on a wide variety of robotic systems. Since no single method can reliably enforce safety on such a wide range of systems with different requirements, this thesis provides the smallest collection of methods that applies to the largest classes of systems.
", "doi": "10.7907/zz10-gv06", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14138", "collection": "thesis", "collection_id": "14138", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05082021-185615529", "primary_object_url": { "basename": "McCardellReed2021thesis.pdf", "content": "final", "filesize": 7370942, "license": "other", "mime_type": "application/pdf", "url": "/14138/7/McCardellReed2021thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Genetic Circuits for the Control of Multi-Strain Bacterial Populations", "author": [ { "family_name": "McCardell", "given_name": "Reed Dillard", "orcid": "0000-0002-0955-3133", "clpid": "McCardell-Reed-Dillard" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Microbial species rarely exist alone. Nearly everywhere you could think to look, microorganisms of various species live together in harmony. Microbes together in their communities are incredibly powerful actors wherever they are found; they perform small miracles---the conversion of milk into yogurt---and large ones---production of most of the planet's oxygen and organic carbon.
\r\n\r\nOur burgeoning knowledge of microbial life combined with modern technologies to manipulate it create a critical, exciting opportunity to harness microbial power for the betterment of technology, people, and the planet. This thesis presents a body of work which explores the manipulation of microbial communities using the intersectional bio-engineering approach of synthetic biology. We demonstrate how molecular tools evolved by bacteria can be repurposed to create rationally designed systems for controlling features of bacterial populations.
\r\n\r\nWe begin by examining a genetic circuit that caps the size of a bacterial population by coordinating the deaths of population members -- the population capping or \"pop cap\" circuit. Briefly, E. coli cells in the pop cap circuit are engineered to synthesize a chemical -- a quorum sensing (QS) signal -- that reports the density of the population, sense this chemical, and produce the ccdB toxin to destroy themselves in response. The molecular tools that make up this circuit are drawn from organisms across the spectrum of bacterial diversity. Brought together, they create a feedback control circuit that controls population size by causing member cells to die when a target population size has been reached. To improve the performance of this population controller and reduce the influence of the environment on the circuit, we add the aiiA quorum sensing signal degradase to allow the experimenter control over the degradation rate of the QS density signal. Additionally, we explore RNA and protein mechanisms to sequester the death-causing toxin---inactivating it---allowing us to release a population cap. The resulting \"cap and release\" circuit is a flexible motif that can be scaled to control multi-strain populations, expanding the scope of control beyond the single-strain populations regulated by the base pop cap circuit.
\r\n\r\nUsing the scalable cap and release motif, we design a genetic circuit to regulate a multi-strain community. Two different cell strains expressing symmetric, interconnected cap and release systems form the \"A=B\" circuit, so named for its ability to control the composition of the community to a target ratio of A cells to B cells, or Apopulation = \u03b1Bpopulation. Through dynamical system models of the system, we explore the effects of active QS signal degradation on composition control performance and perform a parameter sensitivity analysis of the system to help determine the best method for building a functioning A=B system in the laboratory. We use a high throughput construction and screening protocol to create variants of the A=B system with identical architectures, but slightly differing component production rates. We crown the most successful variant with a series of experiments to determine if it indeed recapitulates our model's predictions for its performance. Our implementation of the A=B circuit can successfully regulate the composition of a community, with interesting additional effects on total population density.
\r\n\r\nThe cap and release and A=B circuits need parts that can do three things: 1) send a signal between cells to communicate information, 2) compare two signals, 3) regulate cell growth or death. We highlight bacteriocins, bacterial protein exotoxins that are released from a producer cell to kill other cells of similar species, as attractive tools for bacterial community engineering both for their multi-functionality and modular protein structure. By themselves, bacteriocins can perform all the functions needed for population control: they transmit themselves between cells, have unique high-affinity sequestering antitoxin proteins, and are toxins to receiver cells. We begin the process of their characterization and usage as synthetic biological \"parts\" by creating non-native expression systems that match native expression strengths. Using these experimenter-controlled systems we design preliminarily test a bacteriocin-based bacterial community control circuit. Additionally, given the E. coli colicin bacteriocins' unique, nearly plug-and-play modular domain structure, we explore possibilities for engineering colicin proteins themselves for increased functional diversity or uses outside of growth regulation.
", "doi": "10.7907/wgpp-vj97", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14021", "collection": "thesis", "collection_id": "14021", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12092020-162149429", "type": "thesis", "title": "Online Learning from Human Feedback with Applications to Exoskeleton Gait Optimization", "author": [ { "family_name": "Novoseller", "given_name": "Ellen Rachel", "orcid": "0000-0001-5263-0598", "clpid": "Novoseller-Ellen-Rachel" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel W.", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "thesis_committee": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sadigh", "given_name": "Dorsa", "orcid": "0000-0002-7802-9183", "clpid": "Sadigh-Dorsa" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Systems that intelligently interact with humans could improve people's lives in numerous ways and in numerous settings, such as households, hospitals, and workplaces. Yet, developing algorithms that reliably and efficiently personalize their interactions with people in real-world environments remains challenging. In particular, one major difficulty lies in adapting to human-in-the-loop feedback, in which an algorithm makes sequential decisions while receiving online feedback from humans; throughout this interaction, the algorithm seeks to optimize its decision-making quality, as measured by the utility of its performance to the human users. Such algorithms must balance between exploration and exploitation: on one hand, the algorithm must select uncertain strategies to fully explore the environment and the interacting human's preferences, while on the other hand, it must exploit the empirically-best-performing strategies to maximize its cumulative performance.
\r\n\r\nLearning from human feedback can be difficult, as people are often unreliable in specifying numerical scores. In contrast, humans can often more accurately provide various types of qualitative feedback, for instance pairwise preferences. Yet, sample efficiency is a significant concern in human-in-the-loop settings, as qualitative feedback is less informative than absolute metrics, and algorithms can typically pose only limited queries to human users. Thus, there is a need to create theoretically-grounded online learning algorithms that efficiently, reliably, and robustly optimize their interactions with humans while learning from online qualitative feedback.
\r\n\r\nThis dissertation makes several contributions to algorithm design for human-in-the-loop learning. Firstly, this work develops the Dueling Posterior Sampling (DPS) algorithmic framework, a model-based, Bayesian approach for online learning in the settings of preference-based reinforcement learning and generalized linear dueling bandits. DPS is developed together with a theoretical regret analysis framework, and yields competitive empirical performance in a range of simulations. Additionally, this thesis presents the CoSpar and LineCoSpar algorithms for sample-efficient, mixed-initiative learning from pairwise preferences and coactive feedback. CoSpar and LineCoSpar are both deployed in human subject experiments with a lower-body exoskeleton to identify optimal, user-preferred exoskeleton walking gaits. This work presents the first demonstration of preference-based learning for optimizing dynamic crutchless exoskeleton walking for user comfort, and makes progress toward customizing exoskeletons and other assistive devices for individual users.
", "doi": "10.7907/gvtx-1586", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14083", "collection": "thesis", "collection_id": "14083", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02182021-040721884", "primary_object_url": { "basename": "Shi_Xichen_2021_Thesis.pdf", "content": "final", "filesize": 16708714, "license": "other", "mime_type": "application/pdf", "url": "/14083/1/Shi_Xichen_2021_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Intelligent Control for Fixed-Wing eVTOL Aircraft", "author": [ { "family_name": "Shi", "given_name": "Xichen", "orcid": "0000-0002-5366-9256", "clpid": "Shi-Xichen" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Urban Air Mobility (UAM) holds promise for personal air transportation by deploying \"flying cars\" over cities. As such, fixed-wing electric vertical take-off and landing (eVTOL) aircraft has gained popularity as they can swiftly traverse cluttered areas, while also efficiently covering longer distances. These modes of operation call for an enhanced level of precision, safety, and intelligence for flight control. The hybrid nature of these aircraft poses a unique challenge that stems from complex aerodynamic interactions between wings, rotors, and the environment. Thus accurate estimation of external forces is indispensable for a high performance flight. However, traditional methods that stitch together different control schemes often fall short during hybrid flight modes. On the other hand, learning-based approaches circumvent modeling complexities, but they often lack theoretical guarantees for stability.
\r\n\r\nIn the first part of this thesis, we study the theoretical benefits of these fixed-wing eVTOL aircraft, followed by the derivation of a novel unified control framework. It consists of nonlinear position and attitude controllers using forces and moments as inputs; and control allocation modules that determine desired attitudes and thruster signals. Next, we present a composite adaptation scheme for linear-in-parameter (LiP) dynamics models, which provides accurate realtime estimation for wing and rotor forces based on measurements from a three-dimensional airflow sensor. Then, we introduce a design method to optimize multirotor configuration that ensures a property of robustness against rotor failures.
\r\n\r\nIn the second part of the thesis, we use deep neural networks (DNN) to learn part of unmodeled dynamics of the flight vehicles. Spectral normalization that regulates the Lipschitz constants of the neural network is applied for better generalization outside the training domain. The resultant network is utilized in a nonlinear feedback controller with a contraction mapping update, solving the nonaffine-in-control issue that arises. Next, we formulate general methods for designing and training DNN-based dynamics, controller, and observer. The general framework can theoretically handle any nonlinear dynamics with prior knowledge of its structure. Finally, we establish a delay compensation technique that transforms nominal controllers for an undelayed system into a sample-based predictive controller with numerical integration. The proposed method handles both first-order and transport delays in actuators and balances between numerical accuracy and computational efficiency to guarantee stability under strict hardware limitations.
", "doi": "10.7907/51c6-aa57", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14098", "collection": "thesis", "collection_id": "14098", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03032021-224823348", "primary_object_url": { "basename": "Caltech-Thesis-Mohamad-Final.pdf", "content": "final", "filesize": 7550092, "license": "other", "mime_type": "application/pdf", "url": "/14098/1/Caltech-Thesis-Mohamad-Final.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Thermal Bioswitches for Non-Invasive Control of Cellular Therapies", "author": [ { "family_name": "Abedi", "given_name": "Mohamad", "orcid": "0000-0001-9717-6288", "clpid": "Abedi-Mohamad" } ], "thesis_advisor": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "thesis_committee": [ { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Baltimore", "given_name": "David L.", "orcid": "0000-0001-8723-8190", "clpid": "Baltimore-D-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Temperature is a unique input signal that could be used by engineered therapeutic cells to sense and respond to host conditions or spatially targeted external triggers such as focused ultrasound. To enable these possibilities, I present here a new class of thermal bioswitches that enables thermal control over bacterial and mammalian cells. For bacterial applications, we developed two new families of tunable, orthogonal, temperature-dependent transcriptional repressors providing switch-like control of bacterial gene expression at thresholds spanning the biomedically relevant range of 32\u201346 \u00b0C. We integrated these molecular bioswitches into thermal logic circuits and demonstrated their utility in three in vivo microbial therapy scenarios, including spatially precise activation using focused ultrasound, modulation of activity in response to a host fever, and self-destruction after fecal elimination to prevent environmental escape. This technology provides a critical capability for coupling endogenous or applied thermal signals to cellular function in basic research, biomedical and industrial applications.
\r\n\r\nTo apply this technology in a relevant clinical scenario, we sought to engineer microbial immunotherapies that can be thermally controlled with focused ultrasound. This technology was enabled by rapid advances in synthetic biology that are driving the development of genetically modified microbes as therapeutic agents for a multitude of human diseases, including cancer. In particular, the reduced immune surveillance within the core of some solid tumors creates an ideal environment for microbes to engraft and release therapeutic payloads. However, these therapeutic payloads could be harmful if released in healthy tissues where microbes tend to also engraft in smaller numbers. As described in Chapter 2, my colleagues and I introduced a temperature-actuated state switch that enables tight spatiotemporal control over the activity of therapeutic microbes when combined with focused ultrasound hyperthermia. Through a combination of rational design and high throughput screening, we optimized the behavior of this switch to minimize leakage and maximize inducibility. When tested in a clinically relevant in vivo model, engineered microbes, successfully switched states, and induced a marked suppression of tumor growth upon focal activation. This bioswitch provides a critical tool to attain selective and sustained activity of therapeutic microbes in vivo.
\r\n\r\nEncouraged by the successful development of thermally actuated circuits in microbes, we aimed to establish equivalent technologies for thermal control of human T cells. Genetically engineered T cells are actively being developed to perform a variety of therapeutic functions with great clinical promise. However, no robust mechanisms exist to externally control the activity of T cells at specific locations within the body. Such spatiotemporal control could help mitigate potential off-target toxicity due to incomplete molecular specificity in applications such as T-cell immunotherapy against solid tumors. In Chapter 4, my colleagues and I tested the ability of heat shock promoters to mediate thermal actuation of genetic circuits in primary human T cells in the well-tolerated temperature range of 37\u221242 \u00b0C, and we introduced genetic architectures enabling the tuning of the amplitude and duration of thermal activation. We demonstrated the use of these circuits to control the expression of chimeric antigen receptors and cytokines, and the killing of target tumor cells. Overall, the technologies developed here provide critical tools to direct control therapeutic cells after they have been deployed deep inside the body.
", "doi": "10.7907/z7ac-2g66", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14111", "collection": "thesis", "collection_id": "14111", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03262021-160841703", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 3545856, "license": "other", "mime_type": "application/pdf", "url": "/14111/1/thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Signal Amplification in Synthetic Bacterial Communication", "author": [ { "family_name": "Parkin", "given_name": "James Michael", "orcid": "0000-0002-4058-2338", "clpid": "Parkin-James-Michael" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Bois", "given_name": "Justin S.", "orcid": "0000-0001-7137-8746", "clpid": "Bois-J-S" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Synthetic biology will one day enable embedded control of a variety of chemical and biological contexts, from the human gastrointestinal tract to crop roots. Groups of engineered organisms, also known as synthetic consortia, can inhabit niches of interest while monitoring and intervening according to their genetic design. However, the spatial structure of the deployment environments can obstruct coordination between cosortia members. The mechanisms engineered bacteria use to communicate must contend with these adversarial conditions to maximize group performance.
\r\n\r\nCoordination between synthetic bacteria is typically achieved using small molecules that can traverse cell membranes through passive transport. Cell communicate by producing and sensing these small molecules. In cell-cell signaling relationships composed of a sender population and a receiver population, the concentration of signaling molecule sensed by the receiver cells depends on the spatial patterning of the two groups, the geometry of the diffusive environment, and the sender population\u2019s signal secretion rate.
\r\n\r\nTo make sender-receiver communication more robust to these environmental features, we introduce a third consortium strain that transiently amplifies local signaling molecule concentrations. These amplifier cells employ a synchronized pulse-generating circuit built using Lux-type quorum sensing components and an IFFL transcriptional architecture. When applied to sender-receiver consortia growing on semi-solid media, these amplifier cells respond to sender-secreted signaling molecules by contributing a small amount themselves. The support of amplifier cells enables communication over longer distances than can be achieved by sender cells alone and can partially recover coordination in small consortia where the sender population is too small to successfully signal its receiver population alone. We extend these results using simulation to investigate the benefit that amplifier cells confer to consortia of varying complexity.
", "doi": "10.7907/50p8-bd89", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14115", "collection": "thesis", "collection_id": "14115", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04022021-033321217", "type": "thesis", "title": "Safe and Interpretable Autonomous Systems Design: Behavioral Contracts and Semantic-Based Perception", "author": [ { "family_name": "Cai", "given_name": "Karena Xin", "orcid": "0000-0002-8392-4158", "clpid": "Cai-Karena-Xin" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We are on the verge of experiencing a new, integrated society where autonomous vehicles will become a fabric of our everyday lives. And yet, seamless integration of autonomous vehicles into our society will require vehicles to interface safely with humans in an incredibly complex, fast-paced, and dynamic environment. Premature deployment of these new autonomous systems \u2014 without safety guarantees or interpretability of algorithms, could prove catastrophic. How can algorithms governing vehicle behavior be designed in a way that guarantees safety, performance, interpretability and scalability? This is the question this thesis seeks to answer.
\r\n\r\nFirst, we present a framework for architecting the decision-making module of autonomous vehicles so that safety and progress of agents can be formally guaranteed. In particular, all agents are defined to act according to what is termed an assume-guarantee contract, which is broadly defined as a set of behavioral preferences. The first version of the assume-guarantee contract is a behavioral profile, which is a set of ordered rules that agents must use to select actions in a way that is interpretable. With all agents operating according to a behavioral profile, the interactions however, are not necessarily coordinated. We then constrain agent behavior with an additional set of interaction rules. The behavioral profile combined with these additional constraints, are what we term a behavioral protocol. With all agents operating according to a local, decentralized behavioral protocol, we can provide formal proofs of the correctness of agent behavior, i.e. all agents will never collide and agents will make it to their respective destinations. Not only does the protocol so\u00a0defined allow us to make formal guarantees, but it is also designed in a way that scales well in the number of agents and provides interpretability of agent\u00a0behaviors. Safety and progress guarantees are proven and verified in simulation.
\r\n\r\nSecond, we focus on using information from object classifiers to enhance an autonomous vehicle's ability to localize where it is within its environment. The proposed approach for incorporating this semantic information is based on solving the maximum likelihood problem. With a hierarchical formulation, we are not only able to improve upon the accuracy of traditional localization techniques, but we are also able to improve our confidence in the accuracy of object detection classifications. The improvement in robustness and accuracy of these algorithms are shown in simulation.
", "doi": "10.7907/w3m8-es32", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14188", "collection": "thesis", "collection_id": "14188", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282021-062435188", "primary_object_url": { "basename": "Thesis Jenna Reher.pdf", "content": "final", "filesize": 34967410, "license": "other", "mime_type": "application/pdf", "url": "/14188/1/Thesis Jenna Reher.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Dynamic Bipedal Locomotion: From Hybrid Zero Dynamics to Control Lyapunov Functions via Experimentally Realizable Methods", "author": [ { "family_name": "Reher", "given_name": "Jenna", "orcid": "0000-0002-8297-3847", "clpid": "Reher-Jenna" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Robotic bipedal locomotion has become a rapidly growing field of research as humans increasingly look to augment their natural environments with intelligent machines. In order for these robotic systems to navigate the often unstructured environments of the world and perform tasks, they must first have the capability to dynamically, reliably, and efficiently locomote. Due to the inherently hybrid and underactuated nature of dynamic bipedal walking, the greatest experimental successes in the field have often been achieved by considering all aspects of the problem; with explicit consideration of the interplay between modeling, trajectory planning, and feedback control.
\r\n\r\nThe methodology and developments presented in this thesis begin with the modeling and design of dynamic walking gaits on bipedal robots through hybrid zero dynamics (HZD), a mathematical framework that utilizes hybrid system models coupled with nonlinear controllers that results in stable locomotion. This will form the first half of the thesis, and will be used to develop a solid foundation of HZD trajectory optimization tools and algorithms for efficient synthesis of accurate hybrid motion plans for locomotion on two underactuated and compliant 3D bipeds. While HZD and the associated trajectory optimization are an existing framework, the resulting behaviors shown in these preliminary experiments will extend the limits of what HZD has demonstrated is possible thus far in the literature. Specifically, the core results of this thesis demonstrate the first experimental multi-contact humanoid walking with HZD on the DURUS robot and then through the first compliant HZD motion library for walking over a continuum of walking speeds on the Cassie robot.
\r\n \r\nOn the theoretical front, a novel formulation of an optimization-based control framework is introduced that couples convergence constraints from control Lyapunov functions (CLF)s with desirable formulations existing in other areas of the bipedal locomotion field that have proven successful in practice, such as inverse dynamics control and quadratic programming approaches. The theoretical analysis and experimental validation of this controller thus forms the second half of this thesis. First, a theoretical analysis is developed which demonstrates several useful properties of the approach for tuning and implementation, and the stability of the controller for HZD locomotion is proven. This is then extended to a relaxed version of the CLF controller, which removes a convergence inequality constraint in lieu of a conservative CLF cost within a quadratic program to achieve tracking. It is then explored how this new CLF formulation can fully leverage the planned HZD walking gaits to achieve the target performance on physical hardware. Towards this goal, an experimental implementation of the CLF controller is derived for the Cassie robot, with the resulting experiments demonstrating the first successful realization of a CLF controller for a 3D biped on hardware in the literature. The accuracy of the robot model and synthesized HZD motion library allow the real-time control implementation to regularize the CLF optimization cost about the nominal walking gait. This drives the controller to choose smooth input torques and anticipated spring torques, as well as regulate an optimal distribution of feasible ground reaction forces on hardware while reliably tracking the planned virtual constraints. These final results demonstrate how each component of this thesis were brought together to form an effective end-to-end implementation of a nonlinear control framework for underactuated locomotion on a bipedal robot through modeling, trajectory optimization, and then ultimately real-time control.
", "doi": "10.7907/h8v0-vd47", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14175", "collection": "thesis", "collection_id": "14175", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262021-072231177", "primary_object_url": { "basename": "Ren_Caltech_Thesis_v2.pdf", "content": "final", "filesize": 7116984, "license": "other", "mime_type": "application/pdf", "url": "/14175/1/Ren_Caltech_Thesis_v2.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Principles for Designing Robust and Stable Synthetic Microbial Consortia", "author": [ { "family_name": "Ren", "given_name": "Xinying (Cindy)", "orcid": "0000-0002-8852-6722", "clpid": "Ren-Xinying-Cindy" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Franco", "given_name": "Elisa", "clpid": "Franco-Elisa" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Engineering stable microbial consortia with robust functions are useful in many areas, including bioproduction and human health. Robust and stable properties depend on proper control of dynamics ranging from single cell-level to population-environment interactions. In this thesis, I discuss principles of building microbial consortia with synthetic circuits in two design scenarios.
\r\n\r\nFirst, for one microbial population, strong disturbances in environments often severely perturb cell states and lead to heterogeneous responses. Single cell-level design of control circuits may fail to induce a uniform response as needed. I demonstrate that cell-cell signaling systems can facilitate coordination among cells and achieve robust population-level behaviors. Moreover, I show that heterogeneity can be harnessed for robust adaptation at population-level via a bistable state switch.
\r\n\r\nSecond, multi-pecies consortia are intrinsically unstable due to competitive exclusion. Previous theoretical investigations based on models of pairwise interactions mainly explored what interaction network topology ensures stable coexistence. Yet neglecting detailed interaction mechanisms and spatial context results in contradictory predictions. Focusing on chemical-mediated interaction, I show that detailed mechanisms of chemical consumption/accumulation and chemical-induced growth/death, interaction network topology and spatial structures of environments all are critical factors to maintain stable coexistence. With a two population-system, I demonstrate that the same interaction network topology can exhibit qualitatively different or even opposite behaviors due to interaction mechanisms and spatial conditions.
", "doi": "10.7907/hc8x-3280", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14148", "collection": "thesis", "collection_id": "14148", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05142021-163257155", "primary_object_url": { "basename": "nakka_yashwanth_kumar_2021_thesis.pdf", "content": "final", "filesize": 28258884, "license": "other", "mime_type": "application/pdf", "url": "/14148/2/nakka_yashwanth_kumar_2021_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Spacecraft Motion Planning and Control under Probabilistic Uncertainty for Coordinated Inspection and Safe Learning", "author": [ { "family_name": "Nakka", "given_name": "Yashwanth Kumar", "orcid": "0000-0001-7897-3644", "clpid": "Nakka-Yashwanth-Kumar" } ], "thesis_advisor": [ { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Hadaegh", "given_name": "Fred", "clpid": "Fred-Hadaegh" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "During a spacecraft mission design process, engineers often balance the following three criteria: science return, optimality in performance, and safety. Given a science criterion, engineers design the orbit parameters with predefined performance and safety. Often in this approach, the spacecraft has no understanding of the expected outcome or the knowledge of the mission safety criteria. Autonomous science-driven orbit (or goal) selection and planning for safety under uncertainty enable efficient and adaptable missions. To this end, we propose an architecture for information-based guidance and control for coordinated inspection, motion planning and control algorithms for safe and optimal guidance under uncertainty, and architecture for safe exploration.
\r\n\r\nIn the first part of this thesis, we present an architecture for inspection or mapping of a target spacecraft in a low Earth orbit using multiple observer spacecraft. We use an information gain approach to directly consider the trade-off between gathered data and fuel/energy cost. The estimated information gain is a crucial input to the motion planner, which computes orbits and reconfiguration strategies for each of the observers to maximize the information gain from distributed observations of the target spacecraft. The resulting motion trajectories jointly consider observational coverage of the target spacecraft and fuel/energy cost. We validate our architecture in a mission simulation to visually inspect the target spacecraft and on the three degree-of-freedom robotic spacecraft dynamics simulator testbed.
\r\n\r\nIn the second part of the thesis, we present gPC-SCP, Generalized Polynomial Chaos-based Sequential Convex Programming method, to compute a sub-optimal solution for a continuous-time chance-constrained stochastic nonlinear optimal control (SNOC) problem. The approach enables motion planning and control of robotic systems under uncertainty. The proposed method involves two steps. The first step is to derive a deterministic nonlinear optimal control problem (DNOC) with convex constraints that are surrogate to the SNOC by using gPC expansion and the distributionally-robust convex subset of the chance constraints. The second step is to solve the DNOC problem using sequential convex programming (SCP) for trajectory generation and control. We prove that in the unconstrained case, the optimal value of the DNOC converges to that of SNOC asymptotically and that any feasible solution of the constrained DNOC is a feasible solution of the chance-constrained SNOC. We derive a stable stochastic model predictive controller using the gPC-SCP for tracking a potentially unsafe trajectory in the presence of uncertainty. We empirically demonstrate the efficacy of the gPC-SCP method for the following three test cases: 1) collision checking under uncertainty in actuation, 2) collision checking with stochastic obstacles, and 3) safe trajectory tracking under uncertainty in the dynamics and obstacle location by using a receding horizon control approach. We validate the effectiveness of the gPC-SCP method on the robotic spacecraft testbed.
\r\n\r\n\r\nIn the third part of this thesis, we present a new approach for optimal motion planning for safe exploration that integrates the chance-constrained stochastic optimal control with dynamics learning and feedback control. We derive an iterative convex optimization algorithm that solves an Information-cost Stochastic Nonlinear Optimal Control problem (Info-SNOC). The optimization objective encodes control cost for performance and exploration cost for learning, and the safety is incorporated as distributionally robust chance constraints. The dynamics are predicted from a robust regression model that is learned from data. The Info-SNOC algorithm is used to compute a sub-optimal pool of safe motion plans that aid in exploration for learning unknown residual dynamics under safety constraints. A stable feedback controller is used to execute the motion plan and collect data for model learning. We prove the safety of rollout from our exploration method and reduction in uncertainty over epochs, thereby guaranteeing the consistency of our learning method. We validate the effectiveness of Info-SNOC by designing and implementing a pool of safe trajectories for a planar robot. We demonstrate that our approach has a higher success rate in ensuring safety when compared to a deterministic trajectory optimization approach.
", "doi": "10.7907/6329-sf68", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14132", "collection": "thesis", "collection_id": "14132", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05042021-155258800", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 10181693, "license": "other", "mime_type": "application/pdf", "url": "/14132/1/Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "From Bipedal to Quadrupedal Locomotion, Experimental Realization of Lyapunov Approaches", "author": [ { "family_name": "Ma", "given_name": "Wen-Loong", "orcid": "0000-0002-0115-5632", "clpid": "Ma-Wen-Loong" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Possibly one of the most significant innovations of the past decade is the hybrid zero dynamics (HZD) framework, which formally and rigorously designs a control algorithm for robotic walking. In this methodology, Lyapunov stability, which is often used to certificate a dynamical system's stability, was introduced to the control law design for a hybrid control system. However, the prerequisites of precise modeling to apply the HZD methodology can often be too restrictive to design controllers for uncertain and complex real-world hardware experiments. This thesis addresses the problem raised by noisy measurements and the intricate hybrid structure of locomotion dynamics.
\r\n\r\nFirst, the HZD methodology's construction is based on the full-order, hybrid dynamics of legged locomotion, which can be intractable for control synthesis for high-dimensional systems. This thesis studies the general structure of hybrid control systems for walking systems, ranging from 1D hopping, 2D walking, 2D running, and 3D quadrupedal locomotion on rough terrains. Further, we characterize a walking behavior--gait--as a solution (execution) to a hybrid control system. To find these solutions, which represent a \"gait,\" we employed advanced numerical methods such as collocation methods to parse the solution-finding problem into the open- and closed-loop trajectory optimization problems. The result is that we can find versatile gaits for ten different robotic platforms efficiently. This includes bipedal running, bipedal walking on slippery surfaces, and quadrupedal robots walking on sloped terrains. The numerous solution-finding examples expand the applicability of the HZD framework towards more complex dynamical systems.
\r\n\r\nFurther, for the uncertain and noisy real-world implementation, the exponential stability of the continuous dynamics is an ideal but restrictive condition for hybrid stability. This condition is especially challenging to satisfy for highly dynamical behaviors such as bipedal running, which loses ground support for a short period. This thesis observes the destabilizing effect of the noisy measurements of the phasing variable. By reformulating the traditional input-to-state stability (ISS) concept into phase-uncertainty to state stability, we are able to synthesize a robust controller for bipedal running on DURUS-2D. This time+state-based controller formally guarantees stability under noisy measurements and stabilizes the 1.75 m/s running experiments.
\r\n\r\nLastly, robotic dynamics have long been characterized as the interconnection of rigid-body dynamics. We take this perspective one step further and incorporate controller design into the formulation of coupled control systems (CCS). We first view a quadrupedal robot as two bipedal robots connected via some holonomic constraints. In a dimensional reduction manner, we develop a novel optimization framework, and the computational performance is reduced to a few seconds for gait generation. Furthermore, we can design local controllers for each bipedal subsystem and still guarantee the overall system's stability. This is done by combining the HZD framework and the ISS properties to contain the disturbance induced by the other subsystems' inputs. Utilizing the proposed CCS methods, we will experimentally realize quadrupedal walking on various outdoor rough terrains.
", "doi": "10.7907/j1ty-zb28", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14046", "collection": "thesis", "collection_id": "14046", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01052021-195655093", "primary_object_url": { "basename": "Caltech_Thesis_Richard.pdf", "content": "final", "filesize": 5654612, "license": "other", "mime_type": "application/pdf", "url": "/14046/1/Caltech_Thesis_Richard.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Assuring Safety under Uncertainty in Learning-Based Control Systems", "author": [ { "family_name": "Cheng", "given_name": "Richard", "orcid": "0000-0001-8301-9169", "clpid": "Cheng-Richard" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Learning-based controllers have recently shown impressive results for different robotic tasks in well-defined environments, successfully solving a Rubiks cube and sorting objects in a bin. These advancements promise to enable a host of new capabilities for complex robotic systems. However, these learning-based controllers cannot yet be deployed in highly uncertain environments due to significant issues relating to learning reliability, robustness, and safety.
\r\n\r\nTo overcome these issues, this thesis proposes new methods for integrating model information (e.g. model-based control priors) into the reinforcement learning framework, which is crucial to ensuring reliability and safety. I show, both empirically and theoretically, that this model information greatly reduces variance in learning and can effectively constrain the policy search space, thus enabling significant improvements in sample complexity for the underlying RL algorithms. Furthermore, by leveraging control barrier functions and Gaussian process uncertainty models, I show how system safety can be maintained under uncertainty without interfering with the learning process (e.g. distorting the policy gradients).
\r\n\r\nThe last part of the thesis will discuss fundamental limitations that arise when utilizing machine learning to derive safety guarantees. In particular, I show that widely used uncertainty models can be highly inaccurate when predicting rare events, and examine the implications of this for safe learning. To overcome some of these limitations, a novel framework is developed based on assume-guarantee contracts in order to ensure safety in multi-agent human environments. The proposed approach utilizes contracts to impose loose responsibilities on agents in the environment, which are learned from data. Imposing these responsibilities on agents, rather than treating their uncertainty as a purely random process, allows us to achieve both safety and efficiency in interactions.
", "doi": "10.7907/9kye-rn93", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14052", "collection": "thesis", "collection_id": "14052", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01132021-065636010", "primary_object_url": { "basename": "Tung Phan Caltech Thesis.pdf", "content": "final", "filesize": 7424375, "license": "other", "mime_type": "application/pdf", "url": "/14052/1/Tung Phan Caltech Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Contract-Based Design: Theories and Applications", "author": [ { "family_name": "Phan-Minh", "given_name": "Tung", "orcid": "000-0002-1403-5197", "clpid": "Phan-Minh-Tung" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Most things we know only exist in relation to one another. Their states are strongly coupled due to dependencies that arise from such relations. For a system designer, acknowledging the presence of these dependencies is as crucial to guaranteeing performance as studying them. As the roles played by technology in fields such as transportation, healthcare, and finance continue to be more profound and diverse, modern engineering systems have grown to be more reliant on the integration of technologies across multiple disciplines and their requirements. The need to ensure proper division of labor, integration of system modules, and attribution of legal responsibility calls for a more methodological look into co-design considerations. Originally conceived in computer programming, contract-based reasoning is a design approach whose promise of a formal compositional paradigm is receiving attention from a broader engineering community. Our work is dedicated to narrowing the gap between the theory and application of this yet nascent framework.
\r\n\r\nIn the first half of this dissertation, we introduce a model interface contract theory for input/output automata with guards and a formalization of the directive-response architecture using assume-guarantee contracts and show how these may be used to guide the formal design of a traffic intersection and an automated valet parking system respectively. Next, we address a major drawback of assume-guarantee contracts, i.e., the problem of a void contract due to antecedent failure. Our proposed solution is a reactive version of assume-guarantee contracts that enables direct specification at the assumption and guarantee level along with a novel synthesis algorithm that exposes the effects of failures on the contract structure. This is then used to help optimize, adapt, and robustify our design against an uncertain environment.
\r\n\r\nIn light of ongoing development of autonomous driving technologies and its potential impact on the safety of future transportation, the second half of this work is dedicated to the application of the design-by-contract framework to the distributed control of autonomous vehicles. We start by defining and proving properties of \"assume-guarantee profiles,\" our proposed approach to transparent distributed multi-agent decision making and behavior prediction. Next, we provide a local conflict resolution algorithm in the context of a quasi-simultaneous game which guarantees safety and liveness to the composition of autonomous vehicle systems in this game. Finally, to facilitate the extension of these frameworks to real-life urban driving settings, we also supply an effective method to predict agent behavior that utilizes recent advances in machine learning research.
", "doi": "10.7907/8vp7-kd82", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14052", "collection": "thesis", "collection_id": "14052", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01132021-065636010", "primary_object_url": { "basename": "Tung Phan Caltech Thesis.pdf", "content": "final", "filesize": 7424375, "license": "other", "mime_type": "application/pdf", "url": "/14052/1/Tung Phan Caltech Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Contract-Based Design: Theories and Applications", "author": [ { "family_name": "Phan-Minh", "given_name": "Tung", "orcid": "000-0002-1403-5197", "clpid": "Phan-Minh-Tung" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Most things we know only exist in relation to one another. Their states are strongly coupled due to dependencies that arise from such relations. For a system designer, acknowledging the presence of these dependencies is as crucial to guaranteeing performance as studying them. As the roles played by technology in fields such as transportation, healthcare, and finance continue to be more profound and diverse, modern engineering systems have grown to be more reliant on the integration of technologies across multiple disciplines and their requirements. The need to ensure proper division of labor, integration of system modules, and attribution of legal responsibility calls for a more methodological look into co-design considerations. Originally conceived in computer programming, contract-based reasoning is a design approach whose promise of a formal compositional paradigm is receiving attention from a broader engineering community. Our work is dedicated to narrowing the gap between the theory and application of this yet nascent framework.
\r\n\r\nIn the first half of this dissertation, we introduce a model interface contract theory for input/output automata with guards and a formalization of the directive-response architecture using assume-guarantee contracts and show how these may be used to guide the formal design of a traffic intersection and an automated valet parking system respectively. Next, we address a major drawback of assume-guarantee contracts, i.e., the problem of a void contract due to antecedent failure. Our proposed solution is a reactive version of assume-guarantee contracts that enables direct specification at the assumption and guarantee level along with a novel synthesis algorithm that exposes the effects of failures on the contract structure. This is then used to help optimize, adapt, and robustify our design against an uncertain environment.
\r\n\r\nIn light of ongoing development of autonomous driving technologies and its potential impact on the safety of future transportation, the second half of this work is dedicated to the application of the design-by-contract framework to the distributed control of autonomous vehicles. We start by defining and proving properties of \"assume-guarantee profiles,\" our proposed approach to transparent distributed multi-agent decision making and behavior prediction. Next, we provide a local conflict resolution algorithm in the context of a quasi-simultaneous game which guarantees safety and liveness to the composition of autonomous vehicle systems in this game. Finally, to facilitate the extension of these frameworks to real-life urban driving settings, we also supply an effective method to predict agent behavior that utilizes recent advances in machine learning research.
", "doi": "10.7907/8vp7-kd82", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14234", "collection": "thesis", "collection_id": "14234", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022021-223508132", "primary_object_url": { "basename": "Thesis__Learning_to_Optimize (8).pdf", "content": "final", "filesize": 3672012, "license": "other", "mime_type": "application/pdf", "url": "/14234/1/Thesis__Learning_to_Optimize (8).pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Learning to Optimize: from Theory to Practice", "author": [ { "family_name": "Song", "given_name": "Jialin", "orcid": "0000-0001-5633-9909", "clpid": "Song-Jialin" } ], "thesis_advisor": [ { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "thesis_committee": [ { "family_name": "Wierman", "given_name": "Adam C.", "clpid": "Wierman-A-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Dilkina", "given_name": "Bistra", "orcid": "0000-0002-6784-473X", "clpid": "Dilkina-Bistra" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Optimization is at the heart of everyday applications, from finding the fastest route for navigation to designing efficient drugs for diseases. The study of optimization algorithms has focused on developing general approaches that do not adapt to specific problem instances. While they enjoy wide applicability, they forgo the potentially useful information embedded in the structure of an instance. Furthermore, as new optimization problems appear, the algorithm development process relies heavily on domain expertise to identify special properties and design methods to exploit them. Such design philosophy is labor-intensive and difficult to deploy efficiently to a broad range of domain-specific optimization problems, which are becoming ubiquitous in the pursuit of ever more personalized applications.
\r\n \r\nIn this dissertation, we consider different hybrid versions of classical optimization algorithms with data-driven techniques. We aim to equip classical algorithms with the ability to adapt their behaviors on the fly based on specific problem instances. A common theme in our approaches is to train the data-driven components on a pre-collected batch of representative problem instances to optimize some performance metrics, e.g., wall-clock time. Varying the integration details, we present several approaches to learning data-driven optimization modules for combinatorial optimization problems and study the corresponding fundamental research questions on policy learning. We provide multiple practical experimental results to showcase the practicality of our methods which lead to state-of-the-art performance on some classes of problems.
", "doi": "10.7907/7qaw-kd75", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14234", "collection": "thesis", "collection_id": "14234", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022021-223508132", "primary_object_url": { "basename": "Thesis__Learning_to_Optimize (8).pdf", "content": "final", "filesize": 3672012, "license": "other", "mime_type": "application/pdf", "url": "/14234/1/Thesis__Learning_to_Optimize (8).pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Learning to Optimize: from Theory to Practice", "author": [ { "family_name": "Song", "given_name": "Jialin", "orcid": "0000-0001-5633-9909", "clpid": "Song-Jialin" } ], "thesis_advisor": [ { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" } ], "thesis_committee": [ { "family_name": "Wierman", "given_name": "Adam C.", "clpid": "Wierman-A-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Dilkina", "given_name": "Bistra", "orcid": "0000-0002-6784-473X", "clpid": "Dilkina-Bistra" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Optimization is at the heart of everyday applications, from finding the fastest route for navigation to designing efficient drugs for diseases. The study of optimization algorithms has focused on developing general approaches that do not adapt to specific problem instances. While they enjoy wide applicability, they forgo the potentially useful information embedded in the structure of an instance. Furthermore, as new optimization problems appear, the algorithm development process relies heavily on domain expertise to identify special properties and design methods to exploit them. Such design philosophy is labor-intensive and difficult to deploy efficiently to a broad range of domain-specific optimization problems, which are becoming ubiquitous in the pursuit of ever more personalized applications.
\r\n \r\nIn this dissertation, we consider different hybrid versions of classical optimization algorithms with data-driven techniques. We aim to equip classical algorithms with the ability to adapt their behaviors on the fly based on specific problem instances. A common theme in our approaches is to train the data-driven components on a pre-collected batch of representative problem instances to optimize some performance metrics, e.g., wall-clock time. Varying the integration details, we present several approaches to learning data-driven optimization modules for combinatorial optimization problems and study the corresponding fundamental research questions on policy learning. We provide multiple practical experimental results to showcase the practicality of our methods which lead to state-of-the-art performance on some classes of problems.
", "doi": "10.7907/7qaw-kd75", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14230", "collection": "thesis", "collection_id": "14230", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022021-035141903", "primary_object_url": { "basename": "Thesis__to_submit_0601.pdf", "content": "final", "filesize": 19483726, "license": "other", "mime_type": "application/pdf", "url": "/14230/1/Thesis__to_submit_0601.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Reduced Order Model Inspired Robotic Bipedal Walking: A Step-to-step Dynamics Approximation based Approach", "author": [ { "family_name": "Xiong", "given_name": "Xiaobin", "orcid": "0000-0002-6275-3900", "clpid": "Xiong-Xiaobin" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sreenath", "given_name": "Koushil", "clpid": "Sreenath-S" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Controlling bipedal robotic walking is a challenging task. The dynamics is hybrid, nonlinear, high-dimensional, and typically underactuated. Complex physical constraints have to be satisfied in the walking generation. The stability in terms of not-falling is also hard to be encoded in the walking synthesis. Canonical approaches for enabling robotic walking typically rely on large-scale trajectory optimizations for generating optimal periodic behaviors on the full-dimensional model of the system; then the stabilities of the controlled behaviors are analyzed through the numerically derived Poincar\u00e9 maps. This full-dimensional periodic behavior based synthesis, despite being theoretically rigorous, suffers from several disadvantages. The trajectory optimization problem is computationally challenging to solve. Non-trivial expert-tuning is required on the cost, constraints, and initial conditions to avoid infeasibilities and local optimality. It is cumbersome for realizing non-periodical behaviors, and the synthesized walking can be sensitive to model uncertainties.
\r\n \r\nIn this thesis, we propose an alternative approach of walking synthesis that is based on reduced order modeling and dynamics approximation. We formulate a discrete step-to-step (S2S) dynamics of walking, where the step size is treated as the control input to stabilize the pre-impact horizontal center of mass (COM) state of the robot. Stepping planning thus is converted into a feedback control problem. To effectively and efficiently solve this feedback stepping planning problem, an underactuated Hybrid Linear Inverted Pendulum (H-LIP) model is proposed to approximate the dynamics of underactuated bipedal walking; the linear S2S dynamics of the H-LIP then approximates the robot S2S dynamics. The H-LIP based stepping controller is hence utilized to plan the desired step sizes on the robot to control its pre-impact horizontal COM state. Stable walking behaviors are consequently generating by realizing the desired step size in the output construction and stabilizing the output via optimization-based controllers. We evaluate this approach successfully on several bipedal walking systems with an increase in the system complexity: a planar five-linkage walker AMBER, an actuated version of the Spring Loaded Inverted Pendulum (aSLIP) in both 2D and 3D, and finally the 3D underactuated robot Cassie. The generated dynamic walking behaviors on these systems are shown to be highly versatile and robust. Furthermore, we show that this approach can be effectively extended to realizing more complex walking tasks such as global trajectory tracking and walking on rough terrain.
", "doi": "10.7907/9bz9-x102", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:11888", "collection": "thesis", "collection_id": "11888", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-135312842", "primary_object_url": { "basename": "Hanewich-Hollatz_Mikhail_2020.pdf", "content": "final", "filesize": 16901753, "license": "other", "mime_type": "application/pdf", "url": "/11888/2/Hanewich-Hollatz_Mikhail_2020.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function via Dynamic RNA Nanotechnology", "author": [ { "family_name": "Hanewich-Hollatz", "given_name": "Mikhail Henning", "orcid": "0000-0002-5369-3846", "clpid": "Hanewich-Hollatz-Mikhail-Henning" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "A guide RNA (gRNA) directs the function of a CRISPR protein effector to a target gene of choice, providing a versatile programmable platform for engineering diverse modes of synthetic regulation (edit, silence, induce, bind). However, the fact that gRNAs are constitutively active places limitations on the ability to confine gRNA activity to a desired location and time. To achieve programmable control over the scope of gRNA activity, here we apply principles from dynamic RNA nanotechnology to engineer conditional guide RNAs (cgRNAs) whose activity is dependent on the presence or absence of an RNA trigger. These cgRNAs are programmable at two levels, with the trigger-binding sequence controlling the scope of the effector activity and the target-binding sequence determining the subject of the effector activity. There are two possible logical directions for single-input cgRNAs: constitutively active cgRNAs that are conditionally inactivated by an RNA trigger (ON\u2192OFF logic) and constitutively inactive cgRNAs that are conditionally activated by an RNA trigger (OFF\u2192ON logic). Using an in vitro assay for cgRNA activity with synthetic trigger, in vitro transcribed cgRNA, and recombinant dCas9, we observe a conditional (ON\u2192OFF logic) response for a set of four allosteric constitutively active cgRNAs with a median \u22486% crosstalk between noncognate cgRNA/trigger pairs. Motivated by the observed lack of conditional response of this mechanism when ported to E. coli, we describe a systematic study of unstructured sequence inserts into the standard gRNA structure and report the conditional response of a set of 34 candidate cgRNAs in living cells. Molecular mechanisms for both ON\u2192OFF and OFF\u2192ON cgRNAs are demonstrated in E. coli. For each mechanism, automated sequence design is performed using the reaction pathway designer within NUPACK to produce an orthogonal library of cgRNAs that respond to different RNA triggers. In E. coli expressing cgRNAs, triggers, and silencing dCas9 as the protein effector, we observe a median conditional response of \u224815-fold for a library of three orthogonal ON\u2192OFF \"splinted switch\" cgRNA/trigger pairs, and \u22483-fold for a library of three orthogonal OFF\u2192ON \"toehold switch\" cgRNA/trigger pairs; the median crosstalk within each library is <2% and \u224820% for the two mechanisms, respectively. By providing programmable control over both the scope and target of protein effector function, cgRNA regulators offer a promising platform for conditional gene regulation and synthetic biology.
", "doi": "10.7907/NS2B-DJ96", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13735", "collection": "thesis", "collection_id": "13735", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292020-131840076", "primary_object_url": { "basename": "200529_erik_jue_2020_thesis_final.pdf", "content": "final", "filesize": 13853909, "license": "other", "mime_type": "application/pdf", "url": "/13735/1/200529_erik_jue_2020_thesis_final.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Improved Tools for Point-of-Care Nucleic Acid Amplification Testing", "author": [ { "family_name": "Jue", "given_name": "Erik Bradley", "orcid": "0000-0001-7585-3794", "clpid": "Jue-Erik-Bradley" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "There is a critical need for improved diagnostic tools to detect infectious diseases, especially in low-resource regions. A sample-to-answer point-of-care nucleic acid amplification test (NAAT) would be incredibly valuable for many different applications (e.g. COVID-19, Chlamydia/Gonorrhoeae, Influenza, Ebola, Zika/Chikungunya/Dengue, etc.). However, sample preparation (purification of pure nucleic acids) is a challenging bottleneck. In Chapter 2, commercial NA extraction methods were studied and improved. In Chapter 3, commercial stocks of SARS-CoV-2 RNA used in FDA emergency-use authorizations were found to be inaccurate and were independently quantified using reverse transcription digital PCR. In Chapter 4, a 3D printed meter-mix device was developed for initial processing prior to the sample preparation device. In Chapter 5, a 3D printed sample-to-device interface was prototyped to facilitate loading multi-volume SlipChip devices with purified template mixed with LAMP reactants. In Chapters 6-7, advancements were made for image processing of commercial chips to study digital LAMP reactions. In Chapter 8, additional tools were developed towards sample-to-answer point-of-care NAAT including a sample preparation module, amplification module, cell-phone readout, and automated base station.", "doi": "10.7907/d6mf-5081", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13667", "collection": "thesis", "collection_id": "13667", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04022020-212557295", "type": "thesis", "title": "Mechanisms of Phenazine-Mediated Extracellular Electron Transfer by Pseudomonas aeruginosa", "author": [ { "family_name": "Saunders", "given_name": "Scott Harrison", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-Harrison" } ], "thesis_advisor": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "thesis_committee": [ { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Extracellular electron transfer (EET), the process whereby cells access electron acceptors or donors that reside many cell lengths away, enables metabolic activity by microorganisms, particularly under oxidant-limited conditions that occur in multicellular bacterial biofilms. Although different mechanisms underpin this process in individual organisms, a potentially widespread strategy involves extracellular electron shuttles, redox-active metabolites that are secreted and recycled by diverse bacteria. Here, I first review general aspects of the electron shuttling strategy, such as the chemical diversity and potential distribution of electron shuttle producers and users, and the costs associated with electron shuttle biosynthesis. Then I address the long-standing question: how do these electron shuttles catalyze electron transfer within biofilms without being lost to the environment? I show that phenazine electron shuttles mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms, which are important in nature and disease. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by binding to eDNA. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and phenazines can participate directly in redox reactions through DNA; the biofilm eDNA can also support rapid electron transfer between redox-active intercalators. Electrochemical measurements of biofilms indicate that retained PYO supports an efficient redox cycle with rapid EET and slow loss from the biofilm. Together, these results establish that eDNA facilitates phenazine metabolic processes in P. aeruginosa biofilms, suggesting a model for how extracellular electron shuttles achieve retention and efficient EET in biofilms.
", "doi": "10.7907/P4Z5-5445", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13689", "collection": "thesis", "collection_id": "13689", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292020-165136662", "type": "thesis", "title": "Scalable Synthesis and Verification: Towards Reliable Autonomy", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-Sumanth" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Gao", "given_name": "Sicun", "clpid": "Gao-Sicun" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We have seen the growing deployment of autonomous systems in our daily life, ranging from safety-critical self-driving cars to dialogue agents. While impactful and impressive, these systems do not often come with guarantees and are not rigorously evaluated for failure cases. This is in part due to the limited scalability of tools available for designing correct-by-construction systems, or verifying them posthoc. Another key limitation is the lack of availability of models for the complex environments with which autonomous systems often have to interact with. In the direction of overcoming these above mentioned bottlenecks to designing reliable autonomous systems, this thesis makes contributions along three fronts.
\r\n\r\nFirst, we develop an approach for parallelized synthesis from linear-time temporal logic Specifications corresponding to the generalized reactivity (1) fragment. We begin by identifying a special case corresponding to singleton liveness goals that allows for a decomposition of the synthesis problem, which facilitates parallelized synthesis. Based on the intuition from this special case, we propose a more generalized approach for parallelized synthesis that relies on identifying equicontrollable states.
\r\n\r\nSecond, we consider learning-based approaches to enable verification at scale for complex systems, and for autonomous systems that interact with black-box environments. For the former, we propose a new abstraction refinement procedure based on machine learning to improve the performance of nonlinear constraint solving algorithms on large-scale problems. For the latter, we present a data-driven approach based on chance-constrained optimization that allows for a system to be evaluated for specification conformance without an accurate model of the environment. We demonstrate this approach on several tasks, including a lane-change scenario with real-world driving data.
\r\n\r\nLastly, we consider the problem of interpreting and verifying learning-based components such as neural networks. We introduce a new method based on Craig's interpolants for computing compact symbolic abstractions of pre-images for neural networks. Our approach relies on iteratively computing approximations that provably overapproximate and underapproximate the pre-images at all layers. Further, building on existing work for training neural networks for verifiability in the classification setting, we propose extensions that allow us to generalize the approach to more general architectures and temporal specifications.
", "doi": "10.7907/4j39-v857", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13771", "collection": "thesis", "collection_id": "13771", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022020-154234707", "primary_object_url": { "basename": "My_Thesis.pdf", "content": "final", "filesize": 31028233, "license": "other", "mime_type": "application/pdf", "url": "/13771/1/My_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Applied Safety Critical Control", "author": [ { "family_name": "Gurriet", "given_name": "Thomas", "orcid": "0000-0002-5240-3720", "clpid": "Gurriet-Thomas" } ], "thesis_advisor": [ { "family_name": "Ames", "given_name": "Aaron D.", "clpid": "Ames-A-D" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Ames", "given_name": "Aaron D.", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Feron", "given_name": "Eric M.", "clpid": "Feron-E-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "There is currently a clear gap between control-theoretical results and the reality of robotic implementation, in the sense that it is very difficult to transfer analytical guarantees to practical ones. This is especially problematic when trying to design safety-critical systems where failure is not an option. While there is a vast body of work on safety and reliability in control theory, very little of it is actually used in practice where safety margins are typically empiric and/or heuristic. Nevertheless, it is still widely accepted that a solution to these problems can only emerge from rigorous analysis, mathematics, and methods. In this work, we therefore seek to help bridge this gap by revisiting and expanding existing theoretical results in light of the complexity of hardware implementation.
\r\n\r\nTo that end, we begin by making a clear theoretical distinction between systems and models, and outline how the two need to be related for guarantees to transfer from the latter to the former. We then formalize various imperfections of reality that need to be accounted for at a model level to provide theoretical results with better applicability. We then discuss the reality of digital controller implementation and present the mathematical constraints that theoretical control laws must satisfy for them to be implementable on real hardware. In light of these discussions, we derive new realizable set-invariance conditions that, if properly enforced, can guarantee safety with an arbitrary high levels of confidence. We then discuss how these conditions can be rigorously enforced in a systematic and minimally invasive way through convex optimization-based Safety Filters. Multiple safety filter formulations are proposed with varying levels of complexity and applicability. To enable the use of these safety filters, a new algorithm is presented to compute appropriate control invariant sets and guarantee feasibility of the optimization problem defining these filters. The effectiveness of this approach is demonstrated in simulation on a nonlinear inverted pendulum and experimentally on a simple vehicle. The aptitude of the framework to handle a system's dynamics uncertainty is illustrated by varying the mass of the vehicle and showcasing when safety is conserved. Then, the aptitude of this approach to provide guarantees that account for controller implementation's constraints is illustrated by varying the frequency of the control loop and again showcasing when safety is conserved.
\r\n\r\nIn the second part of this work, we revisit the safety filtering approach in a way that addresses the scalability issues of the first part of this work. There are two main approaches to safety-critical control. The first one relies on computation of control invariant sets and was presented in the first part of this work. The second approach draws from the topic of optimal control and relies on the ability to realize Model-Predictive-Controllers online to guarantee the safety of a system. In that online approach, safety is ensured at a planning stage by solving the control problem subject for some explicitly defined constraints on the state and control input. Both approaches have distinct advantages but also major drawbacks that hinder their practical effectiveness, namely scalability for the first one and computational complexity for the second one. We therefore present an approach that draws from the advantages of both approaches to deliver efficient and scalable methods of ensuring safety for nonlinear dynamical systems. In particular, we show that identifying a backup control law that stabilizes the system is in fact sufficient to exploit some of the set-invariance conditions presented in the first part of this work. Indeed, one only needs to be able to numerically integrate the closed-loop dynamics of the system over a finite horizon under this backup law to compute all the information necessary for evaluating the regulation map and enforcing safety.\r\nThe effect of relaxing the stabilization requirements of the backup law is also studied, and weaker but more practical safety guarantees are brought forward. We then explore the relationship between the optimality of the backup law and how conservative the resulting safety filter is. Finally, methods of selecting a safe input with varying levels of trade-off between conservativeness and computational complexity are proposed and illustrated on multiple robotic systems, namely: a two-wheeled inverted pendulum (Segway), an industrial manipulator, a quadrotor, and a lower body exoskeleton.
", "doi": "10.7907/y97v-b205", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13766", "collection": "thesis", "collection_id": "13766", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012020-230913819", "primary_object_url": { "basename": "Tanner_Melissa_2019.pdf", "content": "final", "filesize": 78028312, "license": "cc_by_nc", "mime_type": "application/pdf", "url": "/13766/1/Tanner_Melissa_2019.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Tethered Motion Planning for a Rappelling Robot", "author": [ { "family_name": "Tanner", "given_name": "Melissa Midori", "orcid": "0000-0003-4610-1379", "clpid": "Tanner-Melissa-Midori" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Nesnas", "given_name": "Issa A.", "clpid": "Nesnas-I-A" }, { "family_name": "Ames", "given_name": "Aaron D.", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The Jet Propulsion Laboratory and Caltech developed the Axel rover to investigate and demonstrate the potential for tethered extreme terrain mobility, such as allowing access to science targets on the steep crater walls of other planets. Tether management is a key issue for Axel and other rappelling rovers. Avoiding tether entanglement constrains the robot's valid motions to the set of outgoing and returning path pairs that are homotopic to each other. In the case of a robot on a steep slope, a motion planner must additionally ensure that this ascent-descent path pair is feasible, based on the climbing forces provided by the tether. This feasibility check relies on the taut tether configuration, which is the shortest path in the homotopy class of the ascent-descent path pair.
\r\n\r\nThis dissertation presents a novel algorithm for tethered motion planning in extreme terrains, produced by combining shortest-homotopic-path algorithms from the topology and computational geometry communities with traditional graph search methods. The resulting tethered motion planning algorithm searches for this shortest path, checks for feasibility, and then generates waypoints for an ascent-descent path pair in the same homotopy class. I demonstrate the implementation of this algorithm on a Martian crater data set such as might be seen for a typical mission. By searching only for the shortest path, and ordering that search according to a heuristic, this algorithm proceeds more efficiently than previous tethered path-planning algorithms for extreme terrain.
\r\n\r\nFrictional tether-terrain interaction may cause dangerously intermittent and unstable tether obstacles, which can be categorized based on their stability. Force-balance equations from the rope physics literature provide a set of tether and terrain conditions for static equilibrium, which can be used to determine if a given tether configuration will stick to a given surface based on tether tension. By estimating the tension of Axel's tether when driving, I divide potential tether tension obstacles into the following categories: acting as obstacles, acting as non-obstacles, and hazardous intermittent obstacles where it is uncertain whether the tether would slip or stick under normal driving tension variance. This dissertation describes how to modify the obstacle map as the categorization of obstacles fluctuates, and how to alter a motion plan around the dangerous tether friction obstacles. Together, these algorithms and methods form a framework for tethered motion planning on extreme terrain.
", "doi": "10.7907/h7d4-ww72", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13687", "collection": "thesis", "collection_id": "13687", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292020-052418975", "type": "thesis", "title": "Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks", "author": [ { "family_name": "Johnson", "given_name": "Robert Francis", "orcid": "0000-0002-5340-8347", "clpid": "Johnson-Robert-Francis" } ], "thesis_advisor": [ { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Qian", "given_name": "Lulu", "orcid": "0000-0003-4115-2409", "clpid": "Qian-Lulu" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Bruck", "given_name": "Jehoshua", "orcid": "0000-0001-8474-0812", "clpid": "Bruck-J" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Qian", "given_name": "Lulu", "orcid": "0000-0003-4115-2409", "clpid": "Qian-Lulu" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "In molecular programming, the Chemical Reaction Network model is often used to describe systems of interacting molecules. This model can describe either real systems, allowing us to analyze and determine their computational function; or describe hypothetical systems, with known computational function but perhaps no known physical example. One significant breakthrough in the field is that any Chemical Reaction Network can be approximated by a system using DNA Strand Displacement mechanisms. This allows the Chemical Reaction Network model to be treated like a programming language, where programs can be written in the abstract and then compiled into physical molecules. Given a programming language and a proof-of-concept compiler, one would want to take the compiler from the proof-of-concept stage into a more reliable, more systematic, and better understood process. This thesis is made up of my contributions to that effort.
\r\n\r\nFirst, given a programming language and a compiler, it would be useful to formally verify that the compiler is correct. My collaborators, Qing Dong and Erik Winfree, and I defined a Chemical Reaction Network-specific form of bisimulation equivalence, which can compare two such networks and verify that one is (or is not) a correct implementation of the other. For example, the compiler-produced DNA circuit can be verified as an implementation of its abstract program, although this is not the only possible use. After defining this concept of equivalence, we show that it can be checked by algorithm; although various parts of the problem are NP-complete or PSPACE-complete, we give algorithms that meet these lower bounds. We also prove a number of interesting properties of Chemical Reaction Network bisimulation equivalence, including transitivity and modularity properties which are particularly useful for stepwise checking of large systems. We further extend this bisimulation method to linear Polymer Reaction Networks, a strictly more powerful abstraction which has been occasionally used in molecular programming. Again we prove complexity hardness results, which in this case are as expected uncomputable in the general case; however, many practical systems can still be verified, and we give one such example. Finally, we use bisimulation to identify a class of single-locus networks that are practical to implement. Thus we show a method of verification which can simplify use of the above-mentioned compiler by proving general statements of correctness about its results.
\r\n\r\nSecond, given a programming language and a concept of compiling it, it would be useful to optimize the result of the compilation. One particular area of optimization is the number of DNA strands per prepared complex; some experiments suggest that systems with no more than 2 strands per complex are more robust. Lulu Qian and I developed some proposed DNA Strand Displacement schemes for general Chemical Reaction Network implementations with no more than 2 strands per complex, and a number of other desirable properties. Meanwhile, having been shown to be useful for many reasons, the mechanisms of DNA Strand Displacement have recently been formalized, abstracted, and analyzed. I show that this formalization, combined with the bisimulation methods above, can prove various statements about the limits of DNA Strand Displacement systems. For example, a set of desirable conditions including the 2-strand limit cannot be achieved by any general Chemical Reaction Network implementation scheme. I also observe that two of the new schemes we discovered, each meeting all but one condition of the impossible set, were found in the process of coming up with this proof. I thus argue that through formalization of DNA Strand Displacement we can have a more systematic method of finding and designing molecular programs, and of knowing when the programs we want do not exist.
", "doi": "10.7907/a74v-kv80", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:13679", "collection": "thesis", "collection_id": "13679", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04222020-163929825", "type": "thesis", "title": "Acoustic Reporter Genes for Noninvasive Imaging of Cellular Function", "author": [ { "family_name": "Farhadi", "given_name": "Arash", "orcid": "0000-0001-9137-8559", "clpid": "Farhadi-Arash" } ], "thesis_advisor": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wang", "given_name": "Lihong", "orcid": "0000-0001-9783-4383", "clpid": "Wang-Lihong" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The study of cellular function within the context of intact living organisms is a grand challenge in biological research. Addressing this challenge requires imaging tools that can visualize cells inside the body. If successful, this would greatly increase our ability to study a battery of processes from brain development to tumorigenesis, to monitoring cell-based therapeutics. To date, most common methods for imaging cellular processes such as gene expression have relied on optical reporters, such as fluorescent or luminescent proteins, which provide high molecular precision for studies in petri dishes and transparent organisms, but have limited performance in large animals due to the poor penetration of light in biological tissue. Conversely, magnetic resonance imaging (MRI) and ultrasound can image tissues at depth with high spatial and temporal resolution, but they lack molecular reporters analogous to the green fluorescent protein (GFP). As a result, they have made limited impact on biological research. To address this, we focus on developing biomolecular reporters for MRI and ultrasound \u2014 based on a unique class of air-filled protein nanostructures called gas vesicles \u2014 using them to image the location and function of cells deep inside the body.
\r\n\r\nThis thesis begins with a brief review of genetically encoded materials for noninvasive imaging, highlighting key advances over the past two decades and providing context for the work below. We discuss the development of increasingly sophisticated tools starting from early efforts to engineer single molecule reporters to recent work on multi-component genetic machinery (including gas vesicles) with multi-modality capabilities. In Chapter 2, we present a platform for engineering the surface of gas vesicles to modulate their acoustic, surface charge, and molecular- targeting properties as injectable acoustic biomolecules. In Chapter 3, we present the recombinant expression of gas vesicles as injectable contrast agents in common lab strain bacteria to facilitate the genetic engineering of the entire gas vesicle gene cluster and to assist this technology\u2019s adoption by other (non-specialist) research groups. This work characterized the ultrasound and hyperpolarized 129Xenon-MRI contrast of gas vesicles as nanoscale contrast agents.
\r\n\r\nIn a parallel effort, we developed a hybrid gene cluster that when introduced to microbes enables the imaging of their gene expression using ultrasound. These bacterial acoustic reporter genes were used to image the location of probiotic cells inside the gastrointestinal tract of mice. However, the ability for these genes to be expressed in mammalian cells had not been demonstrated and presented a major challenge in synthetic biology. In Chapter 4, we addressed this by introducing the first mammalian acoustic reporter genes \u2014 a genetic program whose introduction to mammalian cells resulted in the expression of gas vesicles that can be visualized by ultrasound. These mammalian acoustic reporter genes will enable previously impossible approaches to monitoring the location, viability and function of mammalian cells in vivo.
\r\n\r\nIn Chapter 5, we explore a new paradigm in MRI by taking advantage of the acousto-magnetic property of gas vesicles. Here, we present background-free MRI to address a longstanding challenge in untangling the signal of exogenous contrast agents from the endogenous MRI contrast produced by biological tissues. Chapter 6 explores the optical properties of gas vesicles as genetically encodable phase contrast agents in digital holographic imaging. Chapter 7 is a brief discussion of the potential future directions for this work.
\r\n\r\nThe data presented in this thesis lays the ground for exciting new research on developing noninvasive biomolecular tools that will enable the discovery of novel biological processes.
", "doi": "10.7907/zght-4j47", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:11281", "collection": "thesis", "collection_id": "11281", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11262018-100422941", "primary_object_url": { "basename": "Noah_Olsman_Thesis_Final.pdf", "content": "final", "filesize": 3608771, "license": "other", "mime_type": "application/pdf", "url": "/11281/1/Noah_Olsman_Thesis_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Architecture, Design, and Tradeoffs in Biomolecular Feedback Systems", "author": [ { "family_name": "Olsman", "given_name": "Noah Andrew", "orcid": "0000-0002-4351-3880", "clpid": "Olsman-Noah-Andrew" } ], "thesis_advisor": [ { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Bois", "given_name": "Justin S.", "orcid": "0000-0001-7137-8746", "clpid": "Bois-J-S" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A core pursuit in systems and synthetic biology is the analysis of the connection between the low-level structure and parameters of a biomolecular network and its high-level function and performance. Elucidating this mapping has become increasingly feasible as precise measurements of both input parameters and output dynamics become abundant. At the same time, cross-pollination between biology and engineering has led to the realization that many of the mathematical tools from control theory are well-suited to analyze biological processes.
\r\n\r\nThe goal of this thesis is to use tools from control theory to analyze a variety of biomolecular systems from both natural and synthetic settings, and subsequently yield insight into the architecture, tradeoffs, and limitations of biological network. In Chapter 2, I demonstrate how allosteric proteins can be used to respond logarithmically to changes in signal. In Chapter 3, I show how control theoretic techniques can be used to inform the design of synthetic integral feedback networks that implement feedback with a sequestration mechanism. Finally, in Chapter 4 I present a novel simplified model of the E. coli heat shock response system and show how the the mapping of circuit parameters to function depends on the network's architecture.
\r\n\r\nThe unifying theme of this research is that the conceptual framework used to study engineered systems is remarkably well-suited to biology. That being said, it is important to apply these tools in a way that is informed by the molecular details of biological processes. By combining structural and biochemical data with the functional perspective of engineering, it is possible to understand the architectural principles that underlie living systems.
", "doi": "10.7907/DGPY-1679", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11705", "collection": "thesis", "collection_id": "11705", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-083145024", "primary_object_url": { "basename": "Nakahira_ Yorie_2019_thesis.pdf", "content": "final", "filesize": 5858726, "license": "other", "mime_type": "application/pdf", "url": "/11705/9/Nakahira_ Yorie_2019_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Connecting the Speed-Accuracy Trade-Offs in Sensorimotor Control and Neurophysiology Reveals Diversity Sweet Spots in Layered Control Architectures", "author": [ { "family_name": "Nakahira", "given_name": "Yorie", "orcid": "0000-0003-3324-4602", "clpid": "Nakahira-Yorie" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Adami", "given_name": "Christoph Carl", "clpid": "Adami-C-C" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Nervous systems sense, communicate, compute, and actuate movement using distributed components with trade-offs in speed, accuracy, sparsity, noise, and saturation. Nevertheless, the resulting control can achieve remarkably fast, accurate, and robust performance due to a highly effective layered control architecture. However, this architecture has received little attention from the existing research. This is in part because of the lack of theory that connects speed-accuracy trade-offs (SATs) in the components neurophysiology with system-level sensorimotor control and characterizes the overall system performance when different layers (planning vs. reflex layer) act work jointly. In thesis, we present a theoretical framework that provides a synthetic perspective of both levels and layers. We then use this framework to clarify the properties of effective layered architectures and explain why there exists extreme diversity across layers (planning vs. reflex layers) and within levels (sensorimotor versus neural/muscle hardware levels). The framework characterizes how the sensorimotor SATs are constrained by the component SATs of neurons communicating with spikes and their sensory and muscle endpoints, in both stochastic and deterministic models. The theoretical predictions are also verified using driving experiments. Our results lead to a novel concept, termed ``diversity sweet spots (DSSs)'': the appropriate diversity in the properties of neurons and muscles across layers and within levels help create systems that are both fast and accurate despite being built from components that are individually slow or inaccurate. At the component level, this concept explains why there are extreme heterogeneities in the neural or muscle composition. At the system level, DSSs explain the benefits of layering to allow extreme heterogeneities in speed and accuracy in different sensorimotor loops. Similar issues and properties also extend down to the cellular level in biology and outward to our most advanced network technologies from smart grid to the Internet of Things. We present our initial step in expanding our framework to that area and widely-open area of research for future direction. ", "doi": "10.7907/VYQY-DF47", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11603", "collection": "thesis", "collection_id": "11603", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012019-234115726", "type": "thesis", "title": "Representations of Action Monitoring and Cognitive Control by Single Neurons in the Human Brain", "author": [ { "family_name": "Fu", "given_name": "Zhongzheng", "orcid": "0000-0002-2572-6284", "clpid": "Fu-Zhongzheng" } ], "thesis_advisor": [ { "family_name": "Adolphs", "given_name": "Ralph", "orcid": "0000-0002-8053-9692", "clpid": "Adolphs-R" }, { "family_name": "Rutishauser", "given_name": "Ueli", "clpid": "Rutishauser-U" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Adolphs", "given_name": "Ralph", "orcid": "0000-0002-8053-9692", "clpid": "Adolphs-R" }, { "family_name": "Rutishauser", "given_name": "Ueli", "clpid": "Rutishauser-U" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Allman", "given_name": "John Morgan", "clpid": "Allman-J-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Cognitive control arises whenever a prepotent and often automatic response needs to be overcome by another response. Control is usually effortful and relies on monitoring processes that detect when control is needed and/or when it failed. Control is one of the most important aspects of human behavior in everyday life and is a critical component of executive function. In a series of three empirical chapters, I present results from invasive single-neuron recordings from the frontal cortex of neurosurgical human patients while they perform tasks requiring cognitive control. I show that a substantial proportion of neurons in the pre-supplementary motor area (pre-SMA), and in the dorsal anterior cingulate cortex (dACC), signal response errors shortly after they occurred, but well before onset of feedback. Here I demonstrate that these error neurons signal self-detected errors and that they were separate from neurons signaling conflict. The response of error neurons correlated trial-by-trial with the simultaneously recorded intracranial error-related negativity (iERN), thereby establishing a single-neuron correlate of this important scalp potential. iERN-error neuron synchrony in dACC, but not pre-SMA, predicted whether post-error slowing, which is a measure of control, occurred or not. Spike-field coherence between action potentials and local field potentials in specific frequency bands, and latency differences between the different brain regions, suggest a mechanistic model whereby information relevant to control is passed between sectors of the medial frontal cortex. Multiplexing of different ex-post monitoring signals by individual neurons further documents that control relies on multiple sources of information, which can be dynamically routed in the brain depending on task demands. These findings provide the most complete set of single-neuron data on how errors and conflict signals at the single neuron level contribute to cognitive controls in humans. They provide a first-single neuron correlate of an extensively utilized scalp EEG potential. Together, this work provides a strong complement to investigations of this topic using fMRI in humans, and using electrophysiology in monkeys, and suggests specific future directions.", "doi": "10.7907/RG37-G744", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11586", "collection": "thesis", "collection_id": "11586", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312019-135625690", "primary_object_url": { "basename": "Khazaei Thesis - 5June2019.pdf", "content": "final", "filesize": 2655640, "license": "other", "mime_type": "application/pdf", "url": "/11586/1/Khazaei Thesis - 5June2019.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Metabolic Bi-Stability and Hysteresis in a Model Microbiome Community", "author": [ { "family_name": "Khazaei", "given_name": "Tahmineh", "orcid": "0000-0002-4743-2383", "clpid": "Khazaei-Tahmineh" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Henry", "given_name": "Christopher S.", "clpid": "Henry-Christopher-S" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Changes in the species composition of the human microbiome are associated with a broad range of diseases, but elucidating causal mechanisms has been challenging. Some microbiome disease states persist in seemingly unfavorable conditions, e.g., the proliferation of aerobe\u2013anaerobe communities in oxygen-exposed environments in wounds or small intestinal bacterial overgrowth. In Chapter I, using two microbes relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and control theory to show that multi-stability and hysteresis (MSH) is a mechanism that can describe shifts to a resilient aerobe\u2013anaerobe community. We examine the impact of changing oxygen and nutrient regimes and identify factors, including changes in metabolism and gene expression, that lead to MSH. Where MSH explains microbiome shifts, it can profoundly improve our conceptual understanding of these paradoxically persistent disease states, and thereby facilitate effective interventions.
\r\n\r\nChapter II details a method for rapidly detecting the susceptibility and resistance of Neisseria gonorrhoeae to the antibiotic ciprofloxacin. Antimicrobial-resistant Neisseria gonorrhoeae is an urgent public-health threat, with continued worldwide incidents of infection and rising resistance to antimicrobials. Traditional culture-based methods for antibiotic susceptibility testing are unacceptably slow (1\u20132 days), resulting in the use of broad-spectrum antibiotics and the further development and spread of resistance. Critically needed is a rapid antibiotic susceptibility test (AST) that can guide treatment at the point-of-care. In our approach, we explore the use of RNA signatures, which are among the first cellular responses to drug exposure, as an indicator of antibiotic susceptibility. Using RNA sequencing, we identified antibiotic-responsive transcripts. Significant shifts (>4-fold change) in transcript levels occurred within 5 minutes of antibiotic exposure. We designed assays for responsive transcripts with the highest abundances and fold changes, and validated gene expression using digital PCR. Using the top two markers (porB and rpmB), we correctly determined the antibiotic susceptibility and resistance of 49 clinical isolates after 10-min exposure to ciprofloxacin. RNA signatures are therefore promising as an approach on which to build rapid AST devices for N. gonorrhoeae at the point-of-care, which is critical for disease management, surveillance, and antibiotic stewardship efforts.
", "doi": "10.7907/Z588-5H60", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11489", "collection": "thesis", "collection_id": "11489", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292019-161916232", "primary_object_url": { "basename": "Shan_Kevin_thesis.pdf", "content": "final", "filesize": 3506076, "license": "other", "mime_type": "application/pdf", "url": "/11489/1/Shan_Kevin_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Sparse Deconvolution with Applications to Spike Sorting", "author": [ { "family_name": "Shan", "given_name": "Kevin Qing", "orcid": "0000-0002-2621-1274", "clpid": "Shan-Kevin-Qing" } ], "thesis_advisor": [ { "family_name": "Siapas", "given_name": "Athanassios G.", "clpid": "Siapas-A-G" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" }, { "family_name": "Siapas", "given_name": "Athanassios G.", "clpid": "Siapas-A-G" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Chronic extracellular recording is the use of implanted electrodes to measure the electrical activity of nearby neurons over a long period of time. It presents an unparalleled view of neural activity over a broad range of time scales, offering sub-millisecond resolution of single action potentials while also allowing for continuous recording over the course of many months. These recordings pick up a rich collection of neural phenomena -- spikes, ripples, and theta oscillations, to name a few -- that can elucidate the activity of individual neurons and local circuits.
\r\n\r\nHowever, this also presents an interesting challenge for data analysis. Chronic extracellular recordings contain overlapping signals from multiple sources, requiring these signals to be detected and classified before they can be properly analyzed. The combination of fine temporal resolution with long recording durations produces large datasets, requiring efficient algorithms that can operate at scale.
\r\n\r\nIn this thesis, I consider the problem of spike sorting: detecting spikes (the extracellular signatures of individual neurons' action potentials) and clustering them according to their putative source. First, I introduce a sparse deconvolution approach to spike detection, which seeks to detect spikes and represent them as the linear combination of basis waveforms.\tThis approach is able to separate overlapping spikes without the need for source templates, and produces an output that can be used with a variety of clustering algorithms.
\r\n\r\nSecond, I introduce a clustering algorithm based around a mixture of drifting t-distributions. This model captures two features of chronic extracellular recordings -- cluster drift over time and heavy-tailed residuals in the distribution of spikes -- that are missing from previous models. This enables us to reliably track individual neurons over longer periods of time. I will also show that this model produces more accurate estimates of classification error, which is an important component to proper interpretation of the spike sorting output.
\r\n\r\nFinally, I present a few theoretical results that may assist in the efficient implementation of sparse deconvolution.
", "doi": "10.7907/3JQS-BT21", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11353", "collection": "thesis", "collection_id": "11353", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01222019-133152032", "type": "thesis", "title": "Linearity in Cell Signaling Pathways", "author": [ { "family_name": "Nunns", "given_name": "Harry James Rogan", "orcid": "0000-0002-9669-0039", "clpid": "Nunns-Harry- James-Rogan" } ], "thesis_advisor": [ { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" } ], "thesis_committee": [ { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Accurate cellular communication is of paramount importance for the development, growth, and maintenance of multi-cellular organisms. Communication between cells is carried out by a highly conserved set of signaling pathways, whose dysregulation can lead to many diseases. The molecular details of these signaling pathways are now well-characterized, allowing researchers to investigate the emergent properties that arise from the complex signaling networks. These properties often arise from counter-intuitive or paradoxical mechanisms, meaning that systems-level analysis is necessary. Importantly, mathematical models have been constructed for many pathways that capture measured reaction rates and protein levels. These mathematical models successfully recapitulate dynamic responses of each pathway. Here, I investigated the input-output response of the Wnt, MAPK/ERK, and Tgf\u03b2 pathways using analytical and numerical treatment of mathematical models. Using this approach, I found that the distinct architectures of the three signaling pathways lead to a convergent behavior, linear input-output response. Specifically, mathematical analysis reveals that a futile cycle in the Wnt pathway, a kinase cascade coupled to feedback in the ERK pathway, and nucleocytoplasmic shuttling in the Tgf\u03b2 pathways all yield linear signal transmission. I then verified this finding experimentally in the Wnt and ERK pathways. For the Wnt pathway, direct measurements of the input-output response reveal that \u03b2-catenin is linear with respect to Wnt co-receptor LRP5/6 activity up until receptor saturation. For the ERK pathway, direct measurements indicate a linear relationship between phosphorylated ERK1/2 and the concentration of EGF ligand, up until saturation of ERK1/2. Finally, mathematical modeling reveals that linear response in the Wnt pathway, in conjunction with a recently identified cis-regulatory motif, is sufficient to explain gene expression buffering to perturbations. Therefore, this thesis demonstrates how linearity emerges across three dissimilar architectures, and introduces a novel benefit for linear signal transmission in biology.
", "doi": "10.7907/WP0J-E945", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11161", "collection": "thesis", "collection_id": "11161", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08262018-213846283", "primary_object_url": { "basename": "vipul_singhal_thesis_2018.pdf", "content": "final", "filesize": 5525152, "license": "other", "mime_type": "application/pdf", "url": "/11161/1/vipul_singhal_thesis_2018.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts", "author": [ { "family_name": "Singhal", "given_name": "Vipul", "orcid": "0000-0003-1670-1824", "clpid": "Singhal-Vipul" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Goentoro", "given_name": "Lea A.", "clpid": "Goentoro-L-A" }, { "family_name": "Thomson", "given_name": "Matthew", "clpid": "Thomson-M-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Synthetic biology may be defined as an attempt at using engineering principles to design and build novel biological functionalities. An important class of such functionalities involves the bottom up design of genetic networks (or 'circuits') to control cellular behavior. Performing design iterations on these circuits in vivo is often a time consuming process. One approach that has been developed to address these long design times is to use E. coli cell extracts as simplified circuit prototyping environments. The analogy with similar approaches in engineering, such as prototyping using wind tunnels and breadboards, may be extended by developing accompanying computer aided design tools. In this thesis, we discuss the development of computational and mathematical tools to accelerate circuit prototyping in the TX-TL cell free prototyping platform, and demonstrate some applications of these tools.
\r\n\r\nWe start by discussing the problem of reducing circuit behavior variability between different batches of TX-TL cell extracts. To this end, we demonstrate a model-based methodology for calibrating extract batches, and for using the calibrations to 'correct' the behavior of genetic circuits between batches. We also look at the interaction of this methodology with the phenomenon of parameter non-identifiability, which occurs when the parameter identification inverse problem has multiple solutions. In particular, we derive conditions under which parameter non-identifiability does not hinder our modeling objectives, and subsequently demonstrate the use of such non-identifiable models in performing data variability reduction.
\r\n\r\nNext, we describe txtlsim, a MATLAB Simbiology based toolbox for automatically generating models of genetic circuits in TX-TL, and for using these models for part characterization and circuit behavior prediction. Large genetic circuits can have non-negligible resource usage needs, leading to unintended interactions between circuit nodes arising due to the loading of cellular machinery, transcription factors or other regulatory elements. The usage of consumable resources like nucleotides and amino acids can also have non-trivial effects on complex genetic circuits. These types of effects are handled by the modeling framework of txtlsim in a natural way.
\r\n\r\nWe also highlight mcmc-simbio, a smaller toolbox within txtlsim for performing concurrent Bayesian parameter inference on Simbiology models. Concurrent inference here means that a common set of parameters can be identified using data from an ensemble of different circuits and experiments, with each experiment informing a subset of the parameters. The combination of the concurrence feature with the fact that Markov chain Monte Carlo based Bayesian inference methods allow for the direct visualization of parameter non-identifiability enables the design of ensembles of experiments that reduce such non-identifiability.
\r\n\r\nFinally, we end with a method for performing model order reduction on transcription and translation elongation models while maintaining the ability of these models to track resource consumption. We show that due to their network topology, our models cannot be brought into the two-timescale form of singular perturbation theory when written in species concentration coordinates. We identify a coordinate system in which singular perturbation theory may be applied to chemical reaction networks more naturally, and use this to achieve the desired model reduction.
", "doi": "10.7907/g31j-ch52", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11129", "collection": "thesis", "collection_id": "11129", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07202018-115217471", "primary_object_url": { "basename": "filippidis_ioannis_2019.pdf", "content": "final", "filesize": 700365, "license": "other", "mime_type": "application/pdf", "url": "/11129/39/filippidis_ioannis_2019.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Decomposing Formal Specifications Into Assume-Guarantee Contracts for Hierarchical System Design", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-Ioannis" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Specifications for complex engineering systems are typically decomposed into specifications for individual subsystems in a way that ensures they are implementable and simpler to develop further. We describe a method to algorithmically construct specifications for components that should implement a given specification when assembled. By eliminating variables that are irrelevant to realizability of each component, we simplify the specifications and reduce the amount of information necessary for operation.\r\nTo identify these variables, we parametrize the information flow between components.
\r\n\r\n\r\nThe specifications are written in the Temporal Logic of Actions, TLA+, with liveness properties restricted to an implication of conjoined recurrence properties, known as GR(1). We study whether GR(1) contracts exist in the presence of full information, and prove that memoryless GR(1) contracts that preserve safety do not always exist, whereas contracts in GR(1) with history-determined variables added do exist. We observe that timed stutter-invariant specifications of open-systems in general require GR(2) liveness properties for expressing them.
\r\n\r\n\r\nWe formalize a definition of realizability in TLA+, and define an operator for forming open-systems from closed-systems, based on a variant of the while-plus operator. The resulting open-system properties are realizable when expected to be. We compare stepwise implication operators from the literature, and establish relations between them, and examine the arity required for expressing these operators. We examine which symmetric combinations of stepwise implication and implementation kind avoid circular dependence, and show that only Moore components specified by strictly causal stepwise implication avoid circular dependence.
\r\n\r\n\r\nThe proposed approach relies on symbolic algorithms for computing specifications. To convert the generated specifications from binary decision diagrams to readable formulas over integer variables, we symbolically solve a minimal covering problem. We implemented an algorithm for minimal covering over lattices originally proposed for two-level logic minimization. We formalized the computation of essential elements and cyclic core that is part of this algorithm, and machine-checked the proofs of safety properties using a proof assistant. Proofs supporting the thesis are organized as TLA+ modules in appendices.
", "doi": "10.7907/Z9Q52MTD", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:10966", "collection": "thesis", "collection_id": "10966", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-192944407", "type": "thesis", "title": "Noncommutative Biology: Sequential Regulation of Complex Networks and Connected Matter", "author": [ { "family_name": "Letsou", "given_name": "William Peter", "orcid": "0000-0002-4969-2330", "clpid": "Letsou-William-Peter" } ], "thesis_advisor": [ { "family_name": "Cai", "given_name": "Long", "clpid": "Cai-Long" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Cai", "given_name": "Long", "clpid": "Cai-Long" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "During animal development from zygote to adult, a limited set of regulatory molecules are autonomously deployed in the service of tissue-specific gene expression (reviewed in chapter 1). Inherent in the process is the tension that single cells sample heterogeneous expression states while robustly maintaining a collective final outcome. This thesis addresses theoretical issues that help resolve the paradox that one cell simultaneously contains the fate information of many.
\r\n\r\nPrevious models of development have likened cell fate to minima on a smooth potential energy surface. Such static pictures can be misleading because they suggest the egg knows the path it will take to the adult before it divides even once. Recognition that the potential analogy is an oversimplification has led others to propose that the surface is actually nonsmooth. Chapter 2 reviews the theoretical basis for smooth potentials and resolves these problems by appealing to the tangent space of gene expression. It is then shown that if the potential difference is sufficient to characterize the difference between egg and adult, then the tangent space controls on gene expression are one-dimensional. Furthermore, a shortcoming of models ignoring the connectivity and common origin of dividing cells is that they erect artificial barriers between alternative fates. A fundamentally different picture is sketched wherein the difference between egg and adult is schematized as the shape of the locus of equipotential fates accessible at the same point in time. The conjugacy of space and time is invoked to explain how the requirement that each fate be on a line of equipotential is the same as requiring that each alternative fate move the same distance down the surface at each step. The developmental trajectory is deterministic but not known in advance because it needs to be ascertained at each step which way cells \"turn\" in order to maintain their equipotential relationship. Chapters 3 and 4 refine this sequential model of collective development with specific examples.
\r\n\r\nA simple solution to the problem of cell-type specific gene expression is combinatorial binding of transcription factors at promoters. It is shown in chapter 3 that such models result in substantial information bottlenecks, because all cell fate information is concentrated at the start. We explore a novel, noncommutative model of gene regulation—known as sequential logic—that spreads the information out over time. It is shown using time sequences of noncommutative controllers that targets which otherwise would have been activated together can be regulated independently. We derive scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and show that they scale super-exponentially in the number of regulators. It is also shown that specificity in control is robust to loss of a regulator. Consequently, sequential logic overcomes the information bottleneck in complex problems and enables novel solutions through roundabout strategies. The theoretical results are connected to real biological networks demonstrating specificity in the context of promiscuity.
\r\n\r\nNoncommutative sequential logic has improved storage capacity, but it does not specify who or what supplies the sequences of input that determine cell fate. Chapter 4 offers a solution by way of the seemingly unrelated problem of looping in twisted strings. Cells and strings obey a set of common space-time constraints, ultimately due to the conservation of energy. It is argued that the most parsimonious allocation of energy from the straight to strained string is the one in which each segment sees the same share of the total. Planar looping is shown to be a consequence of the parsimony principle and the Euler-Poincaré equations for rotational motion in the presence an applied torque. We then solve the problem for the looping of a twisted string; with two strains, the Euler-Poincaré predict a different answer than the classical Frenet-Serret equations. Using the results of chapter 2, it is concluded that the Frenet-Serret curvatures assigned ahead of time are not guaranteed to generate space curves that conserve energy: the predicted string has localized strains the Euler-Poincaré solution lacks. Rotational dynamics of strings are connected to developing organisms by postulating conserved RNA polymerase as an analog of angular momentum, and transcriptional activity as energy. Alternative fates along a one-dimensional \"string\" of dividing cells are possible by finding the RNAP distribution that conserves transcriptional activity along a curve of constant developmental potential. Consequently, each alternative fate samples a different sequence of changes to the distribution as it follows a local gradient downhill from high to low developmental potential over time.
\r\n\r\nIn conclusion, regulation in the tangent space of gene expression resolves the paradox that development has a unique solution specified in the DNA of the egg which cannot be determined with certainty until completion of the adult. Noncommutative sequential logic generates complexity that cannot be realized at the start, while interdependent cells (and strings) require time to ensure that each fate is at the same potential difference from a common ancestor. This fundamental reimagining of the Waddington framework can be tested using new multiplexed mRNA imaging technologies that preserve the spatial context of cells in developing tissue.
", "doi": "10.7907/9B5E-F105", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:11021", "collection": "thesis", "collection_id": "11021", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06042018-171639726", "primary_object_url": { "basename": "Baetica-Ania-Ariadna.pdf", "content": "final", "filesize": 3821497, "license": "other", "mime_type": "application/pdf", "url": "/11021/1/Baetica-Ania-Ariadna.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Design, Analysis, And Computational Methods For Engineering Synthetic Biological Networks", "author": [ { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-Ania-Ariadna" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Munsky", "given_name": "Brian", "clpid": "Munsky-Brian" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis advances our understanding of three important aspects of biological systems engineering: analysis, design, and computational methods. First, biological circuit design is necessary to engineer biological systems that behave consistently and follow our design specifications. We contribute by formulating and solving novel problems in stochastic biological circuit design. Second, computational methods for solving biological systems are often limited by the nonlinearity and high dimensionality of the system\u2019s dynamics. This problem is particularly extreme for the parameter identification of stochastic, nonlinear systems. Thus, we develop a method for parameter identification that relies on data-driven stochastic model reduction. Finally, biological system analysis encompasses understanding the stability, performance, and robustness of these systems, which is critical for their implementation. We analyze a sequestration feedback motif for implementing biological control.
\r\n\r\nFirst, we discuss biological circuit design for the stationary and the transient distributional responses of stochastic biochemical systems. Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture their dynamics. The chemical master equation is a commonly used stochastic model that describes how the probability distribution of a chemically reacting system varies with time. Here we design the distributional response of these stochastic models by formulating and solving it as a constrained optimization problem.
\r\n\r\nSecond, we analyze the stability and the performance of a biological controller implemented by a sequestration feedback network motif. Sequestration feedback networks have been implemented in synthetic biology using an array of biological parts. However, their properties of stability and performance are poorly understood. We provide insight into the stability and performance of sequestration feedback networks. Additionally, we provide guidelines for the implementation of sequestration feedback networks.
\r\n\r\nThird, we develop computational methods for the parameter identification of stochastic models of biochemical reaction networks. It is often not possible to find analytic solutions to problems where the dynamics of the underlying biological circuit are stochastic, nonlinear or both. Stochastic models are often challenging due to their high dimensionality and their nonlinearity, which further limits the availability of analytical tools. To address these challenges, we develop a computational method for data-driven stochastic model reduction and we use it to perform parameter identification. Last, we provide concluding remarks and future research directions.
", "doi": "10.7907/98qt-zv92", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10401", "collection": "thesis", "collection_id": "10401", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08302017-121452132", "type": "thesis", "title": "Engineering Biosynthetic Pathways in Cell-Free Systems for Sustainability and Chemical Innovation\r ", "author": [ { "family_name": "Wu", "given_name": "Yong Yi", "orcid": "0000-0002-5401-3662", "clpid": "Wu-Yong-Yi" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "clpid": "Shapiro-M-G" }, { "family_name": "Culler", "given_name": "Stephanie J.", "clpid": "Culler-S-J" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This work presents the cell-free transcription-translation (TX-TL) system as a research and development platform for renewable synthesis and molecular discovery. TX-TL is easy to use and provides a biomolecular breadboard for the rapid prototyping and engineering of biosynthetic pathways. This work has validated the capabilities of the cell-free TX-TL system for simultaneous protein expression and chemical synthesis. Specifically, this work shows that TX-TL supports the conversion of intermediates from carbohydrate metabolism and amino acids into valuable compounds. Metabolic flux through cofactor dependent pathways confirms that active cofactor metabolism is occurring in TX-TL. This work has also demonstrated the industrial relevance of TX-TL through exploring design space of a biosynthetic pathway for improved product yield and expanding substrate scope of another biosynthetic pathway.
\r\n\r\nCurrent methods for assembling biosynthetic pathways in microorganisms require a process of repeated trial and error and have long design-build-test cycles. We describe the use of a cell-free transcription-translation (TX-TL) system as a biomolecular breadboard for the rapid engineering of the 1,4-butanediol (BDO) pathway. In this work, we have verified enzyme expression and enzyme activity and identified the conversion of 4-hydroxybutyrate to downstream metabolites as the pathway bottleneck. We demonstrate the reliability of using linear DNA in TX-TL as a tool for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Pathway constructs of varying pathway enzyme expression levels are tested in TX-TL and in vivo to identify correlations between the two systems, and we find that the production of BDO is correlated to the expression of enzyme ald in both systems. The use of TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Different pathway combinations are also tested in TX-TL for its application in pathway ranking. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied to in vivo strain development.
\r\n\r\nTX-TL simulates a customizable cellular environment that can be controlled by manipulating pH, changing cellular components, or adding exogenous substrates. By adding linear DNA encoding individual enzymes of the violacein pathway and tryptophan analogs in TX-TL reactions, we have discovered new violacein analogs. TX-TL enables rapid production of natural product analogs with diverse substitution, which allows small-scale biosynthesis of potential drug candidates and offers a new platform for drug discovery. This work also presents TX-TL as a platform for protein engineering. Residues targeted for site-saturated mutagenesis were identified with protein-ligand docking. Linear DNAs of individual enzyme mutants were added into TX-TL reactions to screen for improved enzyme variant. Screening result indicates vioE mutant Y17H reduces byproduct formation and redirects metabolic flux towards target metabolites. Protein engineering for improved enzyme activity can further expand the substrate scope of a natural product pathway and result with more natural product analogs that can be applied for medical applications.
\r\n\r\nThis work demonstrates that the cell-free TX-TL system can become a valuable tool that complements the process of engineering biosynthesis in the whole cell in vivo system or the purified protein in vitro system. Future engineering and development of the TX-TL system can further expand the chemical space for biosynthesis.
\r\n", "doi": "10.7907/Z99W0CN1", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10610", "collection": "thesis", "collection_id": "10610", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12162017-121220572", "primary_object_url": { "basename": "leong_yokepeng_2017.pdf", "content": "final", "filesize": 12218687, "license": "other", "mime_type": "application/pdf", "url": "/10610/1/leong_yokepeng_2017.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Optimal Controller Synthesis for Nonlinear Systems", "author": [ { "family_name": "Leong", "given_name": "Yoke Peng", "orcid": "0000-0001-8560-8856", "clpid": "Leong-Yoke-Peng" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Ames", "given_name": "Aaron D.", "clpid": "Ames-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Optimal controller synthesis is a challenging problem to solve. However, in many applications such as robotics, nonlinearity is unavoidable. Apart from optimality, correctness of the system behaviors with respect to system specifications such as stability and obstacle avoidance is vital for engineering applications. Many existing techniques consider either the optimality or the correctness of system behavior. Rarely, a tool exists that considers both. Furthermore, most existing optimal controller synthesis techniques are not scalable because they either require ad-hoc design or they suffer from the curse of dimensionality.
\r\n\r\nThis thesis aims to close these gaps by proposing optimal controller synthesis techniques for two classes of nonlinear systems: linearly solvable nonlinear systems and hybrid nonlinear systems. Linearly solvable systems have associated Hamilton- Jacobi-Bellman (HJB) equations that can be transformed from the original nonlinear partial differential equation (PDE) into a linear PDE through a logarithmic transformation. The first part of this thesis presets two methods to synthesize optimal controller for linearly solvable nonlinear systems. The first technique uses a hierarchy of sums-of-square programs to compute a sequence of suboptimal controllers that have non-increasing suboptimality for first exit and finite horizon problems. This technique is the first systematic approach to provide stability and suboptimal performance guarantees for stochastic nonlinear systems in one framework. The second technique uses the low rank tensor decomposition framework to solve the linear HJB equation for first exit, finite horizon, and infinite horizon problems. This technique scale linearly with dimensions, alleviating the curse of dimensionality and enabling us to solve the linear HJB equation for a quadcopter model that is a twelve-dimensional system on a personal laptop. A new algorithm is proposed for a key step in the controller synthesis algorithm to solve the ill-conditioning issue that arises in the original algorithm. A MATLAB toolbox that implements the algorithms is developed, and the performance of these algorithms is illustrated by a few engineering examples.
\r\n\r\nApart from stability, in many applications, more complex specifications such as obstacle avoidance, reachability, and surveillance are required. The second part of the thesis describes methods to synthesize optimal controllers for hybrid nonlinear systems with quantitative objectives (i.e., minimizing cost) and qualitative objectives (i.e., satisfying specifications). This thesis focuses on two types of qualitative objectives, regular objectives, and \u03c9-regular objectives. Regular objectives capture bounded time behavior such as reachability, and ω-regular objectives capture long term behavior such as surveillance. For both types of objectives, an abstraction-refinement procedure that preserves the cost is developed. A two-player game is solved on the product of the abstract system and the given objectives to synthesize the suboptimal controller for the hybrid nonlinear system. By refining the abstract system, the algorithms are guaranteed to converge to the optimal cost and return the optimal controller if the original systems are robust with respect to the initial states and the optimal controller inputs. The proposed technique is the first abstraction-refinement based technique to combine both quantitative and qualitative objectives into one framework. A Python implementation of the algorithms are developed, and a few engineering examples are presented to illustrate the performance of these algorithms.
", "doi": "10.7907/Z9TX3CK8", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10606", "collection": "thesis", "collection_id": "10606", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12132017-121914940", "type": "thesis", "title": "Application, Computation, and Theory for Synthetic Gene Circuits", "author": [ { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-Anandh" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Goentoro", "given_name": "Lea A.", "clpid": "Goentoro-L-A" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The field of synthetic gene circuits is concerned with engineering novel gene expression dynamics into organisms. This field, a subset of synthetic biology, was started almost two decades ago with the creation of two synthetic circuits: a bistable toggle switch and an oscillator. From the very outset, modeling has played a role in the development of synthetic circuits. However, modeling has been used to gain qualitative insight into dynamics, and actual quantitative modeling has been lagging behind.
\r\n\r\nParameters for quantitative models for biological systems often cannot be adequately estimated from measured data, because far too many sets of parameters can produce the same set of limited measured outputs. Additionally, models for synthetic gene circuits are often not correct the first time, and iterating on cycles of modeling and parameter estimation is difficult. Finally, there is a gap between development of modeling and system identification tools and their application to experiments on actual synthetic gene circuits.
\r\n\r\nThis thesis attempts to work towards addressing these issues with quantitative modeling for synthetic gene circuits. First, we derive theoretical conditions for identifiability of stochastic linear systems from heterogenous types of measurement data. These identifiability conditions can provide insight into what type of model to use and what measurements to collect in order to ensure that the resulting model can be identified.
\r\n\r\nSecond, we develop a software package for fast and flexible modeling and parameter estimation for synthetic gene circuits. The user can input models into our software using a simple text format and perform simulations of all types at optimized speeds. By inputting measured experimental data along with the model, the software can be used to perform Bayesian parameter estimation in an automated manner. To bridge the gap between computation and application, we apply this software to parameter estimation of DNA recombinase dynamics using real experimental data collected in an in vitro cell extract.
\r\n\r\nFinally, we use modeling to guide the design of an improved single gene synthetic oscillator. While the original synthetic genetic oscillator contained three genes, we show that a simple circuit with a single gene can produce robust and synchronized oscillations across a population.
\r\n\r\nOur results constitute an additional step towards the incorporation of quantitative modeling and parameter inference as part of the design-build-test cycle for synthetic gene circuits.
", "doi": "10.7907/Z9833Q67", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10543", "collection": "thesis", "collection_id": "10543", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10242017-193520989", "primary_object_url": { "basename": "fragoso_anthony_2018.pdf", "content": "final", "filesize": 12857622, "license": "other", "mime_type": "application/pdf", "url": "/10543/1/fragoso_anthony_2018.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Egospace Motion Planning Representations for Micro Air Vehicles", "author": [ { "family_name": "Fragoso", "given_name": "Anthony Thomas", "orcid": "0000-0002-5805-9668", "clpid": "Fragoso-Anthony-Thomas" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "McKeon", "given_name": "Beverley J.", "clpid": "McKeon-B-J" }, { "family_name": "Chung", "given_name": "Soon-Jo", "clpid": "Chung-Soon-Jo" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Matthies", "given_name": "Larry H.", "clpid": "Matthies-L-H" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Navigation of micro air vehicles (MAVs) in unknown environments is a complex sensing and trajectory generation task, particularly at high velocities. In this work, we introduce an efficient sense-and-avoid pipeline that compactly represents range measurements from multiple sensors, trajectory generation, and motion planning in a 2.5\u2013dimensional projective data structure called an egospace representation. Egospace coordinates generalize depth image obstacle representations and are a particularly convenient choice for configuration flat mobile robots, which are differentially flat in their configuration variables and include a number of commonly used MAV plant models. After characterizing egospace obstacle avoidance for robots with trivial dynamics and establishing limits on applicability and performance, we generalize to motion planning over full configuration flat dynamics using motion primitives expressed directly in egospace coordinates. In comparison to approaches based on world coordinates, egospace uses the natural sensor geometry to combine the benefits of a multi-resolution and multi-sensor representation architecture into a single simple and efficient layer.\r\nWe also present an experimental implementation, based on perception with stereo vision and an egocylinder obstacle representation, that demonstrates the specialization of our theoretical results to particular mission scenarios. The natural pixel parameterization of the egocylinder is used to quickly identify dynamically feasible maneuvers onto radial paths, expressed directly in egocylinder coordinates, that enable finely detailed planning at extreme ranges within milliseconds. We have implemented our obstacle avoidance pipeline with an Asctec Pelican quadcopter, and demonstrate the efficiency of our approach experimentally with a set of challenging field scenarios. The scalability potential of our system is discussed in terms of sensor horizon, actuation, and computational limitations and the speed limits that each imposes, and its generality to more challenging environments with multiple moving obstacles is developed as an immediate extension to the static framework.", "doi": "10.7907/Z9GX48RJ", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10918", "collection": "thesis", "collection_id": "10918", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05212018-145923990", "primary_object_url": { "basename": "Carey_Y_Zhang_Dissertation.pdf", "content": "final", "filesize": 6246543, "license": "other", "mime_type": "application/pdf", "url": "/10918/1/Carey_Y_Zhang_Dissertation.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Partially Mixed Selectivity and Parietal Cortex", "author": [ { "family_name": "Zhang", "given_name": "Carey Yuzhe", "orcid": "0000-0001-9867-4510", "clpid": "Zhang-Carey-Yuzhe" } ], "thesis_advisor": [ { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Rutishauser", "given_name": "Ueli", "clpid": "Rutishauser-U" }, { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Brain-machine interfaces (BMIs) decode intention signals and other variables from the brain in order to control a computer, tablet, or prosthetic limb. In order to improve the technology, a better understanding of the representational mechanisms within the brain is necessary. Here we study how the anterior intraparietal area (AIP) of human posterior parietal cortex is able to represent many variables within a small patch of cortex. We record single unit activity using a 4 x 4 mm microelectrode array implanted in AIP of a human tetraplegic volunteer. Testing movements of different cognitive strategies, body parts, and body sides, we find that the neural population represents information in a high-dimensional way, termed \"mixed selectivity\", with individual units coding for idiosyncratic combinations of variables. Furthermore, we find that the variables are not randomly mixed but exhibited \"partially mixed selectivity\" with certain variables more randomly mixed than others. Representations were \"functionally segregated\", with representations of the hand and shoulder largely orthogonal despite the high degree of anatomical overlap; representations of body side and strategy were organized by body part. We also examine how the representations changed between BMI training and online BMI control. We find that the structure of the movement representations was preserved, with the different representations found during calibration maintained during online control. Finally, we study the sensory mirror system, a system that processes observed sensations similarly to experienced sensations. We once again find partially mixed selectivity and functional segregation by body parts, showing that this method of encoding information exists not just in the action intention domain but also in the sensory domain. Our results propose partially mixed selectivity as a general mechanism for encoding high dimensional in formation in a small neural population, while also advancing the possibility of limited electrode-array BMIs decoding movements of a large extent of the body.
", "doi": "10.7907/R1RS-RJ59", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10622", "collection": "thesis", "collection_id": "10622", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12312017-234413682", "primary_object_url": { "basename": "park_jin_thesis_composed_5.pdf", "content": "final", "filesize": 4771190, "license": "other", "mime_type": "application/pdf", "url": "/10622/1/park_jin_thesis_composed_5.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Circuits of Dynamically Interacting Sigma Factors in Single Cells", "author": [ { "family_name": "Park", "given_name": "Jin", "clpid": "Park-Jin" } ], "thesis_advisor": [ { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Sternberg", "given_name": "Paul W.", "clpid": "Sternberg-P-W" }, { "family_name": "Goentoro", "given_name": "Lea A.", "clpid": "Goentoro-L-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "How do cells integrate multiple, dynamic genetic circuits? I study this question in the context of the alternative sigma factors of B. subtilis.
\r\n\r\nThe first project proposes a novel mode of gene regulation called timesharing. The key idea is that a limited resource is shared dynamically in time. Here we show that the alternative sigma factors of B. subtilis use dynamic sharing to share a limited supply of core RNA Polymerase (RNAP). We show that 5 alternative sigma factors activate in pulses, and that these pulses operate in a competitive regime. Interestingly, we found that pairwise correlations between these sigma factors contained a mixture of positive and negative correlations, whereas one may naively expect all correlations to be negative. We show with a mathematical model that competitive pulsing can lead to non-intuitive sets of mixed correlations.
\r\n\r\nThe second project take a closer, quantitative look at sigma factor competition. Although competition between the housekeeping sigma and a single alternative sigma has been well studied, competition between alternative sigmas themselves has been relatively unexplored. To address this issue, we systematically investigated the pairwise competitive relationships between 7 alternative sigma factors in B. subtilis. The main experimental tool was a 7x7 'deletion' matrix of strains, where every matrix strain was deleted for one sigma, and reported on another sigma via a fluorescent reporter. The deletion matrix revealed that competition is highly asymmetric. Deletion of any given sigma factor increased \u03c3W activity, but did not affect other sigma factors. These results are recreated by a minimal mathematical model of sigma factor competition, where importantly \u03c3W is relatively high in abundance but weak in affinity for core RNAP. We used the model to predict how overexpressing sigma factors affect each other, and these predictions were matched by experiments.
\r\n\r\nThe third project reports a novel activator for alternative sigma factors. Alternative sigmas factors are activated by many forms of stress, such as nutrient limitation, temperature shifts, and molecular stresses like antibiotics. Here we show that surprisingly, cell lysis causes adjacent cells to specifically activate \u03c3X. This cell lysis-\u03c3X response is a general phenomenon, as it is observed under multiple experimental conditions. We show this relationship between cell death and \u03c3X is causal, since harvested cell extract activates \u03c3X. Finally, we hypothesize that cell death and \u03c3X play an important role in biofilm wrinkle formation.
", "doi": "10.7907/CT0B-Q853", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10973", "collection": "thesis", "collection_id": "10973", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302018-110559204", "primary_object_url": { "basename": "burkhardt_matt_2018_thesis.pdf", "content": "final", "filesize": 44839220, "license": "other", "mime_type": "application/pdf", "url": "/10973/55/burkhardt_matt_2018_thesis.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Dynamic Modeling and Control of Spherical Robots", "author": [ { "family_name": "Burkhardt", "given_name": "Matthew Ryan", "clpid": "Burkhardt-Matthew-Ryan" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Ames", "given_name": "Aaron D.", "clpid": "Ames-A-D" }, { "family_name": "Chung", "given_name": "Soon-Jo", "clpid": "Chung-Soon-Jo" }, { "family_name": "Backes", "given_name": "Paul G.", "clpid": "Backes-Paul-G" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this work, a rigorous framework is developed for the modeling and control of spherical robotic vehicles. Motivation for this work stems from the development of Moball, which is a self-propelled sensor platform that harvests kinetic energy from local wind fields. To study Moball's dynamics, the processes of Lagrangian reduction and reconstruction are extended to robotic systems with symmetry-breaking potential energies, in order to simplify the resulting dynamic equations and expose mathematical structures that play an important role in subsequent control-theoretic tasks. These results apply to robotic systems beyond spherical robots. A formulaic procedure is introduced to derive the reduced equations of motion of most spherical robots from inspection of the Lagrangian. This adaptable procedure is applied to a diverse set of robotic systems, including multirotor aerial vehicles.
\r\n\r\nSmall time local controllability (STLC) results are derived for barycentric spherical robots (BSR), which are spherical vehicles whose locomotion depends on actuating the vehicle's center of mass (COM) location. STLC theorems are introduced for an arbitrary BSR on flat, sloped, or smooth terrain. I show that STLC depends on the surjectivity of a simple steering matrix. An STLC theorem is also derived for a class of commonly encountered multirotor vehicles.
\r\n\r\nFeedback linearizing and PID controllers are proposed to stabilize an arbitrary spherical robot to a desired trajectory over smooth terrain, and direct collocation is used to develop a feedforward controller for Moball specifically. Moball's COM is manipulated by a novel system of magnets and solenoids, which are actuated by a \"ballistic-impulse\" controller that is also presented. Lastly, a motion planner is developed for energy-harvesting vehicles. This planner charts a path over smooth terrain while balancing the desire to achieve scientific objectives, avoid hazards, and the imperative of exposing the vehicle to environmental sources of energy such as local wind fields and topology. Moball's design details and experimental results establishing Moball's energy-harvesting performance (7W while rolling at a speed of 2 m/s), are contained in an Appendix.
", "doi": "10.7907/E5CW-8H41", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10091", "collection": "thesis", "collection_id": "10091", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03082017-163613964", "primary_object_url": { "basename": "Guo_Shaobin_2017_thesis.pdf", "content": "final", "filesize": 27841341, "license": "other", "mime_type": "application/pdf", "url": "/10091/1/Guo_Shaobin_2017_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Prototyping Diverse Synthetic Biological Circuits in a Cell-Free Transcription-Translation System", "author": [ { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Goentoro", "given_name": "Lea A.", "clpid": "Goentoro-L-A" }, { "family_name": "Sternberg", "given_name": "Paul W.", "clpid": "Sternberg-P-W" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Synthetic biological circuits are the foundation for the ultimate goals of controlling cells and building artificial cells from the ground up. To get closer to these goals in a more efficient way, we utilize a cell-free transcription-translation system to help perfect biological circuits for the simplicity, freedom, and convenience that the system offers. In this thesis, we demonstrate three distinct aspects of biological circuits in a cell-free transcription-translation system: circuit dynamics, phosphorylation, and membrane proteins. We start with a simple feedforward circuit, which shows dynamic responses to the input. We first prototype the feedforward circuit in the cell-free system with the aid of mathematical modeling. Then, based on the knowledge learned from prototyping, we successfully implement the circuit in cells. Not only do we show that a circuit with dynamics can be prototyped in the cell- free system, but we also test a more complicated circuit involving a phosphorylation cycle. The phosphorylation-based insulator circuit is prototyped and then a model created for the circuit is shown to be identifiable in the cell-free system. To further expand the capability of the cell-free system, we demonstrate that biologically active membrane proteins can be generated in the cell-free system with engineering, suggesting that even biological circuits requiring membrane proteins can be prototyped in the system. These results help advance our knowledge of both biological circuits and the cell-free transcription-translation system, and bring us one step closer to our ultimate goals of implementing control theory in synthetic biology.", "doi": "10.7907/Z9CR5RDK", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10138", "collection": "thesis", "collection_id": "10138", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04172017-163725367", "primary_object_url": { "basename": "online-learning-control.pdf", "content": "final", "filesize": 12028711, "license": "other", "mime_type": "application/pdf", "url": "/10138/1/online-learning-control.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Online Learning for the Control of Human Standing via Spinal Cord Stimulation", "author": [ { "family_name": "Sui", "given_name": "Yanan", "orcid": "0000-0002-9480-627X", "clpid": "Sui-Yanan" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Yue", "given_name": "Yisong", "clpid": "Yue-Yisong" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Many applications in recommender systems or experimental design need to make decisions online. Each decision leads to a stochastic reward with initially unknown distribution, while new decisions are made based on the observations of previous rewards. To maximize the total reward, one needs to balance between exploring different strategies and exploiting currently optimal strategies within a given set of strategies. This is the underlying trade-off of a number of clinical neural engineering problems, including brain-computer interface, deep brain stimulation, and spinal cord injury therapy. In these systems, complex electronic and computational systems interact with the human central nervous system. A critical issue is how to control the agents to produce results which are optimal under some measure, for example, efficiently decoding the user's intention in a brain-computer interface or performs temporal and spatial specific stimulation in deep brain stimulation. This dissertation is motivated by electrical sipnal cord stimulation with high dimensional inputs(multi-electrode arrays). The stimulation is applied to promote the function and rehabilitation of the remaining neural circuitry below the spinal cord injury, and enable complex motor behaviors such as stepping and standing. To enable the careful tuning of these stimuli for each patient, the electrode arrays which deliver these stimuli have become increasingly more sophisticated, with a corresponding increase in the number of free parameters over which the stimuli need to be optimized. Since the number of stimuli is growing exponentially with the number of electrodes, algorithmic methods of selecting stimuli is necessary, particularly when the feedback is expensive to get.
\r\n\r\nIn many online learning settings, particularly those that involve human feedback, reliable feedback is often limited to pairwise preferences instead of real valued feedback. Examples include implicit or subjective feedback for information retrieval and recommender systems, such as clicks on search results, and subjective feedback on the quality of recommended care. Sometimes with real valued feedback, we require that the sampled function values exceed some prespecified ``safety'' threshold, a requirement that existing algorithms fail to meet. Examples include medical applications where the patients' comfort must be guaranteed; recommender systems aiming to avoid user dissatisfaction; and robotic control, where one seeks to avoid controls that cause physical harm to the platform.
\r\n\r\nThis dissertation provides online learning algorithms for several specific online decision-making problems. \\selfsparring optimizes the cumulative reward with relative feedback. RankComparison deals with ranking feedback. \\safeopt considers the optimization with real valued feedback and safety constraints. \\cduel is designed for specific spinal cord injury therapy.
\r\n\r\nA variant of \\cduel was implemented in closed-loop human experiments, controlling which epidural stimulating electrodes are used in the spinal cord of SCI patients. The results obtained are compared with concurrent stimulus tuning carried out by human experimenter. These experiments show that this algorithm is at least as effective as the human experimenter, suggesting that this algorithm can be applied to the more challenging problems of enabling and optimizing complex, sensory-dependent behaviors, such as stepping and standing in SCI patients.
\r\n\r\nIn order to get reliable quantitative measurements besides comparisons, the standing behaviors of paralyzed patients under spinal cord stimulation are evaluated. The potential of quantifying the quality of bipedal standing in an automatic approach is also shown in this work.
", "doi": "10.7907/Z9BK19DN", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10323", "collection": "thesis", "collection_id": "10323", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06082017-194534497", "primary_object_url": { "basename": "Anu_Thubagere_BBE.pdf", "content": "final", "filesize": 18346331, "license": "other", "mime_type": "application/pdf", "url": "/10323/1/Anu_Thubagere_BBE.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Programming Complex Behavior in DNA-based Molecular Circuits and Robots", "author": [ { "family_name": "Thubagere Jagadeesh", "given_name": "Anupama", "clpid": "Thubagere-Jagadeesh-Anu" } ], "thesis_advisor": [ { "family_name": "Qian", "given_name": "Lulu", "clpid": "Qian-Lulu" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "clpid": "Rothemund-P-W-K" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "clpid": "Shapiro-M-G" }, { "family_name": "Qian", "given_name": "Lulu", "clpid": "Qian-Lulu" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Integrated electronic circuits, like those found in cellphones and computers, are ubiquitous in our information-driven society. The success of electronics has, in part, been due its modular architecture that enables individual components to be independently improved while the overall device functionality remains unchanged. Over the last two decades the emerging field of dynamic DNA nanotechnology has been trying to apply the underlying philosophy of electronics to biochemical circuits. DNA nanotechnology employs rationally designed DNA molecules as building blocks of biochemical circuits that can, in principle, enable powerful applications like diagnostics and therapeutics.
\r\n\r\nResearchers in the field of DNA nanotechnology have developed simple elements to construct biomolecular systems with desired functions. They have also developed molecular compilers for defining design principles. The cost of DNA synthesis has decreased by over three orders of magnitude in the past decade. This has lead to a non-trivial number of small scale circuits, like DNA-based logic gates and chemical oscillators, being implemented. However, the scalability of this approach has yet to be clearly demonstrated. n this thesis, we will discuss our main contributions to facilitating the advancement of DNA nanotechnology by developing systematic approaches for constructing modular DNA building blocks. These modules can be used to construct biochemical circuits and molecular robotic systems. The performance of the modules can be individually tuned and integrated into large-scale systems.
\r\n\r\nUsing automated circuit-design software and cheap unpurified DNA, we demonstrated the design and construction of a complex synthetic biochemical circuit consisting of 78 distinct DNA species. The circuit is capable of computing the transition rules of a cell updating its state based on its neighboring cells, defined in a classic computational model called cellular automata. Using a bottom-up approach, we first characterized the component necessary for basic Boolean logic computation. We then systematically integrated more circuit elements and eventually constructed the full circuit. By developing a systematic procedure for building DNA-based circuits using unpurified components, we significantly simplified the experimental procedure. By using unpurified DNA components, we reduced the cost and technical barrier for circuit construction, thus making the design and synthesis of complex DNA circuits accessible to even novice researchers.
\r\n\r\nNext we demonstrated a cargo sorting DNA nano-robot, using a simple algorithm and modular building blocks. The DNA robot has a leg and two foot domains for exploring a two-dimensional DNA origami surface, and an arm and hand domain for picking up randomly located cargos and dropping them off at their designated locations. It is completely autonomous and is programmed to perform a random walk without requiring an external energy source. Further, we demonstrated sorting multiple copies of two distinct cargo species on the same origami. Additionally, by compartmentalizing each sorting task on a single origami, we showed that two distinct sorting tasks can be implemented on different origami simultaneously in the same test tube. The recognition of a cargo is embedded in its destination, therefore it is possible to scale up the system simply by having multiple types of cargos. The same robot design can be used for performing multiple instances of distinct tasks in parallel. The different modules can be integrated to perform diverse functions, including applications in time-release targeted therapeutics.
", "doi": "10.7907/Z9WD3XMS", "publication_date": "2017-06-16", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9992", "collection": "thesis", "collection_id": "9992", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12122016-113630092", "primary_object_url": { "basename": "Wang_Yuh-Shyang_2017.pdf", "content": "final", "filesize": 2043132, "license": "other", "mime_type": "application/pdf", "url": "/9992/1/Wang_Yuh-Shyang_2017.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A System Level Approach to Optimal Controller Design for Large-Scale Distributed Systems", "author": [ { "family_name": "Wang", "given_name": "Yuh-Shyang", "orcid": "0000-0001-7357-7247", "clpid": "Wang-Yuh-Shyang" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wierman", "given_name": "Adam C.", "orcid": "0000-0002-5923-0199", "clpid": "Wierman-A-C" }, { "family_name": "Chung", "given_name": "Soon-Jo", "orcid": "0000-0002-6657-3907", "clpid": "Chung-Soon-Jo" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Modern cyber-physical systems, such as the smart grid, software-defined networks, and automated highway systems, are large-scale, physically distributed, and interconnected. The scale of these systems poses fundamental challenges for controller design: the traditional optimal control methods are globally centralized, which require solving a large-scale optimization problem with the knowledge of the global plant model, and collecting global measurement instantaneously during implementation. The ultimate goal of distributed control design is to provide a local, distributed, scalable, and coordinated control scheme to achieve centralized control objectives with nearly global transient optimality.
\r\n\r\nThis dissertation provides a novel theoretical and computational contribution to the area of constrained linear optimal control, with a particular emphasis on addressing the scalability of controller design and implementation for large-scale distributed systems. Our approach provides a fundamental rethinking of controller design: we extend a control design problem to a system level design problem, where we directly optimize the desired closed loop behavior of the feedback system. We show that many traditional topics in the optimal control literature, including the parameterization of stabilizing controller and the synthesis of centralized and distributed controller, can all be cast as a special case of a system level design problem. The system level approach therefore unifies many existing results in the field of distributed optimal control, and solves many previously open problems.
\r\n\r\nOur system level approach has at least the following four technical merits. First, we characterize the broadest known class of constrained linear optimal control problem that admits a convex formulation. Specifically, we show that the set of convex system level design problems is a strict superset of those that can be parameterized using quadratic invariance. Second, we identify a class of system level design problems, which we called the localized optimal control problems, that are scalable to arbitrary large-scale systems. In particular, the parallel synthesis and implementation complexity of the localized optimal controller are O(1) compared to the size of the networked system. Third, we provide a unified framework to simultaneously incorporate user-specified design specification on the closed loop and the hardware implementation constraints on the controller into the optimal controller design process. Lastly, we provide a system level approach that supports the co-design of optimal controller and its sensing and actuating architecture.
\r\n\r\nWe demonstrate the effectiveness of our method on a 51200-state randomized heterogeneous power network model, and show that the system level approach provides superior scalability over the centralized and distributed method. For such a large-scale example, the theoretical computation time for the centralized scheme is more than 200 days, and the distributed optimal control scheme is intractable. In contrast, it only takes 38 minutes to synthesize a localized optimal controller that achieves at least 99% global optimality guarantee.
", "doi": "10.7907/Z95M63PF", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9101", "collection": "thesis", "collection_id": "9101", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08122015-172710296", "primary_object_url": { "basename": "siyou_cit_thesis.pdf", "content": "final", "filesize": 1930050, "license": "other", "mime_type": "application/pdf", "url": "/9101/1/siyou_cit_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "A Direct Approach to Robustness Optimization", "author": [ { "family_name": "You", "given_name": "Seungil", "clpid": "You-Seungil" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" }, { "family_name": "Chandrasekaran", "given_name": "Venkat", "clpid": "Chandrasekaran-V" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation reformulates and streamlines the core tools of robustness analysis for linear time invariant systems using now-standard methods in convex optimization. In particular, robust performance analysis can be formulated as a primal convex optimization in the form of a semidefinite program using a semidefinite representation of a set of Gramians. The same approach with semidefinite programming duality is applied to develop a linear matrix inequality test for well-connectedness analysis, and many existing results such as the Kalman-Yakubovich--Popov lemma and various scaled small gain tests are derived in an elegant fashion. More importantly, unlike the classical approach, a decision variable in this novel optimization framework contains all inner products of signals in a system, and an algorithm for constructing an input and state pair of a system corresponding to the optimal solution of robustness optimization is presented based on this information. This insight may open up new research directions, and as one such example, this dissertation proposes a semidefinite programming relaxation of a cardinality constrained variant of the H \u221e norm, which we term sparse H \u221e analysis, where an adversarial disturbance can use only a limited number of channels. Finally, sparse H \u221e analysis is applied to the linearized swing dynamics in order to detect potential vulnerable spots in power networks.\r\n", "doi": "10.7907/Z9X34VDV", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9731", "collection": "thesis", "collection_id": "9731", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05222016-095145651", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 32723348, "license": "other", "mime_type": "application/pdf", "url": "/9731/8/main.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Kinematics and Local Motion Planning for Quasi-static Whole-body Mobile Manipulation", "author": [ { "family_name": "Shankar", "given_name": "Krishna", "clpid": "Shankar-Krishna" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Tropp", "given_name": "Joel A.", "clpid": "Tropp-J-A" }, { "family_name": "Hudson", "given_name": "Nicolas H.", "clpid": "Hudson-N-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis studies mobile robotic manipulators, where one or more robot manipulator arms are\r\nintegrated with a mobile robotic base. The base could be a wheeled or tracked vehicle, or it might be a\r\nmulti-limbed locomotor. As robots are increasingly deployed in complex and unstructured environments,\r\nthe need for mobile manipulation increases. Mobile robotic assistants have the potential to revolutionize human\r\nlives in a large variety of settings including home, industrial and outdoor environments.
\r\n\r\nMobile Manipulation is the use or study of such mobile robots as they interact with physical\r\nobjects in their environment. As compared to fixed base manipulators, mobile manipulators can take\r\nadvantage of the base mechanism\u2019s added degrees of freedom in the task planning and execution process.\r\nBut their use also poses new problems in the analysis and control of base system stability, and the\r\nplanning of coordinated base and arm motions. For mobile manipulators to be successfully and\r\nefficiently used, a thorough understanding of their kinematics, stability, and capabilities is required.\r\nMoreover, because mobile manipulators typically possess a large number of actuators, new and efficient\r\nmethods to coordinate their large numbers of degrees of freedom are needed to make them practically\r\ndeployable. This thesis develops new kinematic and stability analyses of mobile manipulation, and new\r\nalgorithms to efficiently plan their motions.
\r\n\r\nI first develop detailed and novel descriptions of the kinematics governing the operation of multi-\r\nlimbed legged robots working in the presence of gravity, and whose limbs may also be simultaneously\r\nused for manipulation. The fundamental stance constraint that arises from simple assumptions about\r\nfriction and the ground contact and feasible motions is derived. Thereafter, a local relationship between\r\njoint motions and motions of the robot abdomen and reaching limbs is developed. Baseeon these\r\nrelationships, one can define and analyze local kinematic qualities including limberness, wrench\r\nresistance and local dexterity. While previous researchers have noted the similarity between multi-\r\nfingered grasping and quasi-static manipulation, this thesis makes explicit connections between these two\r\nproblems.
\r\n\r\nThe kinematic expressions form the basis for a local motion planning problem that that\r\ndetermines the joint motions to achieve several simultaneous objectives while maintaining stance stability\r\nin the presence of gravity. This problem is translated into a convex quadratic program entitled the\r\nbalanced priority solution, whose existence and uniqueness properties are developed. This problem is\r\nrelated in spirit to the classical redundancy resoxlution and task-priority approaches. With some simple\r\nmodifications, this local planning and optimization problem can be extended to handle a large variety of\r\ngoals and constraints that arise in mobile-manipulation. This local planning problem applies readily to\r\nother mobile bases including wheeled and articulated bases. This thesis describes the use of the local\r\nplanning techniques to generate global plans, as well as for use within a feedback loop. The work in this\r\nthesis is motivated in part by many practical tasks involving the Surrogate and RoboSimian robots at\r\nNASA/JPL, and a large number of examples involving the two robots, both real and simulated, are\r\nprovided.
\r\n\r\nFinally, this thesis provides an analysis of simultaneous force and motion control for multi-\r\nlimbed legged robots. Starting with a classical linear stiffness relationship, an analysis of this problem for\r\nmultiple point contacts is described. The local velocity planning problem is extended to include\r\ngeneration of forces, as well as to maintain stability using force-feedback. This thesis also provides a\r\nconcise, novel definition of static stability, and proves some conditions under which it is satisfied.
", "doi": "10.7907/Z9KK98RX", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9637", "collection": "thesis", "collection_id": "9637", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03312016-100604768", "primary_object_url": { "basename": "matni_nikolai_2015_thesis.pdf", "content": "final", "filesize": 2495362, "license": "other", "mime_type": "application/pdf", "url": "/9637/1/matni_nikolai_2015_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Distributed Optimal Control of Cyber-Physical Systems: Controller Synthesis, Architecture Design and System Identification", "author": [ { "family_name": "Matni", "given_name": "Nikolai", "orcid": "0000-0003-4936-3921", "clpid": "Matni-Nikolai" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Chandrasekaran", "given_name": "Venkat", "clpid": "Chandrasekaran-V" }, { "family_name": "Wierman", "given_name": "Adam C.", "clpid": "Wierman-A-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The centralized paradigm of a single controller and a single plant upon which modern control theory is built is no longer applicable to modern cyber-physical systems of interest, such as the power-grid, software defined networks or automated highways systems, as these are all large-scale and spatially distributed. Both the scale and the distributed nature of these systems has motivated the decentralization of control schemes into local sub-controllers that measure, exchange and act on locally available subsets of the globally available system information. This decentralization of control logic leads to different decision makers acting on asymmetric information sets, introduces the need for coordination between them, and perhaps not surprisingly makes the resulting optimal control problem much harder to solve. In fact, shortly after such questions were posed, it was realized that seemingly simple decentralized optimal control problems are computationally intractable to solve, with the Wistenhausen counterexample being a famous instance of this phenomenon. Spurred on by this perhaps discouraging result, a concerted 40 year effort to identify tractable classes of distributed optimal control problems culminated in the notion of quadratic invariance, which loosely states that if sub-controllers can exchange information with each other at least as quickly as the effect of their control actions propagates through the plant, then the resulting distributed optimal control problem admits a convex formulation.
\r\n\r\nThe identification of quadratic invariance as an appropriate means of \"convexifying\" distributed optimal control problems led to a renewed enthusiasm in the controller synthesis community, resulting in a rich set of results over the past decade. The contributions of this thesis can be seen as being a part of this broader family of results, with a particular focus on closing the gap between theory and practice by relaxing or removing assumptions made in the traditional distributed optimal control framework. Our contributions are to the foundational theory of distributed optimal control, and fall under three broad categories, namely controller synthesis, architecture design and system identification.
\r\n\r\nWe begin by providing two novel controller synthesis algorithms. The first is a solution to the distributed H\u221e optimal control problem subject to delay constraints, and provides the only known exact characterization of delay-constrained distributed controllers satisfying an H\u221e norm bound. The second is an explicit dynamic programming solution to a two player LQR state-feedback problem with varying delays. Accommodating varying delays represents an important first step in combining distributed optimal control theory with the area of Networked Control Systems that considers lossy channels in the feedback loop. Our next set of results are concerned with controller architecture design. When designing controllers for large-scale systems, the architectural aspects of the controller such as the placement of actuators, sensors, and the communication links between them can no longer be taken as given -- indeed the task of designing this architecture is now as important as the design of the control laws themselves. To address this task, we formulate the Regularization for Design (RFD) framework, which is a unifying computationally tractable approach, based on the model matching framework and atomic norm regularization, for the simultaneous co-design of a structured optimal controller and the architecture needed to implement it. Our final result is a contribution to distributed system identification. Traditional system identification techniques such as subspace identification are not computationally scalable, and destroy rather than leverage any a priori information about the system's interconnection structure. We argue that in the context of system identification, an essential building block of any scalable algorithm is the ability to estimate local dynamics within a large interconnected system. To that end we propose a promising heuristic for identifying the dynamics of a subsystem that is still connected to a large system. We exploit the fact that the transfer function of the local dynamics is low-order, but full-rank, while the transfer function of the global dynamics is high-order, but low-rank, to formulate this separation task as a nuclear norm minimization problem. Finally, we conclude with a brief discussion of future research directions, with a particular emphasis on how to incorporate the results of this thesis, and those of optimal control theory in general, into a broader theory of dynamics, control and optimization in layered architectures.
", "doi": "10.7907/Z99884Z0", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9739", "collection": "thesis", "collection_id": "9739", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232016-160307020", "primary_object_url": { "basename": "zhao_changhong_2016_thesis.pdf", "content": "final", "filesize": 2964261, "license": "other", "mime_type": "application/pdf", "url": "/9739/1/zhao_changhong_2016_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Real-Time Load-Side Control of Electric Power Systems", "author": [ { "family_name": "Zhao", "given_name": "Changhong", "orcid": "0000-0003-0539-8591", "clpid": "Zhao-Changhong" } ], "thesis_advisor": [ { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" } ], "thesis_committee": [ { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Kostina", "given_name": "Victoria", "clpid": "Kostina-V" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Wierman", "given_name": "Adam C.", "clpid": "Wierman-A-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Two trends are emerging from modern electric power systems: the growth of renewable (e.g., solar and wind) generation, and the integration of information technologies and advanced power electronics. The former introduces large, rapid, and random fluctuations in power supply, demand, frequency, and voltage, which become a major challenge for real-time operation of power systems. The latter creates a tremendous number of controllable intelligent endpoints such as smart buildings and appliances, electric vehicles, energy storage devices, and power electronic devices that can sense, compute, communicate, and actuate. Most of these endpoints are distributed on the load side of power systems, in contrast to traditional control resources such as centralized bulk generators. This thesis focuses on controlling power systems in real time, using these load side resources. Specifically, it studies two problems.
\r\n\r\n(1) Distributed load-side frequency control: We establish a mathematical framework to design distributed frequency control algorithms for flexible electric loads. In this framework, we formulate a category of optimization problems, called optimal load control (OLC), to incorporate the goals of frequency control, such as balancing power supply and demand, restoring frequency to its nominal value, restoring inter-area power flows, etc., in a way that minimizes total disutility for the loads to participate in frequency control by deviating from their nominal power usage. By exploiting distributed algorithms to solve OLC and analyzing convergence of these algorithms, we design distributed load-side controllers and prove stability of closed-loop power systems governed by these controllers. This general framework is adapted and applied to different types of power systems described by different models, or to achieve different levels of control goals under different operation scenarios. We first consider a dynamically coherent power system which can be equivalently modeled with a single synchronous machine. We then extend our framework to a multi-machine power network, where we consider primary and secondary frequency controls, linear and nonlinear power flow models, and the interactions between generator dynamics and load control.
\r\n\r\n(2) Two-timescale voltage control: The voltage of a power distribution system must be maintained closely around its nominal value in real time, even in the presence of highly volatile power supply or demand. For this purpose, we jointly control two types of reactive power sources: a capacitor operating at a slow timescale, and a power electronic device, such as a smart inverter or a D-STATCOM, operating at a fast timescale. Their control actions are solved from optimal power flow problems at two timescales. Specifically, the slow-timescale problem is a chance-constrained optimization, which minimizes power loss and regulates the voltage at the current time instant while limiting the probability of future voltage violations due to stochastic changes in power supply or demand. This control framework forms the basis of an optimal sizing problem, which determines the installation capacities of the control devices by minimizing the sum of power loss and capital cost. We develop computationally efficient heuristics to solve the optimal sizing problem and implement real-time control. Numerical experiments show that the proposed sizing and control schemes significantly improve the reliability of voltage control with a moderate increase in cost.
", "doi": "10.7907/Z9RN35TJ", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9191", "collection": "thesis", "collection_id": "9191", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10012015-221355676", "primary_object_url": { "basename": "SunZacharyZhipeng2016thesis.pdf", "content": "final", "filesize": 45522801, "license": "other", "mime_type": "application/pdf", "url": "/9191/1/SunZacharyZhipeng2016thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "An in vitro Biomolecular Breadboard for Prototyping Synthetic Biological Circuits", "author": [ { "family_name": "Sun", "given_name": "Zachary Zhipeng", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Zhipeng" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Noireaux", "given_name": "Vincent", "clpid": "Noireaux-V" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Biomolecular circuit engineering is critical for implementing complex functions in vivo, and is a baseline method in the synthetic biology space. However, current methods for conducting biomolecular circuit engineering are time-consuming and tedious. A complete design-build-test cycle typically takes weeks' to months' time due to the lack of an intermediary between design ex vivo and testing in vivo. In this work, we explore the development and application of a \"biomolecular breadboard\" composed of an in-vitro transcription-translation (TX-TL) lysate to rapidly speed up the engineering design-build-test cycle. We first developed protocols for creating and using lysates for conducting biological circuit design. By doing so we simplified the existing technology to an affordable ($0.03/uL) and easy to use three-tube reagent system. We then developed tools to accelerate circuit design by allowing for linear DNA use in lieu of plasmid DNA, and by utilizing principles of modular assembly. This allowed the design-build-test cycle to be reduced to under a business day. We then characterized protein degradation dynamics in the breadboard to aid to implementing complex circuits. Finally, we demonstrated that the breadboard could be applied to engineer complex synthetic circuits in vitro and in vivo. Specifically, we utilized our understanding of linear DNA prototyping, modular assembly, and protein degradation dynamics to characterize the repressilator oscillator and to prototype novel three- and five-node negative feedback oscillators both in vitro and in vivo. We therefore believe the biomolecular breadboard has wide application for acting as an intermediary for biological circuit engineering.", "doi": "10.7907/Z9TB14TW", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9831", "collection": "thesis", "collection_id": "9831", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032016-102336160", "primary_object_url": { "basename": "ipthesis.pdf", "content": "final", "filesize": 1702656, "license": "other", "mime_type": "application/pdf", "url": "/9831/1/ipthesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Robustness, Adaptation, and Learning in Optimal Control", "author": [ { "family_name": "Papusha", "given_name": "Ivan Igorevych", "clpid": "Papusha-Ivan-Igorevych" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Lavretsky", "given_name": "Eugene", "clpid": "Lavretsky-Eugene" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Recent technological advances have opened the door to a wide variety of dynamic control applications, which are enabled by increasing computational power in ever smaller devices. These advances are backed by reliable optimization algorithms that allow specification, synthesis, and embedded implementation of sophisticated learning-based controllers. However, as control systems become more pervasive, dynamic, and complex, the control algorithms governing them become more complex to design and analyze. In many cases, optimal control policies are practically impossible to determine unless the state dimension is small, or the dynamics are simple. Thus, in order to make implementation progress, the control designer must specialize to suboptimal architectures and approximate control. The major engineering challenge in the upcoming decades will be how to cope with the complexity of designing implementable control architectures for these smart systems while certifying their safety, robustness, and performance.
\r\n\r\nThis thesis tackles the design and verification complexity by carefully employing tractable lower and upper bounds on the Lyapunov function, while making connections to robust control, formal synthesis, and machine learning. Specifically, optimization-based upper bounds are used to specify robust controllers, while lower bounds are used to obtain performance bounds and to synthesize approximately optimal policies. Implementation of these bounds depends critically on carrying out learning and optimization in the loop. Examples in aerospace, formal methods, hybrid systems, and networked adaptive systems are given, and novel sources of identifiability and persistence of excitation are discussed.
", "doi": "10.7907/Z9F18WPB", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9348", "collection": "thesis", "collection_id": "9348", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12312015-131513787", "primary_object_url": { "basename": "ScottCLivingston-phdthesis2015.pdf", "content": "final", "filesize": 1707051, "license": "other", "mime_type": "application/pdf", "url": "/9348/1/ScottCLivingston-phdthesis2015.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Incremental Control Synthesis for Robotics in the Presence of Temporal Logic Specifications", "author": [ { "family_name": "Livingston", "given_name": "Scott Carlton", "clpid": "Livingston-Scott-Carlton" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents methods for incrementally constructing controllers in the presence of uncertainty and nonlinear dynamics. The basic setting is motion planning subject to temporal logic specifications. Broadly, two categories of problems are treated. The first is reactive formal synthesis when so-called discrete abstractions are available. The fragment of linear-time temporal logic (LTL) known as GR(1) is used to express assumptions about an adversarial environment and requirements of the controller. Two problems of changes to a specification are posed that concern the two major aspects of GR(1): safety and liveness. Algorithms providing incremental updates to strategies are presented as solutions. In support of these, an annotation of strategies is developed that facilitates repeated modifications. A variety of properties are proven about it, including necessity of existence and sufficiency for a strategy to be winning. The second category of problems considered is non-reactive (open-loop) synthesis in the absence of a discrete abstraction. Instead, the presented stochastic optimization methods directly construct a control input sequence that achieves low cost and satisfies a LTL formula. Several relaxations are considered as heuristics to address the rarity of sampling trajectories that satisfy an LTL formula and demonstrated to improve convergence rates for Dubins car and single-integrators subject to a recurrence task.", "doi": "10.7907/Z94Q7RW3", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9307", "collection": "thesis", "collection_id": "9307", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12062015-164238181", "type": "thesis", "title": "Two and Three Finger Caging of Polygons and Polyhedra", "author": [ { "family_name": "Allen", "given_name": "Thomas F.", "clpid": "Allen-Thomas-F" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Pellegrino", "given_name": "Sergio", "clpid": "Pellegrino-S" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Multi-finger caging offers a rigorous and robust approach to robot grasping. This thesis provides several novel algorithms for caging polygons and polyhedra in two and three dimensions. Caging refers to a robotic grasp that does not necessarily immobilize an object, but prevents it from escaping to infinity. The first algorithm considers caging a polygon in two dimensions using two point fingers. The second algorithm extends the first to three dimensions. The third algorithm considers caging a convex polygon in two dimensions using three point fingers, and considers robustness of this cage to variations in the relative positions of the fingers.
\r\n\r\nThis thesis describes an algorithm for finding all two-finger cage formations of planar polygonal objects based on a contact-space formulation. It shows that two-finger cages have several useful properties in contact space. First, the critical points of the cage representation in the hand\u2019s configuration space appear as critical points of the inter-finger distance function in contact space. Second, these critical points can be graphically characterized directly on the object\u2019s boundary. Third, contact space admits a natural rectangular decomposition such that all critical points lie on the rectangle boundaries, and the sublevel sets of contact space and free space are topologically equivalent. These properties lead to a caging graph that can be readily constructed in contact space. Starting from a desired immobilizing grasp of a polygonal object, the caging graph is searched for the minimal, intermediate, and maximal caging regions surrounding the immobilizing grasp. An example constructed from real-world data illustrates and validates the method.
\r\n\r\nA second algorithm is developed for finding caging formations of a 3D polyhedron for two point fingers using a lower dimensional contact-space formulation. Results from the two-dimensional algorithm are extended to three dimension. Critical points of the inter-finger distance function are shown to be identical to the critical points of the cage. A decomposition of contact space into 4D regions having useful properties is demonstrated. A geometric analysis of the critical points of the inter-finger distance function results in a catalog of grasps in which the cages change topology, leading to a simple test to classify critical points. With these properties established, the search algorithm from the two-dimensional case may be applied to the three-dimensional problem. An implemented example demonstrates the method.
\r\n\r\nThis thesis also presents a study of cages of convex polygonal objects using three point fingers. It considers a three-parameter model of the relative position of the fingers, which gives complete generality for three point fingers in the plane. It analyzes robustness of caging grasps to variations in the relative position of the fingers without breaking the cage. Using a simple decomposition of free space around the polygon, we present an algorithm which gives all caging placements of the fingers and a characterization of the robustness of these cages.
", "doi": "10.7907/Z93X84KR ", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9705", "collection": "thesis", "collection_id": "9705", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05082016-170628018", "primary_object_url": { "basename": "20160509_Hsiao_Victoria_2016.pdf", "content": "final", "filesize": 67580263, "license": "other", "mime_type": "application/pdf", "url": "/9705/1/20160509_Hsiao_Victoria_2016.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Synthetic Circuits for Feedback and Detection in Bacteria", "author": [ { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "clpid": "Rothemund-P-W-K" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Synthetic biology, by co-opting molecular machinery from existing organisms, can be used as a tool for building new genetic systems from scratch, for understanding natural networks through perturbation, or for hybrid circuits that piggy-back on existing cellular infrastructure. Although the toolbox for genetic circuits has greatly expanded in recent years, it is still difficult to separate the circuit function from its specific molecular implementation. In this thesis, we discuss the function-driven design of two synthetic circuit modules, and use mathematical models to understand the fundamental limits of circuit topology versus operating regimes as determined by the specific molecular implementation. First, we describe a protein concentration tracker circuit that sets the concentration of an output protein relative to the concentration of a reference protein. The functionality of this circuit relies on a single negative feedback loop that is implemented via small programmable protein scaffold domains. We build a mass-action model to understand the relevant timescales of the tracking behavior and how the input/output ratios and circuit gain might be tuned with circuit components. Second, we design an event detector circuit with permanent genetic memory that can record order and timing between two chemical events. This circuit was implemented using bacteriophage integrases that recombine specific segments of DNA in response to chemical inputs. We simulate expected population-level outcomes using a stochastic Markov-chain model, and investigate how inferences on past events can be made from differences between single-cell and population-level responses. Additionally, we present some preliminary investigations on spatial patterning using the event detector circuit as well as the design of stationary phase promoters for growth-phase dependent activation. These results advance our understanding of synthetic gene circuits, and contribute towards the use of circuit modules as building blocks for larger and more complex synthetic networks.", "doi": "10.7907/Z9WD3XJW", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9218", "collection": "thesis", "collection_id": "9218", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10132015-121212703", "primary_object_url": { "basename": "jonsson-2016.pdf", "content": "final", "filesize": 5433194, "license": "other", "mime_type": "application/pdf", "url": "/9218/1/jonsson-2016.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Robust Control of Evolutionary Dynamics", "author": [ { "family_name": "Jonsson", "given_name": "Vanessa Danielle", "clpid": "Jonsson-Vanessa-Danielle" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "clpid": "Bjorkman-P-J" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The application of principles from evolutionary biology has long been used to gain new insights into the progression and clinical control of both infectious diseases and neoplasms. This iterative evolutionary process consists of expansion, diversification and selection within an adaptive landscape - species are subject to random genetic or epigenetic alterations that result in variations; genetic information is inherited through asexual reproduction and strong selective pressures such as therapeutic intervention can lead to the adaptation and expansion of resistant variants. These principles lie at the center of modern evolutionary synthesis and constitute the primary reasons for the development of resistance and therapeutic failure, but also provide a framework that allows for more effective control.
\r\n\r\nA model system for studying the evolution of resistance and control of therapeutic failure is the treatment of chronic HIV-1 infection by broadly neutralizing antibody (bNAb) therapy. A relatively recent discovery is that a minority of HIV-infected individuals can produce broadly neutralizing antibodies, that is, antibodies that inhibit infection by many strains of HIV. Passive transfer of human antibodies for the prevention and treatment of HIV-1 infection is increasingly being considered as an alternative to a conventional vaccine. However, recent evolution studies have uncovered that antibody treatment can exert selective pressure on virus that results in the rapid evolution of resistance. In certain cases, complete resistance to an antibody is conferred with a single amino acid substitution on the viral envelope of HIV.
\r\n\r\nThe challenges in uncovering resistance mechanisms and designing effective combination strategies to control evolutionary processes and prevent therapeutic failure apply more broadly. We are motivated by two questions: Can we predict the evolution to resistance by characterizing genetic alterations that contribute to modified phenotypic fitness? Given an evolutionary landscape and a set of candidate therapies, can we computationally synthesize treatment strategies that control evolution to resistance?
\r\n\r\nTo address the first question, we propose a mathematical framework to reason about evolutionary dynamics of HIV from computationally derived Gibbs energy fitness landscapes -- expanding the theoretical concept of an evolutionary landscape originally conceived by Sewall Wright to a computable, quantifiable, multidimensional, structurally defined fitness surface upon which to study complex HIV evolutionary outcomes.
\r\n\r\nTo design combination treatment strategies that control evolution to resistance, we propose a methodology that solves for optimal combinations and concentrations of candidate therapies, and allows for the ability to quantifiably explore tradeoffs in treatment design, such as limiting the number of candidate therapies in the combination, dosage constraints and robustness to error. Our algorithm is based on the application of recent results in optimal control to an HIV evolutionary dynamics model and is constructed from experimentally derived antibody resistant phenotypes and their single antibody pharmacodynamics. This method represents a first step towards integrating principled engineering techniques with an experimentally based mathematical model in the rational design of combination treatment strategies and offers predictive understanding of the effects of combination therapies of evolutionary dynamics and resistance of HIV. Preliminary in vitro studies suggest that the combination antibody therapies predicted by our algorithm can neutralize heterogeneous viral populations despite containing resistant mutations.
", "doi": "10.7907/Z9NP22CH", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9794", "collection": "thesis", "collection_id": "9794", "cite_using_url": "https://resolver.caltech.edu/CaltechThesis:05272016-145559554", "primary_object_url": { "basename": "Yeung-Enoch-2016-thesis_final.pdf", "content": "final", "filesize": 12581127, "license": "other", "mime_type": "application/pdf", "url": "/9794/1/Yeung-Enoch-2016-thesis_final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Reverse Engineering and Quantifying Context Effects in Synthetic Gene Networks", "author": [ { "family_name": "Yeung", "given_name": "Enoch Ho-Yee", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch-Ho-Yee" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John C.", "clpid": "Doyle-J-C" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Goentoro", "given_name": "Lea A.", "clpid": "Goentoro-L-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In the first part of this thesis, we undertake a quantitative investigation of how compositional context, the spatial arrangement and relative orientation of genes, affects individual gene expression in a genetic network. Taking a synthetic biology approach, we construct a series of simple two-reporter biocircuits, each expressing either an mRNA aptamer or a fluorescent protein, and show that by varying the relative orientation of the two genes we obtain a wide range of gene expression profiles, including context-dependent bimodality. We develop a mathematical model to describe the experimental trends observed based on concepts from DNA supercoiling theory. We validate the model through a series of in vitro supercoiling experiments and show that by relaxing positive supercoiling in the plasmids, we can significantly reduce the context effects in gene expression. Most importantly, these insights provide a framework for understanding how compositional context and supercoiling can impose feedback on the intended architecture of a synthetic gene network. As a proof of concept, we engineer a genetic toggle switch exploiting compositional context effects to improve its threshold detection and memory capabilities.
\r\n\r\nIn the second part of this thesis, we examine a series of theoretical and computational tools from dynamical systems theory that assist in engineering novel biochemical reaction networks. We briefly review the concept of dynamical structure functions and network reconstruction as tools for understanding biochemical reaction networks. In particular, we review the concept of resource-loading, show that resource-loading can lead to coupling interactions among biochemical species, and that by estimating a dynamical structure function from experimental data, it is possible to quantify resource loading effects in practice. We illustrate the importance of knowing these loading effects through several example systems, showing that crosstalk imbalance in feed-forward loops can lead to performance limitations. However, since biochemical reaction networks are generally large, in practice, only portions of the global network can be reconstructed at a time. We show, with a combination of theory, simulation, modeling and experiments, it is possible to reconstruct the dynamical structure function of a large-scale biochemical network using a series of network reconstruction experiments. We then demonstrate how the dynamical structure function can be used to analyze context interference and how these perturbations interfere with performance. We illustrate these ideas with several classes of standard biological networks, e.g. autocatalytic systems, cascade systems, and input-coupled systems.
\r\n\r\nFinally, in the third part of this thesis, we consider models for context interference in stochastic chemical reaction networks. We address the problem of representing a biological system and its environment using a stochastic modeling framework. We first introduce a decomposition of the global chemical reaction system into two systems: a system of interest and its environment. We then present and derive a decomposition of the chemical master equation to achieve a representation describing the dynamics of the system of interest, perturbed by an environmental disturbance. We use this decomposition to model examples of two types of environmental disturbances: the disturbance a system experiences through loading effects from limited resources and the disturbance a system experiences when perturbed by an antibiotic that modifies transcription or translation rates.
", "doi": "10.7907/Z9Z31WM4", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9721", "collection": "thesis", "collection_id": "9721", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162016-100757711", "primary_object_url": { "basename": "BillehYN2016.pdf", "content": "final", "filesize": 32112258, "license": "other", "mime_type": "application/pdf", "url": "/9721/1/BillehYN2016.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Functional, Clustered, Feedforward, and Mesoscale Brain Networks", "author": [ { "family_name": "Billeh", "given_name": "Yazan Nicola", "orcid": "0000-0001-5200-4992", "clpid": "Billeh-Yazan-Nicola" } ], "thesis_advisor": [ { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" } ], "thesis_committee": [ { "family_name": "Siapas", "given_name": "Athanassios G.", "orcid": "0000-0001-8837-678X", "clpid": "Siapas-A-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Meister", "given_name": "Markus", "orcid": "0000-0003-2136-6506", "clpid": "Meister-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The brain is a network spanning multiple scales from subcellular to macroscopic. In this thesis I present four projects studying brain networks at different levels of abstraction. The first involves determining a functional connectivity network based on neural spike trains and using a graph theoretical method to cluster groups of neurons into putative cell assemblies. In the second project I model neural networks at a microscopic level. Using diferent clustered wiring schemes, I show that almost identical spatiotemporal activity patterns can be observed, demonstrating that there is a broad neuro-architectural basis to attain structured spatiotemporal dynamics. Remarkably, irrespective of the precise topological mechanism, this behavior can be predicted by examining the spectral properties of the synaptic weight matrix. The third project introduces, via two circuit architectures, a new paradigm for feedforward processing in which inhibitory neurons have the complex and pivotal role in governing information flow in cortical network models. Finally, I analyze axonal projections in sleep deprived mice using data collected as part of the Allen Institute's Mesoscopic Connectivity Atlas. After normalizing for experimental variability, the results indicate there is no single explanatory difference in the mesoscale network between control and sleep deprived mice. Using machine learning techniques, however, animal classification could be done at levels significantly above chance. This reveals that intricate changes in connectivity do occur due to chronic sleep deprivation.", "doi": "10.7907/Z9DB7ZSX", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:8899", "collection": "thesis", "collection_id": "8899", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282015-142013480", "primary_object_url": { "basename": "DenisMartynovThesis.pdf", "content": "final", "filesize": 14459254, "license": "other", "mime_type": "application/pdf", "url": "/8899/1/DenisMartynovThesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Lock Acquisition and Sensitivity Analysis of Advanced LIGO Interferometers", "author": [ { "family_name": "Martynov", "given_name": "Denis V.", "clpid": "Martinov-Denis-V" } ], "thesis_advisor": [ { "family_name": "Adhikari", "given_name": "Rana", "orcid": "0000-0002-5731-5076", "clpid": "Adhikari-R" } ], "thesis_committee": [ { "family_name": "Adhikari", "given_name": "Rana", "orcid": "0000-0002-5731-5076", "clpid": "Adhikari-R" }, { "family_name": "Weinstein", "given_name": "Alan Jay", "orcid": "0000-0002-0928-6784", "clpid": "Weinstein-Alan-J-Physics" }, { "family_name": "Chen", "given_name": "Yanbei", "orcid": "0000-0002-9730-9463", "clpid": "Chen-Yanbei" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "LIGO" }, { "literal": "div_pma" } ], "abstract": "Laser interferometer gravitational wave observatory (LIGO) consists of two complex large-scale laser interferometers designed for direct detection of gravitational waves from distant astrophysical sources in the frequency range 10Hz - 5kHz. Direct detection of space-time ripples will support Einstein's general theory of relativity and provide invaluable information and new insight into physics of the Universe.
\r\n\r\nInitial phase of LIGO started in 2002, and since then data was collected during six science runs. Instrument sensitivity was improving from run to run due to the effort of commissioning team. Initial LIGO has reached designed sensitivity during the last science run, which ended in October 2010.
\r\n\r\nIn parallel with commissioning and data analysis with the initial detector, LIGO group worked on research and development of the next generation detectors. Major instrument upgrade from initial to advanced LIGO started in 2010 and lasted till 2014.
\r\n\r\nThis thesis describes results of commissioning work done at LIGO Livingston site from 2013 until 2015 in parallel with and after the installation of the instrument. This thesis also discusses new techniques and tools developed at the 40m prototype including adaptive filtering, estimation of quantization noise in digital filters and design of isolation kits for ground seismometers.
\r\n\r\nThe first part of this thesis is devoted to the description of methods for bringing interferometer to the linear regime when collection of data becomes possible. States of longitudinal and angular controls of interferometer degrees of freedom during lock acquisition process and in low noise configuration are discussed in details.
\r\n\r\nOnce interferometer is locked and transitioned to low noise regime, instrument produces astrophysics data that should be calibrated to units of meters or strain. The second part of this thesis describes online calibration technique set up in both observatories to monitor the quality of the collected data in real time. Sensitivity analysis was done to understand and eliminate noise sources of the instrument.
\r\n\r\nCoupling of noise sources to gravitational wave channel can be reduced if robust feedforward and optimal feedback control loops are implemented. The last part of this thesis describes static and adaptive feedforward noise cancellation techniques applied to Advanced LIGO interferometers and tested at the 40m prototype. Applications of optimal time domain feedback control techniques and estimators to aLIGO control loops are also discussed.
\r\n\r\nCommissioning work is still ongoing at the sites. First science run of advanced LIGO is planned for September 2015 and will last for 3-4 months. This run will be followed by a set of small instrument upgrades that will be installed on a time scale of few months. Second science run will start in spring 2016 and last for about 6 months. Since current sensitivity of advanced LIGO is already more than factor of 3 higher compared to initial detectors and keeps improving on a monthly basis, upcoming science runs have a good chance for the first direct detection of gravitational waves.
\r\n", "doi": "10.7907/Z9Q81B1F", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8865", "collection": "thesis", "collection_id": "8865", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182015-163708506", "primary_object_url": { "basename": "delossantos_elc_2015_thesis.pdf", "content": "final", "filesize": 11163927, "license": "other", "mime_type": "application/pdf", "url": "/8865/1/delossantos_elc_2015_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits", "author": [ { "family_name": "Cornejo de los Santos", "given_name": "Emmanuel Lorenzo", "clpid": "Cornejo-de-los-Santos-Emmanuel-Lorenzo-Cornejo" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.", "doi": "10.7907/Z9M61H64", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8959", "collection": "thesis", "collection_id": "8959", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012015-171243593", "primary_object_url": { "basename": "NiranjanSrinivas_2015_thesis.pdf", "content": "final", "filesize": 15297188, "license": "other", "mime_type": "application/pdf", "url": "/8959/1/NiranjanSrinivas_2015_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement", "author": [ { "family_name": "Srinivas", "given_name": "Niranjan", "clpid": "Srinivas-Niranjan" } ], "thesis_advisor": [ { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "clpid": "Rothemund-P-W-K" }, { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Seelig", "given_name": "Georg", "clpid": "Seelig-G" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ \"chemical wiring\" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.
\r\n\r\nIn this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.
\r\n\r\nAbstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the \"device physics\" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.
\r\n\r\nIn Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for \"tuning\" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious \"leak\" pathways that compete with desired pathways.
\r\n\r\nWe successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.
", "doi": "10.7907/Z9KD1VVJ", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8648", "collection": "thesis", "collection_id": "8648", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08282014-165029252", "primary_object_url": { "basename": "Gomez_MarcellaM_Thesis_2015.pdf", "content": "final", "filesize": 12301385, "license": "other", "mime_type": "application/pdf", "url": "/8648/1/Gomez_MarcellaM_Thesis_2015.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "On the Role of Delays in Biological Systems : Analysis and Design", "author": [ { "family_name": "Gomez", "given_name": "Marcella Mary", "clpid": "Gomez-Marcella-Mary" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Balas", "given_name": "Mark J.", "clpid": "Balas-M-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system.
\r\n\r\nFurthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.
", "doi": "10.7907/Z9JH3J4W", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8941", "collection": "thesis", "collection_id": "8941", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292015-193747262", "primary_object_url": { "basename": "BorisRevechkisThesis2015.pdf", "content": "final", "filesize": 3838928, "license": "other", "mime_type": "application/pdf", "url": "/8941/10/BorisRevechkisThesis2015.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Neural Prosthetics and Parietal Cortex", "author": [ { "family_name": "Revechkis", "given_name": "Boris", "clpid": "Revechkis-Boris" } ], "thesis_advisor": [ { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" } ], "thesis_committee": [ { "family_name": "Adolphs", "given_name": "Ralph", "clpid": "Adolphs-R" }, { "family_name": "Siapas", "given_name": "Athanassios G.", "clpid": "Siapas-A-G" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In the last decade, research efforts into directly interfacing with the neurons of individuals with motor deficits have increased. The goal of such research is clear: Enable individuals affected by paralysis or amputation to regain control of their environments by manipulating external devices with thought alone. Though the motor cortices are the usual brain areas upon which neural prosthetics depend, research into the parietal lobe and its subregions, primarily in non-human primates, has uncovered alternative areas that could also benefit neural interfaces. Similar to the motor cortical areas, parietal regions can supply information about the trajectories of movements. In addition, the parietal lobe also contains cognitive signals like movement goals and intentions. But, these areas are also known to be tuned to saccadic eye movements, which could interfere with the function of a prosthetic designed to capture motor intentions only. In this thesis, we develop and examine the functionality of a neural prosthetic with a non-human primate model using the superior parietal lobe to examine the effectiveness of such an interface and the effects of unconstrained eye movements in a task that more closely simulates clinical applications. Additionally, we examine methods for improving usability of such interfaces.
\r\n\r\nThe parietal cortex is also believed to contain neural signals relating to monitoring of the state of the limbs through visual and somatosensory feedback. In one of the world\u2019s first clinical neural prosthetics based on the human parietal lobe, we examine the extent to which feedback regarding the state of a movement effector alters parietal neural signals and what the implications are for motor neural prosthetics and how this informs our understanding of this area of the human brain.
", "doi": "10.7907/Z9Z31WNK", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8998", "collection": "thesis", "collection_id": "8998", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06052015-123753277", "primary_object_url": { "basename": "Driggers-JC-2015-thesis.pdf", "content": "final", "filesize": 68440389, "license": "other", "mime_type": "application/pdf", "url": "/8998/1/Driggers-JC-2015-thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Noise Cancellation for Gravitational Wave Detectors", "author": [ { "family_name": "Driggers", "given_name": "Jennifer Clair", "orcid": "0000-0002-6134-7628", "clpid": "Driggers-Jennifer-Clair" } ], "thesis_advisor": [ { "family_name": "Adhikari", "given_name": "Rana", "orcid": "0000-0002-5731-5076", "clpid": "Adhikari-R" } ], "thesis_committee": [ { "family_name": "Adhikari", "given_name": "Rana", "orcid": "0000-0002-5731-5076", "clpid": "Adhikari-R" }, { "family_name": "Weinstein", "given_name": "Alan Jay", "orcid": "0000-0002-0928-6784", "clpid": "Weinstein-Alan-J-Physics" }, { "family_name": "Chen", "given_name": "Yanbei", "orcid": "0000-0002-9730-9463", "clpid": "Chen-Yanbei" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "LIGO" }, { "literal": "div_pma" } ], "abstract": "The LIGO gravitational wave detectors are on the brink of making the first direct detections of gravi- tational waves. Noise cancellation techniques are described, in order to simplify the commissioning of these detectors as well as significantly improve their sensitivity to astrophysical sources. Future upgrades to the ground based detectors will require further cancellation of Newtonian gravitational noise in order to make the transition from detectors striving to make the first direct detection of gravitational waves, to observatories extracting physics from many, many detections. Techniques for this noise cancellation are described, as well as the work remaining in this realm.", "doi": "10.7907/Z94F1NNP", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8020", "collection": "thesis", "collection_id": "8020", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10312013-000733635", "primary_object_url": { "basename": "ThesisMDM_11_1_2013_deposited.pdf", "content": "final", "filesize": 14154152, "license": "other", "mime_type": "application/pdf", "url": "/8020/1/ThesisMDM_11_1_2013_deposited.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Deep Ocean Density Structure at the Last Glacial Maximum: What Was It and Why?", "author": [ { "family_name": "Miller", "given_name": "Madeline Diane", "clpid": "Miller-Madeline-Diane" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Charles", "given_name": "Christopher D.", "clpid": "Charles-C-D" }, { "family_name": "Simons", "given_name": "Mark", "clpid": "Simons-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The search for reliable proxies of past deep ocean temperature and salinity has proved difficult, thereby limiting our ability to understand the coupling of ocean circulation and climate over glacial-interglacial timescales. Previous inferences of deep ocean temperature and salinity from sediment pore fluid oxygen isotopes and chlorinity indicate that the deep ocean density structure at the Last Glacial Maximum (LGM, approximately 20,000 years BP) was set by salinity, and that the density contrast between northern and southern sourced deep waters was markedly greater than in the modern ocean. High density stratification could help explain the marked contrast in carbon isotope distribution recorded in the LGM ocean relative to that we observe today, but what made the ocean's density structure so different at the LGM? How did it evolve from one state to another? Further, given the sparsity of the LGM temperature and salinity data set, what else can we learn by increasing the spatial density of proxy records?
\r\n\r\nWe investigate the cause and feasibility of a highly and salinity stratified deep ocean at the LGM and we work to increase the amount of information we can glean about the past ocean from pore fluid profiles of oxygen isotopes and chloride. Using a coupled ocean--sea ice--ice shelf cavity model we test whether the deep ocean density structure at the LGM can be explained by ice--ocean interactions over the Antarctic continental shelves, and show that a large contribution of the LGM salinity stratification can be explained through lower ocean temperature. In order to extract the maximum information from pore fluid profiles of oxygen isotopes and chloride we evaluate several inverse methods for ill-posed problems and their ability to recover bottom water histories from sediment pore fluid profiles. We demonstrate that Bayesian Markov Chain Monte Carlo parameter estimation techniques enable us to robustly recover the full solution space of bottom water histories, not only at the LGM, but through the most recent deglaciation and the Holocene up to the present. Finally, we evaluate a non-destructive pore fluid sampling technique, Rhizon samplers, in comparison to traditional squeezing methods and show that despite their promise, Rhizons are unlikely to be a good sampling tool for pore fluid measurements of oxygen isotopes and chloride.
", "doi": "10.7907/QHD5-FH77", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8239", "collection": "thesis", "collection_id": "8239", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162014-140751409", "primary_object_url": { "basename": "rydenfelt_mattias_2014_thesis.pdf", "content": "final", "filesize": 19949906, "license": "other", "mime_type": "application/pdf", "url": "/8239/1/rydenfelt_mattias_2014_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Combinatorics of Transcriptional Regulation", "author": [ { "family_name": "Rydenfelt", "given_name": "Mattias Sven Olof", "clpid": "Rydenfelt-Mattias-Sven-Olof" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Refael", "given_name": "Gil", "orcid": "0009-0007-4566-8441", "clpid": "Refael-G" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their internal and external environment. At the transcriptional level, binding of transcription factors (TFs) in the vicinity of promoters can modulate the rate at which transcripts are produced, and as such play an important role in gene regulation. TFs with regulatory action at multiple promoters is the rule rather than the exception, with examples ranging from TFs like the cAMP receptor protein (CRP) in E. coli that regulates hundreds of different genes, to situations involving multiple copies of the same gene, such as on plasmids, or viral DNA. When the number of TFs heavily exceeds the number of binding sites, TF binding to each promoter can be regarded as independent. However, when the number of TF molecules is comparable to the number of binding sites, TF titration will result in coupling (\"entanglement\") between transcription of different genes. The last few decades have seen rapid advances in our ability to quantitatively measure such effects, which calls for biophysical models to explain these data. Here we develop a statistical mechanical model which takes the TF titration effect into account and use it to predict both the level of gene expression and the resulting correlation in transcription rates for a general set of promoters. To test these predictions experimentally, we create genetic constructs with known TF copy number, binding site affinities, and gene copy number; hence avoiding the need to use free fit parameters. Our results clearly prove the TF titration effect and that the statistical mechanical model can accurately predict the fold change in gene expression for the studied cases. We also generalize these experimental efforts to cover systems with multiple different genes, using the method of mRNA fluorescence in situ hybridization (FISH). Interestingly, we can use the TF titration affect as a tool to measure the plasmid copy number at different points in the cell cycle, as well as the plasmid copy number variance. Finally, we investigate the strategies of transcriptional regulation used in a real organism by analyzing the thousands of known regulatory interactions in E. coli. We introduce a \"random promoter architecture model\" to identify overrepresented regulatory strategies, such as TF pairs which coregulate the same genes more frequently than would be expected by chance, indicating a related biological function. Furthermore, we investigate whether promoter architecture has a systematic effect on gene expression by linking the regulatory data of E. coli to genome-wide expression censuses.", "doi": "10.7907/PNX5-Y638", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7990", "collection": "thesis", "collection_id": "7990", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10142013-111401153", "primary_object_url": { "basename": "mihai_florian_thesis.pdf", "content": "final", "filesize": 1272593, "license": "other", "mime_type": "application/pdf", "url": "/7990/1/mihai_florian_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Analysis-Aware Design of Embedded Systems Software", "author": [ { "family_name": "Florian", "given_name": "Mihai", "clpid": "Florian-Mihai" } ], "thesis_advisor": [ { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" } ], "thesis_committee": [ { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Havelund", "given_name": "Klaus", "clpid": "Havelund-K" }, { "family_name": "Joshi", "given_name": "Rajeev", "clpid": "Joshi-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In the past many different methodologies have been devised to support software development and different sets of methodologies have been developed to support the analysis of software artefacts. We have identified this mismatch as one of the causes of the poor reliability of embedded systems software. The issue with software development styles is that they are ``analysis-agnostic.'' They do not try to structure the code in a way that lends itself to analysis. The analysis is usually applied post-mortem after the software was developed and it requires a large amount of effort. The issue with software analysis methodologies is that they do not exploit available information about the system being analyzed.
\r\n\r\nIn this thesis we address the above issues by developing a new methodology, called \"analysis-aware\" design, that links software development styles with the capabilities of analysis tools. This methodology forms the basis of a framework for interactive software development. The framework consists of an executable specification language and a set of analysis tools based on static analysis, testing, and model checking. The language enforces an analysis-friendly code structure and offers primitives that allow users to implement their own testers and model checkers directly in the language. We introduce a new approach to static analysis that takes advantage of the capabilities of a rule-based engine. We have applied the analysis-aware methodology to the development of a smart home application.
", "doi": "10.7907/VB1N-Y042", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7991", "collection": "thesis", "collection_id": "7991", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10162013-111333269", "primary_object_url": { "basename": "han_shuo_2014_thesis.pdf", "content": "final", "filesize": 1628283, "license": "other", "mime_type": "application/pdf", "url": "/7991/1/han_shuo_2014_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Optimal Uncertainty Quantification via Convex Optimization and Relaxation", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Chandrasekaran", "given_name": "Venkat", "clpid": "Chandrasekaran-V" }, { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" }, { "family_name": "Owhadi", "given_name": "Houman", "clpid": "Owhadi-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Many engineering applications face the problem of bounding the expected value of a quantity of interest (performance, risk, cost, etc.) that depends on stochastic uncertainties whose probability distribution is not known exactly. Optimal uncertainty quantification (OUQ) is a framework that aims at obtaining the best bound in these situations by explicitly incorporating available information about the distribution. Unfortunately, this often leads to non-convex optimization problems that are numerically expensive to solve.
\r\n\r\nThis thesis emphasizes on efficient numerical algorithms for OUQ problems. It begins by investigating several classes of OUQ problems that can be reformulated as convex optimization problems. Conditions on the objective function and information constraints under which a convex formulation exists are presented. Since the size of the optimization problem can become quite large, solutions for scaling up are also discussed. Finally, the capability of analyzing a practical system through such convex formulations is demonstrated by a numerical example of energy storage placement in power grids.
\r\n\r\nWhen an equivalent convex formulation is unavailable, it is possible to find a convex problem that provides a meaningful bound for the original problem, also known as a convex relaxation. As an example, the thesis investigates the setting used in Hoeffding's inequality. The naive formulation requires solving a collection of non-convex polynomial optimization problems whose number grows doubly exponentially. After structures such as symmetry are exploited, it is shown that both the number and the size of the polynomial optimization problems can be reduced significantly. Each polynomial optimization problem is then bounded by its convex relaxation using sums-of-squares. These bounds are found to be tight in all the numerical examples tested in the thesis and are significantly better than Hoeffding's bounds.
", "doi": "10.7907/X00K-T615", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8420", "collection": "thesis", "collection_id": "8420", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292014-063852576", "primary_object_url": { "basename": "SharanRangoli_2014_Thesis.pdf", "content": "final", "filesize": 9111864, "license": "other", "mime_type": "application/pdf", "url": "/8420/1/SharanRangoli_2014_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Formal Methods for Control Synthesis in Partially Observed Environments: Application to Autonomous Robotic Manipulation", "author": [ { "family_name": "Sharan", "given_name": "Rangoli", "clpid": "Sharan-Rangoli" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Hudson", "given_name": "Nicolas H.", "clpid": "Hudson-N-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Modern robots are increasingly expected to function in uncertain and dynamically challenging environments, often in proximity with humans. In addition, wide scale adoption of robots requires on-the-fly adaptability of software for diverse application. These requirements strongly suggest the need to adopt formal representations of high level goals and safety specifications, especially as temporal logic formulas. This approach allows for the use of formal verification techniques for controller synthesis that can give guarantees for safety and performance. Robots operating in unstructured environments also face limited sensing capability. Correctly inferring a robot's progress toward high level goal can be challenging.
\r\n\r\nThis thesis develops new algorithms for synthesizing discrete controllers in partially known environments under specifications represented as linear temporal logic (LTL) formulas. It is inspired by recent developments in finite abstraction techniques for hybrid systems and motion planning problems. The robot and its environment is assumed to have a finite abstraction as a Partially Observable Markov Decision Process (POMDP), which is a powerful model class capable of representing a wide variety of problems. However, synthesizing controllers that satisfy LTL goals over POMDPs is a challenging problem which has received only limited attention.
\r\n\r\nThis thesis proposes tractable, approximate algorithms for the control synthesis problem using Finite State Controllers (FSCs). The use of FSCs to control finite POMDPs allows for the closed system to be analyzed as finite global Markov chain. The thesis explicitly shows how transient and steady state behavior of the global Markov chains can be related to two different criteria with respect to satisfaction of LTL formulas. First, the maximization of the probability of LTL satisfaction is related to an optimization problem over a parametrization of the FSC. Analytic computation of gradients are derived which allows the use of first order optimization techniques.
\r\n\r\nThe second criterion encourages rapid and frequent visits to a restricted set of states over infinite executions. It is formulated as a constrained optimization problem with a discounted long term reward objective by the novel utilization of a fundamental equation for Markov chains - the Poisson equation. A new constrained policy iteration technique is proposed to solve the resulting dynamic program, which also provides a way to escape local maxima.
\r\n\r\nThe algorithms proposed in the thesis are applied to the task planning and execution challenges faced during the DARPA Autonomous Robotic Manipulation - Software challenge.
", "doi": "10.7907/RQKC-N871", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8047", "collection": "thesis", "collection_id": "8047", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01032014-164946523", "primary_object_url": { "basename": "vanBreugel_floris_2014_thesis.pdf", "content": "final", "filesize": 21738219, "license": "other", "mime_type": "application/pdf", "url": "/8047/1/vanBreugel_floris_2014_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Complex Behavior and Perception in Drosophila Emerges from Iterative Feedback-Regulated Reflexes", "author": [ { "family_name": "van Breugel", "given_name": "Floris", "orcid": "0000-0001-6538-7179", "clpid": "van-Breugel-Floris" } ], "thesis_advisor": [ { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Riffell", "given_name": "Jeff", "clpid": "Riffell-J" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "For a hungry fruit fly, locating and landing on a fermenting fruit where it can feed, find mates, and lay eggs, is an essential and difficult task requiring the integration of both olfactory and visual cues. Understanding how flies accomplish this will help provide a comprehensive ethological context for the expanding knowledge of their neural circuits involved in processing olfaction and vision, as well as inspire novel engineering solutions for control and estimation in computationally limited robotic applications. In this thesis, I use novel high throughput methods to develop a detailed overview of how flies track odor plumes, land, and regulate flight speed. Finally, I provide an example of how these insights can be applied to robotic applications to simplify complicated estimation problems. To localize an odor source, flies exhibit three iterative, reflex-driven behaviors. Upon encountering an attractive plume, flies increase their flight speed and turn upwind using visual cues. After losing the plume, flies begin zigzagging crosswind, again using visual cues to control their heading. After sensing an attractive odor, flies become more attracted to small visual features, which increases their chances of finding the plume source. Their changes in heading are largely controlled by open-loop maneuvers called saccades, which they direct towards and away from visual features. If a fly decides to land on an object, it begins to decelerate so as to maintain a stereotypical ratio of expansion to retinal size. Once they reach a stereotypical distance from the target, flies extend their legs in preparation for touchdown. Although it is unclear what cues they use to trigger this behavior, previous studies have indicated that it is likely under visual control. In Chapter 3, I use a nonlinear control theoretic analysis and robotic testbed to propose a novel and putative mechanism for how a fly might visually estimate distance by actively decelerating according to a visual control law. Throughout these behaviors, a common theme is the visual control of flight speed. Using genetic tools I show that the neuromodulator octopamine plays an important role in regulating flight speed, and propose a neural circuit for how this controller might be implemented in the flies brain. Two general biological and engineering principles are evident across my experiments: (1) complex behaviors, such as foraging, can emerge from the interactions of simple independent sensory-motor modules; (2) flies control their behavior in such a way that simplifies complex estimation problems.
", "doi": "10.7907/WSE4-WG98", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8078", "collection": "thesis", "collection_id": "8078", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02172014-121159358", "primary_object_url": { "basename": "wolff_eric_thesis.pdf", "content": "final", "filesize": 2659687, "license": "other", "mime_type": "application/pdf", "url": "/8078/1/wolff_eric_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Control of Dynamical Systems with Temporal Logic Specifications", "author": [ { "family_name": "Wolff", "given_name": "Eric McKenzie", "clpid": "Wolff-Eric-McKenzie" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis is motivated by safety-critical applications involving autonomous air, ground, and space vehicles carrying out complex tasks in uncertain and adversarial environments. We use temporal logic as a language to formally specify complex tasks and system properties. Temporal logic specifications generalize the classical notions of stability and reachability that are studied in the control and hybrid systems communities. Given a system model and a formal task specification, the goal is to automatically synthesize a control policy for the system that ensures that the system satisfies the specification. This thesis presents novel control policy synthesis algorithms for optimal and robust control of dynamical systems with temporal logic specifications. Furthermore, it introduces algorithms that are efficient and extend to high-dimensional dynamical systems.
\r\n\r\nThe first contribution of this thesis is the generalization of a classical linear temporal logic (LTL) control synthesis approach to optimal and robust control. We show how we can extend automata-based synthesis techniques for discrete abstractions of dynamical systems to create optimal and robust controllers that are guaranteed to satisfy an LTL specification. Such optimal and robust controllers can be computed at little extra computational cost compared to computing a feasible controller.
\r\n\r\nThe second contribution of this thesis addresses the scalability of control synthesis with LTL specifications. A major limitation of the standard automaton-based approach for control with LTL specifications is that the automaton might be doubly-exponential in the size of the LTL specification. We introduce a fragment of LTL for which one can compute feasible control policies in time polynomial in the size of the system and specification. Additionally, we show how to compute optimal control policies for a variety of cost functions, and identify interesting cases when this can be done in polynomial time. These techniques are particularly relevant for online control, as one can guarantee that a feasible solution can be found quickly, and then iteratively improve on the quality as time permits.
\r\n\r\nThe final contribution of this thesis is a set of algorithms for computing feasible trajectories for high-dimensional, nonlinear systems with LTL specifications. These algorithms avoid a potentially computationally-expensive process of computing a discrete abstraction, and instead compute directly on the system's continuous state space. The first method uses an automaton representing the specification to directly encode a series of constrained-reachability subproblems, which can be solved in a modular fashion by using standard techniques. The second method encodes an LTL formula as mixed-integer linear programming constraints on the dynamical system. We demonstrate these approaches with numerical experiments on temporal logic motion planning problems with high-dimensional (10+ states) continuous systems.
", "doi": "10.7907/TGFR-SS39", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8453", "collection": "thesis", "collection_id": "8453", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312014-011052261", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 4343953, "license": "other", "mime_type": "application/pdf", "url": "/8453/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Efficient Methods for Stochastic Optimal Control", "author": [ { "family_name": "Horowitz", "given_name": "Matanya Benasher", "clpid": "Horowitz-Matanya-Benasher" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Chandrasekaran", "given_name": "Venkat", "clpid": "Chandrasekaran-V" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The Hamilton Jacobi Bellman (HJB) equation is central to stochastic optimal control (SOC) theory, yielding the optimal solution to general problems specified by known dynamics and a specified cost functional. Given the assumption of quadratic cost on the control input, it is well known that the HJB reduces to a particular partial differential equation (PDE). While powerful, this reduction is not commonly used as the PDE is of second order, is nonlinear, and examples exist where the problem may not have a solution in a classical sense. Furthermore, each state of the system appears as another dimension of the PDE, giving rise to the curse of dimensionality. Since the number of degrees of freedom required to solve the optimal control problem grows exponentially with dimension, the problem becomes intractable for systems with all but modest dimension.
\r\n\r\nIn the last decade researchers have found that under certain, fairly non-restrictive structural assumptions, the HJB may be transformed into a linear PDE, with an interesting analogue in the discretized domain of Markov Decision Processes (MDP). The work presented in this thesis uses the linearity of this particular form of the HJB PDE to push the computational boundaries of stochastic optimal control.
\r\n\r\nThis is done by crafting together previously disjoint lines of research in computation. The first of these is the use of Sum of Squares (SOS) techniques for synthesis of control policies. A candidate polynomial with variable coefficients is proposed as the solution to the stochastic optimal control problem. An SOS relaxation is then taken to the partial differential constraints, leading to a hierarchy of semidefinite relaxations with improving sub-optimality gap. The resulting approximate solutions are shown to be guaranteed over- and under-approximations for the optimal value function. It is shown that these results extend to arbitrary parabolic and elliptic PDEs, yielding a novel method for Uncertainty Quantification (UQ) of systems governed by partial differential constraints. Domain decomposition techniques are also made available, allowing for such problems to be solved via parallelization and low-order polynomials.
\r\n\r\nThe optimization-based SOS technique is then contrasted with the Separated Representation (SR) approach from the applied mathematics community. The technique allows for systems of equations to be solved through a low-rank decomposition that results in algorithms that scale linearly with dimensionality. Its application in stochastic optimal control allows for previously uncomputable problems to be solved quickly, scaling to such complex systems as the Quadcopter and VTOL aircraft. This technique may be combined with the SOS approach, yielding not only a numerical technique, but also an analytical one that allows for entirely new classes of systems to be studied and for stability properties to be guaranteed.
\r\n\r\nThe analysis of the linear HJB is completed by the study of its implications in application. It is shown that the HJB and a popular technique in robotics, the use of navigation functions, sit on opposite ends of a spectrum of optimization problems, upon which tradeoffs may be made in problem complexity. Analytical solutions to the HJB in these settings are available in simplified domains, yielding guidance towards optimality for approximation schemes. Finally, the use of HJB equations in temporal multi-task planning problems is investigated. It is demonstrated that such problems are reducible to a sequence of SOC problems linked via boundary conditions. The linearity of the PDE allows us to pre-compute control policy primitives and then compose them, at essentially zero cost, to satisfy a complex temporal logic specification.
", "doi": "10.7907/D40A-9E03", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8173", "collection": "thesis", "collection_id": "8173", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03272014-193400848", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 23888033, "license": "other", "mime_type": "application/pdf", "url": "/8173/8/thesis.pdf", "version": "v10.0.0" }, "type": "thesis", "title": "Design and Analysis of Nucleic Acid Reaction Pathways", "author": [ { "family_name": "Wolfe", "given_name": "Brian Robert", "clpid": "Wolfe-Brian-Robert" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.", "doi": "10.7907/G4XZ-ZF47", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7791", "collection": "thesis", "collection_id": "7791", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312013-122007615", "type": "thesis", "title": "Distributed Optimization in Power Networks and General Multi-agent Systems", "author": [ { "family_name": "Li", "given_name": "Na (Lina)", "clpid": "Li-Na-Lina" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marden", "given_name": "Jason R.", "clpid": "Marden-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The dissertation studies the general area of complex networked systems that consist of interconnected and active heterogeneous components and usually operate in uncertain environments and with incomplete information. Problems associated with those systems are typically large-scale and computationally intractable, yet they are also very well-structured and have features that can be exploited by appropriate modeling and computational methods. The goal of this thesis is to develop foundational theories and tools to exploit those structures that can lead to computationally-efficient and distributed solutions, and apply them to improve systems operations and architecture.
\r\n\r\nSpecifically, the thesis focuses on two concrete areas. The first one is to design distributed rules to manage distributed energy resources in the power network. The power network is undergoing a fundamental transformation. The future smart grid, especially on the distribution system, will be a large-scale network of distributed energy resources (DERs), each introducing random and rapid fluctuations in power supply, demand, voltage and frequency. These DERs provide a tremendous opportunity for sustainability, efficiency, and power reliability. However, there are daunting technical challenges in managing these DERs and optimizing their operation. The focus of this dissertation is to develop scalable, distributed, and real-time control and optimization to achieve system-wide efficiency, reliability, and robustness for the future power grid. In particular, we will present how to explore the power network structure to design efficient and distributed market and algorithms for the energy management. We will also show how to connect the algorithms with physical dynamics and existing control mechanisms for real-time control in power networks.
\r\n\r\nThe second focus is to develop distributed optimization rules for general multi-agent engineering systems. A central goal in multiagent systems is to design local control laws for the individual agents to ensure that the emergent global behavior is desirable with respect to the given system level objective. Ideally, a system designer seeks to satisfy this goal while conditioning each agent\u2019s control on the least amount of information possible. Our work focused on achieving this goal using the framework of game theory. In particular, we derived a systematic methodology for designing local agent objective functions that guarantees (i) an equivalence between the resulting game-theoretic equilibria and the system level design objective and (ii) that the resulting game possesses an inherent structure that can be exploited for distributed learning, e.g., potential games. The control design can then be completed by applying any distributed learning algorithm that guarantees convergence to the game-theoretic equilibrium. One main advantage of this game theoretic approach is that it provides a hierarchical decomposition between the decomposition of the systemic objective (game design) and the specific local decision rules (distributed learning algorithms). This decomposition provides the system designer with tremendous flexibility to meet the design objectives and constraints inherent in a broad class of multiagent systems. Furthermore, in many settings the resulting controllers will be inherently robust to a host of uncertainties including asynchronous clock rates, delays in information, and component failures.
", "doi": "10.7907/NHVJ-FX37", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7789", "collection": "thesis", "collection_id": "7789", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312013-103940337", "primary_object_url": { "basename": "Xu_Huan_Thesis_2013.pdf", "content": "final", "filesize": 16950376, "license": "other", "mime_type": "application/pdf", "url": "/7789/1/Xu_Huan_Thesis_2013.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Design, Specification, and Synthesis of Aircraft Electric Power Systems Control Logic", "author": [ { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-Huan" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Cyber-physical systems integrate computation, networking, and physical processes. Substantial research challenges exist in the design and verification of such large-scale, distributed sensing, ac- tuation, and control systems. Rapidly improving technology and recent advances in control theory, networked systems, and computer science give us the opportunity to drastically improve our approach to integrated flow of information and cooperative behavior. Current systems rely on text-based spec- ifications and manual design. Using new technology advances, we can create easier, more efficient, and cheaper ways of developing these control systems. This thesis will focus on design considera- tions for system topologies, ways to formally and automatically specify requirements, and methods to synthesize reactive control protocols, all within the context of an aircraft electric power system as a representative application area.
\r\n\r\nThis thesis consists of three complementary parts: synthesis, specification, and design. The first section focuses on the synthesis of central and distributed reactive controllers for an aircraft elec- tric power system. This approach incorporates methodologies from computer science and control. The resulting controllers are correct by construction with respect to system requirements, which are formulated using the specification language of linear temporal logic (LTL). The second section addresses how to formally specify requirements and introduces a domain-specific language for electric power systems. A software tool automatically converts high-level requirements into LTL and synthesizes a controller.
\r\n\r\nThe final sections focus on design space exploration. A design methodology is proposed that uses mixed-integer linear programming to obtain candidate topologies, which are then used to synthesize controllers. The discrete-time control logic is then verified in real-time by two methods: hardware and simulation. Finally, the problem of partial observability and dynamic state estimation is ex- plored. Given a set placement of sensors on an electric power system, measurements from these sensors can be used in conjunction with control logic to infer the state of the system.
", "doi": "10.7907/QDJN-BB72", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7753", "collection": "thesis", "collection_id": "7753", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252013-081655550", "primary_object_url": { "basename": "Sojoudi_Somayeh_2013_Thesis.pdf", "content": "final", "filesize": 1227396, "license": "other", "mime_type": "application/pdf", "url": "/7753/1/Sojoudi_Somayeh_2013_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Mathematical Study of Complex Networks: Brain, Internet, and Power Grid", "author": [ { "family_name": "Sojoudi", "given_name": "Somayeh", "clpid": "Sojoudi-Somayeh" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The dissertation is concerned with the mathematical study of various network problems. First, three real-world networks are considered: (i) the human brain network (ii) communication networks, (iii) electric power networks. Although these networks perform very different tasks, they share similar mathematical foundations. The high-level goal is to analyze and/or synthesis each of these systems from a \u201ccontrol and optimization\u201d point of view. After studying these three real-world networks, two abstract network problems are also explored, which are motivated by power systems. The first one is \u201cflow optimization over a flow network\u201d and the second one is \u201cnonlinear optimization over a generalized weighted graph\u201d. The results derived in this dissertation are summarized below.
\r\n\r\nBrain Networks: Neuroimaging data reveals the coordinated activity of spatially distinct brain regions, which may be represented mathematically as a network of nodes (brain regions) and links (interdependencies). To obtain the brain connectivity network, the graphs associated with the correlation matrix and the inverse covariance matrix\u2014describing marginal and conditional dependencies between brain regions\u2014have been proposed in the literature. A question arises as to whether any of these graphs provides useful information about the brain connectivity. Due to the electrical properties of the brain, this problem will be investigated in the context of electrical circuits. First, we consider an electric circuit model and show that the inverse covariance matrix of the node voltages reveals the topology of the circuit. Second, we study the problem of finding the topology of the circuit based on only measurement. In this case, by assuming that the circuit is hidden inside a black box and only the nodal signals are available for measurement, the aim is to find the topology of the circuit when a limited number of samples are available. For this purpose, we deploy the graphical lasso technique to estimate a sparse inverse covariance matrix. It is shown that the graphical lasso may find most of the circuit topology if the exact covariance matrix is well-conditioned. However, it may fail to work well when this matrix is ill-conditioned. To deal with ill-conditioned matrices, we propose a small modification to the graphical lasso algorithm and demonstrate its performance. Finally, the technique developed in this work will be applied to the resting-state fMRI data of a number of healthy subjects.
\r\n\r\nCommunication Networks: Congestion control techniques aim to adjust the transmission rates of competing users in the Internet in such a way that the network resources are shared efficiently. Despite the progress in the analysis and synthesis of the Internet congestion control, almost all existing fluid models of congestion control assume that every link in the path of a flow observes the original source rate. To address this issue, a more accurate model is derived in this work for the behavior of the network under an arbitrary congestion controller, which takes into account of the effect of buffering (queueing) on data flows. Using this model, it is proved that the well-known Internet congestion control algorithms may no longer be stable for the common pricing schemes, unless a sufficient condition is satisfied. It is also shown that these algorithms are guaranteed to be stable if a new pricing mechanism is used.
\r\n\r\nElectrical Power Networks: Optimal power flow (OPF) has been one of the most studied problems for power systems since its introduction by Carpentier in 1962. This problem is concerned with finding an optimal operating point of a power network minimizing the total power generation cost subject to network and physical constraints. It is well known that OPF is computationally hard to solve due to the nonlinear interrelation among the optimization variables. The objective is to identify a large class of networks over which every OPF problem can be solved in polynomial time. To this end, a convex relaxation is proposed, which solves the OPF problem exactly for every radial network and every meshed network with a sufficient number of phase shifters, provided power over-delivery is allowed. The concept of \u201cpower over-delivery\u201d is equivalent to relaxing the power balance equations to inequality constraints.
\r\n\r\nFlow Networks: In this part of the dissertation, the minimum-cost flow problem over an arbitrary flow network is considered. In this problem, each node is associated with some possibly unknown injection, each line has two unknown flows at its ends related to each other via a nonlinear function, and all injections and flows need to satisfy certain box constraints. This problem, named generalized network flow (GNF), is highly non-convex due to its nonlinear equality constraints. Under the assumption of monotonicity and convexity of the flow and cost functions, a convex relaxation is proposed, which always finds the optimal injections. A primary application of this work is in the OPF problem. The results of this work on GNF prove that the relaxation on power balance equations (i.e., load over-delivery) is not needed in practice under a very mild angle assumption.
\r\n\r\nGeneralized Weighted Graphs: Motivated by power optimizations, this part aims to find a global optimization technique for a nonlinear optimization defined over a generalized weighted graph. Every edge of this type of graph is associated with a weight set corresponding to the known parameters of the optimization (e.g., the coefficients). The motivation behind this problem is to investigate how the (hidden) structure of a given real/complex valued optimization makes the problem easy to solve, and indeed the generalized weighted graph is introduced to capture the structure of an optimization. Various sufficient conditions are derived, which relate the polynomial-time solvability of different classes of optimization problems to weak properties of the generalized weighted graph such as its topology and the sign definiteness of its weight sets. As an application, it is proved that a broad class of real and complex optimizations over power networks are polynomial-time solvable due to the passivity of transmission lines and transformers.
", "doi": "10.7907/E750-2M74", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7248", "collection": "thesis", "collection_id": "7248", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10282012-082208075", "primary_object_url": { "basename": "main_dissertation-caltech-oct28.pdf", "content": "final", "filesize": 24248874, "license": "other", "mime_type": "application/pdf", "url": "/7248/4/main_dissertation-caltech-oct28.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Bootstrapping Vehicles: A Formal Approach to Unsupervised Sensorimotor Learning Based on Invariance", "author": [ { "family_name": "Censi", "given_name": "Andrea", "clpid": "Censi-Andrea" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Soatto", "given_name": "Stefano", "clpid": "Soatto-Stefano" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Could a \"brain in a jar\" be able to control an unknown robotic body to which it is connected, and use it to achieve useful tasks, without any prior assumptions on the body's sensors and actuators? Other than of purely intellectual interest, this question is relevant to the medium-term challenges of robotics: as the complexity of robotics applications grows, automated learning techniques might reduce design effort and increase the robustness and reliability of the solutions. In this work, the problem of \"bootstrapping\" is studied in the context of the Vehicles universe, which is an idealization of simple mobile robots, after the work of Braitenberg. The first thread of results consists in analyzing such simple sensorimotor cascades and proposing models of varying complexity that can be learned from data. The second thread regards how to properly formalize the notions of \"absence of assumptions\", as a particular form of invariance that the bootstrapping agent must satisfy, and proposes some invariance-based design techniques.", "doi": "10.7907/PWVS-2Q74", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7665", "collection": "thesis", "collection_id": "7665", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05032013-161632237", "type": "thesis", "title": "A Dynamical Systems Analysis of Vortex Pinch-Off", "author": [ { "family_name": "O'Farrell", "given_name": "Clara", "clpid": "O'Farrell-Clara" } ], "thesis_advisor": [ { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" } ], "thesis_committee": [ { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Vortex rings constitute the main structure in the wakes of a wide class of swimming and flying animals, as well as in cardiac flows and in the jets generated by some moss and fungi. However, there is a physical limit, determined by an energy maximization principle called the Kelvin-Benjamin principle, to the size that axisymmetric vortex rings can achieve. The existence of this limit is known to lead to the separation of a growing vortex ring from the shear layer feeding it, a process known as `vortex pinch-off', and characterized by the dimensionless vortex formation number. The goal of this thesis is to improve our understanding of vortex pinch-off as it relates to biological propulsion, and to provide future researchers with tools to assist in identifying and predicting pinch-off in biological flows.
\r\n\r\nTo this end, we introduce a method for identifying pinch-off in starting jets using the Lagrangian coherent structures in the flow, and apply this criterion to an experimentally generated starting jet. Since most naturally occurring vortex rings are not circular, we extend the definition of the vortex formation number to include non-axisymmetric vortex rings, and find that the formation number for moderately non-axisymmetric vortices is similar to that of circular vortex rings. This suggests that naturally occurring vortex rings may be modeled as axisymmetric vortex rings. Therefore, we consider the perturbation response of the Norbury family of axisymmetric vortex rings. This family is chosen to model vortex rings of increasing thickness and circulation, and their response to prolate shape perturbations is simulated using contour dynamics. Finally, the response of more realistic models for vortex rings, constructed from experimental data using nested contours, to perturbations which resemble those encountered by forming vortices more closely, is simulated using contour dynamics. In both families of models, a change in response analogous to pinch-off is found as members of the family with progressively thicker cores are considered. We posit that this analogy may be exploited to understand and predict pinch-off in complex biological flows, where current methods are not applicable in practice, and criteria based on the properties of vortex rings alone are necessary.
", "doi": "10.7907/AFAA-KF43", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7665", "collection": "thesis", "collection_id": "7665", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05032013-161632237", "type": "thesis", "title": "A Dynamical Systems Analysis of Vortex Pinch-Off", "author": [ { "family_name": "O'Farrell", "given_name": "Clara", "clpid": "O'Farrell-Clara" } ], "thesis_advisor": [ { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" } ], "thesis_committee": [ { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "Vortex rings constitute the main structure in the wakes of a wide class of swimming and flying animals, as well as in cardiac flows and in the jets generated by some moss and fungi. However, there is a physical limit, determined by an energy maximization principle called the Kelvin-Benjamin principle, to the size that axisymmetric vortex rings can achieve. The existence of this limit is known to lead to the separation of a growing vortex ring from the shear layer feeding it, a process known as `vortex pinch-off', and characterized by the dimensionless vortex formation number. The goal of this thesis is to improve our understanding of vortex pinch-off as it relates to biological propulsion, and to provide future researchers with tools to assist in identifying and predicting pinch-off in biological flows.
\r\n\r\nTo this end, we introduce a method for identifying pinch-off in starting jets using the Lagrangian coherent structures in the flow, and apply this criterion to an experimentally generated starting jet. Since most naturally occurring vortex rings are not circular, we extend the definition of the vortex formation number to include non-axisymmetric vortex rings, and find that the formation number for moderately non-axisymmetric vortices is similar to that of circular vortex rings. This suggests that naturally occurring vortex rings may be modeled as axisymmetric vortex rings. Therefore, we consider the perturbation response of the Norbury family of axisymmetric vortex rings. This family is chosen to model vortex rings of increasing thickness and circulation, and their response to prolate shape perturbations is simulated using contour dynamics. Finally, the response of more realistic models for vortex rings, constructed from experimental data using nested contours, to perturbations which resemble those encountered by forming vortices more closely, is simulated using contour dynamics. In both families of models, a change in response analogous to pinch-off is found as members of the family with progressively thicker cores are considered. We posit that this analogy may be exploited to understand and predict pinch-off in complex biological flows, where current methods are not applicable in practice, and criteria based on the properties of vortex rings alone are necessary.
", "doi": "10.7907/AFAA-KF43", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7580", "collection": "thesis", "collection_id": "7580", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04052013-105520483", "primary_object_url": { "basename": "Hebert_thesis_twosided.pdf", "content": "final", "filesize": 14037129, "license": "other", "mime_type": "application/pdf", "url": "/7580/1/Hebert_thesis_twosided.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Estimation and Inference for Grasping and Manipulation Tasks Using Vision and Kinesthetic Sensors", "author": [ { "family_name": "Hebert", "given_name": "Paul", "clpid": "Hebert-Paul" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Hudson", "given_name": "Nicolas H.", "clpid": "Hudson-N-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents a novel framework for state estimation in the context of robotic grasping and manipulation. The overall estimation approach is based on fusing various visual cues for manipulator tracking, namely appearance and feature-based, shape-based, and silhouette-based visual cues. Similarly, a framework is developed to fuse the above visual cues, but also kinesthetic cues such as force-torque and tactile measurements, for in-hand object pose estimation. The cues are extracted from multiple sensor modalities and are fused in a variety of Kalman filters.
\r\n\r\nA hybrid estimator is developed to estimate both a continuous state (robot and object states) and discrete states, called contact modes, which specify how each finger contacts a particular object surface. A static multiple model estimator is used to compute and maintain this mode probability. The thesis also develops an estimation framework for estimating model parameters associated with object grasping. Dual and joint state-parameter estimation is explored for parameter estimation of a grasped object's mass and center of mass. Experimental results demonstrate simultaneous object localization and center of mass estimation.
\r\n\r\nDual-arm estimation is developed for two arm robotic manipulation tasks. Two types of filters are explored; the first is an augmented filter that contains both arms in the state vector while the second runs two filters in parallel, one for each arm. These two frameworks and their performance is compared in a dual-arm task of removing a wheel from a hub.
\r\n\r\nThis thesis also presents a new method for action selection involving touch. This next best touch method selects an available action for interacting with an object that will gain the most information. The algorithm employs information theory to compute an information gain metric that is based on a probabilistic belief suitable for the task. An estimation framework is used to maintain this belief over time. Kinesthetic measurements such as contact and tactile measurements are used to update the state belief after every interactive action. Simulation and experimental results are demonstrated using next best touch for object localization, specifically a door handle on a door.\r\nThe next best touch theory is extended for model parameter determination. Since many objects within a particular object category share the same rough shape, principle component analysis may be used to parametrize the object mesh models. These parameters can be estimated using the action selection technique that selects the touching action which best both localizes and estimates these parameters. Simulation results are then presented involving localizing and determining a parameter of a screwdriver.
\r\n\r\nLastly, the next best touch theory is further extended to model classes. Instead of estimating parameters, object class determination is incorporated into the information gain metric calculation. The best touching action is selected in order to best discern between the possible model classes. Simulation results are presented to validate the theory.
", "doi": "10.7907/PZB6-QJ39", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7864", "collection": "thesis", "collection_id": "7864", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-110839676", "type": "thesis", "title": "Flight Dynamics in Drosophila Through a Dynamically-scaled Robotic Approach", "author": [ { "family_name": "Elzinga", "given_name": "Michael John", "clpid": "Elzinga-Michael-John" } ], "thesis_advisor": [ { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Flies are particularly adept at balancing the competing demands of delay tolerance, performance, and robustness during flight, which invites thoughtful examination of their multimodal feedback architecture. This dissertation examines stabilization requirements for inner-loop feedback strategies in the flapping flight of Drosophila, the fruit fly, against the backdrop of sensorimotor transformations present in the animal. Flies have evolved multiple specializations to reduce sensorimotor latency, but sensory delay during flight is still significant on the timescale of body dynamics. I explored the effect of sensor delay on flight stability and performance for yaw turns using a dynamically-scaled robot equipped with a real-time feedback system that performed active turns in response to measured yaw torque. The results show a fundamental tradeoff between sensor delay and permissible feedback gain, and suggest that fast mechanosensory feedback provides a source of active damping that compliments that contributed by passive effects. Presented in the context of these findings, a control architecture whereby a haltere-mediated inner-loop proportional controller provides damping for slower visually-mediated feedback is consistent with tethered-flight measurements, free-flight observations, and engineering design principles.
\r\n\r\nAdditionally, I investigated how flies adjust stroke features to regulate and stabilize level forward flight. The results suggest that few changes to hovering kinematics are actually required to meet steady-state lift and thrust requirements at different flight speeds, and the primary driver of equilibrium velocity is the aerodynamic pitch moment. This finding is consistent with prior hypotheses and observations regarding the relationship between body pitch and flight speed in fruit flies. The results also show that the dynamics may be stabilized with additional pitch damping, but the magnitude of required damping increases with flight speed. I posit that differences in stroke deviation between the upstroke and downstroke might play a critical role in this stabilization. Fast mechanosensory feedback of the pitch rate could enable active damping, which would inherently exhibit gain scheduling with flight speed if pitch torque is regulated by adjusting stroke deviation. Such a control scheme would provide an elegant solution for flight stabilization across a wide range of flight speeds.
\r\n", "doi": "10.7907/MSRS-JG88", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7863", "collection": "thesis", "collection_id": "7863", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-095239958", "primary_object_url": { "basename": "Venturelli-O-S-2013-thesis.pdf", "content": "final", "filesize": 15828338, "license": "other", "mime_type": "application/pdf", "url": "/7863/13/Venturelli-O-S-2013-thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Role of Feedback and Dynamics of a Gene Regulatory Network", "author": [ { "family_name": "Venturelli", "given_name": "Ophelia Shalini", "clpid": "Venturelli-Ophelia-Shalini" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Deshaies", "given_name": "Raymond Joseph", "orcid": "0000-0002-3671-9354", "clpid": "Deshaies-R-J" }, { "family_name": "El-Samad", "given_name": "Hana", "clpid": "El-Samad-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Cells exhibit a diverse repertoire of dynamic behaviors. These dynamic functions are implemented by circuits of interacting biomolecules. Although these regulatory networks function deterministically by executing specific programs in response to extracellular signals, molecular interactions are inherently governed by stochastic fluctuations. This molecular noise can manifest as cell-to-cell phenotypic heterogeneity in a well-mixed environment. Single-cell variability may seem like a design flaw but the coexistence of diverse phenotypes in an isogenic population of cells can also serve a biological function by increasing the probability of survival of individual cells upon an abrupt change in environmental conditions. Decades of extensive molecular and biochemical characterization have revealed the connectivity and mechanisms that constitute regulatory networks. We are now confronted with the challenge of integrating this information to link the structure of these circuits to systems-level properties such as cellular decision making. To investigate cellular decision-making, we used the well studied galactose gene-regulatory network in Saccharomyces cerevisiae. We analyzed the mechanism and dynamics of the coexistence of two stable on and off states for pathway activity. We demonstrate that this bimodality in the pathway activity originates from two positive feedback loops that trigger bistability in the network. By measuring the dynamics of single-cells in a mixed sugar environment, we observe that the bimodality in gene expression is a transient phenomenon. Our experiments indicate that early pathway activation in a cohort of cells prior to galactose metabolism can accelerate galactose consumption and provide a transient increase in growth rate. Together these results provide important insights into strategies implemented by cells that may have been evolutionary advantageous in competitive environments. \r\n", "doi": "10.7907/WGK3-Y839", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7863", "collection": "thesis", "collection_id": "7863", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-095239958", "primary_object_url": { "basename": "Venturelli-O-S-2013-thesis.pdf", "content": "final", "filesize": 15828338, "license": "other", "mime_type": "application/pdf", "url": "/7863/13/Venturelli-O-S-2013-thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Role of Feedback and Dynamics of a Gene Regulatory Network", "author": [ { "family_name": "Venturelli", "given_name": "Ophelia Shalini", "clpid": "Venturelli-Ophelia-Shalini" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Deshaies", "given_name": "Raymond Joseph", "orcid": "0000-0002-3671-9354", "clpid": "Deshaies-R-J" }, { "family_name": "El-Samad", "given_name": "Hana", "clpid": "El-Samad-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Cells exhibit a diverse repertoire of dynamic behaviors. These dynamic functions are implemented by circuits of interacting biomolecules. Although these regulatory networks function deterministically by executing specific programs in response to extracellular signals, molecular interactions are inherently governed by stochastic fluctuations. This molecular noise can manifest as cell-to-cell phenotypic heterogeneity in a well-mixed environment. Single-cell variability may seem like a design flaw but the coexistence of diverse phenotypes in an isogenic population of cells can also serve a biological function by increasing the probability of survival of individual cells upon an abrupt change in environmental conditions. Decades of extensive molecular and biochemical characterization have revealed the connectivity and mechanisms that constitute regulatory networks. We are now confronted with the challenge of integrating this information to link the structure of these circuits to systems-level properties such as cellular decision making. To investigate cellular decision-making, we used the well studied galactose gene-regulatory network in Saccharomyces cerevisiae. We analyzed the mechanism and dynamics of the coexistence of two stable on and off states for pathway activity. We demonstrate that this bimodality in the pathway activity originates from two positive feedback loops that trigger bistability in the network. By measuring the dynamics of single-cells in a mixed sugar environment, we observe that the bimodality in gene expression is a transient phenomenon. Our experiments indicate that early pathway activation in a cohort of cells prior to galactose metabolism can accelerate galactose consumption and provide a transient increase in growth rate. Together these results provide important insights into strategies implemented by cells that may have been evolutionary advantageous in competitive environments. \r\n", "doi": "10.7907/WGK3-Y839", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7856", "collection": "thesis", "collection_id": "7856", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-224746692", "primary_object_url": { "basename": "thesis_annie.pdf", "content": "final", "filesize": 23718990, "license": "other", "mime_type": "application/pdf", "url": "/7856/1/thesis_annie.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Sensor Networks for Geospatial Event Detection - Theory and Applications", "author": [ { "family_name": "Liu", "given_name": "Annie Hsin-Wen", "clpid": "Liu-Annie-Hsin-Wen" } ], "thesis_advisor": [ { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "thesis_committee": [ { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Clayton", "given_name": "Robert W.", "clpid": "Clayton-R-W" }, { "family_name": "Wierman", "given_name": "Adam C.", "clpid": "Wierman-A-C" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents theories, analyses, and algorithms for detecting and estimating parameters of geospatial events with today's large, noisy sensor networks. A geospatial event is initiated by a significant change in the state of points in a region in a 3-D space over an interval of time. After the event is initiated it may change the state of points over larger regions and longer periods of time.
\r\n\r\nNetworked sensing is a typical approach for geospatial event detection. In contrast to traditional sensor networks comprised of a small number of high quality (and expensive) sensors, trends in personal computing devices and consumer electronics have made it possible to build large, dense networks at a low cost. The changes in sensor capability, network composition, and system constraints call for new models and algorithms suited to the opportunities and challenges of the new generation of sensor networks.
\r\n\r\nThis thesis offers a single unifying model and a Bayesian framework for analyzing different types of geospatial events in such noisy sensor networks. It presents algorithms and theories for estimating the speed and accuracy of detecting geospatial events as a function of parameters from both the underlying geospatial system and the sensor network. Furthermore, the thesis addresses network scalability issues by presenting rigorous scalable algorithms for data aggregation for detection. These studies provide insights to the design of networked sensing systems for detecting geospatial events.
\r\n\r\nIn addition to providing an overarching framework, this thesis presents theories and experimental results for two very different geospatial problems: detecting earthquakes and hazardous radiation. The general framework is applied to these specific problems, and predictions based on the theories are validated against measurements of systems in the laboratory and in the field.
", "doi": "10.7907/MZWJ-T222", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7825", "collection": "thesis", "collection_id": "7825", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032013-143158080", "primary_object_url": { "basename": "ThesisFinal.pdf", "content": "final", "filesize": 2429911, "license": "cc_by", "mime_type": "application/pdf", "url": "/7825/196/ThesisFinal.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Limits and Tradeoffs in the Control of Autocatalytic Systems", "author": [ { "family_name": "Chandra", "given_name": "Fiona Adriani", "clpid": "Chandra-Fiona-Adriani" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "DiStefano", "given_name": "Joseph", "clpid": "DiStefano-J-D" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system\u2019s performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.", "doi": "10.7907/Z1BQ-ZX85", "publication_date": "2013-05-29", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7700", "collection": "thesis", "collection_id": "7700", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05122013-221658522", "primary_object_url": { "basename": "Dabby_Nadine_2013_complete_thesis.pdf", "content": "final", "filesize": 41643872, "license": "other", "mime_type": "application/pdf", "url": "/7700/50/Dabby_Nadine_2013_complete_thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study", "author": [ { "family_name": "Dabby", "given_name": "Nadine L.", "clpid": "Dabby-Nadine-L" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Barr", "given_name": "Alan H.", "clpid": "Barr-A-H" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" }, { "family_name": "Shimojo", "given_name": "Shinsuke", "clpid": "Shimojo-S" }, { "family_name": "Stojanovic", "given_name": "Milan N.", "clpid": "Stojanovic-M-N" }, { "family_name": "Fygenson", "given_name": "Deborah K.", "clpid": "Fygenson-D-K" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast\u2013all while remaining functional.
\r\n\r\nThis thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of \u201cactive self-assembly\u201d of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology\u2019s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.
\r\n\r\nOne of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.
\r\n\r\nOne might think that because a system is Turing-complete, capable of computing \u201canything,\u201d that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not \u201ccomputations\u201d in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.
\r\n\r\n\r\nPassive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors \u201cenergetically incomplete\u201d programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.
\r\n\r\n\r\nAs we will demonstrate and prove, a sufficiently expressive implementation of an \u201cactive\u201d molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not \u201cenergetically incomplete.\u201d But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.
\r\n\r\n\r\nBuilding on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.
\r\n\r\n\r\nWe show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.
\r\n\r\n\r\nWe developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.
\r\n\r\n\r\nIn addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.
", "doi": "10.7907/T0ZG-PA07", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7724", "collection": "thesis", "collection_id": "7724", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182013-191132413", "primary_object_url": { "basename": "caltech_thesis_pete_trautman_small.pdf", "content": "final", "filesize": 11230460, "license": "other", "mime_type": "application/pdf", "url": "/7724/1/caltech_thesis_pete_trautman_small.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Robot Navigation in Dense Crowds: Statistical Models and Experimental Studies of Human Robot Cooperation", "author": [ { "family_name": "Trautman", "given_name": "Peter", "clpid": "Trautman-Peter" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Krause", "given_name": "R. Andreas", "clpid": "Krause-R-A" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Krause", "given_name": "R. Andreas", "clpid": "Krause-R-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis explores the problem of mobile robot navigation in dense human crowds. We begin by considering a fundamental impediment to classical motion planning algorithms called the freezing robot problem: once the environment surpasses a certain level of complexity, the planner decides that all forward paths are unsafe, and the robot freezes in place (or performs unnecessary maneuvers) to avoid collisions. Since a feasible path typically exists, this behavior is suboptimal. Existing approaches have focused on reducing predictive uncertainty by employing higher fidelity individual dynamics models or heuristically limiting the individual predictive covariance to prevent overcautious navigation. We demonstrate that both the individual prediction and the individual predictive uncertainty have little to do with this undesirable navigation behavior. Additionally, we provide evidence that dynamic agents are able to navigate in dense crowds by engaging in joint collision avoidance, cooperatively making room to create feasible trajectories. We accordingly develop interacting Gaussian processes, a prediction density that captures cooperative collision avoidance, and a \"multiple goal\" extension that models the goal driven nature of human decision making. Navigation naturally emerges as a statistic of this distribution.
\r\n\r\nMost importantly, we empirically validate our models in the Chandler dining hall at Caltech during peak hours, and in the process, carry out the first extensive quantitative study of robot navigation in dense human crowds (collecting data on 488 runs). The multiple goal interacting Gaussian processes algorithm performs comparably with human teleoperators in crowd densities nearing 1 person/m2, while a state of the art noncooperative planner exhibits unsafe behavior more than 3 times as often as the multiple goal extension, and twice as often as the basic interacting Gaussian process approach. Furthermore, a reactive planner based on the widely used dynamic window approach proves insufficient for crowd densities above 0.55 people/m2. We also show that our noncooperative planner or our reactive planner capture the salient characteristics of nearly any dynamic navigation algorithm. For inclusive validation purposes, we show that either our non-interacting planner or our reactive planner captures the salient characteristics of nearly any existing dynamic navigation algorithm. Based on these experimental results and theoretical observations, we conclude that a cooperation model is critical for safe and efficient robot navigation in dense human crowds.
\r\n\r\nFinally, we produce a large database of ground truth pedestrian crowd data. We make this ground truth database publicly available for further scientific study of crowd prediction models, learning from demonstration algorithms, and human robot interaction models in general.
\r\n", "doi": "10.7907/BHGM-0C65", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:6718", "collection": "thesis", "collection_id": "6718", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192011-161454857", "type": "thesis", "title": "Analysis, Design, and in vitro Implementation of Robust Biochemical Networks", "author": [ { "family_name": "Franco", "given_name": "Elisa", "clpid": "Franco-Elisa" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "clpid": "Rothemund-P-W-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The functionalities of every living organism are wired in the biochemical interactions among proteins, nucleic acids, and all the other molecules that constitute life's building blocks. Understanding the general design principles of this \"hardware of life\" is an exciting and challenging task for modern bioengineers. In this thesis, I focus on the topic of molecular network robustness: I investigate several design rules guaranteeing desired functionalities in specific systems, despite their components variability. Experimental verifications of such design schemes are carried out using \\emph{in vitro} transcriptional circuits, a minimal analogue of cellular genetic networks.
\r\n \r\nThe first problem I consider is flux control, which is a fundamental feature for the correct performance of biochemical systems. I describe a simple model problem where two reagents bind stoichiometrically to form an output product. In the absence of any regulation, imbalances in the reagent production rates can cause accumulation of unused molecules, and limit the output flow. To match the reagents' flux robustly with respect to the open loop rates, I propose the use of negative or positive feedback schemes that rely on competitive binding. Such schemes are modeled through ordinary differential equations and implemented using transcriptional circuits; data are presented showing the performance of the two approaches.
\r\n \r\nThe second topic I examine is the functional robustness of interconnected networks. Molecular devices characterized in isolation may lose their properties once interconnected. This challenge is illustrated with a case study: a synthetic transcriptional clock is used to time conformational changes in a molecular nanomachine called DNA tweezers. Mass conservation introduces parasitic interactions that perturb the oscillator trajectories proportionally to the total amount of tweezers \"load\". To overcome this problem, we can use a transcriptional switch that acts as a buffer amplifier, achieving signal propagation and at the same time reducing the perturbations on the source of signal.
\r\n\r\nFinally, I describe a general class of control-theoretic methods to analyze structural robustness in natural biological systems. Using Lyapunov theory and set invariance, the stability properties of several well-known case studies are analytically demonstrated. The key feature of this analysis is its reliance on parameter-independent models, which only capture essential dynamic interactions between molecular species.
\r\n \r\n", "doi": "10.7907/1C3S-FA59", "publication_date": "2012-06", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6749", "collection": "thesis", "collection_id": "6749", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12102011-161913831", "primary_object_url": { "basename": "DionysiosBarmpoutis-PhDThesis.pdf", "content": "final", "filesize": 1147053, "license": "other", "mime_type": "application/pdf", "url": "/6749/1/DionysiosBarmpoutis-PhDThesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Network Structure Optimization with Applications to Minimizing Variance and Crosstalk", "author": [ { "family_name": "Barmpoutis", "given_name": "Dionysios", "clpid": "Barmpoutis-Dionysios" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis provides a unified methodology for analyzing structural properties of graphs, along with their applications. In the last several years, the field of complex networks has been extensively studied, and it is now well understood that the way a large network is built is closely intertwined with its function. Structural properties have an impact on the function of the network, and the form of many systems has been evolved in order to optimize for given functions. Despite the great progress, particularly in how structural attributes affect the various network functions, there is a significant gap in the quantitative study of how much these properties can change in a network without a significant impact on the functionality of the system, or what the bounds of these structural attributes are. Here, we find and analytically prove tight bounds of global graph properties, as well as the form of the graphs that achieve these bounds. The attributes studied include the network efficiency, radius, diameter, average distance, betweenness centrality, resistance distance, and average clustering. All of these qualities have a direct impact on the function of the network, and finding the graph that optimizes one or more of them is of interest when designing a large system. In addition, we measure how sensitive these properties are with respect to random rewirings or addition of new edges, since designing a network with a given set of constraints may include a lot of trade-offs. This thesis also studies properties that are of interest in both natural and engineered networks, such as maximum immunity to crosstalk interactions and random noise. We are primarily focused on networks where information is transmitted through a means that is accessible by all the individual units of the network and the interactions among the different entities that comprise it do not necessarily have a dedicated mechanism that facilitates information transmission, or isolates them from other parts of the network. Two examples of this class are biological and chemical reaction networks. Such networks suffer from unwanted crosstalk interactions when two or more units spuriously interact with each other. In addition, they are subject to random fluctuations in their output, both due to noisy inputs and because of the random variance of their parameters. These two types of randomness affect the behavior of the system in ways that are intrinsically different. We examine the network topologies that accentuate or alleviate the effect of random variance in the network for both directed and undirected graphs, and find that increasing the crosstalk among different parts reduces the output variance but also contributes to a slower response.\r\n", "doi": "10.7907/ER8Y-ZK49", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7100", "collection": "thesis", "collection_id": "7100", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302012-155108063", "type": "thesis", "title": "Distributed Control and Computing: Optimal Estimation, Error Correcting Codes, and Interactive Protocols", "author": [ { "family_name": "Sukhavasi", "given_name": "Ravi Teja", "clpid": "Sukhavasi-Ravi-Teja" } ], "thesis_advisor": [ { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" } ], "thesis_committee": [ { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" }, { "family_name": "Vaidyanathan", "given_name": "P. P.", "orcid": "0000-0003-3003-7042", "clpid": "Vaidyanathan-P-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Emerging applications of networked control and distributed computing are characterized by decentralization of information and the need to exchange it over potentially unreliable communication networks. This results in novel interactive communication scenarios that are incompatible with conventional information and coding theoretic approaches. To address this gap, through the early and late 1990's, a new information theoretic notion called anytime reliability and a new coding paradigm called tree codes were proposed. Although the central role of tree codes in several interactive communication problems such as distributed control and computing has been well understood, there have been no practical constructions till date. For the first time, we have an explicit ensemble of linear tree codes with efficient encoding and decoding for the class of erasure channels. In the process, we have developed novel non-asymptotic sufficient conditions on the kind of communication reliability required to stabilize control systems over noisy channels. We also study the application of tree codes to interactive protocols over erasure networks and illustrate their benefits through the example of average consensus.", "doi": "10.7907/7431-FH32", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6798", "collection": "thesis", "collection_id": "6798", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01312012-154032563", "primary_object_url": { "basename": "JCL--Full_Thesis.pdf", "content": "final", "filesize": 5780128, "license": "other", "mime_type": "application/pdf", "url": "/6798/43/JCL--Full_Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "High-Throughput Strategies for the Scalable Generation of RNA Component Functions", "author": [ { "family_name": "Liang", "given_name": "Joe Chih Yao", "clpid": "Liang-Joe-Chih-Yao" } ], "thesis_advisor": [ { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Engineered biological systems hold great promise in providing solutions to many global challenges, including environmental remediation, sustainability, scalable manufacturing, and health and medicine. Synthetic biology is an emerging research field with a primary goal of making the engineering of biology more streamlined and reliable. Recent advances in synthetic RNA biology have led to design of RNA-based gene-regulatory devices from assembly of functional RNA components that encode more basic functions, including sensing, information transmission, and actuation functions. These synthetic RNA control devices allow access and control information on cellular state, thereby advancing our ability to interact with and program biology.
\r\n\r\nA modular ribozyme device platform was recently described to link an aptamer (sensor) to a hammerhead ribozyme (actuator) through a distinct sequence (information transmitter) capable of a strand-displacement event. The utilization of ribozyme as the actuator in the platform, whose mechanism of action is independent of cell-specific machinery, allows transport of the resultant devices to in vitro or different cellular environments. The broad implementation of these devices requires enabling technologies to support efficient generation of new functional RNA components and quantitative tailoring of device regulatory performance for specific cellular applications. Current component generation and device tailoring strategies are limited in their throughputs and efficiencies, and thus have hampered our ability to generate new ribozyme devices for cellular engineering applications.
\r\n\r\nTo support scalable generation and tailoring of ribozyme devices, we have described high-throughput in vitro selection and in vivo screening strategies based on the modular ribozyme device platform. We proposed a high-throughput solution-based in vitro selection strategy to generate new sensing functions within the device platform. A high-throughput and quantitative two-color FACS-based screening strategy was developed to complement the in vitro selection strategy by allowing efficient tailoring of device regulatory activities in the cellular environments. We further developed quantitative assays based on the surface plasmon resonance (SPR) technology to allow rapid measurements of the device and component activities. Together, these enabling strategies will offer a scalable and integrated process for the construction and programming of RNA control devices for broad cellular engineering applications, thus laying an important foundation for engineering more complex biological systems.
", "doi": "10.7907/FQHC-EW36", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7146", "collection": "thesis", "collection_id": "7146", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072012-150636005", "primary_object_url": { "basename": "Fullthesis-KEGALLOWAY-FINAL.pdf", "content": "final", "filesize": 12596632, "license": "other", "mime_type": "application/pdf", "url": "/7146/20/Fullthesis-KEGALLOWAY-FINAL.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "The Development of RNA-based Control Systems to Regulate Signaling and Dictate Cell Fate in a Model MAPK Pathway", "author": [ { "family_name": "Galloway", "given_name": "Kate Elizabeth", "clpid": "Galloway-Kate-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Cells integrate extracellular information via native signaling pathways to spatially and temporally coordinate complex tasks such as development and the immune response. Cellular programming holds the potential of harnessing the sophisticated and complex biological processes of living cells for diverse applications. In the last decade, cellular reprogramming has emerged as a viable therapeutic strategy. In large, reprogramming strategies have relied on statically programmed levels of gene expression to alter cellular behaviors. To construct more sophisticated programs requires dynamic control of expression and strategies for the facile construction of complex control architectures. Additionally, the application of synthetic programs to the control of native regulatory pathways requires the development of tools for interfacing with these pathways, as well as the construction of stringent controllers. Further, control systems composed of modular and tunable elements will facilitate the expansion of synthetic circuitry to a wide array of natural networks with varying system properties.
\r\n \r\nHere we describe the development of RNA-based control systems to regulate signaling and dictate cell fate in a model mitogen-activated protein kinase (MAPK) pathway. We construct networks of RNA-based control systems that interface with the Saccharomyces cerevisiae mating pathway to dictate entry into one of three programmed alternative fates dependent on environmental stimuli. We present a readily translatable method for identifying control points within natural networks that enable the construction of a modular interface between synthetic circuitry and native networks. In building these networks, we demonstrate the rational tuning of circuit performance via the exchange of well-defined parts to compose networks capable of actuating changes in cellular behavior in response to environmental cues. Further, we construct network architectures which facilitate reduced interference from simultaneously integrated opposing programs and identified sensitive parameters for engineering robust circuit performance. Finally, we present the development of a novel RNA-based control element for the regulation of both synthetic and endogenous transcripts. This work provides a model for engineering systems that regulate signaling and direct cell fate which may be applied to additional decision-making pathways to advance tissue engineering strategies, treat diseases, and study the behavior of natural regulatory networks.
\r\n", "doi": "10.7907/CBBN-GX03", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6991", "collection": "thesis", "collection_id": "6991", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04302012-142612208", "type": "thesis", "title": "Geometric Descriptions of Couplings in Fluids and Circuits", "author": [ { "family_name": "Jacobs", "given_name": "Henry Ochi", "clpid": "Jacobs-Henry-Ochi" } ], "thesis_advisor": [ { "family_name": "Desbrun", "given_name": "Mathieu", "clpid": "Desbrun-M" } ], "thesis_committee": [ { "family_name": "Desbrun", "given_name": "Mathieu", "clpid": "Desbrun-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Owhadi", "given_name": "Houman", "clpid": "Owhadi-H" }, { "family_name": "Kanso", "given_name": "Eva", "clpid": "Kanso-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Geometric mechanics is often commended for its breadth (e.g., fluids, circuits, controls) and depth (e.g., identification of stability criteria, controllability criteria, conservation laws). However, on the interface between disciplines it is commonplace for the analysis previously done on each discipline in isolation to break down. For example, when a solid is immersed in a fluid, the particle relabeling symmetry is broken because particles in the fluid behave differently from particles in the solid. This breaks conservation laws, and even changes the configuration manifolds. A second example is that of the interconnection of circuits. It has been verified that LC-circuits satisfy a variational principle. However, when two circuits are soldered together this variational principle must transform to accommodate the interconnection.
\r\n\t\r\nMotivated by these difficulties, this thesis analyzes the following couplings: fluid-particle, fluid-structure, and circuit-circuit. For the case of fluid-particle interactions we understand the system as a Lagrangian system evolving on a Lagrange-Poincare bundle. We leverage this interpretation to propose a class of particle methods by \"ignoring\" the vertical Lagrange-Poincare equation. In a similar vein, we can analyze fluids interacting with a rigid body. We then generalize this analysis to view fluid-structure problems as Lagrangian systems on a Lie algebroid. The simplicity of the reduction process for Lie algebroids allows us to propose a mechanism in which swimming corresponds to a limit-cycle in a reduced Lie algebroid. In the final section we change gears and understand non-energetic interconnection as Dirac structures. In particular we find that any (linear) non-energetic interconnection is equivalent to some Dirac structure. We then explore what this insight has to say about variational principles, using interconnection of LC-circuits as a guiding example.
", "doi": "10.7907/AZXE-PH33", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7017", "collection": "thesis", "collection_id": "7017", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05092012-121922995", "type": "thesis", "title": "Combining Rational and Evolutionary Approaches to Optimize Enzyme Activity in Saccharomyces cerevisiae", "author": [ { "family_name": "Michener", "given_name": "Joshua Kieran", "clpid": "Michener-Joshua-Kieran" } ], "thesis_advisor": [ { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "thesis_committee": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Metabolic engineering has become an increasingly important tool for the production of bulk and fine chemicals. New biosynthetic pathways can be built in a tractable production host using enzymes from a wide variety of organisms. However, these enzymes did not evolve to function in their new host, and as a result their activity may be unacceptably low. Additionally, the host has not adapted to support this new pathway, and its response to any new stresses imposed by the pathway may further limit productivity. I describe two methods for optimizing the host-enzyme interface, using an evolutionary approach to adapt an enzyme to its new host and a rational approach to modify the host in response. Using a synthetic RNA switch to screen for improvements in enzymatic activity in vivo, I increased the activity of a model enzyme more than 30-fold. I then used a systems-level analysis of the host to identify a stress, heme depletion, that the enzyme placed on its host. Alleviating that stress increased the activity of an optimized enzyme by a further 2.3-fold. These results highlight the advantages of combining systems and synthetic biology during the construction of a metabolic pathway. I also consider options for extending the uses of synthetic RNA switches both earlier and later in the pathway development process. An RNA switch could first be used in a functional screen for enzyme discovery and then be used to adapt the newly discovered enzyme to its production host. Finally, a variant of that switch could be used to dynamically regulate a biosynthetic pathway and improve the pathway reliability.", "doi": "10.7907/2KPP-DS46", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6636", "collection": "thesis", "collection_id": "6636", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08312011-003358925", "type": "thesis", "title": "Axel Rover Tethered Dynamics and Motion Planning on Extreme Planetary Terrain", "author": [ { "family_name": "Abad-Manterola", "given_name": "Pablo", "clpid": "Abad-Manterola-Pablo" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Dabiri", "given_name": "John O.", "clpid": "Dabiri-J-O" }, { "family_name": "Nesnas", "given_name": "Issa A.", "clpid": "Nesnas-I-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Some of the most appealing science targets for future exploration missions in our solar system lie in terrains that are inaccessible to state-of-the-art robotic rovers such as NASA's Opportunity, thereby precluding in situ analysis of these rich opportunities. Examples of potential high-yield science areas on Mars include young gullies on sloped terrains, exposed layers of bedrock in the Victoria Crater, sources of methane gas near Martian volcanic ranges, and stepped delta formations in heavily cratered regions. In addition, a recently discovered cryovolcano on Titan and frozen water near the south pole of our own Moon could provide a wealth of knowledge to any robotic explorer capable of accessing these regions.
\r\n\r\nTo address the challenge of extreme terrain exploration, this dissertation presents the Axel rover, a two-wheeled tethered robot capable of rappelling down steep slopes and traversing rocky terrain. Axel is part of a family of reconfigurable rovers, which, when docked, form a four-wheeled vehicle nicknamed DuAxel. DuAxel provides untethered mobility to regions of extreme terrain and serves as an anchor support for a single Axel when it undocks and rappels into low-ground.
\r\n\r\nAxel's performance on extreme terrain is primarily governed by three key system components: wheel design, tether control, and intelligent planning around obstacles. Investigations in wheel design and optimizing for extreme terrain resulted in the development of grouser wheels. Experiments demonstrated that these grouser wheels were very effective at surmounting obstacles, climbing rocks up to 90% of the wheel diameter. Terramechanics models supported by experiments showed that these wheels would not sink excessively or become trapped in deformable terrain.
\r\n\r\nPredicting tether forces in different configurations is also essential to the rover's mobility. Providing power, communication, and mobility forces, the tether is Axel's lifeline while it rappels steep slopes, and a cut, abraded, or ruptured tether would result in an untimely end to the rover's mission. Understanding tether forces are therefore paramount, and this thesis both models and measures tension forces to predict and avoid high-stress scenarios.
\r\n\r\nFinally, incorporating autonomy into Axel is a unique challenge due to the complications that arise during tether management. Without intelligent planning, rappelling systems can easily become entangled around obstacles and suffer catastrophic failures. This motivates the development of a novel tethered planning algorithm, presented in this thesis, which is unique for rappelling systems.
\r\n\r\nRecent field experiments in natural extreme terrains on Earth demonstrate the Axel rover's potential as a candidate for future space operations. Both DuAxel and its rappelling counterpart are rigorously tested on a 20 meter escarpment and in the Arizona desert. Through analysis and experiments, this thesis provides the framework for a new generation of robotic explorers capable of accessing extreme planetary regions and potentially providing clues for life beyond Earth.
", "doi": "10.7907/MPHD-PC75", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6150", "collection": "thesis", "collection_id": "6150", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212010-000757213", "primary_object_url": { "basename": "PHD_Thesis_All.pdf", "content": "final", "filesize": 18174662, "license": "other", "mime_type": "application/pdf", "url": "/6150/19/PHD_Thesis_All.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Interpretation and Scaling of Positional Information During Development", "author": [ { "family_name": "Nahmad Bensusan", "given_name": "Marcos", "clpid": "Nahmad-Bensusan-Marcos" } ], "thesis_advisor": [ { "family_name": "Stathopoulos", "given_name": "Angelike", "clpid": "Stathopoulos-A" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Stathopoulos", "given_name": "Angelike", "clpid": "Stathopoulos-A" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "clpid": "Rothenberg-E-V" }, { "family_name": "Lander", "given_name": "Arthur D.", "clpid": "Lander-A-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Cells in a developing animal require information about their relative position in order to function and differentiate appropriately. In the classical view, cellular positional information is interpreted from the concentration of chemical signals known as morphogens. However, recent studies have questioned the ability of morphogens to establish gene expression patterns in a concentration-dependent manner. Here we combine theoretical tools and experimental work in Drosophila melanogaster to investigate the mechanisms by which positional information is interpreted from a morphogen gradient and the ability of patterns to scale with respect to the size of the system.
\r\n\r\nFirst, we study how a concentration gradient of the signaling molecule Hedgehog establishes multiple patterns of gene expression along the anterior-posterior axis of the Drosophila wing disc. Using mathematical modeling as a hypotheses-generating tool, we predicted that positional information cannot be explained by different concentration thresholds from a static Hedgehog gradient. Instead, we propose that cells take into account their history of Hedgehog signaling exposure to determine patterns of gene expression. We provide experimental evidence that supports our model and conclude that gradient dynamics, resulting from the gene network architecture of the Hedgehog signaling pathway, determine pattern formation in the wing disc.
\r\n\r\nSecond, we introduce a theoretical formalism to study the role of morphogen gradient dynamics in developmental patterning. Given a mathematical model of pattern formation, we define and compute parameter perturbations that leave invariant the steady-state distribution of the relevant morphogen. We propose that this approach can be used as a tool to design genetic experiments that assay the function of morphogen dynamics.
\r\n\r\nLastly, we use dorsal-ventral patterning of the early Drosophila embryo as a model to study scaling of gene expression patterns with respect to natural variations in axis length, that is, the ability to establish positional information relative to the size of the system. We provide evidence that gene expression patterns that depend on the maternal factor Dorsal, scale along the dorsal-ventral axis. Our data suggest that scaling in this system is a gene-dependent rather than a position-dependent property. We propose that the mechanisms for scaling depend on feedback interactions downstream of Dorsal.
", "doi": "10.7907/2ZYV-FF66", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6441", "collection": "thesis", "collection_id": "6441", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252011-164957222", "primary_object_url": { "basename": "Moore_thesis.pdf", "content": "final", "filesize": 9726477, "license": "other", "mime_type": "application/pdf", "url": "/6441/1/Moore_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Discrete Mechanics and Optimal Control for Space Trajectory Design", "author": [ { "family_name": "Moore", "given_name": "Ashley", "clpid": "Moore-Ashley" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Desbrun", "given_name": "Mathieu", "clpid": "Desbrun-M" }, { "family_name": "Ortiz", "given_name": "Michael", "clpid": "Ortiz-M" }, { "family_name": "Ober-Blobaum", "given_name": "Sina", "clpid": "Ober-Blobaum-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Space trajectory design is often achieved through a combination of dynamical systems theory and optimal control. The union of trajectory design techniques utilizing invariant manifolds of the planar circular restricted three-body problem and the optimal control scheme Discrete Mechanics and Optimal Control (DMOC) facilitates the design of low-energy trajectories in the N-body problem. In particular, DMOC is used to optimize a trajectory from the Earth to the Moon in the 4-body problem, removing the mid-course change in velocity usually necessary for such a trajectory while still exploiting the structure from the invariant manifolds.
\r\n\r\nThis thesis also focuses on how to adapt DMOC, a method devised with a constant step size, for the highly nonlinear dynamics involved in trajectory design. Mesh refinement techniques that aim to reduce discretization errors in the solution and energy evolution and their effect on DMOC optimization are explored and compared with trajectories created using time adaptive variational integrators.
\r\n\r\nFurthermore, a time adaptive form of DMOC is developed that allows for a variable step size that is updated throughout the optimization process. Time adapted DMOC is based on a discretization of Hamilton's principle applied to the time adapted Lagrangian of the optimal control problem. Variations of the discrete action of the optimal control Lagrangian lead to discrete Euler-Lagrange equations that can be enforced as constraints for a boundary value problem. This new form of DMOC leads to the accurate and efficient solution of optimal control problems with highly nonlinear dynamics. Time adapted DMOC is tested on several space trajectory problems including the elliptical orbit transfer in the 2-body problem and the reconfiguration of a cubesat.
\r\n", "doi": "10.7907/ZXTG-V056", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6443", "collection": "thesis", "collection_id": "6443", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252011-222115269", "primary_object_url": { "basename": "ssen_complete_thesis.pdf", "content": "final", "filesize": 2949050, "license": "other", "mime_type": "application/pdf", "url": "/6443/1/ssen_complete_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Regulatory Consequences of Bandpass Feedback in a Bacterial Phosphorelay", "author": [ { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" } ], "thesis_advisor": [ { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Garcia-Ojalvo", "given_name": "Jordi", "clpid": "Garcia-Ojalvo-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit structured as a phosphorelay embedded in multiple transcriptional feedback loops, and which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are 'bandpass'-like, in the sense that activation occurs within a limited band of Spo0A~P concentrations, and have recently been shown to pulse in a cell-cycle-dependent fashion. Additionally, the core phosphorelay is an architectural variant of the canonical two-component signaling system, which allows signal integration from a larger number of inputs, including two types of phosphatases that act on different protein components. However, the impact of these pulsed bandpass interactions on the circuit dynamics preceding sporulation and the utility of two types of phosphatases remains unclear. In order to address these questions, we measured key features of the bandpass interactions at the single-cell level and analyzed them in the context of a simple mathematical model. The model predicted the emergence of a delayed phase shift between the pulsing activity of the different sporulation genes, as well as the existence of a stable state, with elevated Spo0A activity but no sporulation, embedded within the dynamical structure of the system. To test the model, we used time-lapse fluorescence microscopy to measure dynamics of single cells initiating sporulation. We observed the delayed phase shift emerging during the progression to sporulation, while a re-engineering of the sporulation circuit revealed behavior resembling the predicted additional state. The core phosphorelay model also showed a post-translational bandpass response, and we find that the two types of phosphatases can independently tune the two bandpass thresholds. These results show that periodically-driven bandpass feedback loops can give rise to complex dynamics in the progression towards sporulation, and that similar inputs can tune different response features. ", "doi": "10.7907/NPZD-G382", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6229", "collection": "thesis", "collection_id": "6229", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01202011-212047218", "primary_object_url": { "basename": "PhD_Thesis_-_Andrew_Babiskin.pdf", "content": "final", "filesize": 3124408, "license": "other", "mime_type": "", "url": "/6229/10/PhD_Thesis_-_Andrew_Babiskin.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Development of RNA-Based Genetic Control Elements for Predictable Tuning of Protein Expression in Yeast", "author": [ { "family_name": "Babiskin", "given_name": "Andrew Harris", "clpid": "Babiskin-Andrew-Harris" } ], "thesis_advisor": [ { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" } ], "thesis_committee": [ { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The proper functioning of many biological processes and synthetic genetic networks depends on the precise tuning of expression levels of key protein components. With growing interests in eukaryotic hosts and the increasing complexity of networks in synthetic biology, there is a need for the expansion of the genetic toolbox, particularly for the bioprocessing and biosynthesis applications in the yeast Saccharomyces cerevisiae. The available control elements in yeast generally focus on the regulation of transcription through alternative promoter systems. Synthetic RNA-based control elements placed in the untranslated regions (UTRs) of transcripts have the ability to regulate the posttranscriptional mechanisms of translation initiation and transcript stability. Such posttranscriptional elements have the added advantage of being coupled to any promoter for enhanced control strategies.
\r\n\r\nTwo types of posttranscriptional elements were examined in this thesis. The first type is a class of RNA hairpins baring AGNN tetraloops that are cleaved by the S. cerevisiae RNase III enzyme Rnt1p. By locating these hairpins in the 3\u2019 UTR of a transcript, the endonucleolytic cleavage due to Rnt1p activity resulted in the rapid degradation of the transcript. We developed two libraries of RNA hairpins based on the randomization of critical regions in Rnt1p substrates that affect the enzyme\u2019s ability to associate and/or cleave the hairpin. The modulation of the strength of binding and cleavage by Rnt1p resulted in changes in the steady-state transcript levels and thus protein levels. Through integration of an aptamer into the stem of an Rnt1p hairpin, we were able to develop a riboswitch based upon the direction inhibition of Rnt1p cleavage through association of the ligand in the sites of cleavage. The second type of posttranscriptional elements examined is the placement of internal ribosome entry sites (IRESes) in the 5\u2019 UTR that initiate translation independent of the 5\u2019 cap through direct interaction with the ribosomal machinery. We propose that the activity of small sequential IRESes can be tuned through varying the complementarity with the 18S ribosomal RNA (rRNA) to advance the creation of yeast multicistronic vectors. The application of Rnt1p hairpins and IRESes provide a key tool in synthetic biology for the construction of complex genetic networks in yeast where the predictable tuning of gene expression is necessitated.
\r\n", "doi": "10.7907/ZVTW-9B37", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6457", "collection": "thesis", "collection_id": "6457", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-171044915", "primary_object_url": { "basename": "MTaoThesis.pdf", "content": "final", "filesize": 8217284, "license": "other", "mime_type": "application/pdf", "url": "/6457/1/MTaoThesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Multiscale Geometric Integration of Deterministic and Stochastic Systems", "author": [ { "family_name": "Tao", "given_name": "Molei", "clpid": "Tao-Molei" } ], "thesis_advisor": [ { "family_name": "Owhadi", "given_name": "Houman", "clpid": "Owhadi-H" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Owhadi", "given_name": "Houman", "clpid": "Owhadi-H" }, { "family_name": "Hou", "given_name": "Thomas Y.", "clpid": "Hou-T-Y" }, { "family_name": "Desbrun", "given_name": "Mathieu", "clpid": "Desbrun-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Ortiz", "given_name": "Michael", "clpid": "Ortiz-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In order to accelerate computations and improve long time accuracy of numerical simulations, this thesis develops multiscale geometric integrators.
\r\n\r\nFor general multiscale stiff ODEs, SDEs, and PDEs, FLow AVeraging integratORs (FLAVORs) have been proposed for the coarse time-stepping without any identification of the slow or the fast variables. In the special case of deterministic and stochastic mechanical systems, symplectic, multisymplectic, and quasi-symplectic multiscale integrators are easily obtained using this strategy.
\r\n\r\nFor highly oscillatory mechanical systems (with quasi-quadratic stiff potentials and possibly high-dimensional), a specialized symplectic method has been devised to provide improved efficiency and accuracy. This method is based on the introduction of two highly nontrivial matrix exponentiation algorithms, which are generic, efficient, and symplectic (if the exact exponential is symplectic).
\r\n\r\nFor multiscale systems with Dirac-distributed fast processes, a family of symplectic, linearly-implicit and stable integrators has been designed for coarse step simulations. An application is the fast and accurate integration of constrained dynamics.
\r\n\r\nIn addition, if one cares about statistical properties of an ensemble of trajectories, but not the numerical accuracy of a single trajectory, we suggest tuning friction and annealing temperature in a Langevin process to accelerate its convergence.
\r\n\r\nOther works include variational integration of circuits, efficient simulation of a nonlinear wave, and finding optimal transition pathways in stochastic dynamical systems (with a demonstration of mass effects in molecular dynamics).
", "doi": "10.7907/6J83-7C18", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6481", "collection": "thesis", "collection_id": "6481", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312011-123940546", "primary_object_url": { "basename": "jwhite.phd.pdf", "content": "final", "filesize": 1446611, "license": "other", "mime_type": "application/pdf", "url": "/6481/1/jwhite.phd.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Applying Formal Methods to Distributed Algorithms Using Local-Global Relations ", "author": [ { "family_name": "White", "given_name": "Jerome S.", "clpid": "White-Jerome-S" } ], "thesis_advisor": [ { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Martin", "given_name": "Alain J.", "clpid": "Martin-A-J" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis deals with the design and analysis of distributed systems in which homogeneous, autonomous agents collaborate to achieve a common goal. The class of problems studied includes consensus algorithms in which all agents eventually come to an agreement about a specific action. The thesis proposes a framework, called local-global, for analyzing these systems. A local interaction is an interaction among subsets of agents, while a global interaction is one among all agents in the system. Global interactions, in practice, are rare, yet they are the basis by which correctness of a system is measured. For example, if the problem is to compute the average of a measurement made separately by each agent, and all the agents in the system could exchange values in a single action, then the solution is straightforward: each agent gets the values of all others and computes the average independently. However, if the system consists of a large number of agents with unreliable communication, this scenario is highly unlikely. Thus, the design challenge is to ensure that sequences of local interactions lead, or converge, to the same state as a global interaction.
\r\n\r\nThe local-global framework addresses this challenge by describing each local interaction as if were a global one, encompassing all agents within the system. This thesis outlines the concept in detail, using it to design algorithms, prove their correctness, and ultimately develop executable implementations that are reliable. To this end, the tools of formal methods are employed: algorithms are modeled, and mechanically checked, within the PVS theorem prover; programs are also verified using the Spin model checker; and interface specification languages are used to ensure local-global properties are still maintained within Java and C# implementations. The thesis presents example applications of the framework and discusses a class of problems to which the framework can be applied.
", "doi": "10.7907/8FRW-ZF17", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6418", "collection": "thesis", "collection_id": "6418", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232011-013046516", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 1636443, "license": "other", "mime_type": "application/pdf", "url": "/6418/1/thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Systematic Design and Formal Verification of Multi-Agent Systems ", "author": [ { "family_name": "Pilotto", "given_name": "Concetta", "clpid": "Pilotto-Concetta" } ], "thesis_advisor": [ { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "thesis_committee": [ { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Ledyard", "given_name": "John O.", "clpid": "Ledyard-J-O" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents methodologies for verifying the correctness of multi-agent systems operating in hostile environments. Verification of these systems is challenging because of their inherent concurrency and unreliable communication medium. The problem is exacerbated if the model representing the multi-agent system includes infinite or uncountable data types.
\r\n\r\nWe first consider message-passing multi-agent systems operating over an unreliable communication medium. We assume that messages in transit may be lost, delayed or received out-of-order. We present conditions on the system that reduce the design and verification of a message-passing system to the design and verification of the corresponding shared-state system operating in a friendly environment. Our conditions can be applied both to discrete and continuous agent trajectories.
\r\n\r\nWe apply our results to verify a general class of multi-agent system whose goal is solving a system of linear equations. We discuss this class in detail and show that mobile robot linear pattern-formation schemes are instances of this class. In these protocols, the goal of the team of robots is to reach a given pattern formation.
\r\n\r\nWe present a framework that allows verification of message-passing systems operating over an unreliable communication medium. This framework is implemented as a library of PVS theorem prover meta-theories and is built on top of the timed automata framework. We discuss the applicability of this tool. As an example, we automatically check correctness of the mobile robot linear pattern formation protocols.
\r\n\r\nWe conclude with an analysis of the verification of multi-agent systems operating in hostile environments. Under these more general assumptions, we derive conditions on the agents' protocols and properties of the environment that ensure bounded steady-state system error. We apply these results to message-passing multi-agent systems that allow for lost, delayed, received out-of-order or forged messages, and to multi-agent systems whose goal is tracking time-varying quantities. We show that pattern formation schemes are robust to leaders dynamics, i.e., in these schemes, followers eventually form the pattern defined by the new positions of the leaders.
", "doi": "10.7907/SCQF-VP66", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:11763", "collection": "thesis", "collection_id": "11763", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312011-123357339", "primary_object_url": { "basename": "CEWard-ThesisDone.pdf", "content": "final", "filesize": 3810119, "license": "other", "mime_type": "application/pdf", "url": "/11763/1/CEWard-ThesisDone.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Medea Selfish Genetic Elements as Tools for Altering Traits of Wild Populations: A Theoretical Analysis", "author": [ { "family_name": "Ward", "given_name": "Catherine Marie", "clpid": "Ward-Catherine-Marie" } ], "thesis_advisor": [ { "family_name": "Hay", "given_name": "Bruce", "clpid": "Hay-B-A" } ], "thesis_committee": [ { "family_name": "Sternberg", "given_name": "Paul W.", "clpid": "Sternberg-P-W" }, { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hay", "given_name": "Bruce A.", "clpid": "Hay-B-A" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Insect-borne diseases kill millions of people annually. One strategy for controlling transmission of insect-borne disease involves replacing the native insect population with transgenic animals unable to transmit disease. Population replacement requires a drive mechanism to ensure the rapid spread of linked transgenes conferring disease refractoriness. Medea selfish genetic elements have the feature that when present in a female, only offspring that inherit the element survive, a behavior that can lead to spread. Here we use modeling to identify conditions under which Medea elements spread. We derive equations describing the allele frequencies required for spread of Medea elements with a fitness cost, and the equilibrium allele frequencies attained. We validate our model against a synthetic Medea element created in Drosophila and find that the model fits the data without parameter fitting. We show that when Medea spreads, it drives the non-Medea genotype out of the population, and we provide estimates of the number of generations required to achieve this goal. We also characterize two contexts in which Medea elements with fitness costs drive the non-Medea allele from the population: an autosomal element in which zygotic rescue is incomplete and an X-linked element in species in which X/Y individuals are male. Finally, we explore costs and benefits associated with the introduction of multiple Medea elements. Our results suggest that Medea elements can drive population replacement under a wide range of conditions, potentially reducing disease burden.", "doi": "10.7907/T656-ZN91", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6490", "collection": "thesis", "collection_id": "6490", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022011-110025485", "primary_object_url": { "basename": "lamperskidissertationfinal.pdf", "content": "final", "filesize": 2293278, "license": "other", "mime_type": "application/pdf", "url": "/6490/1/lamperskidissertationfinal.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Hierarchies, Spikes, and Hybrid Systems: Physiologically Inspired Control Problems", "author": [ { "family_name": "Lamperski", "given_name": "Andrew G.", "clpid": "Lamperski-Andrew-G" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Lall", "given_name": "Sanjay", "clpid": "Lall-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In animal motor control and locomotion, neurons process information, muscles are the actuators, and the body is the plant. Control theory is the standard mathematical language for describing motor control and locomotion, but many phenomena in physiological control remain outside of the scope of control theoretic reasoning. Unlike traditional engineering control systems, nearly all the components of physiological control systems have complex dynamics. Instead of a fast centralized computer, an animal implements controllers using a distributed network of slow, nonlinear, and noisy neurons. Rather than having linear plants and actuators, the animal must control limbs with nonlinear and hybrid dynamics.
\r\n\r\nThis dissertation develops basic control theory motivated by physiological systems. Dynamical phenomena that arise in physiology but remain outside the scope of mathematical methods are isolated and studied in general control theoretic frameworks. In particular, three problems are discussed: distributed linear quadratic Gaussian (LQG) control with communication delays, control over communication channels modeled after spiking neurons, and Zeno stability of hybrid systems.
\r\n\r\nMotivated by the presence of delays in the human motor system, Chapter 2 explores the architecture of distributed LQG controllers when communication between subsystems is limited by delays. Sensory and motor command information is processed in several different regions throughout the nervous system. Since processing speed in neurons is limited, information from different sensory and motor regions can only be integrated after a time delay. In spite of this difficulty, humans make efficient and reliable motions that are well-described by optimal feedback control. Optimal delay compensation is studied in a distributed LQG framework. The structure that emerges as the result of optimization resembles a management hierarchy, bearing similarities with the organization of the motor system.
\r\n\r\nNetworked control systems, in which communication between the controller and the plant occurs over a special neuron-inspired channel, are analyzed in Chapter 3. In addition to being the basic computing elements, neurons are the long-range communication channels of the body. Neurons transmit information in the form of short-lived voltage spikes, called action potentials. Sufficient conditions for stable control over the spiking channel are presented, along with bounds on tracking error and data rates.
\r\n\r\nThe final technical chapter studies the connections between Zeno behavior and Lyapunov stability. Zeno behavior occurs in a hybrid system when an infinite number of discrete transitions occurs in a finite amount of time. While Zeno behavior results from modeling abstractions, it is commonly observed in models of mechanical systems undergoing impacts, including models important for locomotion. Often, Zeno behavior is associated with dynamical mode transitions, such as knee locking and the transition between bouncing and sliding. To reason about such transitions without modifying the models, the chapter on hybrid systems gives Lyapunov-like sufficient conditions for Zeno behavior. A technique for constructing the Lyapunov-like certificates is presented for a general class of mechanical systems undergoing impacts.
\r\n", "doi": "10.7907/0ANZ-8209", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6495", "collection": "thesis", "collection_id": "6495", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022011-214438378", "type": "thesis", "title": "Random Matrix Recursions in Estimation, Control, and Adaptive Filtering", "author": [ { "family_name": "Vakili", "given_name": "Ali", "clpid": "Vakili-Ali" } ], "thesis_advisor": [ { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" } ], "thesis_committee": [ { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Tropp", "given_name": "Joel A.", "clpid": "Tropp-J-A" }, { "family_name": "Vaidyanathan", "given_name": "P. P.", "clpid": "Vaidyanathan-P-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation is devoted to the study of estimation and control over systems that can be described by linear time-varying state-space models. Examples of such systems are encountered frequently in systems theory, e.g., wireless sensor networks, adaptive filtering, distributed control, etc. Recent developments in distributed catastrophe surveillance, smart transportation, and power grid control systems further motivate such a study.
\r\n\r\nWhile linear time-invariant systems are well-understood, there is no general theory that captures various aspects of time-varying counterparts. With little exception, tackling these problems normally boils down to studying time-varying linear or non-linear recursive matrix equations, known as Lyapunov and Riccati recursions that are notoriously hard to analyze. We employ the theory of random matrices to elucidate different facets of these recursions and answer several important questions about the performance, stability, and convergence of estimation and control over such systems.
\r\n\r\nWe make two general assumptions. First, we assume that the coefficient matrices are drawn from jointly stationary matrix-valued random processes. The stationarity assumption hardly restricts the analysis since almost all cases of practical interest fall into this category. We further assume that the state vector size, n, is relatively large. The law of large numbers however guarantees fast convergence to the asymptotic results for n being as small as 10. Under these assumptions, we develop a framework capable of characterizing steady-state and transient behavior of adaptive filters and control and estimation over communication networks. This framework proves promising by successfully tackling several problems for the first time in the literature.
\r\n\r\nWe first study random Lyapunov recursions and characterize their transient and steady-state behavior. Lyapunov recursions appear in several classes of adaptive filters and also as lower bounds of random Riccati recursions in distributed Kalman filtering. We then look at random Riccati recursions whose nonlinearity makes them much more complicated to study. We investigate standard recursive-least-squares (RLS) filtering and extend our analysis beyond the standard case to filtering with multiple measurements, as well as the case of intermittent measurements. Finally, we study Kalman filtering with intermittent observations, which is frequently used to model wireless sensor networks. In all of these cases we obtain interesting universal laws that depend on the structure of the problem, rather than specific model parameters. We verify the accuracy of our results through various simulations for systems with as few as 10 states.
\r\n", "doi": "10.7907/HCKN-7W53", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6510", "collection": "thesis", "collection_id": "6510", "cite_using_url": "https://resolver.caltech.edu/CaltechThesis:06082011-191034348", "primary_object_url": { "basename": "sbfuller_dissertation2011.pdf", "content": "final", "filesize": 16285464, "license": "other", "mime_type": "application/pdf", "url": "/6510/1/sbfuller_dissertation2011.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Steady as She Goes: Visual Autocorrelators and Antenna-Mediated Airspeed Feedback in the Control of Flight Dynamics in Fruit Flies and Robotics ", "author": [ { "family_name": "Fuller", "given_name": "Sawyer Buckminster", "clpid": "Fuller-Sawyer-Buckminster" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Straw", "given_name": "Andrew", "clpid": "Straw-A" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Achieving agile autonomous flight by an insect-sized micro aerial vehicle (MAV) will require improved technology that is radically smaller, lighter, and more power-efficient. One animal that has solved the problem is the fly, a virtuoso among insect flyers whose nervous system can perform sophisticated aerial maneuvers under severe computational constraints. This thesis is concerned with understanding and emulating the dynamics of the fly's feedback control system. Because vision is noisy and information rich, processing time may a problem for a fast-moving MAV or fly. By tracking the fruit fly Drosophila melanogaster in free flight in gusts of wind, I found that they incorporate feedback from wind-sensing antennae in a fast feedback loop that dampens the forward-flight dynamics. The slower dynamics are easier to control for long-delay visual feedback, making the fly more robust to the limitations of its visual system. Using the fly as inspiration, I designed a minimal, visual autocorrelation based controller that used a small array of visual sensors to stabilize a fan-actuated hovercraft robot in a narrow corridor. Using a model for correlators developed for the robot, I showed that a uniform array of visual correlators was sufficient to explain the free-flight velocity regulation behavior of flies, rather than a different model. In addition to illustrating the benefits of concurrent scientific analysis and engineering synthesis, the results give new insight into how to control small biological and man-made flying vehicles using limited, noisy sensors.", "doi": "10.7907/Z3D0-GG27", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6391", "collection": "thesis", "collection_id": "6391", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05132011-113642762", "primary_object_url": { "basename": "Thesis_Caltech.pdf", "content": "final", "filesize": 3285748, "license": "other", "mime_type": "application/pdf", "url": "/6391/1/Thesis_Caltech.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Large-Scale Complex Systems: From Antenna Circuits to Power Grids", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaeiyanesi-Javad" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation is motivated by the lack of scalable methods for the analysis and synthesis of different large-scale complex systems appearing in electrical and computer engineering. The systems of interest in this work are power networks, analog circuits, antenna systems, communication networks and distributed control systems. By combining theories from control and optimization, the high-level objective is to develop new design tools and algorithms that explicitly exploit the physical properties of these practical systems (e.g., passivity of electrical elements or sparsity of network topology). To this end, the aforementioned systems are categorized intro three classes of systems, and then studied in Parts I, II, and III of this dissertation, as explained below:
\r\n\r\nPower networks: In Part I of this work, the operation planning of power networks using efficient algorithms is studied. The primary focus is on the optimal power flow (OPF) problem, which has been studied by the operations research and power communities in the past 50 years with little success. In this part, it is shown that there exists an efficient method to solve a practical OPF problem along with many other energy-related optimization problems such as dynamic OPF or security-constrained OPF. The main reason for the successful convexification of these optimization problems is also identified to be the physical properties of a power circuit, especially the passivity of transmission lines.
\r\n\r\nCircuits and systems: Motivated by different applications in power networks, electromagnetics and optics, Part II of this work studies the fundamental limits associated with the synthesis of a particular type of linear circuit. It is shown that the optimal design of the parameters of this type of circuit can be performed in polynomial time if the circuit is passive and there are sufficient number of controllable (unknown) parameters. This result introduces a trade-off between the design simplicity and the implementation complexity for an important class of linear circuits. As an application of this methodology, the design of smart antennas is also studied; the goal is to devise an intelligent wireless communication device in order to avoid co-channel interference, power consumption in undesired directions and security issues. Since the existing smart antennas are either hard to program or hard to implement, a new type of smart antenna is synthesized by utilizing tools from algebraic geometry, control, communications, and circuits, which is both easy to program and easy to implement.
\r\n \r\nDistributed computation: The first problem tackled in Part III of this work is a very simple type of distributed computation, referred to as quantized consensus, which aims to compute the average of a set of numbers using a distributed algorithm subject to a quantization error. It is shown that quantized consensus is reached by means of a recently proposed gossip algorithm, and the convergence time of the algorithm is also derived. The second problem studied in Part III is a more advanced type of distributed computation, which is the distributed resource allocation problem for the Internet. The existing distributed resource allocation algorithms aim to maximize the utility of the network only at the equilibrium point and ignore the transient behavior of the network. To address this issue, it is shown that optimal control theory provides powerful tools for designing distributed resource allocation algorithms with a guaranteed real-time performance.
\r\n\r\nThe results of this work can all be integrated to address real-world interdisciplinary problems, such as the design of the next generation of the electrical power grid, named the Smart Grid.
\r\n\r\n", "doi": "10.7907/CM46-5R54", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:5864", "collection": "thesis", "collection_id": "5864", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272010-153304667", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 3350152, "license": "other", "mime_type": "application/pdf", "url": "/5864/1/main.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Formal Methods for Design and Verification of Embedded Control Systems: Application to an Autonomous Vehicle", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-Tichakorn" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The design of reliable embedded control systems inherits the difficulties involved in designing both control systems and distributed (concurrent) computing systems. Design bugs in these systems may arise from the unforeseen interactions among the computing, communication and control subsystems. Motivated by the difficulties of finding this type of design bugs, this thesis develops mathematical frameworks, based on formal methods, to facilitate the design and analysis of such embedded systems. An expressive specification language of linear temporal logic (LTL) is used to specify the desired system properties. The practicality of the proposed frameworks is demonstrated through autonomous vehicle case studies and autonomous urban driving problems.
\r\n\r\nOur approach incorporates methodology from computer science and control, including model checking, theorem proving, synthesis of digital designs, reachability analysis, Lyapunov-type methods and receding horizon control. This thesis consists of two complementary parts, namely, verification and design. First, we introduce Periodically Controlled Hybrid Automata (PCHA), a subclass of hybrid automata that abstractly captures a common design pattern in embedded control systems. New sufficient conditions that exploit the structure of PCHAs in order to simplify their invariant verification are presented.
\r\n\r\nAlthough the aforementioned technique simplifies an invariant verification of PCHAs, finding a proper invariant remains a challenging problem. To complement the verification efforts, in the second part of the thesis, we present a methodology for automatic synthesis of embedded control software that provides a formal guarantee of system correctness, with respect to its desired properties expressed in linear temporal logic. The correctness of the system is guaranteed even in the presence of an adversary (typically arising from changes in the environments), disturbances and modeling errors. A receding horizon framework is proposed to alleviate the associated computational complexity of LTL synthesis. The effectiveness of this framework is demonstrated through the autonomous urban driving problems.
\r\n", "doi": "10.7907/XZ3X-7V51", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5559", "collection": "thesis", "collection_id": "5559", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02262010-130618704", "primary_object_url": { "basename": "ThesisFinal_Buzi.pdf", "content": "final", "filesize": 1849654, "license": "other", "mime_type": "application/pdf", "url": "/5559/1/ThesisFinal_Buzi.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Control Theoretic Analysis of Autocatalytic Networks in Biology with Applications to Glycolysis ", "author": [ { "family_name": "Buzi", "given_name": "Gentian", "clpid": "Buzi-Gentian" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "El-Samad", "given_name": "Hana", "clpid": "El-Samad-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Metabolic networks in the cell break down food and resources to create useful energy and components. At the same time they use those same components and energy in the process, thus making autocatalysis an unavoidable part of core metabolism. The simplest and most widely studied autocatalytic network is the glycolytic pathway. It is common to every cell of living organisms, from bacteria to humans. Its special autocatalytic structure, like the structure of many similar autocatalytic networks, makes the pathway hard to control and can lead to instabilities.
\r\n\r\nIn this thesis, we study autocatalytic metabolic networks, specifically glycolysis, to investigate fundamental performance tradeoffs in these network topologies. We hypothesize that instabilities in glycolysis are a result of performance tradeoffs that stem from the structure of the pathways and a conservation law, mathematically described by a special form of the Bode Sensitivity Integral. We show that pathway size and intermediate metabolite consumption adversely affect the performance of the pathway, while reversibility of chemical reactions improves performance. We establish tight bounds for the feedback control gains that guarantee stability of pathways of arbitrary size and arbitrary parameter values for the intermediate reactions.
\r\n\r\nIn addition, we investigate effects of perturbations in metabolite concentrations through the estimation of invariant subsets of the region of attraction around nominal operating conditions. To this end we use a numerical procedure composed of system theoretic characterizations and optimization-based formulations. For large, computationally intractable systems we employ a different technique based on the underlying biological structure, which offers a natural decomposition of the system into a feedback interconnection of two input-output subsystems. This decomposition simplifies the analysis and leads to analytical construction of Lyapunov functions for a large family of autocatalytic pathways.
\r\n\r\nThe results of our analysis reveal fundamental tradeoffs between performance and robustness, energy efficiency, pathway evolvability and computational complexity in these networks.
", "doi": "10.7907/MHMV-9M59", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5545", "collection": "thesis", "collection_id": "5545", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02042010-152638957", "type": "thesis", "title": "Robot Motion Planning in Dynamic, Cluttered, and Uncertain Environments: the Partially Closed-Loop Receding Horizon Control Approach", "author": [ { "family_name": "Du Toit", "given_name": "Noel Eduard", "clpid": "Du-Toit-Noel-Eduard" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Blackmore", "given_name": "James C.", "clpid": "Blackmore-J-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis is concerned with robot motion planning in dynamic, cluttered, and uncertain environments. Successful and efficient robot operation in such environments requires reasoning about the future system evolution and the uncertainty associated with obstacles and moving agents in the environment. Current motion planning strategies ignore future information and are limited by the resulting growth of uncertainty as the system is evolved. This thesis presents an approach that accounts for future information gathering (and the quality of that information) in the planning process. The Partially Closed-Loop Receding Horizon Control approach, introduced in this thesis, is based on Dynamic Programming with imperfect state information. Probabilistic collision constraints, due to the need for obstacle avoidance between the robot and obstacles with uncertain locations and geometries, are developed and imposed. By accounting for the anticipated future information, the uncertainty associated with the system evolution is managed, allowing for greater numbers of moving agents and more complex agent behaviors to be handled. Simulation results demonstrate the benefit of the proposed approach over existing approaches in static and dynamic environments. Complex agent behaviors, including multimodal and interactive agent-robot models, are considered.", "doi": "10.7907/SD3N-JR18", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5293", "collection": "thesis", "collection_id": "5293", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10072009-165901284", "primary_object_url": { "basename": "philipdutoit_thesis.pdf", "content": "final", "filesize": 47249560, "license": "other", "mime_type": "application/pdf", "url": "/5293/19/philipdutoit_thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Transport and Separatrices in Time-Dependent Flows", "author": [ { "family_name": "Du Toit", "given_name": "Philip Christopher", "clpid": "Du-Toit-Philip-Christopher" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Dabiri", "given_name": "John O.", "clpid": "Dabiri-J-O" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The method of using Finite Time Liapunov Exponents (FTLE) to extract Lagrangian Coherent Structures (LCS) in aperiodic flows, as originally developed by Haller, is applied to geophysical flows, and flows in the phase space of second order dynamical systems. In this approach, the LCS are identified as surfaces of greatest separation that parse the flow into regions with different dynamical behavior. In this way, the LCS reveal the underlying skeleton of turbulence. The time-dependence of the LCS provides insight into the mechanisms by which fluid is transported from one region to another. Of especial interest in this study, is the utility with which the FTLE-LCS method can be used to reveal homoclinic and horseshoe dynamics in aperiodic flows.
\r\n\r\nThe FTLE-LCS method is applied to turbulent flow in hurricanes and reveals LCS that delineate sharp boundaries to a storm. Moreover, intersections of the LCS define lobes that mediate transport into and out of a storm through the action of homoclinic lobe dynamics. Using FTLE-LCS, the same homoclinic structures are seen to be a dominant transport mechanism in the Global Ocean, and provide insights into the role of mesoscale eddies in enhancing lateral mixing.
\r\n\r\nBeyond geophysical flows, we also study transport in the phase space of a coupled oscillator model for biomolecules. Before we can analyze transport in this model, we first introduce an appropriate model reduction that captures the relevant statistics of the full system. In the reduced model, we see that transport is again mediated by the process of horseshoe dynamics in a perturbed homoclinic tangle.
\r\n\r\nWe also consider some theoretical aspects of FTLE-LCS, including the relationship between LCS and stable/unstable manifolds, the invariance of LCS, and the possibility of an evolution equation describing the motion of the LCS. A parallelized software for computing FTLE is also introduced.
", "doi": "10.7907/X0Y5-N133", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5522", "collection": "thesis", "collection_id": "5522", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01152010-143831008", "primary_object_url": { "basename": "thesis_single.pdf", "content": "final", "filesize": 7707375, "license": "other", "mime_type": "application/pdf", "url": "/5522/1/thesis_single.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Real-Time Applications of 3D Object Detection and Tracking", "author": [ { "family_name": "Ma", "given_name": "Jeremy Chee-Ming", "clpid": "Ma-Jeremy-Chee-Ming" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Robot perception is a fundamental aspect of any autonomous system. It gives the robot the capacity to make sense of vast amounts of data and gain an understanding of the world around it. An active problem in the area of robot perception is real-time detection and pose estimation of 3D objects. This thesis presents an approach to 3D object detection and tracking utilizing a stereo-camera sensor. Geometric object models are learned in short order time via a training phase and real-time detection and tracking is made possible by performing sparse stereo calculations on the chosen features within an adaptive region of interest of the camera image. The experimental results obtained by using this method will show the effectiveness of the approach as compared against ground truth measures in real-time. Using that framework as a basis, extensions to two other problems in robot sensing are then considered: (1) sensor-planning for model identification, and (2) sensor-planning for object-search. In the former, a novel algorithm for determining the next-best-view for a mobile sensor to identify an unknown 3D object from among a database of known models is presented and tested across two experiments involving real robotic systems. An information theoretic approach is taken to quantify the utility of each potential sensing action and the validity of the algorithm is discussed. In the latter area, a novel approach is presented that allows an autonomous mobile robot to search for a 3D object using an onboard stereo camera sensor mounted on a pan-tilt head. Search efficiency is realized by the combination of a coarse-scale global search coupled with a fine-scale local search, guided by a grid-based probability map. Obstacle avoidance during the search is naturally integrated into the method with additional experimental results on a mobile robot presented to illustrate and validate the proposed search strategy. All presented experiments were carried out in real-time processing with modest computation done by a single laptop computer.", "doi": "10.7907/4N1K-GK74", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5878", "collection": "thesis", "collection_id": "5878", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282010-094801935", "type": "thesis", "title": "Variational Methods for Control and Design of Bipedal Robot Models", "author": [ { "family_name": "Pekarek", "given_name": "David N.", "clpid": "Pekarek-David-N" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Desbrun", "given_name": "Mathieu", "clpid": "Desbrun-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis investigates nonsmooth mechanics using variational methods for the modeling, control, and design of bipedal robots.
\r\n\r\nThe theory of Lagrangian mechanics is extended to capture a variety of nonsmooth collision behaviors in rigid body systems. Notably, a variational impact model is presented for the transition of constraints behavior that describes a biped switching stance feet at the conclusion of a step.
\r\n\r\nNext, discretizations of the impact mechanics are developed using the framework of variational discrete mechanics. The resulting variational collision integrators are consistent with the continuous time theory and have an underlying symplectic structure.
\r\n\r\nIn addition to their role as integrators, the discrete equations of motion capturing nonsmooth dynamics enable a direct method for trajectory optimization. Upon specifically defining the optimal control problem for nonsmooth systems, examples demonstrate this optimization method in the task of determining periodic gaits for\r\ntwo rigid body biped models.
\r\n\r\nAn additional effort is made to optimize bipedal walking motions through modifications in system design. A method for determining optimal designs using a combination\r\nof trajectory optimization methods and surrogate function optimization methods is defined. This method is demonstrated in the task of determining knee joint placement\r\nin a given biped model.
", "doi": "10.7907/KATX-3233", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:3252", "collection": "thesis", "collection_id": "3252", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08272008-121822", "primary_object_url": { "basename": "Ling_Shi_thesis.pdf", "content": "final", "filesize": 1526490, "license": "other", "mime_type": "application/pdf", "url": "/3252/1/Ling_Shi_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Resource Optimization for Networked Estimator with Guaranteed Estimation Quality", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Johansson", "given_name": "Karl Henrik", "clpid": "Johansson-K-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Advances in fabrication, modern sensor and communication technologies, and computer architecture have enabled a variety of new networked sensing and control applications. However, many difficulties are inherent with these systems, for example, the constrained communication and computation capabilities, and limited energy resources, which are frequently seen in a wireless sensor network. As a consequence, the networks typically induce many new issues such as limited bandwidth, packet loss, and delay. Estimation and control over such networks thus require new design paradigms beyond traditional sampled-data control, as the aforementioned constraints undoubtedly affect system performance or even stability. In this thesis work, I consider the problem of state estimation over networks. As communication, computation, and energy are scarce resources in such networks, I focus on optimizing the use of them. When the state estimation is carried out over a sensor network, I consider the problem of minimizing the sensor energy usage and maximizing the network lifetime. When the state estimation is carried out over a packet-delaying network, I consider the problem of minimizing the buffer length at the remote state estimator. In each scenario, a certain desired level of estimation quality is guaranteed.\r\n", "doi": "10.7907/DTCJ-BN07", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:5174", "collection": "thesis", "collection_id": "5174", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12312008-184713", "primary_object_url": { "basename": "hudson_thesis.pdf", "content": "final", "filesize": 2221233, "license": "other", "mime_type": "application/pdf", "url": "/5174/1/hudson_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Inference in Hybrid Systems with Applications in Neural Prosthetics", "author": [ { "family_name": "Hudson", "given_name": "Nicolas Henry", "clpid": "Hudson-Nicolas-Henry" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis develops new hybrid system models and associated inference algorithms to create a ``supervisory decoder' for cortical neural prosthetic devices that aim to help the severely handicapped. These devices are a brain-machine interface, consisting of surgically implanted electrode arrays and associated computer decoding algorithms, that enable a human to control external electromechanical devices, such as artificial limbs, by thought alone.
\r\n\r\nHybrid systems are characterized by discrete switching between sets of continuous dynamical activity. New hybrid models, which are flexible enough to model neurological activity, are created that incorporate both duration and dynamical state based switching paradigms. Combining generalized linear models with nonstationary and semi-Markov chains gives rise to three new hybrid systems: generalized linear hidden Markov models (GLHMM), hidden semi-Markov models (HSMM) with generalized linear model dynamics, and hidden regressor dependent Markov models (HRDMM). Bayesian inference methods, including variational Bayes and Gibbs sampling, are derived for the identification of existing and developed hybrid models. The developed inference algorithms provide advances over the current hybrid system identification literature by providing a principled way to incorporate prior knowledge and select between alternative model classes and orders, including the number of discrete system states.
\r\n\r\nFuture neuroprostheses that seek to provide a facile interface for the paralyzed patient will require a supervisory decoder that classifies, in real time, the discrete cognitive, behavioral, or planning state of the brain. The developed hybrid models and inference algorithms provide a framework for supervisory decoding, where first, a hybrid-state neurological activity model is identified from data, and then used to estimate the discrete state in real time. The electrical activity of multiple neurons from a cortical area in the brain associated with motor planning (the parietal reach region), and multiple signal types, including both spike arrival times and local field potentials, are fused to give more accurate results. The model structure, including the number of discrete cognitive states, can also be estimated from the data, resulting in significantly improved decoding performance compared to existing methods.
\r\n\r\nAdditional demonstrated applications include the automated segmentation of honey bee motion into discrete primitives, and generating mechanical system models for a pick-and-place machine.
\r\n", "doi": "10.7907/REB5-BB43", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:3823", "collection": "thesis", "collection_id": "3823", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09292008-204618", "primary_object_url": { "basename": "Akellythesis090408.pdf", "content": "final", "filesize": 1100957, "license": "other", "mime_type": "application/pdf", "url": "/3823/1/Akellythesis090408.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Constitutive Relation for Shape-Memory Alloys", "author": [ { "family_name": "Kelly", "given_name": "Alex", "clpid": "Kelly-Alex" } ], "thesis_advisor": [ { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The novel nonlinear thermoelastic behavior of shape-memory alloys (SMAs) makes them increasingly desirable as components in many advanced technological applications. In order to incorporate these materials into engineering designs, it is important to develop an understanding of their constitutive response. The purpose of this thesis is to develop a constitutive model of shape-memory polycrystals that is faithful to the underlying micromechanics while remaining simple enough for utility in engineering analysis and design.
\r\n\r\nWe present a model in which the material microstructure is represented macroscopically as a recoverable transformation strain that is constrained by the texture of the polycrystal. The point of departure in this model is the recognition that the mechanics of the onset of martensitic transformation are fundamentally different from those of its saturation. Consequently, the constraint on the set of recoverable strains varies throughout the transformation process. The effects of constraint geometry on the constitutive response of SMAs are studied. Several well known properties of SMAs are demonstrated. Finally the model is simply implemented in a commercial finite-element package as a proof of the concept.
\r\n", "doi": "10.7907/YMT5-AX47", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2271", "collection": "thesis", "collection_id": "2271", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-111937", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 5631440, "license": "other", "mime_type": "application/pdf", "url": "/2271/11/thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Safety Verification and Failure Analysis of Goal-Based Hybrid Control Systems", "author": [ { "family_name": "Braman", "given_name": "Julia Marie Badger", "clpid": "Braman-Julia-Marie-Badger" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The success of complex autonomous robotic systems depends on the quality and correctness of their fault tolerant control systems. A goal-based approach to fault tolerant control, which is modeled after a software architecture developed at the Jet Propulsion Laboratory, uses networks of goals to control autonomous systems. The complex conditional branching of the control program makes safety verification necessary. Three novel verification methods are presented. In the first, goal networks are converted to linear hybrid automata via a bisimulation. The converted automata can then be verified against an unsafe set of conditions using an existing symbolic model checker such as PHAVer. Due to the complexity issues that result from this method, a design for verification software tool, the SBT Checker, was developed to create goal networks that have state-based transitions. Goal networks that have state-based transitions can be converted to hybrid automata whose locations' invariants contain all information necessary to determine the transitions between the locations. An original verification software called InVeriant can then be used to find unsafe locations of linear hybrid systems based on the locations\u2019 invariants and rate conditions, which are compared to the unsafe set of conditions. The reachability of the unsafe locations depends only on the reachability of the states of the state variables constrained in the locations' invariants from those state variables' initial conditions. In cases where this reachability condition is not trivially true, the software efficiently searches for a path to the unsafe locations using properties of the system. The third verification method is the calculation of the failure probability of the verified hybrid control system due to state estimation uncertainty, which is extremely important in autonomous systems that rely heavily on the state estimates made from sensor measurements. Finally, two significant example goal network control programs, one for a complex rover and another for a proposed aerobot mission to Titan, a moon of Saturn, are verified using the three techniques presented.", "doi": "10.7907/3H42-BF56", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2269", "collection": "thesis", "collection_id": "2269", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-102458", "primary_object_url": { "basename": "SH_Cheung_thesis.pdf", "content": "final", "filesize": 2231044, "license": "other", "mime_type": "application/pdf", "url": "/2269/1/SH_Cheung_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Stochastic Analysis, Model and Reliability Updating of Complex Systems with Applications to Structural Dynamics", "author": [ { "family_name": "Cheung", "given_name": "Sai Hung", "orcid": "0000-0003-2324-3884", "clpid": "Cheung-Sai-Hung" } ], "thesis_advisor": [ { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Krishnan", "given_name": "Swaminathan", "clpid": "Krishnan-S" }, { "family_name": "Heaton", "given_name": "Thomas H.", "clpid": "Heaton-T-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In many engineering applications, it is a formidable task to construct mathematical models that are expected to produce accurate predictions of the behavior of a system of interest. During the construction of such predictive models, errors due to imperfect modeling and uncertainties due to incomplete information about the system and its environment (e.g., input or excitation) always exist and can be accounted for appropriately by using probability logic. To assess the system performance subjected to dynamic excitations, a stochastic system analysis considering all the uncertainties involved has to be performed. In engineering, evaluating the robust failure probability (or its complement, robust reliability) of the system is a very important part of such stochastic system analysis. The word \u2018robust\u2019 is used because all uncertainties, including those due to modeling of the system, are taken into account during the system analysis, while the word \u2018failure\u2019 is used to refer to unacceptable behavior or unsatisfactory performance of the system output(s). Whenever possible, the system (or subsystem) output (or maybe input as well) should be measured to update models for the system so that a more robust evaluation of the system performance can be obtained. In this thesis, the focus is on stochastic system analysis, model and reliability updating of complex systems, with special attention to complex dynamic systems which can have high-dimensional uncertainties, which are known to be a very challenging problem. Here, full Bayesian model updating approach is adopted to provide a robust and rigorous framework for these applications due to its ability to characterize modeling uncertainties associated with the underlying system and to its exclusive foundation on the probability axioms.
\r\n\r\nFirst, model updating of a complex system which can have high-dimensional uncertainties within a stochastic system model class is considered. To solve the challenging computational problems, stochastic simulation methods, which are reliable and robust to problem complexity, are proposed. The Hybrid Monte Carlo method is investigated and it is shown how this method can be used to solve Bayesian model updating problems of complex dynamic systems involving high-dimensional uncertainties. New formulae for Markov Chain convergence assessment are derived. Advanced hybrid Markov Chain Monte Carlo simulation algorithms are also presented in the end.
\r\n\r\nNext, the problem of how to select the most plausible model class from a set of competing candidate model classes for the system and how to obtain robust predictions from these model classes rigorously, based on data, is considered. To tackle this problem, Bayesian model class selection and averaging may be used, which is based on the posterior probability of different candidate classes for a system. However, these require calculation of the evidence of the model class based on the system data, which requires the computation of a multi-dimensional integral involving the product of the likelihood and prior defined by the model class. Methods for solving the computationally challenging problem of evidence calculation are reviewed and new methods using posterior samples are presented.
\r\n\r\nMultiple stochastic model classes can be created even there is only one embedded deterministic model. These model classes can be viewed as a generalization of the stochastic models considered in Kalman filtering to include uncertainties in the parameters characterizing the stochastic models. State-of-the-art algorithms are used to solve the challenging computational problems resulting from these extended model classes. Bayesian model class selection is used to evaluate the posterior probability of an extended model classe and the original one to allow a data-based comparison. The problem of calculating robust system reliability is also addressed. The importance and effectiveness of the proposed method is illustrated with examples for robust reliability updating of structural systems. Another significance of this work is to show the sensitivity of the results of stochastic analysis, especially the robust system reliability, to how the uncertainties are handled, which is often ignored in past studies.
\r\n\r\nA model validation problem is then considered where a series of experiments are conducted that involve collecting data from successively more complex subsystems and these data are to be used to predict the response of a related more complex system. A novel methodology based on Bayesian updating of hierarchical stochastic system model classes using such experimental data is proposed for uncertainty quantification and propagation, model validation, and robust prediction of the response of the target system. Recently-developed stochastic simulation methods are used to solve the computational problems involved.
\r\n\r\nFinally, a novel approach based on stochastic simulation methods is developed using current system data, to update the robust failure probability of a dynamic system which will be subjected to future uncertain dynamic excitations. Another problem of interest is to calculate the robust failure probability of a dynamic system during the time when the system is subjected to dynamic excitation, based on real-time measurements of some output from the system (with or without corresponding input data) and allowing for modeling uncertainties; this generalizes Kalman filtering to uncertain nonlinear dynamic systems. For this purpose, a novel approach is introduced based on stochastic simulation methods to update the reliability of a nonlinear dynamic system, potentially in real time if the calculations can be performed fast enough.
", "doi": "10.7907/K5T7-4B72", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2119", "collection": "thesis", "collection_id": "2119", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262009-100436", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 9040987, "license": "other", "mime_type": "application/pdf", "url": "/2119/1/thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Bifurcations in Single Atom Cavity QED", "author": [ { "family_name": "Armen", "given_name": "Michael A.", "clpid": "Armen-Michael-A" } ], "thesis_advisor": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" } ], "thesis_committee": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Thorne", "given_name": "Kip S.", "clpid": "Thorne-K-S" }, { "family_name": "Painter", "given_name": "Oskar J.", "clpid": "Painter-O" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "Current research in single-atom cavity quantum electrodynamics largely emphasizes the input-output properties of strongly coupled systems, from normal mode splitting to photon blockade. But over the last decade, experiments have, with few exceptions, focused on relatively weak driving conditions. This thesis concentrates on a range of quantum nonlinear phenomena in the strong driving regime. In particular, I discuss the observation of random-telegraph phase switching in the light transmitted through a Fabry-Perot resonator containing one strongly coupled atom and 10-100 photons, confirming long-standing predictions of a phenomenon known as single-atom phase bistability. These results highlight the relevance of cavity quantum electrodynamics in the development of attojoule nanophotonic logic and signal processing. In addition, I consider a general class of bifurcation phenomena that are manifest within this physical setting. Here, focus is placed on the investigation of quantum-classical correspondence near semiclassical bifurcation points. ", "doi": "10.7907/2G57-2609", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2172", "collection": "thesis", "collection_id": "2172", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272008-161801", "primary_object_url": { "basename": "FontaineThesisV1.pdf", "content": "final", "filesize": 24200211, "license": "other", "mime_type": "application/pdf", "url": "/2172/1/FontaineThesisV1.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Automated Visual Tracking for Behavioral Analysis of Biological Model Organisms", "author": [ { "family_name": "Fontaine", "given_name": "Ebraheem Ihsan", "clpid": "Fontaine-Ebraheem-Ihsan" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Barr", "given_name": "Alan H.", "clpid": "Barr-A-H" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Capturing the detailed motion and behavior of biological organisms plays an important role in a wide variety of research disciplines. Many studies in biomechanics, neuroethology, and developmental biology rely on analysis of video sequences to understand the underlying behavior. However, the efficient and rapid quantification of these complex behavioral traits imposes a major bottleneck on the elucidation of many interesting scientific questions. The goal of this thesis is to develop a suite of model-based visual tracking algorithms that will apply across a variety of model organisms used in biology. These automated tracking algorithms operate in a high-throughput, high-resolution manner needed for a productive synthesis with modern genetic approaches. To this end, I demonstrate automated estimation of the detailed body posture of nematodes, zebrafish, and fruit flies from calibrated video.
\r\n\r\nThe current algorithm utilizes a generative geometric model to capture the organism's shape and appearance. To accurately predict the organism's motion between video frames, I incorporate a motion model that matches tracked motion patterns to patterns in a training set. This technique is invariant with respect to the organism's velocity and can easily incorporate training data from completely different motion patterns. The prediction of the motion model is refined using measurements from the image. In addition to high-contrast feature points, I introduce a region, segmentation model based on level sets that are formally integrated into the observation framework of an Iterated Kalman Filter (IKF). The prior knowledge provided by the geometric and motion models improves tracking accuracy in the presence of partial occlusions and misleading visual cues.
\r\n\r\nThe method is used to track the position and shape of multiple nematodes during mating behavior, zebrafish of different ages during escape response, and fruit flies during take off maneuvers. These applications demonstrate the modular design of this model-based visual tracking system, where the user can specify which components are appropriate to a given experiment. In contrast to other approaches, which are customized to a particular organism or experimental setup, my approach provides a foundation that requires little re-engineering whenever the experimental parameters are changed.
", "doi": "10.7907/TSQ7-SN68", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2320", "collection": "thesis", "collection_id": "2320", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05302008-141602", "primary_object_url": { "basename": "00_mjdunlop_complete_thesis.pdf", "content": "final", "filesize": 4934029, "license": "other", "mime_type": "application/pdf", "url": "/2320/1/00_mjdunlop_complete_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Dynamics and Correlated Noise in Gene Regulation", "author": [ { "family_name": "Dunlop", "given_name": "Mary Julia", "orcid": "0000-0002-9261-8216", "clpid": "Dunlop-Mary-Julia" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Gene regulatory interactions are context dependent, active in some cell types or cellular states but not in others. In this thesis we present a method for determining when a regulatory link is active given temporal measurements of gene expression. Correlations in time-series data are used to determine how genes influence each other and their causal relationships. Natural stochastic noise is shown to aid in the process of network identification by perturbing the expression of genes; the speed and direction at which the noisy signal propagates shows how the network is connected. Cross correlation functions are used to reveal time-delayed correlations.
\r\n\r\nWe develop a stochastic model of gene expression and show that by measuring correlations in cellular noise, it is possible to infer network activity and temporal properties of gene regulation. Using a linearized version of the model, we introduce a method for analytically deriving cross correlation functions for arbitrary networks. These results are validated experimentally using a synthetic gene circuit in E. coli bacteria. Single-cell time-lapse microscopy is used to measure noisy expression of multiple genes over time. Extending this work to natural systems, we study feed-forward loops and determine that certain classes of feed-forward loops are more robust to noise and parameter variations that others. Noise in two naturally occurring feed-forward loops involved in galactose utilization is measured experimentally and it is shown that neither is actively regulating its target in the conditions tested.
", "doi": "10.7907/AC8V-6S05", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2318", "collection": "thesis", "collection_id": "2318", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05302008-134607", "type": "thesis", "title": "Adaptive Feature Selection in Pattern Recognition and Ultra-Wideband Radar Signal Analysis", "author": [ { "family_name": "Jiang", "given_name": "Hao", "clpid": "Jiang-Hao" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Feature selection from measured data aims to extract informative features to reveal the statistic or stochastic mechanism underlying the complicated or high dimensional original data. In this thesis, the feature selection problem is probed under two situations, one is pattern recognition and the other is ultra-wideband radar signal analysis.
\r\n\r\nClassical pattern recognition methods select features by their ability to separate the multiple classes with certain gauge measure. The deficiency in this general strategy is its lack of adaptation in specific situations. This deficiency may be overcome by viewing the selected features as a function of not only the training samples but also the unlabeled test data. From this perspective, this thesis proposes an adaptive sequential feature selection algorithm which utilizes an information-theoretic measure to reduce the classification task complexity sequentially, and finally outputs the probabilistic classification result and its variation level. To verify the potential advantage of this algorithm, this thesis applies it to one important problem of neural prosthesis, which concerns decoding a finite number of classes, intended reach directions, from recordings of neural activities in the Parietal Reach Region of one rhesus monkey. Experimental results show that the classification scheme of combining the adaptive sequential feature selection algorithm and the information fusion method outperforms some classical pattern recognition rules, such as the nearest neighbor rule and support vector machine, in decoding performance.
\r\n\r\nThe second scenario in this thesis targets developing a human presence and motion pattern detector through ultra-wideband radar signal analysis. To augment the detection robustness, both static and dynamic features should be utilized. The static features reflect the information of target geometry and its variability, while the dynamic features extract the temporal structure among radar scans. The problem of static feature selection is explored in this thesis, which utilizes the Procrustes shape analysis to generate the representative template for the target images, and makes statistical inference in the tangent space through the Hotelling one sample test. After that, the waveform shape variation structure is decomposed in the tangent space through the principal component analysis. The selected principal components not only accentuate the prominent dynamics of the target motion, but also generate another informative classification feature.
\r\n", "doi": "10.7907/7NR6-AR24", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:1664", "collection": "thesis", "collection_id": "1664", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05072008-131735", "primary_object_url": { "basename": "Carson_Thesis_1sided.pdf", "content": "final", "filesize": 1904222, "license": "other", "mime_type": "application/pdf", "url": "/1664/1/Carson_Thesis_1sided.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Robust Model Predictive Control with a Reactive Safety Mode", "author": [ { "family_name": "Carson", "given_name": "John Maurice, III", "clpid": "Carson-John-Maurice-III" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "MacMynowski", "given_name": "Douglas G.", "clpid": "MacMynowski-D-G" }, { "family_name": "Acikmese", "given_name": "Behcet", "clpid": "Acikmese-B" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Acikmese", "given_name": "Behcet", "clpid": "Acikmese-B" }, { "family_name": "MacMynowski", "given_name": "Douglas G.", "clpid": "MacMynowski-D-G" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Control algorithms suitable for online implementation in engineering applications, such as aerospace and mechanical vehicles, often require adherence to physical state and control constraints. Additionally, the chosen algorithms must provide robustness to uncertainty affecting both the system dynamics and the constraints. As further autonomy is built into these systems, the algorithms must be capable of blending multiple operational modes without violating the intrinsic constraints. Further, for real-time applications, the implemented control algorithms must be computationally efficient and reliable. The research in this thesis approaches these application needs by building upon the framework of MPC (Model Predictive Control).
\r\n\r\nThe MPC algorithm makes use of a nominal dynamics model to predict and optimize the response of a system under the application of a feedforward control policy, which is computed online in a finite-horizon optimization problem. The MPC algorithm is quite general and can be applied to linear and nonlinear systems and include explicit state and control constraints. The finite-horizon optimization is advantageous given the finite online computational capabilities in practical applications. Further, recursively re-solving the finite-horizon optimization in a compressing- or receding-horizon manner provides a form of closed-loop control that updates the feedforward control policy by setting the nominal state at re-solve to the current actual state. However, uncertainty between the nominal model and the actual system dynamics, along with constraint uncertainty can cause feasibility, and hence, robustness issues with the traditional MPC algorithm.
\r\n\r\nIn this thesis, an R-MPC (Robust and re-solvable MPC) algorithm is developed for uncertain nonlinear systems to address uncertainty affecting the dynamics. The R-MPC control policy consists of two components: the feedforward component that is solved online as in traditional MPC; and a separate feedback component that is determined offline, based on a characterization of the uncertainty between the nominal model and actual system. The addition of the feedback policy generates an invariant tube that ensures the actual system trajectories remain in the proximity of the nominal feedforward trajectory for all time. Further, this tube provides a means to theoretically guarantee continued feasibility and thus re-solvability of the R-MPC algorithm, both of which are required to guarantee asymptotic stability.
\r\n\r\nTo address uncertainty affecting the state constraints, an SR-MPC (Safety-mode augmented R-MPC) algorithm is developed that blends a reactive safety mode with the R-MPC algorithm for uncertain nonlinear systems. The SR-MPC algorithm has two separate operational modes: standard mode implements a modified version of the R-MPC algorithm to ensure asymptotic convergence to the origin; safety mode, if activated, guarantees containment within an invariant set about a safety reference for all time. The standard mode modifies the R-MPC algorithm with a special constraint to ensure safety-mode availability at any time. The safety-mode control is provided by an offline designed control policy that can be activated at any time during standard mode. The separate, reactive safety mode provides robustness to unexpected state-constraint changes; e.g., other vehicles crossing/stopping in the feasible path, or unexpected ground proximity in landing scenarios.
\r\n\r\nExplicit design methods are provided for implementation of the R-MPC and SR-MPC algorithms on a class of systems with uncertain nonlinear terms that have norm-bounded derivatives. Further, a discrete SR-MPC algorithm is developed that is more broadly applicable to real engineering systems. The discrete algorithm is formulated as a second-order cone program that can be solved online in a computationally efficient manner by using interior-point algorithms, which provide convergence guarantees in finite time to a prescribed level of accuracy.
\r\n\r\nThis discrete SR-MPC algorithm is demonstrated in simulation of a spacecraft descent toward a small asteroid where there is an uncertain gravity model, as well as errors in the expected surface altitude. Further, realistic effects such as control-input uncertainty, sensor noise, and unknown disturbances are included to further demonstrate the applicability of the discrete SR-MPC algorithm in a realistic implementation.
", "doi": "10.7907/S0VN-VE35", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2254", "collection": "thesis", "collection_id": "2254", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-105504", "primary_object_url": { "basename": "Wolf_PhD_1sided.pdf", "content": "final", "filesize": 8416466, "license": "other", "mime_type": "application/pdf", "url": "/2254/1/Wolf_PhD_1sided.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Target Tracking Using Clustered Measurements, with Applications to Autonomous Brain-Machine Interfaces", "author": [ { "family_name": "Wolf", "given_name": "Michael Timothy", "clpid": "Wolf-Michael-Timothy" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents new methods for classifying and tracking the signals of targets that produce clusters of observations, measured in successive recording intervals or scans. This multitarget tracking problem arises, for instance, in extracellular neural recordings, in which an electrode is inserted into the brain to detect the spikes of individual neurons. Since multiple active neurons may lie near the electrode, each detected spike must be assigned to the neuron that produced it, a task known as spike sorting. In the scenario considered in this thesis, the electrode signal is sampled over many brief recording intervals. In each recording interval, all spikes must first be clustered according to their generating neurons, and then each cluster must be associated to clusters from previous recording intervals, thus tracking the signals of putative neuron \"targets.\"
\r\n\r\nThis thesis introduces a novel multitarget tracking solution for the above problem, called multiple hypothesis tracking for clusters (MHTC). The MHTC algorithm has two main parts: a Bayesian clustering algorithm for associating observations to clusters in each interval and a probabilistic supervisory system that manages association hypotheses across intervals. The clustering procedure provides significantly more consistent results than previously available methods, enabling more accurate tracking of targets over time. Such consistency is promoted by a maximum a posteriori (MAP) approach to optimizing a Gaussian mixture model via expectation-maximization (EM), in which information from the preceding intervals serves as a prior for the current interval while still allowing the number and locations of targets to change. MHTC's hypothesis management system, like that of traditional multiple hypothesis tracking (MHT) algorithms, propagates various possibilities for how to assign measurements to existing targets and uses a delayed decision-making logic to resolve data association ambiguities. It also, however, maintains several options, termed model hypotheses, for how to cluster the observations of each interval. This combination of clustering and tracking in a single solution enables MHTC to robustly maintain the identities of cluster-producing targets in challenging recording scenarios.
\r\n\r\nIn addition to these classification and tracking techniques, this thesis presents advances in a miniature robotic electrode microdrive capable of extracellular recordings lasting for days at a time. As a whole, these contributions can play an important role in enabling an autonomous neural interface, which, by frequent automatic repositioning of its recording electrodes, can optimize the recording quality of extracellular signals associated with individual neurons and maintain high quality recordings for long periods of time. Such autonomous movable electrodes may eventually overcome key barriers to engineering a practical neuroprosthetic device and, in the near term, can significantly improve state-of-the-art neuroscience experimental procedures.
\r\n", "doi": "10.7907/6Y3F-8M87", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:3666", "collection": "thesis", "collection_id": "3666", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09202007-135027", "primary_object_url": { "basename": "final_thesis.pdf", "content": "final", "filesize": 3271723, "license": "other", "mime_type": "application/pdf", "url": "/3666/1/final_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Robotic Training for Motor Rehabilitation after Complete Spinal Cord Injury", "author": [ { "family_name": "Liang", "given_name": "Yongqiang", "clpid": "Liang-Yongqiang" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Edgerton", "given_name": "V. Reggie", "clpid": "Edgerton-V-R" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Edgerton", "given_name": "V. Reggie", "clpid": "Edgerton-V-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The spinal cord circuits have a great degree of automaticity and plasticity. They are able to generate complex locomotor patterns such as stepping and scratching even without input from supraspinal nervous systems. When provided with ensembles of afferent sensory information input associated with a specific motor task, e.g., stepping, the spinal cord can \"learn\" to perform that task even if it is isolated from the supraspinal nervous systems.
\r\n\r\nThe plasticity of the spinal cord led researchers to study the use of physical locomotor training, e.g., treadmill step training with body weight support, to rehabilitate locomotor function after spinal cord injury (SCI). With intensive training, the spinal-cord-injured subject can recover some level of stepping ability. Explorations were made in this thesis to find an optimal training paradigm. Novel assist-as-needed paradigms were developed to allow variability during training since it is an intrinsic feature of normal stepping. Comparative experiments were conducted against fixed-trajectory training. Results demonstrated that variability is an important factor to induce more improvement in step training.
\r\n\r\nStanding is another important function in one's daily life, though it received less research attention than stepping. A prototype stand platform with 6 degrees of freedom was developed as an experimental tool for stand and postural study. Analogous to step training, we tested the effect of daily training on extensor responses in the hind limbs of complete spinal rats. The results showed no significant effect of the training. This led to the conclusion that without tonic input, the spinal cord has very limited ability to generate enough extensor muscle tone and to respond to postural disturbance. Further studies in standing rehabilitation should combine other methods to provide tonic inputs to the spinal cord.
", "doi": "10.7907/T01R-P904", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:3886", "collection": "thesis", "collection_id": "3886", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10032007-121619", "primary_object_url": { "basename": "Angelova_PhD_Thesis.pdf", "content": "final", "filesize": 8076859, "license": "other", "mime_type": "application/pdf", "url": "/3886/1/Angelova_PhD_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Visual Prediction of Rover Slip: Learning Algorithms and Field Experiments", "author": [ { "family_name": "Angelova", "given_name": "Anelia Nedelcheva", "orcid": "0000-0003-1822-7943", "clpid": "Angelova-Anelia-Nedelcheva" } ], "thesis_advisor": [ { "family_name": "Matthies", "given_name": "Larry H.", "clpid": "Matthies-L-H" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "thesis_committee": [ { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Matthies", "given_name": "Larry H.", "clpid": "Matthies-L-H" }, { "family_name": "Lapusta", "given_name": "Nadia", "clpid": "Lapusta-N" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Perception of the surrounding environment is an essential tool for intelligent navigation in any autonomous vehicle. In the context of Mars exploration, there is a strong motivation to enhance the perception of the rovers beyond geometry-based obstacle avoidance, so as to be able to predict potential interactions with the terrain. In this thesis we propose to remotely predict the amount of slip, which reflects the mobility of the vehicle on future terrain. The method is based on learning from experience and uses visual information from stereo imagery as input. We test the algorithm on several robot platforms and in different terrains. We also demonstrate its usefulness in an integrated system, onboard a Mars prototype rover in the JPL Mars Yard.
\r\n\r\nAnother desirable capability for an autonomous robot is to be able to learn about its interactions with the environment in a fully automatic fashion. We propose an algorithm which uses the robot's sensors as supervision for vision-based learning of different terrain types. This algorithm can work with noisy and ambiguous signals provided from onboard sensors. To be able to cope with rich, high-dimensional visual representations we propose a novel, nonlinear dimensionality reduction technique which exploits automatic supervision. The method is the first to consider supervised nonlinear dimensionality reduction in a probabilistic framework using supervision which can be noisy or ambiguous.
\r\n\r\nFinally, we consider the problem of learning to recognize different terrains, which addresses the time constraints of an onboard autonomous system. We propose a method which automatically learns a variable-length feature representation depending on the complexity of the classification task. The proposed approach achieves a good trade-off between decrease in computational time and recognition performance.
\r\n", "doi": "10.7907/F7FY-5T13", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:4374", "collection": "thesis", "collection_id": "4374", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11022007-104734", "primary_object_url": { "basename": "waydo-thesis-final-oneside.pdf", "content": "final", "filesize": 5568170, "license": "other", "mime_type": "application/pdf", "url": "/4374/1/waydo-thesis-final-oneside.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Explicit Object Representation by Sparse Neural Codes", "author": [ { "family_name": "Waydo", "given_name": "Stephen J.", "clpid": "Waydo-Stephen-J" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" } ], "thesis_committee": [ { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Olshausen", "given_name": "Bruno", "clpid": "Olshausen-B" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Neurons have been identified in the human medial temporal lobe (MTL) that display a strong selectivity for only a few stimuli (such as familiar individuals or landmark buildings) out of perhaps 100 presented to the test subject. While highly selective for a particular object or category, these cells are remarkably insensitive to different presentations (i.e., different poses and views) of their preferred stimulus. This invariant, sparse, and explicit representation of the world may be crucial to the transformation of complex visual stimuli into more abstract memories. In this thesis I first discuss the issue of how best to quantify sparseness, particularly in very sparse systems where biases are significant, and show the results of this analysis applied to human MTL data. I also provide an overview of existing results from other investigators on measuring sparseness both elsewhere along the primate visual pathway and in selected other sensory processing systems. From there I move into the computational realm. Sparse coding as a computational constraint applied to the representation of natural images has been shown to produce receptive fields strikingly similar to those observed in mammalian primary visual cortex. I apply sparse coding as a model for processing further along the visual hierarchy: not directly to images but rather to an invariant feature-based representation of images analogous to that found in the inferotemporal cortex. This combination of sparseness and invariance naturally leads to explicit category representation. That is, by exposing the model to different images drawn from different categories, units develop that respond selectively to different categories. After extending an existing model of sparse coding and providing some mathematical analysis of its operation, I show results obtained by applying this method both to unsupervised category discovery in images and to differentiation between images of different individuals.\r\n", "doi": "10.7907/1XY7-2H19", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:682", "collection": "thesis", "collection_id": "682", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02192008-153449", "type": "thesis", "title": "Real-Time Trajectory Generation for Constrained Nonlinear Dynamical Systems Using Non-Uniform Rational B-Spline Basis Functions", "author": [ { "family_name": "Flores Contreras", "given_name": "Melvin Estuardo", "clpid": "Flores-Contreras-Melvin-Estuardo" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Milam", "given_name": "Mark B.", "clpid": "Milam-M-B" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The thesis describes a new method for obtaining minimizers for optimal control problems whose minima serve as control policies for guiding nonlinear dynamical systems to achieve prescribed goals under imposed trajectory and actuator constraints. One of the major contributions of the present work resides in the approximation of such minimizers by piecewise polynomial functions expressed in terms of a linear combination of non-uniform rational B-spline (NURBS) basis functions and the judicious exploitation of the properties of the resulting NURBS curves to improve the computational effort often associated with solving optimal control problems for constrained dynamical systems.
\r\n\r\nIn particular, by exploiting the two structures combined in a NURBS curve, NURBS basis functions and an associated union of overlapping polytopes constructed from the coefficients of the linear combination, we are able to separate an optimal control problem into two subproblems | guidance and obstacle avoidance, making the original problem tractable. This is accomplished by laying out the union of overlapping polytopes in such a way that they delineate a section of space that avoids all obstacles and then manipulating the NURBS basis functions to obtain trajectories that are guaranteed to remain bounded by this section of space without explicitly including the conjunction of disjunctions naturally induced from obstacles into the guidance problem.
\r\n\r\nIn addition, we show how one can construct systematically a feasible region that corresponds to a NURBS parameterization starting from an ordered union of pairwise adjacently overlapping nonempty compact convex sets. Specifically, we show how to setup a nonlinear programming problem to solve for the feasible region in terms of an ordered union of pairwise adjacently overlapping polytopes with nonempty interiors by maximizing the sum of their volumes and starting from a feasible region described by an ordered union of pairwise adjacently overlapping nonempty convex compact simi-algebraic sets. Finally, we show how this strategy can be implemented practically for an autonomous system traversing an urban environment.
\r\n\r\nFinally, this work culminated in the filing of patent US20070179685 on behalf of Northrop Grumman for the Space Technology sector and in the development of the NURBS-based OTG software package. This C++ package contains the theoretical results of this thesis in the form of an object-oriented implementation optimized for real-time trajectory generation.
\r\n\r\n", "doi": "10.7907/TK01-9X60", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:5073", "collection": "thesis", "collection_id": "5073", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12192007-153619", "primary_object_url": { "basename": "MSE_thesis.pdf", "content": "final", "filesize": 1506285, "license": "other", "mime_type": "application/pdf", "url": "/5073/2/MSE_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Managing Information in Networked and Multi-Agent Control Systems", "author": [ { "family_name": "Epstein", "given_name": "Michael Steven", "clpid": "Epstein-Michael-Steven" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "MacMynowski", "given_name": "Douglas G.", "clpid": "MacMynowski-D-G" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Traditional feedback control systems give little attention to issues associated with the flow of information through the feedback loop. Typically implemented with dedicated communication links that deliver nearly precise, reliable and non-delayed information, researchers have not needed to concern themselves with issues related to quantized, delayed and even lost information. With the advent of newer technologies and application areas that pass information through non-reliable networks, these issues can not be ignored. In recent years the field of Networked Control Systems (NCS) has emerged to describe situations where these issues are present. The research in this field focuses on quantifying performance degradations in the presence of network effects and proposing algorithms for managing the information flow to counter those negative effects. In this thesis I propose and analyze algorithms for managing information flow for several NCS scenarios; state estimation with lossy measurement signals, using input buffers to reduce the frequency of communication with a remote plant, and performing state estimation when control signals are transmitted to a remote plant via a lossy communication link with no acknowledgement signal at the estimator. Multi-agent coordinated control systems serve as a prime example of an emerging area of feedback control systems that utilize feedback loops with information passed through possibly imperfect communication networks. In these systems, agents use a communication network to exchange information in order to achieve a desired global objective. Hence managing the information flow has a direct impact on the performance of the system. I also explore this area by focusing on the problem of multi-agent average consensus. I propose an algorithm based on a hierarchical decomposition of the communication topology to speed up the time to convergence. For all these topics I focus on designing intuitive algorithms that intelligently manage the information flow and provide analysis and simulations to illustrate their effectiveness.\r\n", "doi": "10.7907/84NT-9N46", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:3625", "collection": "thesis", "collection_id": "3625", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09182006-162259", "primary_object_url": { "basename": "Thesis_ZJ_Caltech_07.pdf", "content": "final", "filesize": 1131131, "license": "other", "mime_type": "application/pdf", "url": "/3625/1/Thesis_ZJ_Caltech_07.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Coordinated Control for Networked Multi-Agent Systems", "author": [ { "family_name": "Jin", "given_name": "Zhipu", "clpid": "Jin-Zhipu" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Coordination in networked multi-agent systems attracts significant interest in the realm of engineering. Typical examples include formations of unmanned aerial vehicles, automated highway systems, and sensor networks. One common feature for these systems is that coordinated behaviors are exhibited by interactions among agents where information exchange and manipulation are necessary. In this work, three relevant issues are investigated in detail: uniform strategy for multi-agent formation control, fast-converging consensus protocols, and packet-based state estimation over communication networks.
\r\n\r\nFormation control of multi-agent systems involves harmony among local controller design, interaction topology analysis, and objective agreement among networked agents. We propose a novel control strategy so that each agent responds to neighbors' behaviors as well as acts towards the global goal. Thus, information flows for local interactions and global objective synchronization are studied separately. Using the tools from signal flow graphs and algebraic graph theory, we show that this new strategy eases the design of local controllers by relaxing stabilizing conditions. Robustness against the link failure and scalable disturbance resistance are also discussed based on small-gain theory. Experimental results on the Caltech multi-vehicle wireless testbed are provided to verify the feasibility and efficiency of this control strategy.
\r\n\r\nConsensus protocols over communication networks are used to achieve agreement among agents. One important issue is the convergence speed. We propose multi-hop relay protocols for fast consensus seeking. Without physically changing the topology of the communication network, this type of distributed protocol increases the algebraic connectivity by employing multi-hop paths in the network. We also investigate the convergence behaviors of consensus protocols with communication delays. It is interesting that, the faster the protocol converges, the more sensitive it is to the delay. This tradeoff is identified when we investigate delay margins of multi-hop relay protocols using the frequency sweep method.
\r\n\r\nEfficiently estimating the states of other agents over communication links is also discussed in this work. When information flows in the network, packet-based data is normally not retransmitted in order to satisfy real-time requirements. Thus, packet drops and random delays are inevitable. In this context, observation data that the estimator can receive is intermittent. In order to decrease the chance of losing packets and efficiently using the limited bandwidth, we introduce multiple description source codes to manipulate the data before transmission. Using modified algebraic Riccati equations, we show that multiple description codes improve the performance of Kalman filters over a large set of packet-dropping scenarios. This problem is also generalized to the case where observation data has an independent and identical static distribution over a finite set of observation noise. Moreover, Kalman filtering with bursty packet drops is also discussed based on the two-state Markov chain model.
", "doi": "10.7907/ZRAD-XN95", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:3157", "collection": "thesis", "collection_id": "3157", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08172006-130145", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 2051167, "license": "other", "mime_type": "application/pdf", "url": "/3157/1/main.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Distributed Estimation and Control in Networked Systems", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-Vijay" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" }, { "family_name": "Bruck", "given_name": "Jehoshua", "clpid": "Bruck-J" }, { "family_name": "Schulman", "given_name": "Leonard J.", "clpid": "Schulman-L-J" }, { "family_name": "Vaidyanathan", "given_name": "P. P.", "clpid": "Vaidyanathan-P-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Rapid advances in information processing, communication and sensing technologies have enabled more and more devices to be provided with embedded processors, networking capabilities and sensors. For the field of estimation and control, it is now possible to consider an architecture in which many simple components communicate and cooperate to achieve a joint team goal. This distributed (or networked) architecture promises much in terms of performance, reliability and simplicity of design; however, at the same time, it requires extending the traditional theories of control, communication and computation and, in fact, looking at a unified picture of the three fields. A systematic theory of how to design distributed systems is currently lacking.
\r\n\r\nThis dissertation takes the first steps towards understanding the effects of imperfect information flow in distributed systems from an estimation and control perspective and coming up with new design principles to counter these effects. Designing networked systems is difficult because such systems challenge two basic assumptions of traditional control theory - presence of a central node with access to all the information about the system and perfect transmission of information among components. We formulate and solve many problems that deal with the removal of one, or both, of these assumptions. The chief idea explored in this dissertation is the joint design of information flow and the control law. While traditional control design has concentrated on calculating the optimal control input by assuming a particular information flow between the components, our approach seeks to synthesize the optimal information flow along with the optimal control law that satisfies the constraints of the information flow. Thus besides the question of 'What should an agent do?', the questions of 'Whom should an agent talk to?', 'What should an agent communicate?', 'When should an agent communicate?' and so on also have to be answered. The design of the information flow represents an important degree of freedom available to the system designer that has hitherto largely been ignored. As we demonstrate in the dissertation, the joint design of information flow and the optimal control input satisfying the constraints of that information flow yields large improvements in performance over simply trying to fit traditional design theories on distributed systems.
\r\n\r\nWe begin by formulating a distributed control problem in which many agents in a formation need to cooperate to minimize a joint cost function. We provide numerical algorithms to synthesize the optimal constrained control law that involve solving linear equations only and hence are free from numerical issues plaguing the other approaches proposed in the literature. We then provide and analyze a model to understand the issue of designing the topology according to which the agents interact. The results are very surprising since there are cases when allowing communication to happen between two agents may, in fact, be detrimental to the performance.
\r\n\r\nWe then move on to consider the effects of communication channels on control performance. To counter such effects, we propose the idea of encoding information for the purpose of estimation and control prior to transmission. Although information theoretic techniques are not possible in our problem, we are able to solve for a recursive yet optimal encoder / decoder structure in many cases. This information flow design oriented approach has unique advantages such as being optimal for any packet drop pattern, being able to include the effect of known but random delays easily, letting us escape the limits set by reliability for transmission of data across a network by using intermediate nodes as 'repeaters' similar to a digital communication network and so on.
\r\n\r\nWe finally take a look at combining the effects of multiple sources of information and communication channels on estimation and control. We look at a distributed estimation problem in which, at every time step, only a subset out of many sensors can transmit information to the estimator. This is also a representative resource allocation problem. We propose the idea of stochastic communication patterns that allows us to include the effects of communication channels explicitly during system design. Thus, instead of tree-search based algorithms proposed in the literature, we provide stochastic scheduling algorithms that can take into account the random packet drop effect of the channels. We also consider a distributed control problem with switching topologies and solve for the optimal controller. The tools that we develop are applicable to many other scenarios and we demonstrate some of them in the dissertation.
\r\n\r\nAlong the way, we look at many other related problems in the dissertation. As an example, we provide initial results about the issue of robustness of a distributed system design to a malfunctioning agent. This notion is currently lacking in the control and estimation community, but has to be a part of any effective theory for designing networked or distributed systems.
", "doi": "10.7907/KWN2-X741", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:864", "collection": "thesis", "collection_id": "864", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03042007-163003", "primary_object_url": { "basename": "thesis-ds.pdf", "content": "final", "filesize": 1530757, "license": "other", "mime_type": "application/pdf", "url": "/864/1/thesis-ds.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Elements of Feed-Forward and Feedback Control in Drosophila Body Saccades", "author": [ { "family_name": "Bender", "given_name": "John Andrew", "clpid": "Bender-John-Andrew" } ], "thesis_advisor": [ { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "thesis_committee": [ { "family_name": "Laurent", "given_name": "Gilles J.", "clpid": "Laurent-G-J" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Siapas", "given_name": "Athanassios G.", "clpid": "Siapas-A-G" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "I have developed a new experimental preparation of the fruit fly, Drosophila melanogaster. A fly is glued to a steel pin, which is held in the field between two magnets such that the fly is free to rotate about only one axis. Such \"magnetically tethered\" flies perform rapid yaw turns, similar to the behaviors termed \"body saccades\" in free flight. Saccades can be evoked by visual stimulation, in a manner suggesting that the underlying neural circuitry may be performing an angular threshold calculation. Once a saccade is initiated, however, visual feedback has very little effect on its dynamics, but rotational feedback from the haltere system plays an important role in structuring the time course of saccades. Vision is important, though, in maintaining a stable orientation in both intact flies and flies with asymmetrical wing alterations. The halteres are known to mediate responses to Coriolis forces correlated with the fly's rotations in flight, but flies with modified halteres also exhibit distorted saccade dynamics when they are not free to rotate. This suggests that the halteres may be involved in saccade initiation, although the precise mechanisms are not clear. There is preliminary evidence suggesting that the haltere strokes may be actively modulated during flight.", "doi": "10.7907/HEVK-7T03", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1951", "collection": "thesis", "collection_id": "1951", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05222007-101946", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 5076548, "license": "other", "mime_type": "application/pdf", "url": "/1951/1/main.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Treatise on Econometric Forecasting", "author": [ { "family_name": "Martinez Estrada", "given_name": "Alfredo", "clpid": "Martinez-Estrada-Alfredo" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We investigate the effects of model misspecification and stochastic dynamics in the problem of forecasting. In economics and many fields of engineering, many researchers are guilty of the dangerous practice of treating their mathematical models as the true data generating mechanisms responsible for the observed phenomena and downplaying or omitting all together the important step of model verification. In recent years, econometricians have acknowledged the need to account for model misspecification in the problems of estimation and forecasting. In particular, a large body of work has emerged to address properties of estimators under model misspecification, along with a plethora of misspecification testing methodologies. In this work, we investigate the combined effects of model misspecification and various types of stochastic dynamics on forecasts based on linear regression models. The data generating process (DGP) is assumed unknown to the forecaster except for the nature of process dependencies, i.e., independent identically distributed, covariance stationary, or nonstationary. Estimation is carried out by means of ordinary least squares, and forecasts are evaluated with the mean squared forecast error (MSFE) or mean square error of prediction. We investigate the sample size dependence of the MSFE. For this purpose, we develop an algorithm to approximate the MSFE by an expression depending only on the sample size n and moments of the processes. The approximation is constructed by Taylor series expansions of the squared forecast error which do not require knowledge of the functional form of the DGP. The approximation can be used to determine the existence of optimal observation windows which result in the minimum MSFE. We assess the accuracy of the approximating algorithm with Monte Carlo experiments.\r\n", "doi": "10.7907/WXN5-9A47", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:5160", "collection": "thesis", "collection_id": "5160", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12282006-181735", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 628105, "license": "other", "mime_type": "application/pdf", "url": "/5160/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Wireless Network Design and Control", "author": [ { "family_name": "Chen", "given_name": "Lijun", "orcid": "0000-0001-6694-4299", "clpid": "Chen-Lijun" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Optimization theory and game theory provide a suite of tools that are flexible in modelling various network systems, and a rich series of equilibrium solution concepts and convergent algorithms. In this thesis, we view network protocols as distributed algorithms achieving the corresponding network equilibria, and study wireless network design and control in optimization and game-theoretic frameworks.
\r\n\r\nSpecifically, we first take a holistic approach and design an overall framework for the protocol architecture in ad hoc wireless networks. The goal is to integrate various protocol layers into a unified framework, by regarding them as distributed computations over the network to solve some optimization problem. Our current theory integrates three functions--congestion control, routing and scheduling--in transport, network and link layers into a coherent framework. These three functions interact through and are regulated by congestion price so as to achieve a global optimality, even in a time-varying environment. This framework is promising to be extended to provide a mathematical theory for network architecture, and to allow us to systematically carry out cross-layer design.
\r\n\r\nWe then develop a general game-theoretic framework for contention control. We define a general game-theoretic model, called random access game, to study the contention/interaction among wireless nodes, and propose a novel medium access method derived from carrier sensing multiple access with collision avoidance in which each node estimates its conditional collision probability and adjusts its persistence probability or contention window, according to a distributed strategy update mechanism achieving the Nash equilibrium of random access game. This results in simple dynamics, controllable performance objectives, good short-term fairness, low collision, and high throughput. As wireless nodes can estimate conditional collision probabilities by observing consecutive idle slots between transmissions, we can decouple contention control from handling failed transmissions. This also opens up other opportunities such as rate adaptation to channel variations. In addition to providing a general and systematic design methodology for medium access control, the random access game model also provides an analytical framework to understand the equilibrium properties such as throughput, loss and fairness, and dynamic properties of different medium access protocols and their interactions.
\r\n\r\nFinally, we conclude this work with some suggestions for future research.
", "doi": "10.7907/TEVD-PK95", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:64", "collection": "thesis", "collection_id": "64", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01082007-033253", "primary_object_url": { "basename": "Reiser_thesis.pdf", "content": "final", "filesize": 45856229, "license": "other", "mime_type": "application/pdf", "url": "/64/1/Reiser_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Visually Mediated Control of Flight in Drosophila: Not Lost in Translation", "author": [ { "family_name": "Reiser", "given_name": "Michael Bernard", "orcid": "0000-0002-4108-4517", "clpid": "Reiser-Michael-Bernard" } ], "thesis_advisor": [ { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Flying insects exhibit stunning behavioral repertoires that are largely mediated by the visual control of flight. For this reason, presenting a controlled visual environment to tethered insects has been and continues to be a powerful tool for studying the sensory control of complex behaviors. The work presented in this dissertation concerns several robust behavioral responses exhibited by Drosophila that shed light on some of the challenges of visual navigation. To address questions of visual flight control in Drosophila, a modular display system has been designed and has proven to be a robust experimental instrument. The display system has enabled the wide variety of experimental paradigms presented in the thesis.
\r\n\r\nMuch is known about the responses of tethered Drosophila to rotational stimuli. However, the processing of the more complex patterns of motion that occur during translatory flight is largely unknown. Recent experimental results have demonstrated that Drosophila turn away from visual patterns of expansion. However, the avoidance of expansion is so vigorous, that flies robustly orient towards the focus of contraction of a translating flow field. Much of the effort documented in this thesis has sought to explain this paradox.
\r\n\r\nThe paradox has been largely resolved by several significant findings. When undergoing flight directed towards a prominent object, Drosophila will tolerate a level of expansion that would otherwise induce avoidance. The expansion-avoidance behavior is also critically dependent on the speed of image motion; in response to reduced speeds of expansion, Drosophila exhibit a centering response in which they steer towards the focus of expansion by balancing the image motion seen by both eyes. Taken together, these behaviors contribute to a model of Drosophila's visual flight control as emerging from multiple behavioral modules that operate concurrently.
\r\n\r\nSimple computational models of Drosophila's visual system are used to demonstrate that the experimental results arrived at by doing psychophysics on tethered animals actually yield sensible navigation strategies. This final component of the thesis documents an effort to close the feedback loop around the experimenter, by using computational models of Drosophila behavior to constrain the design of future experiments.
", "doi": "10.7907/YYSN-7C82", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:4496", "collection": "thesis", "collection_id": "4496", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11102006-021149", "primary_object_url": { "basename": "ShreeshPMysorePhDThesis.pdf", "content": "final", "filesize": 18609611, "license": "other", "mime_type": "application/pdf", "url": "/4496/1/ShreeshPMysorePhDThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structural Plasticity in Neuronal Networks", "author": [ { "family_name": "Mysore", "given_name": "Shreesh Pranesh", "orcid": "0000-0002-7781-8252", "clpid": "Mysore-Shreesh-Pranesh" } ], "thesis_advisor": [ { "family_name": "Schuman", "given_name": "Erin Margaret", "orcid": "0000-0002-7053-1005", "clpid": "Schuman-E-M" }, { "family_name": "Quartz", "given_name": "Steven R.", "clpid": "Quartz-S-R" } ], "thesis_committee": [ { "family_name": "Schuman", "given_name": "Erin Margaret", "orcid": "0000-0002-7053-1005", "clpid": "Schuman-E-M" }, { "family_name": "Quartz", "given_name": "Steven R.", "clpid": "Quartz-S-R" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Neuronal networks are established during development by the formation of connections (synapses) between neurons. Once formed, these synapses undergo experience-dependent modifications throughout the lifespan of the animal (synaptic plasticity). Additionally, the connectivity pattern itself can be modified in an activity-dependent manner (architectural plasticity). Changes in the structure of synapses, neurons, and networks \u2013 collectively called structural plasticity \u2013 are the predominant mechanisms for changes in the network architecture in the brain. Structural plasticity forms the focus of this thesis and motivates both the experimental and the computational modeling work reported here. With experiments, we look in detail at one form of structural plasticity, namely dendritic spine dynamics. We develop a unified approach to characterize motility and use this both to detect subtle forms of structural dynamics and to uncover novel phenomena in it. We show that disruption of N-cadherin, a synaptic adhesion molecule, causes spines to first be more motile and to shrink in length, and then to be lost. Along with this, synapses are eliminated as well. For the first time, we show that early structural changes can predict later synapse elimination, suggesting that early dynamics may be readouts for future changes in the neural wiring diagram. We also address some of the related mechanistic questions. In our computational modeling work, we address structural plasticity at the next higher scale of complexity. We provide a novel, neurobiologically plausible, and experimentally consistent explanation for how changes in visual experience may produce axogenesis and the formation of new synaptic pathways in the barn owl auditory localization system. We discuss implications of architectural plasticity to the representational power of networks and explore links with statistical learning theory. Taken together, our work argues that architectural changes are a powerful and indispensable form of neural plasticity and sheds new light on the mechanisms of structural plasticity in the brain, thereby contributing to our understanding of learning and memory.", "doi": "10.7907/EVYW-EY02", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:4496", "collection": "thesis", "collection_id": "4496", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11102006-021149", "primary_object_url": { "basename": "ShreeshPMysorePhDThesis.pdf", "content": "final", "filesize": 18609611, "license": "other", "mime_type": "application/pdf", "url": "/4496/1/ShreeshPMysorePhDThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structural Plasticity in Neuronal Networks", "author": [ { "family_name": "Mysore", "given_name": "Shreesh Pranesh", "orcid": "0000-0002-7781-8252", "clpid": "Mysore-Shreesh-Pranesh" } ], "thesis_advisor": [ { "family_name": "Schuman", "given_name": "Erin Margaret", "orcid": "0000-0002-7053-1005", "clpid": "Schuman-E-M" }, { "family_name": "Quartz", "given_name": "Steven R.", "clpid": "Quartz-S-R" } ], "thesis_committee": [ { "family_name": "Schuman", "given_name": "Erin Margaret", "orcid": "0000-0002-7053-1005", "clpid": "Schuman-E-M" }, { "family_name": "Quartz", "given_name": "Steven R.", "clpid": "Quartz-S-R" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Neuronal networks are established during development by the formation of connections (synapses) between neurons. Once formed, these synapses undergo experience-dependent modifications throughout the lifespan of the animal (synaptic plasticity). Additionally, the connectivity pattern itself can be modified in an activity-dependent manner (architectural plasticity). Changes in the structure of synapses, neurons, and networks \u2013 collectively called structural plasticity \u2013 are the predominant mechanisms for changes in the network architecture in the brain. Structural plasticity forms the focus of this thesis and motivates both the experimental and the computational modeling work reported here. With experiments, we look in detail at one form of structural plasticity, namely dendritic spine dynamics. We develop a unified approach to characterize motility and use this both to detect subtle forms of structural dynamics and to uncover novel phenomena in it. We show that disruption of N-cadherin, a synaptic adhesion molecule, causes spines to first be more motile and to shrink in length, and then to be lost. Along with this, synapses are eliminated as well. For the first time, we show that early structural changes can predict later synapse elimination, suggesting that early dynamics may be readouts for future changes in the neural wiring diagram. We also address some of the related mechanistic questions. In our computational modeling work, we address structural plasticity at the next higher scale of complexity. We provide a novel, neurobiologically plausible, and experimentally consistent explanation for how changes in visual experience may produce axogenesis and the formation of new synaptic pathways in the barn owl auditory localization system. We discuss implications of architectural plasticity to the representational power of networks and explore links with statistical learning theory. Taken together, our work argues that architectural changes are a powerful and indispensable form of neural plasticity and sheds new light on the mechanisms of structural plasticity in the brain, thereby contributing to our understanding of learning and memory.", "doi": "10.7907/EVYW-EY02", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2204", "collection": "thesis", "collection_id": "2204", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282007-223415", "primary_object_url": { "basename": "thesis_main_lun.pdf", "content": "final", "filesize": 3008643, "license": "other", "mime_type": "application/pdf", "url": "/2204/1/thesis_main_lun.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Topologies of Complex Networks: Functions and Structures", "author": [ { "family_name": "Li", "given_name": "Lun", "clpid": "Li-Lun" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" }, { "family_name": "Willinger", "given_name": "Walter", "clpid": "Willinger-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "During the last decade, significant efforts have been made toward improving our understanding of the topological structures underlying complex networks and illuminating some of the intriguing large-scale properties exhibited by these systems. The dominant theme of these efforts has been on studying the graph-theoretic properties of the corresponding connectivity structures and on developing universal theories and models that transcend system-specific details and describe the different systems well in a statistical sense.
\r\n\r\nHowever, in this thesis we argue that these efforts have had limited success and are in need of substantial correction. Using a highly engineered system, the Internet, as a case study we demonstrate that networks are designed for a purpose, and ignoring that aspect or obscuring it with the use of some generic but random mechanism can result in models that misrepresent what matters for system functions. By accounting in a minimal manner for both the functional requirements and structural features inherent in the design of an engineered system, we propose an alternative, optimization-based modeling approach that highlights the necessary trade-offs between system performance and the technological and economic constraints that are crucial when designing the system. We show that our proposed approach yields network models that not only match the large-scale graph-theoretic properties of measured router-level topologies well but are also fully consistent with engineering intuition and networking reality, especially as far as their performance aspects and robustness properties are concerned. In fact, we show that our design-inspired network models can be easily distinguished from previously considered probabilistic network models and efficiently achieve the level of performance for which they were designed in the first place.
\r\n\r\nWhile this thesis focuses on the Internet, it has much broader implications for complex networks and graph theory generally. To better differentiate between different graphs that are identical in certain graph statistics, we introduce a structural metric, the s-metric, and demonstrate that it provides insights into the diversity of graphs constrained by certain common properties and sheds new light on many classic graph concepts such as the various notions of self-similarity, likelihood, and assortativity. Our s-metric clarifies much of the confusion surrounding the sensational qualitative claims in the current graph theory literature for complex networks and offers a rigorous and quantitative alternative.
\r\n\r\nMoreover, to examine the space of graphs that satisfy certain common properties, we propose a new approach that is based on establishing a link between two graphs if and only if one can be obtained from the other via a local transformation. Exploring the resulting connected space of graphs by dividing it into countable subspaces provides a much clearer picture on the whole space. We also show that this space of graphs has a rich and interesting structure and that some properties of the latter can be related to features of the individual graphs in this space (e.g., degree variability of a node $g$ in the space of graphs and the s-metric for g).
", "doi": "10.7907/9G3P-7F13", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2336", "collection": "thesis", "collection_id": "2336", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312007-024822", "primary_object_url": { "basename": "THC_thesis.pdf", "content": "final", "filesize": 2999095, "license": "other", "mime_type": "application/pdf", "url": "/2336/1/THC_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Intelligent Information-Gathering: Using Control for Sensing and Decision-Making", "author": [ { "family_name": "Chung", "given_name": "Timothy Hahn Deut", "clpid": "Chung-Timothy-Hahn-Deut" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Information is everywhere and evolving, which necessitates both deliberate and efficient processing to acquire a good understanding of the dynamic situation, environment, or system of interest. Intelligent agents such as autonomous mobile sensors can control the way they gather information and thereby take advantage of feedback to improve the quality of that information. This approach reflects a shift from traditional \"sensing for control\" notions to \"control for sensing\" methods for addressing information-based objectives. This thesis presents several algorithms for distributed sensing tasks in the context of a team of mobile sensing agents. Applications of these types of mobile sensor networks include target tracking, dynamic environment monitoring, and distributed classification. These methods point beyond the use of sensory data for control and toward a framework for using control to improve information-based decisions made by intelligent agents. The sequential decision-theoretic framework presented herein has relevant applications in engineered systems such as search and rescue using a robotic team, as well as potential connections to natural systems including search strategies in the human vision system.", "doi": "10.7907/V5S4-4197", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1897", "collection": "thesis", "collection_id": "1897", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05202007-135411", "primary_object_url": { "basename": "thesis_main.pdf", "content": "final", "filesize": 1027735, "license": "other", "mime_type": "application/pdf", "url": "/1897/1/thesis_main.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Geometrical Analysis of Spatio-temporal Planning Problems", "author": [ { "family_name": "Tiwari", "given_name": "Abhishek", "clpid": "Tiwari-Abhishek" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hassibi", "given_name": "Babak", "clpid": "Hassibi-B" }, { "family_name": "Jeffcoat", "given_name": "David E.", "clpid": "Jeffcoat-D-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this thesis I represent and analyze spatially and temporally constrained multi-agent planning problems using tools from geometry and advanced calculus. The two problems considered in this thesis are multi-agent rendezvous and dynamic sensor coverage. Together, these problems encompass the cooperation, constraint representation,and task scheduling aspects of multi-agent planning problems. I have represented the constraint of the rendezvous problem on the phase space and shown that the fulfilment of rendezvous constraints is equivalent to certain conical regions being invariant. Alternatively, for the dynamic coverage problem, the constraints can be adequately represented on the uncertainty space and sensor motion laws can be obtained by partitioning the uncertainty space and making decisions based on which partition the uncertainty lies in. I have examined convergence behavior of sensor motion under such laws.", "doi": "10.7907/917G-MJ20", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2166", "collection": "thesis", "collection_id": "2166", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272007-214755", "primary_object_url": { "basename": "XinThesis.pdf", "content": "final", "filesize": 670893, "license": "other", "mime_type": "application/pdf", "url": "/2166/1/XinThesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Robustness, Complexity, Validation and Risk", "author": [ { "family_name": "Liu", "given_name": "Xin", "clpid": "Liu-Xin" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Yi", "given_name": "Tau-Mu", "clpid": "Yi-Tau-Mu" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A robust design process starts with modeling of the physical system and the uncertainty it faces. Robust design tools are then applied to achieve specified performance criteria. Verification of system properties is crucial as improvements on the modeling and design practices can be made based on results of such verification. In this thesis, we discuss three aspects of this closed-loop process.
\r\n\r\nFirst and the most important aspect is the possibility of the feedback from verification to system modeling and design. When verification is hard, what does it tell us about our system? When the system is robust, would it be easy to verify so? We study the relation between robustness of a system property posed as a decision problem and the proof complexity of verifying such property. We examine this relation in two classes of problems: percolation lattices and linear programming problems, and show complexity is upper-bounded by the reciprocal of robustness, i.e. fragility.
\r\n\r\nThe second aspect we study is model validation. More precisely, when given a candidate model and experiment data, how do we rigorously refute the model or gain information about the consistent parameter set? Different methods for model invalidation and parameter inference are demonstrated with the G-protein signaling system in yeast to show the advantages and hurdles in their applications.
\r\n\r\nWhile quantification of robustness requirements has been well-studied in engineering, it is just emerging in the field of finance. Robustness specification in finance is closely related to the availability of proper risk measures. We study the estimation of a coherent risk measure, Expected Shortfall (ES). A consistent and asymptotically normal estimator for ES based on empirical likelihood is proposed. Although empirical likelihood based estimators usually involve numerically solving optimization problems that are not necessarily convex, computation of our estimator can be carried out in a sequential manner, avoiding solving non-convex optimization problems.
", "doi": "10.7907/JZX4-QN41", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:3996", "collection": "thesis", "collection_id": "3996", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10092006-165831", "primary_object_url": { "basename": "BerglundThesis.pdf", "content": "final", "filesize": 4782590, "license": "other", "mime_type": "application/pdf", "url": "/3996/1/BerglundThesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Feedback Control of Brownian Motion for Single-Particle Fluorescence Spectroscopy", "author": [ { "family_name": "Berglund", "given_name": "Andrew John", "clpid": "Berglund-Andrew-John" } ], "thesis_advisor": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" } ], "thesis_committee": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Libbrecht", "given_name": "Kenneth George", "clpid": "Libbrecht-K-G" }, { "family_name": "Painter", "given_name": "Oskar J.", "clpid": "Painter-O" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The stochastic Brownian motion of individual particles in solution constrains the utility of single-particle fluorescence microscopy both by limiting the dwell time of particles in the observation volume and by convolving their internal degrees of freedom with their random spatial trajectories. This thesis describes the use of active feedback control to eliminate these undesirable effects. We designed and implemented a feedback tracking system capable of locking the position of a fluorescent particle to the optic axis of our microscope, i.e., capable of tracking the two-dimensional, planar Brownian motion of a free particle in solution. A full theoretical description of the experiment is given in the language of linear stochastic control theory. The model describes both the statistics of the tracking system and provides a generalization of the theory of open-loop Fluorescence Correlation Spectroscopy (FCS) that accounts for fluctuations in fluorescence arising from competition between diffusion and damping. We find excellent agreement between theory and experiment. Using fluorescent polymer microspheres as test particles, we find that the observation time for these particles can be increased by 2-3 orders of magnitude over the open-loop scenario. The system achieves nearly optimal performance for moderately fast-moving particles at very low fluorescent count rates, comparable to those of a single fluorescent protein molecule. The system can classify particles in a binary mixture based on a real-time estimate of their diffusion coefficients (differing by a factor of ~4), achieving 90% success using fewer than 600 photons detected over 120 ms. Future directions for both the experimental and theoretical techniques are briefly discussed.", "doi": "10.7907/EBKX-BP40", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:104", "collection": "thesis", "collection_id": "104", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01102007-010550", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 990506, "license": "other", "mime_type": "application/pdf", "url": "/104/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Distributed Averaging and Efficient File Sharing on Peer-to-Peer Networks", "author": [ { "family_name": "Mehyar", "given_name": "Mortada", "clpid": "Mehyar-Mortada" } ], "thesis_advisor": [ { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" } ], "thesis_committee": [ { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "orcid": "0000-0001-9190-1290", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The work presented in this thesis is mainly divided in two parts. In the first part we study the problem of distributed averaging, which has attracted a lot of interest in the research community in recent years. Our work focuses on the issues of implementing distributed averaging algorithms on peer-to-peer networks such as the Internet. We present algorithms that eliminate the need for global coordination or synchronization, as many other algorithms require, and show mathematical analysis of their convergence.
\r\n\r\nDiscrete-event simulations that verify the theoretical results are presented. We show that the algorithms proposed converge rapidly in practical scenarios. Real-world experiments are also presented to further corroborate these results. We present experiments conducted on the PlanetLab research network. Finally, we present several promising applications of distributed averaging that can be implemented in a wide range of areas of interest.
\r\n\r\nThe second part of this thesis, also related to peer-to-peer networking, is about modelling and understanding peer-to-peer file sharing. The BitTorrent protocol has become one of the most popular peer-to-peer file sharing systems in recent years. Theoretical understanding of the global behavior of BitTorrent and similar peer-to-peer file sharing systems is however not very complete yet. We study a model that requires very simple assumptions yet exhibits a lot structure. We show that it is possible to consider a wide range of performance criteria within the framework, and that the model captures many of the important issues of peer-to-peer file sharing.
\r\n\r\nWe believe the results provide fundamental insights to practical peer-to-peer file sharing systems. We show that many optimization criteria can be studied within our framework. Many new directions of research are also opened up.
", "doi": "10.7907/Q9EV-S167", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2445", "collection": "thesis", "collection_id": "2445", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06042006-160620", "primary_object_url": { "basename": "thesis_Branchaud_Edward_A.pdf", "content": "final", "filesize": 9429095, "license": "other", "mime_type": "application/pdf", "url": "/2445/1/thesis_Branchaud_Edward_A.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "A Control System for Positioning Recording Electrodes to Isolate Neurons in Extracellular Recordings", "author": [ { "family_name": "Branchaud", "given_name": "Edward Allan", "clpid": "Branchaud-Edward-Allan" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" }, { "family_name": "Andersen", "given_name": "Richard A.", "clpid": "Andersen-R-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents an algorithm that autonomously positions recording electrodes inside cortical tissue so as to isolate and then maintain optimal extracellular signal recording quality without human intervention. The algorithm is used to improve the quality and efficiency of acute (daily insertion) recordings that are needed for basic research in neurophysiology. It also offers the potential to increase the longevity and quality of chronic (long-term implant) recordings by controlling an emerging class of chronic arrays in which the electrodes can be continually repositioned after implantation.
\r\n\r\nThe challenges encountered in attempting to isolate neurons are studied. A solution is proposed in which a finite state machine oversees a number of signal processing steps, computes various metrics of the recording quality and issues commands to move the electrode close to neurons without causing them damage. A number of metrics of the quality of neuron isolation are compared.
\r\n\r\nThe algorithm has been used to control a number of commercial microdrive systems, including a single-electrode FHC microdrive and multielectrode microdrives from Thomas Recording and NAN, as well as a novel miniature microdrive. The autonomous positioning software is used by several neuroscientists to perform basic neurophysiology research. Analysis of the system's performance in isolating neurons is included.
", "doi": "10.7907/6HHC-5456", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2402", "collection": "thesis", "collection_id": "2402", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06022006-140421", "primary_object_url": { "basename": "tapus-phd.pdf", "content": "final", "filesize": 1531668, "license": "other", "mime_type": "application/pdf", "url": "/2402/1/tapus-phd.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Distributed Speculations: Providing Fault-Tolerance and Improving Performance", "author": [ { "family_name": "\u021a\u0103pu\u0219", "given_name": "Cristian", "clpid": "\u021a\u0103pu\u0219-Cristian" } ], "thesis_advisor": [ { "family_name": "Hickey", "given_name": "Jason J.", "clpid": "Hickey-J-J" } ], "thesis_committee": [ { "family_name": "Hickey", "given_name": "Jason J.", "clpid": "Hickey-J-J" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis introduces a new programming model based on speculative execution and it examines the use of speculations, a form of distributed transactions, for improving the performance, reliability and fault tolerance of distributed systems. A speculation is defined as a computation that is based on an assumption that is not validated before the computation is started. If the assumption is later invalidated the computation is aborted and the state of the program is rolled back; if the assumption is validated, the results of the computation are committed. The primary difference between a speculation and a transaction is that a speculation is not isolated---for example, a speculative computation may send and receive messages, and it may modify shared objects. As a result, processes that share those objects may be absorbed into a speculation.
\r\n\r\nThe contributions presented in this thesis include:\r\n
In the last several years, significant progress has been made in modelling the Internet congestion control using theories from convex optimization and feedback control. In this dissertation, the equilibrium and dynamics of various congestion control schemes are rigorously studied using these mathematical frameworks.
\r\n\r\nFirst, we study the dynamics of TCP/AQM systems. We demonstrate that the dynamics of queue and average window in Reno/RED networks are determined predominantly by the protocol stability, not by AIMD probing nor noise traffic. Our study shows that Reno/RED becomes unstable when delay increases and more strikingly, when link capacity increases. Therefore, TCP Reno is ill suited for the future high-speed network, which has motivated the design of FAST TCP. Using a continuous-time model, we prove that FAST TCP is globally stable without feedback delays and provide a sufficient condition for local stability when feedback delays are present. We also introduce a discrete-time model for FAST TCP that fully captures the effect of self-clocking and derive the local stability condition for general networks with feedback delays.
\r\n\r\nSecond, the equilibrium properties (i.e., fairness, throughput, and capacity) of TCP/AQM systems are studied using the utility maximization framework. We quantitatively capture the variations in network throughput with changes in link capacity and allocation fairness. We clarify the open conjecture of whether a fairer allocation is always more efficient. The effects of changes in routing are studied using a joint optimization problem over both source rates and their routes. We investigate whether minimal-cost routing with proper link costs can solve this joint optimization problem in a distributed way. We also identify the tradeoff between achievable utility and routing stability.
\r\n\r\nAt the end, two other related projects are briefly described.
", "doi": "10.7907/4DQ0-GA49", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2110", "collection": "thesis", "collection_id": "2110", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-130209", "primary_object_url": { "basename": "pfister_thesis_full.pdf", "content": "final", "filesize": 11870951, "license": "other", "mime_type": "application/pdf", "url": "/2110/1/pfister_thesis_full.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Algorithms for Mobile Robot Localization and Mapping, Incorporating Detailed Noise Modeling and Multi-scale Feature Extraction", "author": [ { "family_name": "Pfister", "given_name": "Samuel Thomas", "clpid": "Pfister-Samuel-Thomas" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Mobile robot localization and mapping in unknown environments is a fundamental requirement for effective autonomous navigation. Three different approaches to localization and mapping are presented. Each is based on data collected from a robot using a dense range scanner to generate a planar representation of the surrounding environment. This externally sensed range data is then overlayed and correlated to estimate the robot's position and build a map.
\r\n\r\nThe three approaches differ in the choice of representation of the range data, but all achieve improvements over prior work using detailed sensor modeling and rigorous bookkeeping of the modeled uncertainty in the estimation processes. In the first approach, the raw range data points collected from two different positions are individually weighted and aligned to estimate the relative robot displacement. In the second approach, line segment features are extracted from the raw point data and are used as the basis for efficient and robust global map construction and localization. In the third approach, a new multi-scale data representation is introduced. New methods of localization and mapping are developed, taking advantage of this multi-scale representation to achieve significant improvements in computational complexity. A central focus of all three approaches is the determination of accurate and robust solutions to the data association problem, which is critical to the accuracy of any sensor-based localization and mapping method.
\r\n\r\nExperiments using data collected from a Sick LMS-200 laser scanner illustrate the effectiveness of the algorithms and improvements over prior work. All methods are capable of being run in real time on a mobile robot, and can be used to support fully autonomous navigation applications.
", "doi": "10.7907/FN3J-M568", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:1876", "collection": "thesis", "collection_id": "1876", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05192006-063455", "primary_object_url": { "basename": "thesistwoside.pdf", "content": "final", "filesize": 14253494, "license": "other", "mime_type": "application/pdf", "url": "/1876/1/thesistwoside.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Multi-robot Systems: Modeling Swarm Dynamics and Designing Inspection Planning Algorithms", "author": [ { "family_name": "Williams", "given_name": "Kjerstin Irja", "clpid": "Williams-Kjerstin-Irja" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Martinoli", "given_name": "Alcherio", "clpid": "Martinoli-A" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Martinoli", "given_name": "Alcherio", "clpid": "Martinoli-A" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "For a variety of applications, the capability of simultaneous sensing and action in multiple locations that is inherent to multi-robot approaches offers potential advantages over single robot systems in robustness, efficiency, and application feasibility.
\r\n\r\nAt the fully distributed and reactive end of the multi-robot system spectrum, I present mathematical modeling methodologies developed to predict and optimize a self-organized robotic swarm\u2019s performance for several tasks. These models allow us to better understand the relationship between agent and group behavior by capturing the dynamics of these highly stochastic, nonlinear, asynchronous systems at various levels of abstraction, in some cases even achieving mathematical tractability. The models deliver qualitatively and quantitatively correct predictions several orders of magnitude more quickly than an embodied simulator can. Swarm modeling lays the foundation for more generalized SI system design methodology by saving time, enabling generalization to different robotic platforms, and estimating optimal design and control parameters.
\r\n\r\nIn considering more complex target tasks and behaviors, efficiency and completeness of execution may be of concern, and a swarm approach may not be appropriate. In such cases a more deliberative approach may be warranted. In that context, I introduce the multi-robot boundary coverage problem, in which a group of robots is required to completely inspect the boundary of all two-dimensional objects in a specified environment. To make such a guarantee, I present a centralized planning approach that constructs a two-component abstraction of the problem: a graph representing the particular instance of the inspection task and a graph problem whose solution represents a complete plan for inspection. Using the building blocks of this approach, related inspection tasks that require the robotic system to adapt to a changes in team size and task assignment are also explored. The application of these planning methods to the case of long-term deployment for surveillance applications that require repetitive coverage is also discussed.
\r\n\r\nThe recurring theme of this thesis is that we must look beyond implementation and validation of a particular system and ask how its design can contribute to the development of a more general design methodology.
", "doi": "10.7907/G1T2-FB74", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2014", "collection": "thesis", "collection_id": "2014", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242006-190748", "primary_object_url": { "basename": "cremean_thesis.pdf", "content": "final", "filesize": 4480525, "license": "other", "mime_type": "application/pdf", "url": "/2014/1/cremean_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "System Architectures and Environment Modeling for High-Speed Autonomous Navigation", "author": [ { "family_name": "Cremean", "given_name": "Lars Br\u00f6r", "clpid": "Cremean-Lars-Br\u00f6r" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Successful high-speed autonomous navigation requires integration of tools from robotics, control theory, computer vision, and systems engineering. This thesis presents work that develops and combines these tools in the context of navigating desert terrain.
\r\n\r\nA comparative analysis of reactive, behavior-based, and deliberative control architectures provides important guidelines for design of robotic systems. These guidelines depend on the particular task and environment of the vehicle. Two important factors are identified which guide an effective choice between these architectures: dynamic feasibility for the vehicle, and predictability of the environment. This is demonstrated by parallels to control theory, illustrative examples, simulations, and analysis of Bob and Alice---Caltech's full-scale autonomous ground vehicle entries in the 2004 and 2005 Grand Challenge races, respectively.
\r\n\r\nFurther, new model-based methods are developed for constructing and maintaining estimates of terrain elevation and road geometry. These are demonstrated in simulation and in fully autonomous operation of Alice, including accurate detection and tracking of the centerline of desert roads at speeds up to 5 m/s. Finally, Alice's navigation architecture is presented in full along with experimental results that demonstrate its capabilities.
", "doi": "10.7907/8HT2-N165", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2363", "collection": "thesis", "collection_id": "2363", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012006-150109", "primary_object_url": { "basename": "kriechbaum-thesis.pdf", "content": "final", "filesize": 1921860, "license": "other", "mime_type": "application/pdf", "url": "/2363/1/kriechbaum-thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Tools and Algorithms for Mobile Robot Navigation with Uncertain Localization", "author": [ { "family_name": "Kriechbaum", "given_name": "Kristopher Lars", "clpid": "Kriechbaum-Kristopher-Lars" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Collins", "given_name": "Curtis L.", "clpid": "Collins-C-L" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The ability for a mobile robot to localize itself is a basic requirement for reliable long range autonomous navigation. This thesis introduces new tools and algorithms to aid in robot localization and navigation. I introduce a new range scan matching method that incorporates realistic sensor noise models. This method can be thought of as an improved form of odometry. Results show an order of magnitude of improvement over typical mobile robot odometry. In addition, I have created a new sensor-based planning algorithm where the robot follows the locally optimal path to the goal without exception, regardless of whether or not the path moves towards or temporarily away from the goal. The cost of a path is defined as the path length. This new algorithm, which I call \"Optim-Bug,\" is complete and correct. Finally, I developed a new on-line motion planning procedure that determines a path to a goal that optimally allows the robot to localize itself at the goal. This algorithm is called \"Uncertain Bug.\" In particular, the covariance of the robot's pose estimate at the goal is minimized. This characteristic increases the likelihood that the robot will actually be able to reach the desired goal, even when uncertainty corrupts its localization during movement along the path. The robot's path is chosen so that it can use known features in the environment to improve its localization. This thesis is a first step towards bringing the tools of mobile robot localization and mapping together with ideas from sensor-based motion planning.", "doi": "10.7907/R6YB-NQ21", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2062", "collection": "thesis", "collection_id": "2062", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05252006-221412", "primary_object_url": { "basename": "thesis052606.pdf", "content": "final", "filesize": 3500508, "license": "other", "mime_type": "application/pdf", "url": "/2062/1/thesis052606.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Engineering Design Synthesis of Sensor and Control Systems for Intelligent Vehicles", "author": [ { "family_name": "Zhang", "given_name": "Yizhen", "clpid": "Zhang-Yizhen" } ], "thesis_advisor": [ { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" } ], "thesis_committee": [ { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Martinoli", "given_name": "Alcherio", "clpid": "Martinoli-A" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Pickar", "given_name": "Kenneth A.", "clpid": "Pickar-K-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis investigates the application of formal engineering design synthesis methodologies to the development of sensor and control systems for intelligent vehicles.
\r\n\r\nA formal engineering design synthesis methodology based on evolutionary computation is presented, with special emphasis on dealing with modern engineering design challenges, such as high or variable complexity of design solutions, multiple conflicting design objectives, and noisy evaluation results, etc. The efficacy of the evolutionary design synthesis method is validated through multiple different case studies, where a variety of novel design solutions are generated to represent different engineering design trade-offs, and they have achieved performances comparable to, if not better than, that of hand-coded solutions in the same simplified environment. More importantly, this automatic design synthesis method shows great potential to handle more complex design problems, where a good hand-coded solution may be very difficult or even impossible to obtain. Moreover, the evolutionary design synthesis methodology appears promising to deal with uncertainty in the problem efficiently and adapt to the collective task nature well.
\r\n\r\nIn addition, multiple levels of vehicle simulation models with different computational cost and fidelity as well as necessary driver behaviors are implemented for different types of simulation experiments conducted for different research purposes. Efforts are made to try to generate good candidate solutions efficiently with less computational time and human engineering effort.
\r\n\r\nFurthermore, a new threat assessment measure, time-to-last-second-braking (Tlsb), is proposed, which directly characterizes human natural judgment of the urgency and severity of threats in terms of time. Based on driver reaction time experimental results, new warning and overriding criteria are proposed in terms of the new Tlsb measure, and the performance is analyzed statistically in terms of two typical sample pre-crash traffic scenarios. Less affected by driver behavior variability, the new criteria characterize the current dynamic situations better than the previous ones, providing more appropriate warning and more effective overriding at the last moment. Finally, the possibility of frontal collision avoidance through steering (lane-changing) is discussed, and similarly the time-to-last-second-steering (Tlss) measure is proposed and compared with Tlsb.
", "doi": "10.7907/NB6H-S822", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2735", "collection": "thesis", "collection_id": "2735", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06262006-171822", "primary_object_url": { "basename": "thesis_master.pdf", "content": "final", "filesize": 676842, "license": "other", "mime_type": "application/pdf", "url": "/2735/1/thesis_master.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Distributed Gradient Systems and Dynamic Coordination", "author": [ { "family_name": "Spanos", "given_name": "Demetri Polychronis", "clpid": "Spanos-Demetri-Polychronis" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Many systems comprised of interconnected sub-units exhibit coordinated behaviors; social groups, networked computers, financial markets, and numerous biological systems come to mind. There has been long-standing interest in developing a scientific understanding of coordination, both for explanatory power in the natural and economic sciences, and also for constructive power in engineering and applied sciences. This thesis is an abstract study of coordination, focused on developing a systematic \"design theory\" for producing interconnected systems with specifiable coordinated behavior; this is in contrast to the bulk of previous work on this subject, in which any design component has been primarily ad-hoc.
\r\n\r\nThe main theoretical contribution of this work is a geometric formalism in which to cast distributed systems. This has numerous advantages and \"naturally\" parametrizes a wide class of distributed interaction mechanisms in a uniform way. We make use of this framework to present a model for distributed optimization, and we introduce the distributed gradient as a general design tool for synthesizing dynamics for distributed systems. The distributed optimization model is a useful abstraction in its own right and motivates a definition for a distributed extremum. As one might expect, the distributed gradient is zero at a distributed extremum, and the dynamics of a distributed gradient flow must converge to a distributed extremum. This forms the basis for a wide variety of designs, and we are in fact able to recover a widely studied distributed averaging algorithm as a very special case.
\r\n\r\nWe also make use of our geometric model to introduce the notion of coordination capacity; intuitively, this is an upper bound on the \"complexity\" of coordination that is feasible given a particular distributed interaction structure. This gives intuitive results for local, distributed, and global control architectures, and allows formal statements to be made regarding the possibility of \"solving\" certain optimization problems under a particular distributed interaction model.
\r\n\r\nFinally, we present a number of applications to illustrate the theoretical approach presented; these range from \"standard\" distributed systems tasks (leader election and clock synchronization) to more exotic tasks like graph coloring, distributed account balancing, and distributed statistical computations.
", "doi": "10.7907/D1NJ-KF96", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2968", "collection": "thesis", "collection_id": "2968", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07232004-075729", "primary_object_url": { "basename": "GregoryPhD0704.pdf", "content": "final", "filesize": 2678591, "license": "other", "mime_type": "application/pdf", "url": "/2968/1/GregoryPhD0704.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Design and Stability Analysis of an Integrated Controller for Highly Flexible Advanced Aircraft Utilizing the Novel Nonlinear Dynamic Inversion", "author": [ { "family_name": "Gregory", "given_name": "Irene Michelle", "clpid": "Gregory-Irene-Michelle" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Davidson", "given_name": "John B.", "clpid": "Davidson-J-B" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "High performance aircraft of the future will be designed to be lighter, more maneuverable, and operate over an ever expanding flight envelope. This set of conditions will necessarily mean highly flexible vehicles operating in nonlinear regimes. A methodology proposed to better optimize their responses to both pilot input and external disturbances, as well as to decrease the cost of vehicle design is the novel dynamic inversion. The attractiveness of this methodology lies in the fact that the inherent nonlinearities of the problem and the coupled nature of flexible dynamics are explicitly considered.
\r\n\r\nThe contribution of this work to the state of the art is predicated on the development and application of the novel dynamic inversion methodology to handle highly flexible aircraft in an integrated flight/structural mode control manner. The unprecedented small separation between rigid body and flexible dynamics as well as the reciprocal interaction between them due to flight control action are the key elements of the aircraft model. The novel approach to the nonlinear dynamic inversion allows the methodology to more intelligently handle flexible dynamics in the context of the dual objectives of integrated flight/SMC control by altering flexible mode damping without cancellation; thus, improving disturbance response and avoiding the potentially destabilizing effect of pole cancellation close to the j-omega-axis in case of modeling uncertainty. The necessary level of model complexity for design has been established with particular attention given to understanding physics. The effect of uncertainty in the structural mode dynamics has been addressed.
\r\n\r\nFurther contribution of this work addresses the issue of stability of the dynamic systems driven by nonlinear controllers. One result shows how assessing stability of an n-dimensional system can be reduced to checking stability of a two-dimensional one using algebraic expressions that are based on the vehicle characteristics such as aerodynamic coefficients. This reduces a complicated dynamical problem to something purely algebraic and manageably complex. Another approach is based on algorithmically finding a local Lyapunov function using sum of squares. The presented results are the first to address the question of stability for the nonlinear dynamic inversion in the presence of flexible dynamics.
\r\n", "doi": "10.7907/Y6B1-ZZ55", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2089", "collection": "thesis", "collection_id": "2089", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-100534", "primary_object_url": { "basename": "BhatThesis_05_26_2005.pdf", "content": "final", "filesize": 1917954, "license": "other", "mime_type": "application/pdf", "url": "/2089/1/BhatThesis_05_26_2005.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Lagrangian Averaging, Nonlinear Waves, and Shock Regularization", "author": [ { "family_name": "Bhat", "given_name": "Harish Subrahmanya", "orcid": "0000-0001-7631-1831", "clpid": "Bhat-Harish-Subrahmanya" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Hajimiri", "given_name": "Ali", "clpid": "Hajimiri-A" }, { "family_name": "Fetecau", "given_name": "Razvan Constantin", "clpid": "Fetecau-R-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Schneider", "given_name": "Tapio", "clpid": "Schneider-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this thesis, we explore various models for the flow of a compressible fluid as well as model equations for shock formation, one of the main features of compressible fluid flows.
\r\n\r\nWe begin by reviewing the variational structure of compressible fluid mechanics. We derive the barotropic compressible Euler equations from a variational principle in both material and spatial frames. Writing the resulting equations of motion requires certain Lie-algebraic calculations that we carry out in detail for expository purposes.
\r\n\r\nNext, we extend the derivation of the Lagrangian averaged Euler (LAE-alpha) equations to the case of barotropic compressible flows. The derivation in this thesis involves averaging over a tube of trajectories centered around a given Lagrangian flow. With this tube framework, the LAE-alpha equations are derived by following a simple procedure: start with a given action, expand via Taylor series in terms of small-scale fluid fluctuations, truncate, average, and then model those terms that are nonlinear functions of the fluctuations.
\r\n\r\nWe then analyze a one-dimensional subcase of the general models derived above. We prove the existence of a large family of traveling wave solutions. Computing the dispersion relation for this model, we find it is nonlinear, implying that the equation is dispersive. We carry out numerical experiments that show that the model possesses smooth, bounded solutions that display interesting pattern formation.
\r\n\r\nFinally, we examine a Hamiltonian partial differential equation (PDE) that regularizes the inviscid Burgers equation without the addition of standard viscosity. Here alpha is a small parameter that controls a nonlinear smoothing term that we have added to the inviscid Burgers equation. We show the existence of a large family of traveling front solutions. We analyze the initial-value problem and prove well-posedness for a certain class of initial data. We prove that in the zero-alpha limit, without any standard viscosity, solutions of the PDE converge strongly to weak solutions of the inviscid Burgers equation. We provide numerical evidence that this limit satisfies an entropy inequality for the inviscid Burgers equation. We demonstrate a Hamiltonian structure for the PDE.
", "doi": "10.7907/8DJ2-F672", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:5225", "collection": "thesis", "collection_id": "5225", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06072005-163739", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 4892392, "license": "other", "mime_type": "application/pdf", "url": "/5225/2/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Bio-Inspired Visuomotor Convergence in Navigation and Flight Control Systems", "author": [ { "family_name": "Humbert", "given_name": "James Sean", "orcid": "0000-0002-0863-875X", "clpid": "Humbert-James-Sean" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "MacMynowski", "given_name": "Douglas G.", "clpid": "MacMynowski-D-G" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Dickinson", "given_name": "Michael H.", "clpid": "Dickinson-M-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Insects exhibit incredibly robust closed loop flight dynamics in the face of uncertainties. A fundamental principle contributing to this unparalleled behavior is rapid processing and convergence of visual sensory information to flight motor commands via spatial wide-field integration, accomplished by retinal motion pattern sensitive interneurons (LPTCs) in the lobula plate portion of the visual ganglia. Within a control-theoretic framework, an inner product model for wide-field integration of retinal image flow is developed, representing the spatial decompositions performed by LPTCs in the insect visuomotor system. A rigorous characterization of the information available from this visuomotor convergence technique for motion within environments exhibiting non-homogeneous spatial distributions is performed, establishing the connection between retinal motion sensitivity shape and closed loop behavior. The proposed output feedback methodology is shown to be sufficient to give rise to experimentally observed insect navigational heuristics, including forward speed regulation, obstacle avoidance, hovering, and terrain following behaviors. Hence, extraction of global retinal motion cues through computationally efficient wide-field integration processing provides a novel and promising methodology for utilizing visual sensory information in autonomous robotic navigation and flight control applications.\r\n", "doi": "10.7907/T5QZ-QS18", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2147", "collection": "thesis", "collection_id": "2147", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-113928", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 752980, "license": "other", "mime_type": "application/pdf", "url": "/2147/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "State Estimation in Multi-Agent Decision and Control Systems", "author": [ { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-Domitilla" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Klavins", "given_name": "Eric", "clpid": "Klavins-E" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "his thesis addresses the problem of estimating the state in multi-agent decision and control systems. In particular, a novel approach to state estimation is developed that uses partial order theory in order to overcome some of the severe computational complexity issues arising in multi-agent systems. Within this approach, state estimation algorithms are developed that enjoy provable convergence properties and are scalable with the number of agents.
\r\n\r\nThe dynamic evolution of the systems under study are characterized by the interplay of continuous and discrete variables. Continuous variables usually represent physical quantities such as position, velocity, voltage, and current, while the discrete variables usually represent quantities internal to the decision protocol that are used for coordination, communication, and control. Within the proposed state estimation approach, the estimation of continuous and discrete variables is developed in the same mathematical framework as a joint continuous-discrete space is considered for the estimator. This way, the dichotomy between the continuous and discrete world is overcome for the purpose of state estimation.
\r\n\r\nApplication examples are considered, which include the state estimation in competitive multi-robot systems and in multi-agent discrete event systems, and the monitoring of distributed environments.
", "doi": "10.7907/SAX3-ED56", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2163", "collection": "thesis", "collection_id": "2163", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-165938", "primary_object_url": { "basename": "jf_cit_phdthesis.pdf", "content": "final", "filesize": 4884172, "license": "other", "mime_type": "application/pdf", "url": "/2163/1/jf_cit_phdthesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Coarse Analysis of Multiscale Systems: Diffuser Flows, Charged Particle Motion, and Connections to Averaging Theory", "author": [ { "family_name": "Fung", "given_name": "Jimmy", "orcid": "0000-0002-6612-2209", "clpid": "Fung-Jimmy" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "We describe a technique for the efficient computation of the dominant-scale dynamics of a fluid system when only a high-fidelity simulation is available. Such a technique is desirable when governing equations for the dominant scales are unavailable, when model reduction is impractical, or when the original high-fidelity computation is expensive. We adopt the coarse analysis framework proposed by I. G. Kevrekidis (Comm. Math. Sci. 2003), where a computational superstructure is designed to use short-time, high-fidelity simulations to extract the dominant features for a multiscale system. We apply this technique to compute the dominant features of the compressible flow through a planar diffuser. We apply the proper orthogonal decomposition to classify the dominant and subdominant scales of diffuser flows. We derive a suitable coarse projective Adams-Bashforth time integration routine and apply it to compute averaged diffuser flows. The results include accurate tracking of the dominant-scale dynamics for a range of parameter values for the computational superstructure. These results demonstrate that coarse analysis methods are useful for solving fluid flow problems of a multiscale nature.
\r\n\r\nIn order to elucidate the behavior of coarse analysis techniques, we make comparisons to averaging theory. To this end, we derive governing equations for the average motion of charged particles in a magnetic field in a number of different settings. First, we apply a novel procedure, inspired by WKB theory and Whitham averaging, to average the variational principle. The resulting equations are equivalent to the guiding center equations for charged particle motion; this marks an instance where averaging and variational principles commute. Secondly, we apply Lagrangian averaging techniques, previously applied in fluid mechanics, to derive averaged equations. Making comparisons to the WKB/Whitham-style derivation allows for the necessary closure of the Lagrangian averaging formulation. We also discuss the Hamiltonian setting and show that averaged Hamiltonian systems may be derivable using concepts from coarse analysis. Finally, we apply a prototypical coarse analysis procedure to the system of charged particles and generate trajectories that resemble guiding center trajectories. We make connections to perturbation theory to derive guidelines for the design of coarse analysis techniques and comment on the prototypical coarse analysis application.
", "doi": "10.7907/wn0z-gn57", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2155", "collection": "thesis", "collection_id": "2155", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-144358", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 856631, "license": "other", "mime_type": "application/pdf", "url": "/2155/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Optimization-Based Methods for Nonlinear and Hybrid Systems Verification", "author": [ { "family_name": "Prajna", "given_name": "Stephen", "clpid": "Prajna-Stephen" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Rantzer", "given_name": "Anders", "clpid": "Rantzer-A" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Complex behaviors that can be exhibited by hybrid systems make the verification of such systems both important and challenging. Due to the infinite number of possibilities taken by the continuous state and the uncertainties in the system, exhaustive simulation is impossible, and also computing the set of reachable states is generally intractable. Nevertheless, the ever-increasing presence of hybrid systems in safety critical applications makes it evident that verification is an issue that has to be addressed.
\r\n\r\nIn this thesis, we develop a unified methodology for verifying temporal properties of continuous and hybrid systems. Our framework does not require explicit computation of reachable states. Instead, functions of state termed barrier certificates and density functions are used in conjunction with deductive inference to prove properties such as safety, reachability, eventuality, and their combinations. As a consequence, the proposed methods are directly applicable to systems with nonlinearity, uncertainty, and constraints. Moreover, it is possible to treat safety verification of stochastic systems in a similar fashion, by computing an upper-bound on the probability of reaching the unsafe states.
\r\n\r\nWe formulate verification using barrier certificates and density functions as convex programming problems. For systems with polynomial descriptions, sum of squares optimization can be used to construct polynomial barrier certificates and density functions in a computationally scalable manner. Some examples are presented to illustrate the use of the methods. At the end, the convexity of the problem formulation is also exploited to prove a converse theorem in safety verification using barrier certificates.
", "doi": "10.7907/S3BJ-4M47", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:1678", "collection": "thesis", "collection_id": "1678", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05082005-100243", "primary_object_url": { "basename": "finalthesis.pdf", "content": "final", "filesize": 1604788, "license": "other", "mime_type": "application/pdf", "url": "/1678/1/finalthesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Scalable Analysis of Nonlinear Systems Using Convex Optimization", "author": [ { "family_name": "Papachristodoulou", "given_name": "Antonis", "orcid": "0000-0002-3565-8967", "clpid": "Papachristodoulou-Antonis" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Rantzer", "given_name": "Anders", "clpid": "Rantzer-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Low", "given_name": "Steven H.", "clpid": "Low-S-H" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "In this thesis, we investigate how convex optimization can be used to analyze different classes of nonlinear systems at various scales algorithmically. The methodology is based on the construction of appropriate Lyapunov-type certificates using sum of squares techniques.
\r\n\r\nAfter a brief introduction on the mathematical tools that we will be using, we turn our attention to robust stability and performance analysis of systems described by Ordinary Differential Equations. A general framework for constrained systems analysis is developed, under which stability of systems with polynomial, non polynomial vector fields and switching systems, as well as estimating the region of attraction and the L2 gain can be treated in a unified manner. Examples from biology and aerospace illustrate our methodology.
\r\n\r\nWe then consider systems described by Functional Differential Equations (FDEs), i.e., time-delay systems. Their main characteristic is that they are infinite dimensional, which complicates their analysis. We first show how the complete Lyapunov-Krasovskii functional can be constructed algorithmically for linear time delay systems. Then, we concentrate on delay-independent and delay-dependent stability analysis of nonlinear FDEs using sum of squares techniques. An example from ecology is given.
\r\n\r\nThe scalable stability analysis of congestion control algorithms for the Internet is investigated next. The models we use result in an arbitrary interconnection of FDE subsystems, for which we require that stability holds for arbitrary delays, network topologies and link capacities. Through a constructive proof, we develop a Lyapunov functional for FAST - a recently developed network congestion control scheme - so that the Lyapunov stability properties scale with the system size. We also show how other network congestion control schemes can be analyzed in the same way.
\r\n\r\nFinally, we concentrate on systems described by Partial Differential Equations. We show that axially constant perturbations of the Navier-Stokes equations for Hagen-Poiseuille flow are globally stable, even though the background noise is amplified as R3 where R is the Reynolds number, giving a 'robust yet fragile' interpretation. We also propose a sum of squares methodology for the analysis of systems described by parabolic PDEs.
\r\n\r\nWe conclude this work with an account for future research.
", "doi": "10.7907/5YG6-JG32", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2347", "collection": "thesis", "collection_id": "2347", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012004-063432", "primary_object_url": { "basename": "etd_1.pdf", "content": "final", "filesize": 2865121, "license": "other", "mime_type": "application/pdf", "url": "/2347/1/etd_1.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structural Control Using Regenerative Force Actuation Networks", "author": [ { "family_name": "Scruggs", "given_name": "Jeffrey Thomas", "orcid": "0000-0002-1560-6211", "clpid": "Scruggs-Jeffrey-Thomas" } ], "thesis_advisor": [ { "family_name": "Iwan", "given_name": "Wilfred D.", "clpid": "Iwan-W-D" } ], "thesis_committee": [ { "family_name": "Iwan", "given_name": "Wilfred D.", "clpid": "Iwan-W-D" }, { "family_name": "Hall", "given_name": "John F.", "clpid": "Hall-J-F" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A Regenerative Force Actuation (RFA) Network consists of multiple electromechanical forcing devices distributed throughout a structural system and actuated in such a way as to reduce the response of the structure when subject to an excitation. The associated electronics of the devices are connected together such that they are capable of sharing electrical power with each other. This makes it possible for some devices to extract mechanical energy from the structure, while others re-inject a portion of that energy back into the structure at other locations. The forcing capability of an RFA network is constrained only by the requirement that in the aggregate the total network must always dissipate energy.
\r\n\r\nThe electromechanical currents generated by RFA networks must be controlled to create the desired structural forces. This control is facilitated by the alternation of a multitude of power-electronic transistor switches in the electrical network. In this study, a sliding-mode switching controller is proposed for realizing zero-error force command tracking. It is shown that parameter uncertainty is a critical issue for force commands which require the network to operate near its optimum transmissive efficiency.
\r\n\r\nRFA networks can be used to create velocity-proportional damping forces in structures. However, unlike traditional structural damping, RFA networks have the ability to create non-local and asymmetric damping forces. It is shown that this more generalized damping capability can lead to significant improvements in the forced response of a structure, as compared with traditional linear damping.
\r\n\r\nRFA networks may also be used for feedback control. In this context, the forcing capability of the RFA network is constrained by its physical limitations. In this study, a systematic method of nonlinear control design called \"Damping-Reference\" control is proposed, which guarantees a certain level of quadratic performance for the structural response. Variants of the control law synthesis are proposed for quadratic regulation, stochastic control, and H[infinity] control contexts.
\r\n\r\nThese ideas are illustrated in the context of earthquake engineering through a simulation example, involving a three-story structure with a two-actuator RFA network installed. In this example, it is shown that the \"power sharing\" nature of the RFA network has a significant influence on the response.
", "doi": "10.7907/W3M9-ZW72", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:1854", "collection": "thesis", "collection_id": "1854", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05182004-154045", "primary_object_url": { "basename": "rossthesis_5_11.pdf", "content": "final", "filesize": 6185364, "license": "other", "mime_type": "application/pdf", "url": "/1854/1/rossthesis_5_11.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Cylindrical Manifolds and Tube Dynamics in the Restricted Three-Body Problem", "author": [ { "family_name": "Ross", "given_name": "Shane David", "orcid": "0000-0001-5523-2376", "clpid": "Ross-Shane-David" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Scheeres", "given_name": "Daniel", "clpid": "Scheeres-D" }, { "family_name": "Lo", "given_name": "Martin", "clpid": "Lo-Martin" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Within the phase space of the planar circular restricted three-body problem, stable and unstable manifolds of periodic orbits with a S x R (cylindrical) geometry are shown to exist. The periodic orbits considered reside in bottleneck regions of the energy manifold, separating large zones associated with motion about one mass, the other mass, or both masses.
\r\n\r\nThe cylinders have the physical property that all motion through the bottleneck in which the periodic orbit resides must occur through the interior of these surfaces. The cylinders thus mediate the global transport of test particles between large zones of the energy surface which are separated by the bottlenecks.
\r\n\r\nBy elucidating the structuring role of the cylinders, we provide a new language for discussing some important problems in celestial mechanics. Furthermore, we propose that these cylindrical structures are the natural objects of study for the design of space mission trajectories which take advantage of three-body effects.
", "doi": "10.7907/KHYT-A428", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:831", "collection": "thesis", "collection_id": "831", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03022004-000251", "primary_object_url": { "basename": "01_thesis_double_sided_mleok.pdf", "content": "final", "filesize": 3867316, "license": "other", "mime_type": "application/pdf", "url": "/831/1/01_thesis_double_sided_mleok.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Foundations of Computational Geometric Mechanics", "author": [ { "family_name": "Leok", "given_name": "Melvin", "orcid": "0000-0002-8326-0830", "clpid": "Leok-Melvin" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Weinstein", "given_name": "Alan Jay", "clpid": "Weinstein-Alan-J-Physics" }, { "family_name": "Ortiz", "given_name": "Michael", "clpid": "Ortiz-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hou", "given_name": "Thomas Y.", "clpid": "Hou-T-Y" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Geometric mechanics involves the study of Lagrangian and Hamiltonian mechanics using geometric and symmetry techniques. Computational algorithms obtained from a discrete Hamilton's principle yield a discrete analogue of Lagrangian mechanics, and they exhibit excellent structure-preserving properties that can be ascribed to their variational derivation.
\r\n\r\nWe construct discrete analogues of the geometric and symmetry methods underlying geometric mechanics to enable the systematic development of computational geometric mechanics. In particular, we develop discrete theories of reduction by symmetry, exterior calculus, connections on principal bundles, as well as generalizations of variational integrators.
\r\n\r\nDiscrete Routh reduction is developed for abelian symmetries, and extended to systems with constraints and forcing. Variational Runge-Kutta discretizations are considered in detail, including the extent to which symmetry reduction and discretization commute. In addition, we obtain the Reduced Symplectic Runge-Kutta algorithm, which is a discrete analogue of cotangent bundle reduction.
\r\n\r\nDiscrete exterior calculus is modeled on a primal simplicial complex, and a dual circumcentric cell complex. Discrete notions of differential forms, exterior derivatives, Hodge stars, codifferentials, sharps, flats, wedge products, contraction, Lie derivative, and the Poincar?emma are introduced, and their discrete properties are analyzed. In examples such as harmonic maps and electromagnetism, discretizations arising from discrete exterior calculus commute with taking variations in Hamilton's principle, which implies that directly discretizing these equations yield numerical schemes that have the structure-preserving properties associated with variational schemes.
\r\n\r\nDiscrete connections on principal bundles are obtained by introducing the discrete Atiyah sequence, and considering splittings of the sequence. Equivalent representations of a discrete connection are considered, and an extension of the pair groupoid composition that takes into account the principal bundle structure is introduced. Discrete connections provide an intrinsic coordinatization of the reduced discrete space, and the necessary discrete geometry to develop more general discrete symmetry reduction techniques.
\r\n\r\nGeneralized Galerkin variational integrators are obtained by discretizing the action integral through appropriate choices of finite-dimensional function space and numerical quadrature. Explicit expressions for Lie group, higher-order Poincar\u00e9, higher-order symplectic-energy-momentum, and pseudospectral variational integrators are presented, and extensions such as spatio-temporally adaptive and multiscale variational integrators are briefly described.
", "doi": "10.7907/KDV0-WR34", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:2198", "collection": "thesis", "collection_id": "2198", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282004-170123", "primary_object_url": { "basename": "WBDdissertation.pdf", "content": "final", "filesize": 1540394, "license": "other", "mime_type": "application/pdf", "url": "/2198/1/WBDdissertation.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Distributed Receding Horizon Control of Multiagent Systems", "author": [ { "family_name": "Dunbar", "given_name": "William Bruce", "orcid": "0000-0002-0913-318X", "clpid": "Dunbar-William-Bruce" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hickey", "given_name": "Jason J.", "clpid": "Hickey-J-J" }, { "family_name": "Shamma", "given_name": "Jeff", "clpid": "Shamma-J" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Multiagent systems arise in several domains of engineering. Examples include arrays of mobile sensor networks for aggregate imagery, autonomous highways, and formations of unmanned aerial vehicles. In these contexts, agents are governed by vehicle dynamics and often constraints, and the control objective is achieved by cooperation. Cooperation refers to the agreement of the agents to 1) have a common objective with neighboring agents, with the objective typically decided offline, and 2) share information online to realize the objective. To be viable, the control approach for multiagent systems should be distributed, for autonomy of the individual agents and for scalability and improved tractability over centralized approaches.
\r\n\r\nOptimization-based techniques are suited to multiagent problems, in that such techniques can admit very general objectives. Receding horizon control is an optimization-based approach that is applicable when dynamics and constraints on the system are present. Several researchers have recently explored the use of receding horizon control to achieve multi-vehicle objectives. In most cases, the common objective is formulated, and the resulting control law implemented, in a centralized way.
\r\n\r\nThis dissertation provides a distributed implementation of receding horizon control with guaranteed convergence and performance comparable to a centralized implementation. To begin with, agents are presumed to be individually governed by heterogeneous dynamics, modelled by a nonlinear ordinary differential equation. Coupling between agents occurs in a generic quadratic cost function of a single optimal control problem. The distributed implementation is generated by decomposition of the single optimal control problem into local problems, and the inclusion of local compatibility constraints in each local problem. The coordination requirements are globally synchronous timing and local information exchanges between neighboring agents. For sufficiently fast update times, the distributed implementation is proven to be asymptotically stabilizing. Extensions for handling inter-agent coupling constraints and partially synchronous timing are also explored. The venue of multi-vehicle formation stabilization demonstrates the efficacy of the implementation in numerical experiments. Given the generality of the receding horizon control mechanism, there is great potential for the implementation presented here in dynamic and constrained distributed systems.
", "doi": "10.7907/1N74-MZ62", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:2431", "collection": "thesis", "collection_id": "2431", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06042003-181857", "primary_object_url": { "basename": "Radford_je_2003.pdf", "content": "final", "filesize": 3658533, "license": "other", "mime_type": "application/pdf", "url": "/2431/1/Radford_je_2003.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Symmetry, Reduction and Swimming in a Perfect Fluid", "author": [ { "family_name": "Radford", "given_name": "James Edward", "clpid": "Radford-James-Edward" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents a geometric picture of a deformable body in a perfect fluid and a way to approximate its dynamics and the motion, resulting from cyclic shape deformations, of the body and, interestingly, the fluid as well. Emphasis is placed on the group structure of the configuration space of the body fluid system and the resulting symmetry in their equations of motion. Symmetry is also used to reduce a series expansion for the flow of a time dependent vector field in order to obtain a novel expansion for the path-ordered exponential. This can be used to approximate holonomy, or geometric phase, in a principal bundle when its evolution is governed by a connection on the bundle and it is subject to periodic shape inputs. Simple models for swimming in and the stirring of a perfect fluid are proposed and examined.", "doi": "10.7907/CE65-XM80", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2378", "collection": "thesis", "collection_id": "2378", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06022003-114340", "primary_object_url": { "basename": "mbmthesis_ds.pdf", "content": "final", "filesize": 3135332, "license": "other", "mime_type": "application/pdf", "url": "/2378/1/mbmthesis_ds.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Real-Time Optimal Trajectory Generation for Constrained Dynamical Systems", "author": [ { "family_name": "Milam", "given_name": "Mark Bradley", "clpid": "Milam-Mark-Bradley" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Hauser", "given_name": "John", "clpid": "Hauser-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "With the advent of powerful computing and efficient computational algorithms, real-time solutions to constrained optimal control problems are nearing a reality. In this thesis, we develop a computationally efficient Nonlinear Trajectory Generation (NTG) algorithm and describe its software implementation to solve, in real-time, nonlinear optimal trajectory generation problems for constrained systems. NTG is a nonlinear trajectory generation software package that combines nonlinear control theory, B-spline basis functions, and nonlinear programming. We compare NTG with other numerical optimal control problem solution techniques, such as direct collocation, shooting, adjoints, and differential inclusions.
\r\n\r\nWe demonstrate the performance of NTG on the Caltech Ducted Fan testbed. Aggressive, constrained optimal control problems are solved in real-time for hover-to-hover, forward flight, and terrain avoidance test cases. Real-time trajectory generation results are shown for both the two-degree of freedom and receding horizon control designs. Further experimental demonstration is provided with the station-keeping, reconfiguration, and deconfiguration of micro-satellite formation with complex nonlinear constraints. Successful application of NTG in these cases demonstrates reliable real-time trajectory generation, even for highly nonlinear and non-convex systems. The results are among the first to apply receding horizon control techniques for agile flight in an experimental setting, using representative dynamics and computation.
", "doi": "10.7907/1X68-E370", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2182", "collection": "thesis", "collection_id": "2182", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282003-094253", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 2203138, "license": "other", "mime_type": "application/pdf", "url": "/2182/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Averaging and Control of Nonlinear Systems", "author": [ { "family_name": "Vela", "given_name": "Patricio Antonio", "orcid": "0000-0002-6888-7002", "clpid": "Vela-Patricio-Antonio" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Ostrowski", "given_name": "James P.", "clpid": "Ostrowski-J-P" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation investigates three principal areas regarding the dynamics and control of nonlinear systems: averaging theory, controllability of mechanical systems, and control of underactuated nonlinear systems. The most effective stabilizing controllers for underactuated nonlinear systems are time-periodic, which leads to the study of averaging theory for understanding the nonlinear effect generated by resonant oscillatory inputs.
\r\n\r\nThe research on averaging theory generalizes averaging theory to arbitrary order by synthesizing series expansion methods for nonlinear time-varying vector fields and their flows with nonlinear Floquet theory. It is shown that classical averaging theory is the application of perturbation methods in conjunction with nonlinear Floquet theory. Many known properties and consequences of averaging theory are placed within a single framework.
\r\n\r\nThe generalized averaging theory is merged with controllability analysis of underactuated nonlinear systems to derive exponentially stabilizing controllers. Although small-time local controllability (STLC) is easily demonstrated for driftless systems via the Lie algebra rank condition, STLC for systems with drift is more complicated. Furthermore, there exists a variety of techniques and canonical forms for determining STLC. This thesis exploits notions of geometric homogeneity to show that STLC results for a large class of mechanical systems with drift can be recovered by considering a class of nonlinear dynamical systems satisfying certain homogeneity conditions. These theorems generalize the controllability results for simple mechanical control systems found in Lewis and Murray [85]. Most nonlinear controllability results for classes of mechanical systems may be obtained using these methods.
\r\n\r\nThe stabilizing controllers derived using the generalized averaging theory and STLC analysis can be used to stabilize both systems with and without drift. Furthermore, they result in a set of tunable gains and oscillatory parameters for modification and improvement of the feedback strategy. The procedure can not only derive known controllers from the literature, but can also be used to improve them. Examples demonstrate the diversity of controllers constructed using the generalized averaging theory.
\r\n\r\nThis dissertation concludes with a chapter devoted to biomimetic and biomechanical locomotive control systems that have been stabilized using the generalized averaging theory and the controller construction procedure. The locomotive control systems roll, wriggle, swim, and walk, demonstrating the universal nature of the control strategy proposed.
", "doi": "10.7907/N7HH-PM67", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2182", "collection": "thesis", "collection_id": "2182", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282003-094253", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 2203138, "license": "other", "mime_type": "application/pdf", "url": "/2182/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Averaging and Control of Nonlinear Systems", "author": [ { "family_name": "Vela", "given_name": "Patricio Antonio", "orcid": "0000-0002-6888-7002", "clpid": "Vela-Patricio-Antonio" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Ostrowski", "given_name": "James P.", "clpid": "Ostrowski-J-P" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation investigates three principal areas regarding the dynamics and control of nonlinear systems: averaging theory, controllability of mechanical systems, and control of underactuated nonlinear systems. The most effective stabilizing controllers for underactuated nonlinear systems are time-periodic, which leads to the study of averaging theory for understanding the nonlinear effect generated by resonant oscillatory inputs.
\r\n\r\nThe research on averaging theory generalizes averaging theory to arbitrary order by synthesizing series expansion methods for nonlinear time-varying vector fields and their flows with nonlinear Floquet theory. It is shown that classical averaging theory is the application of perturbation methods in conjunction with nonlinear Floquet theory. Many known properties and consequences of averaging theory are placed within a single framework.
\r\n\r\nThe generalized averaging theory is merged with controllability analysis of underactuated nonlinear systems to derive exponentially stabilizing controllers. Although small-time local controllability (STLC) is easily demonstrated for driftless systems via the Lie algebra rank condition, STLC for systems with drift is more complicated. Furthermore, there exists a variety of techniques and canonical forms for determining STLC. This thesis exploits notions of geometric homogeneity to show that STLC results for a large class of mechanical systems with drift can be recovered by considering a class of nonlinear dynamical systems satisfying certain homogeneity conditions. These theorems generalize the controllability results for simple mechanical control systems found in Lewis and Murray [85]. Most nonlinear controllability results for classes of mechanical systems may be obtained using these methods.
\r\n\r\nThe stabilizing controllers derived using the generalized averaging theory and STLC analysis can be used to stabilize both systems with and without drift. Furthermore, they result in a set of tunable gains and oscillatory parameters for modification and improvement of the feedback strategy. The procedure can not only derive known controllers from the literature, but can also be used to improve them. Examples demonstrate the diversity of controllers constructed using the generalized averaging theory.
\r\n\r\nThis dissertation concludes with a chapter devoted to biomimetic and biomechanical locomotive control systems that have been stabilized using the generalized averaging theory and the controller construction procedure. The locomotive control systems roll, wriggle, swim, and walk, demonstrating the universal nature of the control strategy proposed.
", "doi": "10.7907/N7HH-PM67", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2183", "collection": "thesis", "collection_id": "2183", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282003-205506", "primary_object_url": { "basename": "thesis_twoside.pdf", "content": "final", "filesize": 2966187, "license": "other", "mime_type": "application/pdf", "url": "/2183/1/thesis_twoside.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Modeling Artificial, Mobile Swarm Systems", "author": [ { "family_name": "Agassounon", "given_name": "William B. G.", "clpid": "Agassounon-William-B-G" } ], "thesis_advisor": [ { "family_name": "McEliece", "given_name": "Robert J.", "clpid": "McEliece-R-J" } ], "thesis_committee": [ { "family_name": "McEliece", "given_name": "Robert J.", "clpid": "McEliece-R-J" }, { "family_name": "Martinoli", "given_name": "Alcherio", "clpid": "Martinoli-A" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Behrens", "given_name": "Wilhelm", "clpid": "Behrens-W" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Swarm intelligence is a new research paradigm that offers novel approaches for studying and solving distributed problems using solutions inspired by social insects and other natural behaviors of vertebrates. In this thesis, we present methodologies for modeling artificial, mobile systems within the swarm intelligence framework. The proposed methodologies provide guidelines in the study and design of artificial swarm systems for the following two classes of experiments: distributed sensing and distributed manipulation.
\r\n\r\nEvent discovery and information dissemination through local communication in artificial swarm systems present similar characteristics as natural phenomena such as foraging and food discovery in insect colonies and the spread of infectious diseases in animal populations, respectively. We show that the artificial systems can be described in similar mathematical terms as those used to describe the natural systems. The proposed models can be classified in two main categories: non-embodied and embodied models. In the first category agents are modeled as mobile bodiless points, whereas the other models take into account the physical interference between agents resulting from embodiment. Furthermore, within each category, we distinguish two subcategories: spatial and nonspatial models. In the spatial models we keep track of the trajectory of each agent, the correlation between the positions occupied by the agents over consecutive time steps, or make use of the spatial distribution resulting from the movement pattern of the agents. In the nonspatial models we assume that agents hop around randomly and occupy independent positions over consecutive time steps.
\r\n\r\nIn our description of distributed manipulation in swarm robotic systems we present two case studies of non-collaborative and collaborative manipulations, respectively. The general approach proposed here consists of first representing the group behavior of the active agents with a Finite State Machine (FSM) then describing mathematically the dynamics of the group. The first case study is the aggregation experiment that consists of collecting and gathering objects scattered around an enclosed arena. We present a macroscopic model that accurately captures the dynamics of the experiment and a suite of threshold-based, scalable, and fully distributed algorithms for allocating the workers to the task optimally. The second case study is that of the stick-pulling experiment in which a group of robots is used to pull sticks from the ground. This task requires the collaborative effort of two robots to be successful. Here, we present a discrete-time macroscopic model that helps us uncover counter-intuitive behaviors that result from collaboration between the agents.
\r\n\r\nWe complete each proposed modeling methodology by showing how the parameters of the models can be calculated using solely the characteristics of the environment and those of the agents and by analyzing the constraints and limitations of the different models. Finally, we use different tools (simulations and real robots) to validate the proposed models.
\r\n", "doi": "10.7907/EJYZ-3Y55", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:4207", "collection": "thesis", "collection_id": "4207", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10222002-115711", "primary_object_url": { "basename": "mgthesis.pdf", "content": "final", "filesize": 3074987, "license": "other", "mime_type": "application/pdf", "url": "/4207/1/mgthesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling and Control of Epitaxial Thin Film Growth", "author": [ { "family_name": "Gallivan", "given_name": "Martha Anne", "orcid": "0000-0002-7036-776X", "clpid": "Gallivan-Martha-Anne" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Christofides", "given_name": "Panagiotis D.", "clpid": "Christofides-P-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Thin film deposition is a manufacturing process in which tolerances may approach the size of individual atoms. The final film is highly sensitive to the processing conditions, which can be intentionally manipulated to control film properties. A lattice model of surface evolution during thin film growth captures many important features, including the nucleation and growth of clusters of atoms and the propagation of atomic-height steps. The dimension of this probabilistic master equation is too large to directly simulate for any physically realistic domain, and instead stochastic realizations of the lattice model are obtained with kinetic Monte Carlo simulations.
\r\n\r\nIn this thesis simpler representations of the master equation are developed for use in analysis and control. The static map between macroscopic process conditions and microscopic transition rates is first analyzed. In the limit of fast periodic process parameters, the surface responds only to the mean transition rates, and, since the map between process parameters and transition rates is nonlinear, new effective combinations of transition rates may be generated. These effective rates are the convex hull of the set of instantaneous rates.
\r\n\r\nThe map between transition rates and expected film properties is also studied. The dimension of a master equation can be reduced by eliminating or grouping configurations, yielding a reduced-order master equation that approximates the original one. A linear method for identifying the coefficients in a master equation is then developed, using only simulation data. These concepts are extended to generate low-order master equations that approximate the dynamic behavior seen in large Monte Carlo simulations. The models are then used to compute optimal time-varying process parameters.
\r\n\r\nThe thesis concludes with an experimental and modeling study of germanium film growth, using molecular beam epitaxy and reflection high-energy electron diffraction. Growth under continuous and pulsed flux is compared in experiment, and physical parameters for the lattice model are extracted. The pulsing accessible in the experiment does not trigger a change in growth mode, which is consistent with the Monte Carlo simulations. The simulations are then used to suggest other growth strategies to produce rougher or smoother surfaces.
", "doi": "10.7907/FXZB-XT91", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:3884", "collection": "thesis", "collection_id": "3884", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10032002-214953", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 2300841, "license": "other", "mime_type": "application/pdf", "url": "/3884/1/main.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Set Mapping in the Method of Imprecision", "author": [ { "family_name": "Wang", "given_name": "Xiaoou", "clpid": "Wang-Xiaoou" } ], "thesis_advisor": [ { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" } ], "thesis_committee": [ { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Pickar", "given_name": "Kenneth A.", "clpid": "Pickar-K-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The Method of Imprecision, or MoI, is a semi-automated set-based approach which uses mathematics of fuzzy sets to aid the designer making decisions with imprecise information in the preliminary design stage.
\r\n\r\nThe Method of Imprecision uses preference to represent the imprecision in engineering design. The preferences are specified both in the design variable space (DVS) and the performance variable space (PVS). To reach the overall preference which is needed to evaluate designs, the mapping between the DVS and the PVS should be explored. Many engineering design tools can only produce precise results with precise specifications, and usually the cost is high. In the preliminary stage, the specifications are imprecise and resources are limited. Hence, it is not cost-effective nor necessary to use these engineering design tools directly to study the mapping between the DVS and the PVS. An interpolation model is introduced to the MoI to construct metamodels for the actual mapping function between the DVS and the PVS. Due to the nature of engineering design, multistage metamodels are needed. Experimental design is used to choose design points for the first metamodel. In order to find an efficient way to choose design points when a priori information is available, many sampling criteria are discussed and tested on two specific examples. The difference between different sampling criteria when the number of added design points is small, while more design points do improve the accuracy of the metamodel substantially.
\r\n\r\nThe metamodels can be used to induce preferences in the DVS or the PVS according to the extension principle. The Level Interval Algorithm (LIA) is a discrete approximate implementation of the extension principle. The resulting preference by the LIA is presented as an alpha-cut, which is the set of designs or performances with a certain level of preference. There are some limitations of the LIA, especially for multidimensional DVS and PVS. A new extension of the LIA is proposed to compute alpha-cuts with more accuracy and less limitations. The designers have more control over the trade-off between the cost and accuracy of the computation with the new extension of the LIA.
\r\n\r\nThe results of the Method of Imprecision should be the set of alternative designs in the DVS at a certain preference level, and the set of achievable performances in the PVS. The information about preferences in the DVS and the PVS is needed to transfer back and forth. Usually the mapping from the PVS to the DVS is unavailable, while it is needed to induce preference in the DVS from the PVS. A new method is constructed to compute the alpha-cuts in both spaces from preferences specified in the DVS and the PVS.
\r\n\r\nFinally, a new measure is proposed to find the most cost-effective sampling region of new design points for a metamodel. Also, the full implementation of the Method of Imprecision is listed in detail. Then it is applied to an example of the structure design of a passenger vehicle, and comparisons are made between the new results and previous results.
", "doi": "10.7907/J0JH-M190", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:3884", "collection": "thesis", "collection_id": "3884", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10032002-214953", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 2300841, "license": "other", "mime_type": "application/pdf", "url": "/3884/1/main.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Set Mapping in the Method of Imprecision", "author": [ { "family_name": "Wang", "given_name": "Xiaoou", "clpid": "Wang-Xiaoou" } ], "thesis_advisor": [ { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" } ], "thesis_committee": [ { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Pickar", "given_name": "Kenneth A.", "clpid": "Pickar-K-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The Method of Imprecision, or MoI, is a semi-automated set-based approach which uses mathematics of fuzzy sets to aid the designer making decisions with imprecise information in the preliminary design stage.
\r\n\r\nThe Method of Imprecision uses preference to represent the imprecision in engineering design. The preferences are specified both in the design variable space (DVS) and the performance variable space (PVS). To reach the overall preference which is needed to evaluate designs, the mapping between the DVS and the PVS should be explored. Many engineering design tools can only produce precise results with precise specifications, and usually the cost is high. In the preliminary stage, the specifications are imprecise and resources are limited. Hence, it is not cost-effective nor necessary to use these engineering design tools directly to study the mapping between the DVS and the PVS. An interpolation model is introduced to the MoI to construct metamodels for the actual mapping function between the DVS and the PVS. Due to the nature of engineering design, multistage metamodels are needed. Experimental design is used to choose design points for the first metamodel. In order to find an efficient way to choose design points when a priori information is available, many sampling criteria are discussed and tested on two specific examples. The difference between different sampling criteria when the number of added design points is small, while more design points do improve the accuracy of the metamodel substantially.
\r\n\r\nThe metamodels can be used to induce preferences in the DVS or the PVS according to the extension principle. The Level Interval Algorithm (LIA) is a discrete approximate implementation of the extension principle. The resulting preference by the LIA is presented as an alpha-cut, which is the set of designs or performances with a certain level of preference. There are some limitations of the LIA, especially for multidimensional DVS and PVS. A new extension of the LIA is proposed to compute alpha-cuts with more accuracy and less limitations. The designers have more control over the trade-off between the cost and accuracy of the computation with the new extension of the LIA.
\r\n\r\nThe results of the Method of Imprecision should be the set of alternative designs in the DVS at a certain preference level, and the set of achievable performances in the PVS. The information about preferences in the DVS and the PVS is needed to transfer back and forth. Usually the mapping from the PVS to the DVS is unavailable, while it is needed to induce preference in the DVS from the PVS. A new method is constructed to compute the alpha-cuts in both spaces from preferences specified in the DVS and the PVS.
\r\n\r\nFinally, a new measure is proposed to find the most cost-effective sampling region of new design points for a metamodel. Also, the full implementation of the Method of Imprecision is listed in detail. Then it is applied to an example of the structure design of a passenger vehicle, and comparisons are made between the new results and previous results.
", "doi": "10.7907/J0JH-M190", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:4917", "collection": "thesis", "collection_id": "4917", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12102002-113833", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 1898611, "license": "other", "mime_type": "application/pdf", "url": "/4917/1/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A Probabilistic Approach to Human Motion Detection and Labeling", "author": [ { "family_name": "Song", "given_name": "Yang", "clpid": "Song-Yang" } ], "thesis_advisor": [ { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "thesis_committee": [ { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Bruck", "given_name": "Jehoshua", "clpid": "Bruck-J" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Soatto", "given_name": "Stefano", "clpid": "Soatto-Stefano" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Human motion analysis is a very important task for computer vision with many potential applications. There are several problems in human motion analysis: detection, tracking, and activity interpretation. Detection is the most fundamental problem of the three, but remains untackled due to its inherent difficulty. This thesis develops a solution to the problem. It is based on a learned probabilistic model of the joint positions and velocities of the body parts, where detection and labeling are performed by hypothesis testing on the maximum a posterior estimate of the pose and motion of the body. To achieve efficiency in learning and testing, a graphical model is used to approximate the conditional independence of human motion. This model is also shown to provide a natural way to deal with clutter and occlusion.
\r\n\r\nOne key factor in the proposed method is the probabilistic model of human motion. In this thesis, an unsupervised learning algorithm that can obtain the probabilistic model automatically from unlabeled training data is presented. The training data include useful foreground features as well as features that arise from irrelevant background clutter. The correspondence between parts and detected features is also unknown in the training data. To learn the best model structure as well as model parameters, a variant of the EM algorithm is developed where the labeling of the data (part assignments) is treated as hidden variables. We explore two classes of graphical models: trees and decomposable triangulated graphs and find that the later are superior for our application. To better model human motion, we also consider the case when the model consists of mixtures of decomposable triangulated graphs.
\r\n \r\nThe efficiency and effectiveness of the algorithm have been demonstrated by applying it to generate models of human motion automatically from unlabeled image sequences, and testing the learned models on a variety of sequences. We find detection rates of over 95% on pairs of frames. This is very promising for building a real-life system, for example, a pedestrian detector.
", "doi": "10.7907/945J-QX86", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:1304", "collection": "thesis", "collection_id": "1304", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04082003-180353", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 40124312, "license": "other", "mime_type": "application/pdf", "url": "/1304/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Time-Dependent Dynamical Systems and Geophysical Flows", "author": [ { "family_name": "Lekien", "given_name": "Francois Paul", "clpid": "Lekien-Francois-Paul" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Haller", "given_name": "George", "clpid": "Haller-G" }, { "family_name": "Mezic", "given_name": "Igor", "clpid": "Mezic-I" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents a dynamical systems approach to transport and mixing in geophysical flows. First, new algorithms are developed that allow one to study a dynamical system that is described in a variety of ways such as by means of observational data or numerical simulations of differential equations.
\r\n\r\nNext, methods available to study non-autonomous systems, such as hyperbolic trajectories and Lagrangian coherent structures, are developed. These concepts are applied to examples of interests: Monterey Bay, the coast of Florida and the circulation in the North Atlantic. Combining accurate current measurements and recent developments in dynamical systems theory provides new and original answers to many problems, such as the minimization of the impact of released contaminants in a coastal area or the optimization of the coverage by a group of drifters.
\r\n\r\nThe appendices give details about MANGEN, a software package developed to produce the numerical results of this thesis. Some projects that make use of its algorithms, such as the dissociation rate of a molecule and efficient space mission design, are also described.
", "doi": "10.7907/A83E-VZ73", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:859", "collection": "thesis", "collection_id": "859", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03042003-102221", "primary_object_url": { "basename": "matveev_thesis.pdf", "content": "final", "filesize": 2117824, "license": "other", "mime_type": "application/pdf", "url": "/859/1/matveev_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Thermoacoustic Instabilities in the Rijke Tube: Experiments and Modeling", "author": [ { "family_name": "Matveev", "given_name": "Konstantin Ivanovich", "clpid": "Matveev-Konstantin-Ivanovich" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Pickar", "given_name": "Kenneth A.", "clpid": "Pickar-K-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Thermoacoustic instability can appear in thermal devices when unsteady heat release is coupled with pressure perturbations. This effect results in excitation of eigen acoustic modes of the system. These instabilities are important in various technical applications, for instance, in rocket motors and thermoacoustic engines.
\r\n\r\nA Rijke tube, representing a resonator with a mean flow and a concentrated heat source, is a convenient system for studying the fundamental physics of thermoacoustic instabilities. At certain values of the main system parameters, a loud sound is generated through a process similar to that in real-world devices prone to thermoacoustic instability. Rijke devices have been extensively employed for research purposes. The current work is intended to overcome the serious deficiencies of previous investigations with regard to estimating experimental errors and the influence of parameter variation on the results. Also, part of the objective here is to account for temperature field non-uniformity and to interpret nonlinear phenomena. The major goals of this study are to deliver accurate experimental results for the transition to instability and the scope and nature of the excited regimes, and to develop a theory that explains and predicts the effects observed.
\r\n\r\nAn electrically heated, horizontally oriented, Rijke tube is used for the experimental study of transition to instability. The stability boundary is quantified as a function of major system parameters with measured uncertainties for the data collected. Hysteresis in the stability boundary is observed for certain operating regimes of the Rijke tube.
\r\n\r\nAn innovative theory is developed for modeling the Rijke oscillations. First, linear theory, incorporating thermal analysis that accurately determines the properties of the modes responsible for the transition to instability, is used to predict the stability boundary. Then, a nonlinear extension of the theory is derived by introducing a hypothesis for a special form of the nonlinear heat transfer function. This nonlinear modeling is shown to predict the hysteresis phenomenon and the limit cycles observed during the tests.
\r\n\r\nA new, reduced-order modeling approach for combustion instabilities in systems with vortex shedding is derived using the developed analytical framework. A hypothesis for the vortex detachment criterion is introduced, and a kicked oscillator model is applied to produce nonlinear results characteristic for unstable combustion systems.
\r\n\r\nThe experimental system and the mathematical model, developed in this work for the Rijke tube, are recommended for preliminary design and analysis of real-world thermal devices, where thermoacoustic instability is a concern.
", "doi": "10.7907/3X6A-6D11", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:859", "collection": "thesis", "collection_id": "859", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03042003-102221", "primary_object_url": { "basename": "matveev_thesis.pdf", "content": "final", "filesize": 2117824, "license": "other", "mime_type": "application/pdf", "url": "/859/1/matveev_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Thermoacoustic Instabilities in the Rijke Tube: Experiments and Modeling", "author": [ { "family_name": "Matveev", "given_name": "Konstantin Ivanovich", "clpid": "Matveev-Konstantin-Ivanovich" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Pickar", "given_name": "Kenneth A.", "clpid": "Pickar-K-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Thermoacoustic instability can appear in thermal devices when unsteady heat release is coupled with pressure perturbations. This effect results in excitation of eigen acoustic modes of the system. These instabilities are important in various technical applications, for instance, in rocket motors and thermoacoustic engines.
\r\n\r\nA Rijke tube, representing a resonator with a mean flow and a concentrated heat source, is a convenient system for studying the fundamental physics of thermoacoustic instabilities. At certain values of the main system parameters, a loud sound is generated through a process similar to that in real-world devices prone to thermoacoustic instability. Rijke devices have been extensively employed for research purposes. The current work is intended to overcome the serious deficiencies of previous investigations with regard to estimating experimental errors and the influence of parameter variation on the results. Also, part of the objective here is to account for temperature field non-uniformity and to interpret nonlinear phenomena. The major goals of this study are to deliver accurate experimental results for the transition to instability and the scope and nature of the excited regimes, and to develop a theory that explains and predicts the effects observed.
\r\n\r\nAn electrically heated, horizontally oriented, Rijke tube is used for the experimental study of transition to instability. The stability boundary is quantified as a function of major system parameters with measured uncertainties for the data collected. Hysteresis in the stability boundary is observed for certain operating regimes of the Rijke tube.
\r\n\r\nAn innovative theory is developed for modeling the Rijke oscillations. First, linear theory, incorporating thermal analysis that accurately determines the properties of the modes responsible for the transition to instability, is used to predict the stability boundary. Then, a nonlinear extension of the theory is derived by introducing a hypothesis for a special form of the nonlinear heat transfer function. This nonlinear modeling is shown to predict the hysteresis phenomenon and the limit cycles observed during the tests.
\r\n\r\nA new, reduced-order modeling approach for combustion instabilities in systems with vortex shedding is derived using the developed analytical framework. A hypothesis for the vortex detachment criterion is introduced, and a kicked oscillator model is applied to produce nonlinear results characteristic for unstable combustion systems.
\r\n\r\nThe experimental system and the mathematical model, developed in this work for the Rijke tube, are recommended for preliminary design and analysis of real-world thermal devices, where thermoacoustic instability is a concern.
", "doi": "10.7907/3X6A-6D11", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2235", "collection": "thesis", "collection_id": "2235", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292003-160843", "primary_object_url": { "basename": "mason_thesis.pdf", "content": "final", "filesize": 4082068, "license": "other", "mime_type": "application/pdf", "url": "/2235/1/mason_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Fluid Locomotion and Trajectory Planning for Shape-Changing Robots", "author": [ { "family_name": "Mason", "given_name": "Richard James", "clpid": "Mason-Richard-James" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wu", "given_name": "Theodore Yao-tsu", "clpid": "Wu-T-Y-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Motivated by considerations of shape changing propulsion of underwater robotic vehicles, I analyze the mechanics of deformable bodies operating in an ideal fluid. I give particular attention to fishlike robots which may be considered as one or more flexing or oscillating hydrofoils. I then describe methods of planning trajectories for a fishlike robot or any other sort of robot whose locomotion has a periodic or quasi-periodic nature.", "doi": "10.7907/MFM1-0866", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2235", "collection": "thesis", "collection_id": "2235", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292003-160843", "primary_object_url": { "basename": "mason_thesis.pdf", "content": "final", "filesize": 4082068, "license": "other", "mime_type": "application/pdf", "url": "/2235/1/mason_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Fluid Locomotion and Trajectory Planning for Shape-Changing Robots", "author": [ { "family_name": "Mason", "given_name": "Richard James", "clpid": "Mason-Richard-James" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wu", "given_name": "Theodore Yao-tsu", "clpid": "Wu-T-Y-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Motivated by considerations of shape changing propulsion of underwater robotic vehicles, I analyze the mechanics of deformable bodies operating in an ideal fluid. I give particular attention to fishlike robots which may be considered as one or more flexing or oscillating hydrofoils. I then describe methods of planning trajectories for a fishlike robot or any other sort of robot whose locomotion has a periodic or quasi-periodic nature.", "doi": "10.7907/MFM1-0866", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:6128", "collection": "thesis", "collection_id": "6128", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10112010-161816245", "primary_object_url": { "basename": "Chang_de_2002.pdf", "content": "final", "filesize": 57952667, "license": "other", "mime_type": "application/pdf", "url": "/6128/1/Chang_de_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Controlled Lagrangian and Hamiltonian Systems", "author": [ { "family_name": "Chang", "given_name": "Dong Eui", "clpid": "Chang-Dong-Eui" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "any control systems are mechanical systems. The unique feature of mechanical systems is the notion of energy, which gives much information on the stability of equilibria. Two kinds of forces are associated with the energy: dissipative force and gyroscopic force. A dissipative force is, by definition, a force which decreases the energy, and a gyroscopic force is, by definition, a force that does not change the energy. Gyroscopic forces add couplings to the dynamics. In this thesis, we develop a control design methodology which makes full use of these three physical notions: energy, dissipation, and coupling.
\r\n\r\nFirst, we develop the method of controlled Lagrangian systems. It is a systematic procedure for designing stabilizing controllers for mechanical systems by making use of energy, dissipative forces, and gyroscopic forces. The basic idea is as follows: Suppose that we are given a mechanical system and want to design a controller to asymptotically stabilize an equilibrium of interest. We look for a feedback control law such that the closed-loop dynamics can be also described by a new Lagrangian with a dissipative force and a gyroscopic force where the energy of the new Lagrangian has a minimum at the equilibrium. Then we check for asymptotic stability by applying the Lyapunov stability theory with the new energy as a Lyapunov function.
\r\n\r\nNext, we show that the method of controlled Lagrangian systems and its Hamiltonian counterpart, the method of controlled Hamiltonian systems, are equivalent for simple mechanical systems where the underlying Lagrangian is of the form kinetic minus potential energy. In addition, we extend both the Lagrangian and Hamiltonian sides of this theory to include systems with symmetry and discuss the relevant reduction theory.
", "doi": "10.7907/3DRR-ZV53", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:4742", "collection": "thesis", "collection_id": "4742", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12032004-075012", "primary_object_url": { "basename": "cwr_thesis.pdf", "content": "final", "filesize": 10860896, "license": "other", "mime_type": "application/pdf", "url": "/4742/1/cwr_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling, Simulation, and Control of Cavity Flow Oscillations", "author": [ { "family_name": "Rowley", "given_name": "Clarence Worth, III", "clpid": "Rowley-Clarence-Worth-III" } ], "thesis_advisor": [ { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "thesis_committee": [ { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis involves the modeling of self-sustained oscillations in the flow past a rectangular cavity. The emphasis is on developing low-dimensional models that are suitable for analysis using tools from dynamical systems and control theory. Two-dimensional direct numerical simulations are performed, and indicate the presence of a \u201cwake mode,\u201d which has been observed previously in experiments, but which is much less well understood than the \u201cshear-layer mode\u201d usually observed. We characterize the flow in both shear-layer mode and wake mode, and provide a criterion for predicting the onset of wake mode, as a function of the various geometrical and flow-related parameters. We focus on the modeling of shear-layer mode, and employ two distinct modeling approaches: first, we use the method of Proper Orthogonal Decomposition (POD) and Galerkin projection to reduce the Navier-Stokes equations to a lowdimensional system of ordinary differential equations (ODEs). We extend the method to compressible flows, using approximations that are valid for cold flows at moderate Mach number. In a compressible flow, both the kinematic and thermodynamic variables contribute to the total energy, and an inner product is introduced which respects this, and allows one to use vector-valued POD modes for the Galerkin projection. We obtain models in the form of ODEs with between 2 and 60 states, and compare models based on scalar-valued and vector-valued POD modes. All of the models work well for short times (a few periods of oscillation), but the models based on scalar-valued modes deviate for longer times, while in general the models based on vector-valued modes retain qualitatively correct dynamical behavior. In the second modeling approach, we model the underlying physical mechanisms separately (shear-layer amplification, acoustic scattering, acoustic propagation), and obtain linear models that are suitable for control design and analysis. We design a controller which stabilizes the model, and implement a similar control law on an experiment, demonstrating significant reduction in the amplitude of the oscillations, but revealing some limitations of feedback control.", "doi": "10.7907/G4ZX-KH73", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:2989", "collection": "thesis", "collection_id": "2989", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07312002-091923", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 2313008, "license": "other", "mime_type": "application/pdf", "url": "/2989/1/thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Control of Multiple Model Systems", "author": [ { "family_name": "Murphey", "given_name": "Todd David", "clpid": "Murphey-Todd-David" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis considers the control of multiple model systems. These are systems for which only one model out of some finite set of models gives the system dynamics at any given time. In particular, the model that gives the system dynamics can change over time. This thesis covers some of the theoretical aspects of these systems, including controllability and stabilizability. As an application, ``overconstrained' mechanical systems are modeled as multiple model systems. Examples of such systems include distributed manipulation problems such as microelectromechanical systems and many wheeled vehicles such as the Sojourner vehicle of the Mars Pathfinder mission. Such systems are typified by having more Pfaffian constraints than degrees of freedom. Conventional classical motion planning and control theories do not directly apply to overconstrained systems. Control issues for two examples are specifically addressed. The first example is distributed manipulation. Distributed manipulation systems control an object's motion through contact with a high number of actuators. Stability results are shown for such systems and control schemes based on these results are implemented on a distributed manipulation test-bed. The second example is that of overconstrained vehicles, of which the Mars rover is an example. The nonlinear controllability test for multiple model systems is used to answer whether a kinematic model of the rover is or is not controllable.", "doi": "10.7907/17Q7-Y019", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:4742", "collection": "thesis", "collection_id": "4742", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12032004-075012", "primary_object_url": { "basename": "cwr_thesis.pdf", "content": "final", "filesize": 10860896, "license": "other", "mime_type": "application/pdf", "url": "/4742/1/cwr_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling, Simulation, and Control of Cavity Flow Oscillations", "author": [ { "family_name": "Rowley", "given_name": "Clarence Worth, III", "clpid": "Rowley-Clarence-Worth-III" } ], "thesis_advisor": [ { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "thesis_committee": [ { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis involves the modeling of self-sustained oscillations in the flow past a rectangular cavity. The emphasis is on developing low-dimensional models that are suitable for analysis using tools from dynamical systems and control theory. Two-dimensional direct numerical simulations are performed, and indicate the presence of a \u201cwake mode,\u201d which has been observed previously in experiments, but which is much less well understood than the \u201cshear-layer mode\u201d usually observed. We characterize the flow in both shear-layer mode and wake mode, and provide a criterion for predicting the onset of wake mode, as a function of the various geometrical and flow-related parameters. We focus on the modeling of shear-layer mode, and employ two distinct modeling approaches: first, we use the method of Proper Orthogonal Decomposition (POD) and Galerkin projection to reduce the Navier-Stokes equations to a lowdimensional system of ordinary differential equations (ODEs). We extend the method to compressible flows, using approximations that are valid for cold flows at moderate Mach number. In a compressible flow, both the kinematic and thermodynamic variables contribute to the total energy, and an inner product is introduced which respects this, and allows one to use vector-valued POD modes for the Galerkin projection. We obtain models in the form of ODEs with between 2 and 60 states, and compare models based on scalar-valued and vector-valued POD modes. All of the models work well for short times (a few periods of oscillation), but the models based on scalar-valued modes deviate for longer times, while in general the models based on vector-valued modes retain qualitatively correct dynamical behavior. In the second modeling approach, we model the underlying physical mechanisms separately (shear-layer amplification, acoustic scattering, acoustic propagation), and obtain linear models that are suitable for control design and analysis. We design a controller which stabilizes the model, and implement a similar control law on an experiment, demonstrating significant reduction in the amplitude of the oscillations, but revealing some limitations of feedback control.", "doi": "10.7907/G4ZX-KH73", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:2989", "collection": "thesis", "collection_id": "2989", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07312002-091923", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 2313008, "license": "other", "mime_type": "application/pdf", "url": "/2989/1/thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Control of Multiple Model Systems", "author": [ { "family_name": "Murphey", "given_name": "Todd David", "clpid": "Murphey-Todd-David" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis considers the control of multiple model systems. These are systems for which only one model out of some finite set of models gives the system dynamics at any given time. In particular, the model that gives the system dynamics can change over time. This thesis covers some of the theoretical aspects of these systems, including controllability and stabilizability. As an application, ``overconstrained' mechanical systems are modeled as multiple model systems. Examples of such systems include distributed manipulation problems such as microelectromechanical systems and many wheeled vehicles such as the Sojourner vehicle of the Mars Pathfinder mission. Such systems are typified by having more Pfaffian constraints than degrees of freedom. Conventional classical motion planning and control theories do not directly apply to overconstrained systems. Control issues for two examples are specifically addressed. The first example is distributed manipulation. Distributed manipulation systems control an object's motion through contact with a high number of actuators. Stability results are shown for such systems and control schemes based on these results are implemented on a distributed manipulation test-bed. The second example is that of overconstrained vehicles, of which the Mars rover is an example. The nonlinear controllability test for multiple model systems is used to answer whether a kinematic model of the rover is or is not controllable.", "doi": "10.7907/17Q7-Y019", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:1200", "collection": "thesis", "collection_id": "1200", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03302004-115559", "primary_object_url": { "basename": "th2s.pdf", "content": "final", "filesize": 6054226, "license": "other", "mime_type": "application/pdf", "url": "/1200/1/th2s.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Time-Frequency Analysis Based on Wavelets for Hamiltonian Systems", "author": [ { "family_name": "Vela-Arevalo", "given_name": "Luz Vianey", "clpid": "Vela-Arevalo-Luz-Vianey" } ], "thesis_advisor": [ { "family_name": "Wiggins", "given_name": "Stephen R.", "clpid": "Wiggins-S-R" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Candes", "given_name": "Emmanuel J.", "clpid": "Candes-E-J" }, { "family_name": "Haller", "given_name": "George", "clpid": "Haller-G" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this work, we present the method of time-frequency analysis based on wavelets for Hamiltonian systems and demonstrate its applications and consequences in the general dynamics of higher dimensional systems.\r\n\r\nBy extracting instantaneous frequencies from the wavelet transform of numerical solutions, we can distinguish regular from chaotic motions, and characterize the global structure of the phase space. The method allows us to determine resonance areas that persists even for high energy levels. We can also show how the existence of resonant motion affects the dynamics of the chaotic motion: we detect when chaotic trajectories are temporarily trapped around resonance areas, or undergo transitions between different resonances. This process is a good indicator of intrinsic transport in the phase space.\r\n\r\nThe method can be applied to a large class of systems, since it is not restricted to nearly integrable systems expressed in action-angle variables, which is the traditional framework for the definition of frequencies.\r\n\r\nThe main contribution of this method is that we have included the time variable in the analysis. We can determine exactly when the trajectories exchange between different regions by keeping records of resonance trappings. This allows us to analyze chaotic trajectories and not only quasiperiodic trajectories. And, we do not require any assumption about the regularity of chaotic trajectories.\r\n\r\nWe present three different applications of the method.\r\n\r\nThe first application consists of the analysis of dynamics and global phase space structure of the classical version of a quantum Hamiltonian for the water molecule. In the second application, we study the planar circular restricted three body problem, and show how resonance transitions of chaotic orbits are related to transport between different regions of the Solar system. Finally, we applied our method to a vibrational three-degrees-of-freedom Hamiltonian of the planar OCS molecule. We study the global dynamics at an energy level close to dissociation, which corresponds to a highly excited state of the molecule.", "doi": "10.7907/8MBB-3Z60", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:4230", "collection": "thesis", "collection_id": "4230", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10242005-105000", "primary_object_url": { "basename": "Fax_ja_2002.pdf", "content": "final", "filesize": 6899741, "license": "other", "mime_type": "application/pdf", "url": "/4230/1/Fax_ja_2002.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Optimal and Cooperative Control of Vehicle Formations", "author": [ { "family_name": "Fax", "given_name": "Joseph Alexander", "clpid": "Fax-Joseph-Alexander" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Hickey", "given_name": "Jason J.", "clpid": "Hickey-J-J" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Control of vehicle formations has emerged as a topic of significant interest to the controls community. In applications such as microsatellites and underwater vehicles, formations have the potential for greater functionality and versatility than individual vehicles. In this thesis, we investigate two topics relevant to control of vehicle formations: optimal vehicle control and cooperative control.\r\n\r\nThe framework of optimal control is often employed to generate vehicle trajectories. We use tools from geometric mechanics to specialize the two classical approaches to optimal control, namely the calculus of variations and the Hamilton-Jacobi-Bellman (HJB) equation, to the case of vehicle dynamics. We employ the formalism of the covariant derivative, useful in geometric representations of vehicle dynamics, to relate variations of position to variations of velocity. When variations are computed in this setting, the evolution of the adjoint variables is shown to be governed by the covariant derivative, thus inheriting the geometric structure of the vehicle dynamics. To simplify the HJB equation, we develop the concept of time scalability enjoyed by many vehicle systems. We employ this property to eliminate time from the HJB equation, yielding a purely spatial PDE whose solution supplies both finite-time optimal trajectories and a time-invariant stabilizing control law.\r\n\r\nCooperation among vehicles in formation depends on intervehicle communication. However, vehicle communication is often subject to disruption, especially in an adversarial setting. We apply tools from graph theory to relate the topology of the communication network to formation stability. We prove a Nyquist criterionthat uses the eigenvalues of the graph Laplacian matrix to determine the effect of the graph on formation stability. We also propose a method for decentralized information exchange between vehicles. This approach realizes a dynamical system that supplies each vehicle with a common reference to be used for cooperative motion. We prove a separation principle that states that formation stability is achieved if the information flow is stable for the given graph and if the local controller stabilizes the vehicle. The information flow can be rendered highly robust to changes in the graph, thus enabling tight formation control despite limitations in intervehicle communication capability.", "doi": "10.7907/M4N7-AK02", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:6128", "collection": "thesis", "collection_id": "6128", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10112010-161816245", "primary_object_url": { "basename": "Chang_de_2002.pdf", "content": "final", "filesize": 57952667, "license": "other", "mime_type": "application/pdf", "url": "/6128/1/Chang_de_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Controlled Lagrangian and Hamiltonian Systems", "author": [ { "family_name": "Chang", "given_name": "Dong Eui", "clpid": "Chang-Dong-Eui" } ], "thesis_advisor": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Low", "given_name": "Steven H.", "orcid": "0000-0001-6476-3048", "clpid": "Low-S-H" }, { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "any control systems are mechanical systems. The unique feature of mechanical systems is the notion of energy, which gives much information on the stability of equilibria. Two kinds of forces are associated with the energy: dissipative force and gyroscopic force. A dissipative force is, by definition, a force which decreases the energy, and a gyroscopic force is, by definition, a force that does not change the energy. Gyroscopic forces add couplings to the dynamics. In this thesis, we develop a control design methodology which makes full use of these three physical notions: energy, dissipation, and coupling.
\r\n\r\nFirst, we develop the method of controlled Lagrangian systems. It is a systematic procedure for designing stabilizing controllers for mechanical systems by making use of energy, dissipative forces, and gyroscopic forces. The basic idea is as follows: Suppose that we are given a mechanical system and want to design a controller to asymptotically stabilize an equilibrium of interest. We look for a feedback control law such that the closed-loop dynamics can be also described by a new Lagrangian with a dissipative force and a gyroscopic force where the energy of the new Lagrangian has a minimum at the equilibrium. Then we check for asymptotic stability by applying the Lyapunov stability theory with the new energy as a Lyapunov function.
\r\n\r\nNext, we show that the method of controlled Lagrangian systems and its Hamiltonian counterpart, the method of controlled Hamiltonian systems, are equivalent for simple mechanical systems where the underlying Lagrangian is of the form kinetic minus potential energy. In addition, we extend both the Lagrangian and Hamiltonian sides of this theory to include systems with symmetry and discuss the relevant reduction theory.
", "doi": "10.7907/3DRR-ZV53", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:1200", "collection": "thesis", "collection_id": "1200", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03302004-115559", "primary_object_url": { "basename": "th2s.pdf", "content": "final", "filesize": 6054226, "license": "other", "mime_type": "application/pdf", "url": "/1200/1/th2s.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Time-Frequency Analysis Based on Wavelets for Hamiltonian Systems", "author": [ { "family_name": "Vela-Arevalo", "given_name": "Luz Vianey", "clpid": "Vela-Arevalo-Luz-Vianey" } ], "thesis_advisor": [ { "family_name": "Wiggins", "given_name": "Stephen R.", "clpid": "Wiggins-S-R" } ], "thesis_committee": [ { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Candes", "given_name": "Emmanuel J.", "clpid": "Candes-E-J" }, { "family_name": "Haller", "given_name": "George", "clpid": "Haller-G" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this work, we present the method of time-frequency analysis based on wavelets for Hamiltonian systems and demonstrate its applications and consequences in the general dynamics of higher dimensional systems.\r\n\r\nBy extracting instantaneous frequencies from the wavelet transform of numerical solutions, we can distinguish regular from chaotic motions, and characterize the global structure of the phase space. The method allows us to determine resonance areas that persists even for high energy levels. We can also show how the existence of resonant motion affects the dynamics of the chaotic motion: we detect when chaotic trajectories are temporarily trapped around resonance areas, or undergo transitions between different resonances. This process is a good indicator of intrinsic transport in the phase space.\r\n\r\nThe method can be applied to a large class of systems, since it is not restricted to nearly integrable systems expressed in action-angle variables, which is the traditional framework for the definition of frequencies.\r\n\r\nThe main contribution of this method is that we have included the time variable in the analysis. We can determine exactly when the trajectories exchange between different regions by keeping records of resonance trappings. This allows us to analyze chaotic trajectories and not only quasiperiodic trajectories. And, we do not require any assumption about the regularity of chaotic trajectories.\r\n\r\nWe present three different applications of the method.\r\n\r\nThe first application consists of the analysis of dynamics and global phase space structure of the classical version of a quantum Hamiltonian for the water molecule. In the second application, we study the planar circular restricted three body problem, and show how resonance transitions of chaotic orbits are related to transport between different regions of the Solar system. Finally, we applied our method to a vibrational three-degrees-of-freedom Hamiltonian of the planar OCS molecule. We study the global dynamics at an energy level close to dissociation, which corresponds to a highly excited state of the molecule.", "doi": "10.7907/8MBB-3Z60", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:2544", "collection": "thesis", "collection_id": "2544", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06112002-132034", "primary_object_url": { "basename": "aththesis.pdf", "content": "final", "filesize": 4110318, "license": "other", "mime_type": "application/pdf", "url": "/2544/1/aththesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Self-Organized Robotic System Design and Autonomous Odor Localization", "author": [ { "family_name": "Hayes", "given_name": "Adam Thomas", "clpid": "Hayes-Adam-Thomas" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents a methodology for designing self-organized autonomous robotic systems and demonstrates how this process can be applied to the problem of finding the source of an airborne odor plume. The design methodology is applicable to other task domains and the resulting odor localization system extends the state of the art.\r\n\r\nThe design procedure centers on the ability to define a specific task performance metric, systematically evaluate performance in a realistic environment, and define abstract relationships between system parameters and system performance. Once such relationships have been experimentally validated in a test environment, they can be used to guide the design of a deployable system. Because this process relies heavily on evaluative feedback, this work emphasizes the development of tools that allow the collection of accurate performance data. It presents a reliable multiple robot test-bed and some task-enabling sensory hardware, as well as validation of the sensory and kinematic models used in simulation. Also, a reinforcement learning methodology is described that provides consistent optimization performance while minimizing the amount of required evaluation.\r\n\r\nThe design methodology is applied to the task of odor localization. Specifically, this thesis analyzes a basic collective search task and derives the optimal group size and expected performance bounds for random and coordinated search. It also investigates a set of biologically inspired behaviors that permit an agent to traverse an odor plume to its source and describes the common characteristics of successful algorithms. One of these algorithms is implemented on the real test-bed and in simulation to verify that plume traversal is taking place and that the use of multiple collaborating robots can expand the reachable performance space. Collective search and plume traversal are then combined (along with egocentric source declaration) into the full odor localization task which is optimized in simulation. Then, following the design methodology, a model is presented which can aid in the prediction of performance and choice of algorithm parameters in more complex environments. Finally, a flocking behavior is designed, and the addition of this flocking behavior to the plume tracing algorithm is shown to produce a more capable system", "doi": "10.7907/KH16-XH33", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:6161", "collection": "thesis", "collection_id": "6161", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10262010-112027161", "type": "thesis", "title": "Receding horizon control of nonlinear systems: a control Lyapunov function approach", "author": [ { "family_name": "Jadbabaie", "given_name": "Ali", "clpid": "Jadbabaie-A" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "With the advent of faster and cheaper computers, optimization based control methodologies have become a viable candidate for control of nonlinear systems. Over the past twenty years, a group of such control schemes have been successfully used in the process control industry where the processes are either intrinsically stable or have very large time constants.
\r\n\r\nThe purpose of this thesis is to provide a theoretical framework for synthesis of a class of optimization based control schemes, known as receding horizon control techniques for nonlinear systems such as unmanned aerial vehicles.
\r\n\r\nIt is well known that unconstrained infinite horizon optimal control may be used to construct a stabilizing controller for a nonlinear system. In this thesis, we show that similar stabilization results may be achieved using unconstrained finite horizon optimal control. The key idea is to approximate the tail of the infinite horizon cost-to-go using, as terminal cost, an appropriate control Lyapunov function (CLF). A CLF can be thought of as generalization of the concept of a Lyapunov function to systems with inputs.
\r\n\r\nRoughly speaking, the terminal CLF should provide an (incremental) upper bound on the cost. In this fashion, important stability characteristics may be retained without the use of terminal constraints such as those employed by a number of other researchers. The absence of constraints allows a significant speedup in computation.
\r\n\r\nFurthermore, it is shown that in order to guarantee stability, it suffices to satisfy an improvement property, thereby relaxing the requirement that truly optimal trajectories be found.
\r\n\r\nWe provide a complete analysis of the stability and region of attraction/operation properties of receding horizon control strategies that utilize finite horizon approximations in the proposed class. It is shown that the guaranteed region of operation contains that of the CLF controller and may be made as large as desired by increasing the optimization horizon (restricted, of course, to the infinite horizon domain). Moreover, it is easily seen that both CLF and infinite horizon optimal control approaches are limiting cases of our receding horizon strategy. The key results are illustrated using a familiar example, the inverted pendulum, as well as models of the Caltech ducted fan at hover and forward flight, where significant improvements in guaranteed region of operation and cost are noted.
\r\n\r\nWe also develop an optimization based scheme for generation of aggressive trajectories for hover and forward flight models of the Caltech ducted fan experiment, using a technique known as trajectory morphing. The main idea behind trajectory morphing is to develop a simplified model of the nonlinear system and solve the trajectory generation problem for that model. The resulting trajectory is then used as a reference in a receding horizon optimization scheme to generate trajectories of the original nonlinear system. Several aggressive trajectories are obtained in this fashion for the forward flight model of the Caltech ducted fan experiment.
", "doi": "10.7907/CRHD-3202", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:1143", "collection": "thesis", "collection_id": "1143", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03262007-112838", "primary_object_url": { "basename": "Duttweiler_me_2001.pdf", "content": "final", "filesize": 20766786, "license": "other", "mime_type": "application/pdf", "url": "/1143/1/Duttweiler_me_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Surge Instability on a Cavitating Propeller", "author": [ { "family_name": "Duttweiler", "given_name": "Mark Edward", "clpid": "Duttweiler-Mark-Edward" } ], "thesis_advisor": [ { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" } ], "thesis_committee": [ { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Acosta", "given_name": "Allan J.", "clpid": "Acosta-A-J" }, { "family_name": "Raichlen", "given_name": "Fredric", "clpid": "Raichlen-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The present study details results from experiments investigating a surge instability on a cavitating propeller. Initially, the stable behavior of the propeller is explored, and the nature and extent of the cavitation is documented at various experimental conditions, including propeller yaw. The cavitation surge instability is first explored through visual observation of the cavitation on the propeller blades and in the tip vortices. Particular note is made of similarities between the behavior of the re-entrant jets and that noted by other investigators. It is also observed that the nature of the instability is closely related to the partial cavity instability observed on single, two-dimensional hydrofoils.
\r\n\r\nThe flow conditions that lead to instability are determined and it is shown that onset corresponds to a specific configuration of attached cavity lengths on an individual propeller blade. Pressure measurements are obtained from transducers within the experimental facility, and the acoustic signature of the instability is identified. The magnitude of the fluctuating pressures is very large, presumably capable of producing severe hull vibration. A simple model is developed based on cavity volume estimates obtained from high speed video footage, and the predictions of the model are compared with the experimentally obtained pressures.
\r\n\r\nTo assess the significance of the surrounding facility in initiating and sustaining the instability, a model is developed for the experimental facility dynamics. The predictions of this model are then compared with an experimentally determined facility response to a volumetric excitation imposed by an oscillating piston. To quantify the response of the cavitation to fluctuations in test section conditions, quasistatic estimates are obtained for the cavitation compliance and mass flow gain factor of the propeller. These parameters have previously been employed in developing system transfer functions for cavitating pumps.
\r\n\r\nFinally, a model is developed for the complete system, incorporating both the cavitation and facility dynamics. The model predicts active system dynamics and therefore potentially unstable behavior for two distinct frequency ranges, and one such range is hypothesized to correspond to the observed instability. The ability of the model to predict the observed characteristics of the instability is then evaluated.
", "doi": "10.7907/07RB-NX02", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3785", "collection": "thesis", "collection_id": "3785", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09262005-143545", "primary_object_url": { "basename": "Tripathi_ab_2001.pdf", "content": "final", "filesize": 12407063, "license": "other", "mime_type": "application/pdf", "url": "/3785/1/Tripathi_ab_2001.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "In-Situ Diagnostics for Metalorganic Chemical Vapor Deposition of YBCO", "author": [ { "family_name": "Tripathi", "given_name": "Ashok Burton", "clpid": "Tripathi-Ashok-Burton" } ], "thesis_advisor": [ { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" } ], "thesis_committee": [ { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Raja", "given_name": "L.", "clpid": "Raja-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A new stagnation flow MOCVD research reactor is described that is designed to serve as a testbed to develop tools for \"intelligent\" thin film deposition, such as in-situ sensors and diagnostics, control algorithms, and thin film growth models. The reactor is designed in particular for the deposition of epitaxial YBa2Cu3O7-\u03b4 on MgO, although with minor modifications it would be suitable for deposition of any metal-oxide thin films.
\r\n\r\nThe reactor is specifically designed to permit closed-loop thermal and stoichiometric control of the film growth process. Closed-loop control of precursor flow rates is accomplished by using ultraviolet absorption spectroscopy on each precursor line. Also integrated into the design is a Fourier Transform Infrared (FTIR) spectroscopy system which collects real-time, in-situ infrared polarized reflectance spectra of the film as it grows. Numerical simulation was used extensively to optimize the fluid dynamics and heat transfer to provide uniform fluxes to the substrate. As a result, thickness uniformity across the substrate is typically within 3% from the center to the edge of the substrate.
\r\n\r\nExperimental studies of thin films grown in the Y/Ba/Cu/O system have been carried out. The films have been characterized by Rutherford Backscattering Spectrometry and X-ray Diffraction. Results indicate c-axis oriented grains with pure 1:2:3 phase YBCO, good spatial uniformity, and a low degree of c-axis wobble. Experimental growth data is used in a gas phase and surface chemistry model to calculate sticking coefficients for yttrium oxide, barium oxide, and copper oxide on YBCO.
\r\n\r\nIn-situ FTIR and Coherent Gradient Sensing (CGS) analysis of growing films has been performed, yielding accurate substrate temperature, film thickness monitoring, and full-field, real-time curvature maps of the films. In addition, we have implemented CGS to obtain full-field in-situ images of local curvature during oxygenation and deoxygenation of YBCO films. An analysis of the oxygen diffusion is performed, and diffusivity constants are presented for a variety of temperature and film conditions.
", "doi": "10.7907/3ZJS-BE38", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3192", "collection": "thesis", "collection_id": "3192", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08222001-170336", "primary_object_url": { "basename": "punthesis.pdf", "content": "final", "filesize": 6296651, "license": "other", "mime_type": "application/pdf", "url": "/3192/1/punthesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Measurements of Thermo-Acoustic Coupling", "author": [ { "family_name": "Pun", "given_name": "Winston", "clpid": "Pun-Winston" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The problem of combustion instabilities has existed since the early 1940s, when they were observed during the development of solid and liquid rocket engines. While various engineering solutions have served well in these fields, the problem is revisited in modern gas-turbine engines. The purpose of this work is to provide experimental measurements of laboratory devices that exhibit thermo-acoustic coupling, similar to the interaction observed during combustion instabilities, which will aid in the design and development of stable systems.\r\n\r\nPossibly the simplest device which exhibits these characteristics is a Rijke tube. An electrical, horizontally mounted, 1 m long version of the original Rijke tube is presented, with measurements taken during unstable and stable operation. An accurate stability boundary with uncertainty is determined for a heater position of x/L = ?, as a function of mass flow rate and heater power. Hysteresis, not previously reported, is observed at flow rates above 3 g/s. A one-dimensional model of the stability boundary with linear acoustics is shown to have qualitative agreement with experimental data.\r\n\r\nA novel technique has also been devised which can provide insight into the local dynamic response of a flame to an acoustic field. In the experiments, a test chamber is acoustically excited by a pair of low-frequency drivers. The response of the flame is visualized by two techniques; chemiluminescence and planar laser-induced fluorescence (PLIF) of the hydroxyl (OH) radical, both of which are well-known indicators for heat release in flames. The resulting images are phase-resolved and averaged to yield a qualitative picture of the fluctuation of the heat release. The images are correlated with a pressure transducer near the flame, which allows stability to be evaluated using Rayleigh?s criterion and a combustion response function. This is the first known measurement of the combustion dynamics of a flame over a range of frequencies. Results indicate that the drive frequency and burner configuration have a pronounced effect on the response of the flame. Drive frequencies ranging from 22 Hz to 55 Hz are applied to the jet mixed burner, supplied with a premixed 50/50 mixture of methane and carbon dioxide at a Reynolds number of 20,000. The burner is operated in two configurations; with an aerodynamically stabilized flame and with a flame stabilized by two protruding bluff-bodies. Results indicate that in general the bluff-body stabilized flame is less sensitive to chamber acoustic excitation.", "doi": "10.7907/SPSR-VD18", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:338", "collection": "thesis", "collection_id": "338", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01252007-135242", "primary_object_url": { "basename": "Seywert_c_2001.pdf", "content": "final", "filesize": 6353138, "license": "other", "mime_type": "application/pdf", "url": "/338/1/Seywert_c_2001.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Combustion Instabilities: Issues in Modeling and Control", "author": [ { "family_name": "Seywert", "given_name": "Claude", "clpid": "Seywert-Claude" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Hornung", "given_name": "Hans G.", "orcid": "0000-0002-4903-8419", "clpid": "Hornung-H-G" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "This study deals with various aspects in the development of active control of combustion instabilities.\r\n\r\nA low-order model is developed, reconciling along the way two different approaches taken by researchers to attack the description of combustion instabilities. The model is demonstrated with application to a Rijke tube and compared to experiments. The Rijke burner experiments suggest two major discrepancies with the model: the presence of a hysteresis loop is unaccounted for and the model does not describe the seemingly random fluctuations in the amplitude of the pressure oscillations in the 'unstable' regime. So far no explanation for the hysteresis can be given; however, this phenomenon is successfully exploited by using a novel nonlinear control technique to expand the stable operating range of the burner. The origin of the 'noise' in the pressure trace is explained by considering entropy and vorticity waves in the combustor. Their presence leads to a slight modification of the original model, introducing stochastic source terms into the oscillator equations. The consequences of the presence of these terms is analyzed by means of simulations. One interesting result is that they allow for the identification of model parameters from a single experimental run of a stable combustion system.\r\n\r\nFinally, a unified approach to controlling combustion instabilities is presented. The formulation and analysis account for truncation to a few modes; uncertainties in the description of the system (including uncertain sensing and actuating); external disturbances; and intrinsic noise sources. An explicit expression is derived against which any controller can be checked for stability.", "doi": "10.7907/JKFD-7W43", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:338", "collection": "thesis", "collection_id": "338", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01252007-135242", "primary_object_url": { "basename": "Seywert_c_2001.pdf", "content": "final", "filesize": 6353138, "license": "other", "mime_type": "application/pdf", "url": "/338/1/Seywert_c_2001.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Combustion Instabilities: Issues in Modeling and Control", "author": [ { "family_name": "Seywert", "given_name": "Claude", "clpid": "Seywert-Claude" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Hornung", "given_name": "Hans G.", "orcid": "0000-0002-4903-8419", "clpid": "Hornung-H-G" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "This study deals with various aspects in the development of active control of combustion instabilities.\r\n\r\nA low-order model is developed, reconciling along the way two different approaches taken by researchers to attack the description of combustion instabilities. The model is demonstrated with application to a Rijke tube and compared to experiments. The Rijke burner experiments suggest two major discrepancies with the model: the presence of a hysteresis loop is unaccounted for and the model does not describe the seemingly random fluctuations in the amplitude of the pressure oscillations in the 'unstable' regime. So far no explanation for the hysteresis can be given; however, this phenomenon is successfully exploited by using a novel nonlinear control technique to expand the stable operating range of the burner. The origin of the 'noise' in the pressure trace is explained by considering entropy and vorticity waves in the combustor. Their presence leads to a slight modification of the original model, introducing stochastic source terms into the oscillator equations. The consequences of the presence of these terms is analyzed by means of simulations. One interesting result is that they allow for the identification of model parameters from a single experimental run of a stable combustion system.\r\n\r\nFinally, a unified approach to controlling combustion instabilities is presented. The formulation and analysis account for truncation to a few modes; uncertainties in the description of the system (including uncertain sensing and actuating); external disturbances; and intrinsic noise sources. An explicit expression is derived against which any controller can be checked for stability.", "doi": "10.7907/JKFD-7W43", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3192", "collection": "thesis", "collection_id": "3192", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08222001-170336", "primary_object_url": { "basename": "punthesis.pdf", "content": "final", "filesize": 6296651, "license": "other", "mime_type": "application/pdf", "url": "/3192/1/punthesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Measurements of Thermo-Acoustic Coupling", "author": [ { "family_name": "Pun", "given_name": "Winston", "clpid": "Pun-Winston" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The problem of combustion instabilities has existed since the early 1940s, when they were observed during the development of solid and liquid rocket engines. While various engineering solutions have served well in these fields, the problem is revisited in modern gas-turbine engines. The purpose of this work is to provide experimental measurements of laboratory devices that exhibit thermo-acoustic coupling, similar to the interaction observed during combustion instabilities, which will aid in the design and development of stable systems.\r\n\r\nPossibly the simplest device which exhibits these characteristics is a Rijke tube. An electrical, horizontally mounted, 1 m long version of the original Rijke tube is presented, with measurements taken during unstable and stable operation. An accurate stability boundary with uncertainty is determined for a heater position of x/L = ?, as a function of mass flow rate and heater power. Hysteresis, not previously reported, is observed at flow rates above 3 g/s. A one-dimensional model of the stability boundary with linear acoustics is shown to have qualitative agreement with experimental data.\r\n\r\nA novel technique has also been devised which can provide insight into the local dynamic response of a flame to an acoustic field. In the experiments, a test chamber is acoustically excited by a pair of low-frequency drivers. The response of the flame is visualized by two techniques; chemiluminescence and planar laser-induced fluorescence (PLIF) of the hydroxyl (OH) radical, both of which are well-known indicators for heat release in flames. The resulting images are phase-resolved and averaged to yield a qualitative picture of the fluctuation of the heat release. The images are correlated with a pressure transducer near the flame, which allows stability to be evaluated using Rayleigh?s criterion and a combustion response function. This is the first known measurement of the combustion dynamics of a flame over a range of frequencies. Results indicate that the drive frequency and burner configuration have a pronounced effect on the response of the flame. Drive frequencies ranging from 22 Hz to 55 Hz are applied to the jet mixed burner, supplied with a premixed 50/50 mixture of methane and carbon dioxide at a Reynolds number of 20,000. The burner is operated in two configurations; with an aerodynamically stabilized flame and with a flame stabilized by two protruding bluff-bodies. Results indicate that in general the bluff-body stabilized flame is less sensitive to chamber acoustic excitation.", "doi": "10.7907/SPSR-VD18", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:820", "collection": "thesis", "collection_id": "820", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03012006-093758", "primary_object_url": { "basename": "Isella_gc_2001.pdf", "content": "final", "filesize": 7393215, "license": "other", "mime_type": "application/pdf", "url": "/820/1/Isella_gc_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling and Simulation of Combustion Chamber and Propellant Dynamics and Issues in Active Control of Combustion Instabilities", "author": [ { "family_name": "Isella", "given_name": "Giorgio Carlo", "clpid": "Isella-Giorgio-Carlo" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "A method for a comprehensive approach to analysis of the dynamics of an actively controlled combustion chamber, with detailed analysis of the combustion models for the case of a solid rocket propellant, is presented here. The objective is to model the system as interconnected blocks describing the dynamics of the chamber, combustion and control (including sensors and actuators).
\r\n\r\nThe analytical framework for the analysis of the dynamics of a combustion chamber is based on spatial averaging, as introduced by Culick. This method results in the determination of a set of coupled oscillator equations that are then integrated with the appropriate forcing terms deriving from combustion and control.
\r\n\r\nCombustion dynamics are analyzed for the case of a solid propellant. Considerable data exists suggesting that the response functions for many solid propellants tend to have higher values, in some ranges of frequencies, than predicted by the conventional quasi-steady theory. Hence, quasi-steady theory is extended to include the dynamics of the gas-phase and also of a surface layer interposed between the gaseous flame zone and the heated solid phase of the propellant. The models are constructed so that they produce a combustion response function for the solid propellant that can be immediately introduced in the our analytical framework. The principal objective of this analysis is to determine which characteristics of the solid propellant are responsible for the large sensitivity, observed experimentally, of propellant burning response to small variations in the conditions. We show that velocity coupling, and not pressure coupling, has the potential to be the mechanism responsible for that high sensitivity. Some issues related to the modeling of solid propellant are also discussed, namely the importance of particulate modeling and its effect on the global dynamics of the chamber and a revisited interpretation of the intrinsic stability limit for burning of solid propellants.
\r\n\r\nActive control is also considered in the analysis. A critical discussion about the most commonly used control strategies used in combustion allows us to define which are the most promising algorithms to use on future experiments. Particular attention is devoted to the effect of time delay (between sensing and actuation) on the control strategy; several methods to compensate for it are presented and discussed, with numerical examples based on the approximate analysis produced by our framework.
\r\n\r\nExperimental results are presented for the case of a Dump Combustor. The combustor exhibits an unstable burning mode, defined through the measurement of the pressure trace and shadowgraph imaging. The transition between stable and unstable modes of operation is characterized by the presence of hysteresis, also observed in other experimental works, and hence not a special characteristic of this combustor. Control is introduced in the form of pulsed secondary fuel. We show the capability of forcing the transition from unstable to stable burning, hence extending the stable operating regime of the combustor. The transition, characterized by the use of a shadowgraph movie sequence, is attributed to a combined fluid-mechanic and combustion mechanism.
", "doi": "10.7907/k1rf-a525", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:1143", "collection": "thesis", "collection_id": "1143", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03262007-112838", "primary_object_url": { "basename": "Duttweiler_me_2001.pdf", "content": "final", "filesize": 20766786, "license": "other", "mime_type": "application/pdf", "url": "/1143/1/Duttweiler_me_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Surge Instability on a Cavitating Propeller", "author": [ { "family_name": "Duttweiler", "given_name": "Mark Edward", "clpid": "Duttweiler-Mark-Edward" } ], "thesis_advisor": [ { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" } ], "thesis_committee": [ { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Acosta", "given_name": "Allan J.", "clpid": "Acosta-A-J" }, { "family_name": "Raichlen", "given_name": "Fredric", "clpid": "Raichlen-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The present study details results from experiments investigating a surge instability on a cavitating propeller. Initially, the stable behavior of the propeller is explored, and the nature and extent of the cavitation is documented at various experimental conditions, including propeller yaw. The cavitation surge instability is first explored through visual observation of the cavitation on the propeller blades and in the tip vortices. Particular note is made of similarities between the behavior of the re-entrant jets and that noted by other investigators. It is also observed that the nature of the instability is closely related to the partial cavity instability observed on single, two-dimensional hydrofoils.
\r\n\r\nThe flow conditions that lead to instability are determined and it is shown that onset corresponds to a specific configuration of attached cavity lengths on an individual propeller blade. Pressure measurements are obtained from transducers within the experimental facility, and the acoustic signature of the instability is identified. The magnitude of the fluctuating pressures is very large, presumably capable of producing severe hull vibration. A simple model is developed based on cavity volume estimates obtained from high speed video footage, and the predictions of the model are compared with the experimentally obtained pressures.
\r\n\r\nTo assess the significance of the surrounding facility in initiating and sustaining the instability, a model is developed for the experimental facility dynamics. The predictions of this model are then compared with an experimentally determined facility response to a volumetric excitation imposed by an oscillating piston. To quantify the response of the cavitation to fluctuations in test section conditions, quasistatic estimates are obtained for the cavitation compliance and mass flow gain factor of the propeller. These parameters have previously been employed in developing system transfer functions for cavitating pumps.
\r\n\r\nFinally, a model is developed for the complete system, incorporating both the cavitation and facility dynamics. The model predicts active system dynamics and therefore potentially unstable behavior for two distinct frequency ranges, and one such range is hypothesized to correspond to the observed instability. The ability of the model to predict the observed characteristics of the instability is then evaluated.
", "doi": "10.7907/07RB-NX02", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3785", "collection": "thesis", "collection_id": "3785", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09262005-143545", "primary_object_url": { "basename": "Tripathi_ab_2001.pdf", "content": "final", "filesize": 12407063, "license": "other", "mime_type": "application/pdf", "url": "/3785/1/Tripathi_ab_2001.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "In-Situ Diagnostics for Metalorganic Chemical Vapor Deposition of YBCO", "author": [ { "family_name": "Tripathi", "given_name": "Ashok Burton", "clpid": "Tripathi-Ashok-Burton" } ], "thesis_advisor": [ { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" } ], "thesis_committee": [ { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Raja", "given_name": "L.", "clpid": "Raja-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A new stagnation flow MOCVD research reactor is described that is designed to serve as a testbed to develop tools for \"intelligent\" thin film deposition, such as in-situ sensors and diagnostics, control algorithms, and thin film growth models. The reactor is designed in particular for the deposition of epitaxial YBa2Cu3O7-\u03b4 on MgO, although with minor modifications it would be suitable for deposition of any metal-oxide thin films.
\r\n\r\nThe reactor is specifically designed to permit closed-loop thermal and stoichiometric control of the film growth process. Closed-loop control of precursor flow rates is accomplished by using ultraviolet absorption spectroscopy on each precursor line. Also integrated into the design is a Fourier Transform Infrared (FTIR) spectroscopy system which collects real-time, in-situ infrared polarized reflectance spectra of the film as it grows. Numerical simulation was used extensively to optimize the fluid dynamics and heat transfer to provide uniform fluxes to the substrate. As a result, thickness uniformity across the substrate is typically within 3% from the center to the edge of the substrate.
\r\n\r\nExperimental studies of thin films grown in the Y/Ba/Cu/O system have been carried out. The films have been characterized by Rutherford Backscattering Spectrometry and X-ray Diffraction. Results indicate c-axis oriented grains with pure 1:2:3 phase YBCO, good spatial uniformity, and a low degree of c-axis wobble. Experimental growth data is used in a gas phase and surface chemistry model to calculate sticking coefficients for yttrium oxide, barium oxide, and copper oxide on YBCO.
\r\n\r\nIn-situ FTIR and Coherent Gradient Sensing (CGS) analysis of growing films has been performed, yielding accurate substrate temperature, film thickness monitoring, and full-field, real-time curvature maps of the films. In addition, we have implemented CGS to obtain full-field in-situ images of local curvature during oxygenation and deoxygenation of YBCO films. An analysis of the oxygen diffusion is performed, and diffusivity constants are presented for a variety of temperature and film conditions.
", "doi": "10.7907/3ZJS-BE38", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:820", "collection": "thesis", "collection_id": "820", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03012006-093758", "primary_object_url": { "basename": "Isella_gc_2001.pdf", "content": "final", "filesize": 7393215, "license": "other", "mime_type": "application/pdf", "url": "/820/1/Isella_gc_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling and Simulation of Combustion Chamber and Propellant Dynamics and Issues in Active Control of Combustion Instabilities", "author": [ { "family_name": "Isella", "given_name": "Giorgio Carlo", "clpid": "Isella-Giorgio-Carlo" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Leonard", "given_name": "Anthony", "clpid": "Leonard-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "A method for a comprehensive approach to analysis of the dynamics of an actively controlled combustion chamber, with detailed analysis of the combustion models for the case of a solid rocket propellant, is presented here. The objective is to model the system as interconnected blocks describing the dynamics of the chamber, combustion and control (including sensors and actuators).
\r\n\r\nThe analytical framework for the analysis of the dynamics of a combustion chamber is based on spatial averaging, as introduced by Culick. This method results in the determination of a set of coupled oscillator equations that are then integrated with the appropriate forcing terms deriving from combustion and control.
\r\n\r\nCombustion dynamics are analyzed for the case of a solid propellant. Considerable data exists suggesting that the response functions for many solid propellants tend to have higher values, in some ranges of frequencies, than predicted by the conventional quasi-steady theory. Hence, quasi-steady theory is extended to include the dynamics of the gas-phase and also of a surface layer interposed between the gaseous flame zone and the heated solid phase of the propellant. The models are constructed so that they produce a combustion response function for the solid propellant that can be immediately introduced in the our analytical framework. The principal objective of this analysis is to determine which characteristics of the solid propellant are responsible for the large sensitivity, observed experimentally, of propellant burning response to small variations in the conditions. We show that velocity coupling, and not pressure coupling, has the potential to be the mechanism responsible for that high sensitivity. Some issues related to the modeling of solid propellant are also discussed, namely the importance of particulate modeling and its effect on the global dynamics of the chamber and a revisited interpretation of the intrinsic stability limit for burning of solid propellants.
\r\n\r\nActive control is also considered in the analysis. A critical discussion about the most commonly used control strategies used in combustion allows us to define which are the most promising algorithms to use on future experiments. Particular attention is devoted to the effect of time delay (between sensing and actuation) on the control strategy; several methods to compensate for it are presented and discussed, with numerical examples based on the approximate analysis produced by our framework.
\r\n\r\nExperimental results are presented for the case of a Dump Combustor. The combustor exhibits an unstable burning mode, defined through the measurement of the pressure trace and shadowgraph imaging. The transition between stable and unstable modes of operation is characterized by the presence of hysteresis, also observed in other experimental works, and hence not a special characteristic of this combustor. Control is introduced in the form of pulsed secondary fuel. We show the capability of forcing the transition from unstable to stable burning, hence extending the stable operating regime of the combustor. The transition, characterized by the use of a shadowgraph movie sequence, is attributed to a combined fluid-mechanic and combustion mechanism.
", "doi": "10.7907/k1rf-a525", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:1647", "collection": "thesis", "collection_id": "1647", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05062004-055516", "primary_object_url": { "basename": "Parrilo-Thesis.pdf", "content": "final", "filesize": 911166, "license": "other", "mime_type": "application/pdf", "url": "/1647/1/Parrilo-Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization", "author": [ { "family_name": "Parrilo", "given_name": "Pablo A.", "clpid": "Parrilo-P-A" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In the first part of this thesis, we introduce a specific class of Linear Matrix Inequalities (LMI) whose optimal solution can be characterized exactly. This family corresponds to the case where the associated linear operator maps the cone of positive semidefinite matrices onto itself. In this case, the optimal value equals the spectral radius of the operator. It is shown that some rank minimization problems, as well as generalizations of the structured singular value ($mu$) LMIs, have exactly this property.\n\nIn the same spirit of exploiting structure to achieve computational efficiency, an algorithm for the numerical solution of a special class of frequency-dependent LMIs is presented. These optimization problems arise from robustness analysis questions, via the Kalman-Yakubovich-Popov lemma. The procedure is an outer approximation method based on the algorithms used in the computation of hinf norms for linear, time invariant systems. The result is especially useful for systems with large state dimension.\n\nThe other main contribution in this thesis is the formulation of a convex optimization framework for semialgebraic problems, i.e., those that can be expressed by polynomial equalities and inequalities. The key element is the interaction of concepts in real algebraic geometry (Positivstellensatz) and semidefinite programming.\n\nTo this end, an LMI formulation for the sums of squares decomposition for multivariable polynomials is presented. Based on this, it is shown how to construct sufficient Positivstellensatz-based convex tests to prove that certain sets are empty. Among other applications, this leads to a nonlinear extension of many LMI based results in uncertain linear system analysis.\n\nWithin the same framework, we develop stronger criteria for matrix copositivity, and generalizations of the well-known standard semidefinite relaxations for quadratic programming.\n\nSome applications to new and previously studied problems are presented. A few examples are Lyapunov function computation, robust bifurcation analysis, structured singular values, etc. It is shown that the proposed methods allow for improved solutions for very diverse questions in continuous and combinatorial optimization.\n", "doi": "10.7907/2K6Y-CH43", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:2753", "collection": "thesis", "collection_id": "2753", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06282005-103901", "primary_object_url": { "basename": "Wang_y_2000.pdf", "content": "final", "filesize": 8520722, "license": "other", "mime_type": "application/pdf", "url": "/2753/1/Wang_y_2000.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Effects of actuator limits in bifurcation control with applications to active control of fluid instabilities in turbomachinery", "author": [ { "family_name": "Wang", "given_name": "Yong", "clpid": "Wang-Yong" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Paduano", "given_name": "James D.", "clpid": "Paduano-J-D" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Feedback stabilization is one of the most dominant issues in modern control theory. The validity of linear control design is based on the assumption that the system is stabilizable. With rapid broadening of control applications to complex systems during the past two decades, the attainability of linear stabilizability sometimes has to compromise with system constraints and affordability of distributed actuation. The goal of this thesis is to tackle some of the problems in control of nonequilibrium behavior and to apply the theory to active control of fluid instabilities in gas turbine engines.\r\n\r\nWe consider two of the simplest nontrivial scenarios in local smooth feedback stabilization: the steady-state case, when the linearly unstabilizable eigenvalue is zero; and the Hopf case, when the unstabilizable eigenvalues are a pair of pure imaginary numbers. Under certain nondegeneracy conditions, we give explicit algebraic conditions for stabilizability. And when the system is stabilizable, the stabilizing feedback can be explicitly constructed.\r\n\r\nThe problem of local smooth feedback stabilization for systems with critical unstabilizable modes is closely related to bifurcation control. Under certain nondegeneracy conditions, a steady-state/Hopf bifurcation can be turned into a supercritical pitchfork/Hopf bifurcation if and only if the system is locally stabilizable at the bifurcation point. Algebraic necessary and sufficient conditions are derived under which the criticality of a simple steady-state or Hopf bifurcation can be changed to supercritical by a smooth feedback. The effects of magnitude saturation, bandwidth, and rate limits are important issues in control engineering. We give qualitative estimates of the region of attraction to the stabilized bifurcating equilibrium/periodic orbits under these constraints.\r\n\r\nWe apply the above theoretical results to the Moore-Greitzer model in active control of rotating stall and surge in gas turbine engines. Though linear stabilizability can be achieved using distributed actuation, it limits the practical usefulness due to considerations of affordability and reliability. On the other hand, simple but practically promising actuation schemes such as outlet bleed valves, a couple of air injectors, and magnetic bearings will make the system loss of linear stabilizability, thus the control design becomes a challenging task. The above mentioned results in bifurcation stabilization can be applied to these cases. We analyze the effects of magnitude and rate saturations in active stall and surge control using bleed valves and magnetic bearings using the Moore-Greitzer model. The analytical formulas for bleed valve actuation give good qualitative predictions when compared with experiments. Our conclusion is that these constraints are serious limiting factors in stall control and must be addressed in practical implementation to the aircraft engines.", "doi": "10.7907/229f-f376", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:1607", "collection": "thesis", "collection_id": "1607", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05042006-131410", "primary_object_url": { "basename": "Zhu_x_2000.pdf", "content": "final", "filesize": 7149117, "license": "other", "mime_type": "application/pdf", "url": "/1607/1/Zhu_x_2000.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Hard vs. soft bounds in probablilistic robustness analysis and generalized source coding and optimal web layout design", "author": [ { "family_name": "Zhu", "given_name": "Xiaoyun", "clpid": "Zhu-Xiaoy" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Effros", "given_name": "Michelle", "clpid": "Effros-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Hou", "given_name": "Thomas Y.", "clpid": "Hou-T-Y" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I:\r\n\r\nThe relationship between hard vs. soft bounds and probabilistic vs. worst-case problem formulations for robustness analysis has been a source of some apparent confusion in the control community, and this thesis attempts to clarify some of these issues. Essentially, worst-case analysis involves computing the maximum of a function which measures performance over some set of uncertainty. Probabilistic analysis assumes some distribution on the uncertainty and computes the resulting probability measure on performance. Exact computation in each case is intractable in general. In the past most research focused on computing hard bounds on worst-case performance. This thesis explores the use of both hard and soft bounds in probabilistic robustness analysis, and investigates the computational complexity of the problems through extensive numerical experimentation. We focus on the simplest possible problem formulations that we believe reveal the difficulties associated with more general probabilistic analysis.\r\n\r\nBy extending the standard structured singular value [...] framework to allow for probabilistic descriptions of uncertainty, probabilistic [...] is defined, which characterizes the probability distribution of some performance function. The computation of probabilistic [...] involves approximating the level surface of the function in the parameter space, which is even more complex than the worst-case [...] computation, a well-known NP-hard problem. In particular, providing sufficiently tight bounds in the tail of the distribution is extremely difficult. This thesis proposes three different methods for computing a hard upper bound on probabilistic [...] whose tightness can be tested by comparison with the soft bound provided by Monte-Carlo simulations. At the same time, the efficiency of the soft bounds can be significantly improved with the information from the hard bound computation. Among the three algorithms proposed, the LC-BNB algorithm is proven by numerical experiments to provide the best average performance on random examples. One particular example is shown in the end to demonstrate the effectiveness of the method.\r\n\r\nPart II: \r\n\r\nThe design of robust and reliable networks and network services has become an increasingly challenging task in today's Internet world. To achieve this goal, understanding the characteristics of Internet traffic plays a more and more critical role. Empirical studies of measured traffic traces have led to the wide recognition of self-similarity in network traffic. Moreover, a direct link has been established between the self-similar nature of measured aggregate network traffic and the underlying heavy-tailed distributions of the Web traffic at the source level.\r\n\r\nThis thesis provides a natural and plausible explanation for the origin of heavy tails in Web traffic by introducing a series of simplified models for optimal Web layout design with varying levels of realism and analytic tractability. The basic approach is to view the minimization of the average file download time as a generalization of standard source coding for data compression, but with the design of the Web layout rather than the codewords. The results, however, are quite different from standard source coding, as all assumptions produce power law distributions for a wide variety of user behavior models.\r\n\r\nIn addition, a simulation model of more complex Web site layouts is proposed, with more detailed hyperlinks and user behavior. The throughput of a Web site can be maximized by taking advantage of information on user access patterns and rearranging (splitting or merging) files on the Web site accordingly, with a constraint on available resources. A heuristic optimization on random graphs is formulated, with user navigation modeled as Markov Chains. Simulations on different classes of graphs as well as more realistic models with simple geometries in individual Web pages all produce power law tails in the resulting size distributions of the files transferred from the Web sites. This again verifies our conjecture that heavy-tailed distributions result naturally from the tradeoff between the design objective and limited resources, and suggests a methodology for aiding in the design of high-throughput Web sites.", "doi": "10.7907/1f3r-va82", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:785", "collection": "thesis", "collection_id": "785", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02272008-083453", "primary_object_url": { "basename": "Yeung_ch_1999.pdf", "content": "final", "filesize": 7060334, "license": "other", "mime_type": "application/pdf", "url": "/785/1/Yeung_ch_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Nonlinear control of rotating stall and surge with axisymmetric bleed and air injection on axial flow compressors", "author": [ { "family_name": "Yeung", "given_name": "Chung-hei (Simon)", "clpid": "Yeung-C-S" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Caughey", "given_name": "Thomas Kirk", "clpid": "Caughey-T-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The study of compressor instabilities in gas turbine engines has received much attention in recent ears. In particular, rotating stall and surge are major causes of problems ranging from component stress and lifespan reduction to engine explosion. In this thesis, modeling and control of rotating stall and surge using bleed valve and air injection is studied and validated on a low speed, single stage, axial compressor at Caltech.\n\nBleed valve control of stall is achieved only when the compressor characteristic is actuated, due to the fast growth rate of the stall cell compared to the rate limit of the valve. Furthermore, experimental results show that the actuator rate requirement for stall control is reduced by a factor of fourteen via compressor characteristic actuation. Analytical expressions based on low order models (2-3 states) and a high fidelity simulation (37 states) tool are developed to estimate the minimum rate requirement of a bleed valve for control of stall. A comparison of the tools to experiments show a good qualitative agreement, with increasing quantitative accuracy as the complexity of the underlying model increases.\n\nAir injection control of stall and surge is also investigated. Simultaneous control of stall and surge is achieved using axisymmetric air injection. Three cases with different injector back pressure are studied. Surge control via binary air injection is achieved in all three cases. Simultaneous stall and surge control is achieved for two of the cases, but is not achieved for the lowest authority case. This is consistent with previous results for control of stall with axisymmetric air injection without a plenum attached.\n\nNon\u2014axisymmetric air injection control of stall and surge is also studied. Three existing control algorithms found in literature are modeled and analyzed. A three\u2014state model is obtained for each algorithm. For two cases, conditions for linear stability and bifurcation criticality on control of rotating stall are derived and expressed in terms of implementation\u2014oriented variables such as number of injectors. For the third case, bifurcation criticality conditions are not obtained due to complexity, though linear stability property is derived. A theoretical comparison between the three algorithms is made, via the use of low\u2014order models, to investigate pros and cons of the algorithms in the context of operability.\n\nThe effects of static distortion on the compressor facility at Caltech is characterized experimentally. Results consistent with literature are obtained. Simulations via a high fidelity model (34 states) are also performed and show good qualitative as well as quantitative agreement to experiments. A non\u2014axisymmetric pulsed air injection controller for stall is shown to be robust to static distortion.", "doi": "10.7907/1wef-gp10", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:5051", "collection": "thesis", "collection_id": "5051", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12182007-111636", "primary_object_url": { "basename": "Owen_rl_1999.pdf", "content": "final", "filesize": 3303518, "license": "other", "mime_type": "application/pdf", "url": "/5051/1/Owen_rl_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Detection and Analysis of Musical Events Using Model-Based Signal Processing", "author": [ { "family_name": "Owen", "given_name": "Randall Lee", "clpid": "Owen-Randall-Lee" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Vaidyanathan", "given_name": "P. P.", "orcid": "0000-0003-3003-7042", "clpid": "Vaidyanathan-P-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The present work is directed to the detection and analysis of notes, chords and other musical events produced by a stringed musical instrument, specifically the guitar. The chords generated by a guitar are polyphonic, meaning that they comprise multiple notes sounded simultaneously. Each note is also spectrally complex, in that it comprises a\r\nfundamental tone and several harmonics. Despite this complexity, the statistics of the signal containing the notes and chords are expected to be similar to those of human speech. This similarity will allow the signal to be characterized as a parametric random process so that established mathematical and speech recognition techniques can be used\r\nto extract the events from the signal. The analysis of musical signals is an important application since it is a logical extension to the problem of speech recognition. Moreover, a robust computer-based solution to this problem could have both research and commercial applications.
\r\n\r\n\r\nA system for automated detection and analysis of musical events, such as notes and chords, has been designed. The system is comprised of two main elements: the event library and a set of match measures. The event library contains a hierarchy of event models each corresponding to a distinct musical note or chord. Each event model is structured as a hidden Markov model (HMM), \u03bb = (A, B, \u03c0), having the four distinct states labeled attack, sustain, decay or silence, that correspond to the specific physical states of the musical event. Associated with each model state Q={q1, \u2022\u2022\u2022 , q4} are a set of M observation symbols V={ v1,v2, \u2022\u2022\u2022 , vM} and a set of three probability distributions: a transition probability distribution A={aij} , an observable probability distribution B={bj(k)} and an initial probability distribution \u03c0=\u03c0{i}. Three match measures are developed for solving the recognition problem: one for estimating the HMM parameters, one for determining the optimal state sequence of the HMM and one for evaluating the probability that a given observation sequence was produced by a specific HMM. The observation sequence is derived from the input signal by sampling, converting to a spectral representation, and digitally coding using standard speech recognition\r\ntechniques. The three match measures correspond, respectively, to training the model, refining the model and matching an event to a model, each of which is performed using conventional speech processing algorithms.
", "doi": "10.7907/GPBA-SM95", "publication_date": "1999", "thesis_type": "engd", "thesis_year": "1999" }, { "id": "thesis:5051", "collection": "thesis", "collection_id": "5051", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12182007-111636", "primary_object_url": { "basename": "Owen_rl_1999.pdf", "content": "final", "filesize": 3303518, "license": "other", "mime_type": "application/pdf", "url": "/5051/1/Owen_rl_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Detection and Analysis of Musical Events Using Model-Based Signal Processing", "author": [ { "family_name": "Owen", "given_name": "Randall Lee", "clpid": "Owen-Randall-Lee" } ], "thesis_advisor": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" } ], "thesis_committee": [ { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Vaidyanathan", "given_name": "P. P.", "orcid": "0000-0003-3003-7042", "clpid": "Vaidyanathan-P-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The present work is directed to the detection and analysis of notes, chords and other musical events produced by a stringed musical instrument, specifically the guitar. The chords generated by a guitar are polyphonic, meaning that they comprise multiple notes sounded simultaneously. Each note is also spectrally complex, in that it comprises a\r\nfundamental tone and several harmonics. Despite this complexity, the statistics of the signal containing the notes and chords are expected to be similar to those of human speech. This similarity will allow the signal to be characterized as a parametric random process so that established mathematical and speech recognition techniques can be used\r\nto extract the events from the signal. The analysis of musical signals is an important application since it is a logical extension to the problem of speech recognition. Moreover, a robust computer-based solution to this problem could have both research and commercial applications.
\r\n\r\n\r\nA system for automated detection and analysis of musical events, such as notes and chords, has been designed. The system is comprised of two main elements: the event library and a set of match measures. The event library contains a hierarchy of event models each corresponding to a distinct musical note or chord. Each event model is structured as a hidden Markov model (HMM), \u03bb = (A, B, \u03c0), having the four distinct states labeled attack, sustain, decay or silence, that correspond to the specific physical states of the musical event. Associated with each model state Q={q1, \u2022\u2022\u2022 , q4} are a set of M observation symbols V={ v1,v2, \u2022\u2022\u2022 , vM} and a set of three probability distributions: a transition probability distribution A={aij} , an observable probability distribution B={bj(k)} and an initial probability distribution \u03c0=\u03c0{i}. Three match measures are developed for solving the recognition problem: one for estimating the HMM parameters, one for determining the optimal state sequence of the HMM and one for evaluating the probability that a given observation sequence was produced by a specific HMM. The observation sequence is derived from the input signal by sampling, converting to a spectral representation, and digitally coding using standard speech recognition\r\ntechniques. The three match measures correspond, respectively, to training the model, refining the model and matching an event to a model, each of which is performed using conventional speech processing algorithms.
", "doi": "10.7907/GPBA-SM95", "publication_date": "1999", "thesis_type": "engd", "thesis_year": "1999" }, { "id": "thesis:540", "collection": "thesis", "collection_id": "540", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02072008-100242", "primary_object_url": { "basename": "Bullo_f_1999.pdf", "content": "final", "filesize": 5715647, "license": "other", "mime_type": "application/pdf", "url": "/540/1/Bullo_f_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Nonlinear control of mechanical systems : a Riemannian geometry approach", "author": [ { "family_name": "Bullo", "given_name": "Francesco", "clpid": "Bullo-F" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Nonlinear control of mechanical systems is a challenging discipline that lies at the intersection between control theory and geometric mechanics. This thesis sheds new light on this interplay while investigating motion control problems for Lagrangian systems. Both stability and motion planning aspects are treated within a unified framework that accounts for a large class of devices such as robotic manipulators, autonomous vehicles and locomotion systems.\n\nOne distinguishing feature of mechanical systems is the number of control forces. For systems with as many input forces as degrees of freedom, many control problems are tractable. One contribution of this thesis is a set of trajectory tracking controllers designed via the notions of configuration and velocity error. The proposed approach includes as special cases a variety of results on joint and workspace control of manipulators as well as on attitude and position control of vehicles.\n\nWhenever fewer input forces are available than degrees of freedom, various control questions arise. The main contribution of this thesis is the design of motion algorithms for vehicles, i.e., rigid bodies moving in Euclidean space. First, an algebraic controllability analysis characterizes the set of reachable configurations and velocities for a system starting at rest. Then, provided a certain controllability condition is satisfied, various motion algorithms are proposed to perform tasks such as short range reconfiguration and hovering.\n\nFinally, stabilization techniques for underactuated systems are investigated. The emphasis is on relative equilibria, i.e., steady motions for systems that have a conserved momentum. Local exponential stabilization is achieved via an appropriate splitting of the control authority.", "doi": "10.7907/xrak-3409", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:15018", "collection": "thesis", "collection_id": "15018", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08312022-180047419", "primary_object_url": { "basename": "Grigoriev_RO_1998.pdf", "content": "final", "filesize": 46993645, "license": "other", "mime_type": "application/pdf", "url": "/15018/1/Grigoriev_RO_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Symmetry and Localized Control of Extended Chaotic Systems", "author": [ { "family_name": "Grigoriev", "given_name": "Roman O.", "clpid": "Grigoriev-Roman-O" } ], "thesis_advisor": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" } ], "thesis_committee": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Roukes", "given_name": "Michael Lee", "orcid": "0000-0002-2916-6026", "clpid": "Roukes-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The present study is prompted by the failure of conventional chaos control theory to provide a practically sound algorithm for controlling the chaos in general spatially extended experimental systems. The primary reason for this failure is the presence of symmetry, which is a feature of most extended dynamical systems and which violates a number of assumptions of genericity made by conventional control theory. These\r\nassumptions can be relaxed, but at a price that increases with increasing symmetry of the target state. This price includes the larger number of independent control parameters that must be adjusted to steer the system towards the target trajectory, as well as the larger number of independent observables required to reconstruct the dynamics of an experimental system with symmetries.
\r\n\r\nWe show that spatially extended chaotic systems can be controlled by monitoring and perturbing them at multiple spatial locations, or pinning sites, with separations determined by the noise in the system. We show that the arrangement of pinning sites must comply with constraints determined by the symmetry of the system in order to achieve control. We determine how the system can be forced from the spatiotemporally chaotic state into the controllable target state. Finally, we determine the maxim al distance between pinning sites and the maximal level of noise tolerated\r\nby a given arrangement of pinning sites for a model extended system.
", "doi": "10.7907/zxm1-n119", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:4124", "collection": "thesis", "collection_id": "4124", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10172005-103315", "primary_object_url": { "basename": "Primbs_ja_1999.pdf", "content": "final", "filesize": 688728, "license": "other", "mime_type": "application/pdf", "url": "/4124/1/Primbs_ja_1999.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Nonlinear optimal control: a receding horizon appoach", "author": [ { "family_name": "Primbs", "given_name": "James A.", "clpid": "Primbs-J-A" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Krener", "given_name": "Arthur", "clpid": "Krener-A" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Chandy", "given_name": "K. Mani", "clpid": "Chandy-K-M" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "As advances in computing power forge ahead at an unparalleled rate, an increasingly compelling question that spans nearly every discipline is how best to exploit these advances. At one extreme, a tempting approach is to throw as much computational power at a problem as possible. Unfortunately, this is rarely a justifiable approach unless one has some theoretical guarantee of the efficacy of the computations. At the other extreme, not taking advantage of available computing power is unnecessarily limiting. In general, it is only through a careful inspection of the strengths and weaknesses of all available approaches that an optimal balance between analysis and computation is achieved. This thesis addresses the delicate interaction between theory and computation in the context of optimal control.\n\nAn exact solution to the nonlinear optimal control problem is known to be prohibitively difficult, both analytically and computationally. Nevertheless, a number of alternative (suboptimal) approaches have been developed. Many of these techniques approach the problem from an off-line, analytical point of view, designing a controller based on a detailed analysis of the system dynamics. A concept particularly amenable to this point of view is that of a control Lyapunov function. These techniques extend the Lyapunov methodology to control systems. In contrast, so-called receding horizon techniques rely purely on on-line computation to determine a control law. While offering an alternative method of attacking the optimal control problem, receding horizon implementations often lack solid theoretical stability guarantees.\n\nIn this thesis, we uncover a synergistic relationship that holds between control Lyapunov function based schemes and on-line receding horizon style computation. These connections derive from the classical Hamilton-Jacobi-Bellman and Euler-Lagrange approaches to optimal control. By returning to these roots, a broad class of control Lyapunov schemes are shown to admit natural extensions to receding horizon schemes, benefiting from the performance advantages of on-line computation. From the receding horizon point of view, the use of a control Lyapunov function is a convenient solution to not only the theoretical properties that receding horizon control typically lacks, but also unexpectedly eases many of the difficult implementation requirements associated with on-line computation. After developing these schemes for the unconstrained nonlinear optimal control problem, the entire design methodology is illustrated on a simple model of a longitudinal flight control system. They are then extended to time-varying and input constrained nonlinear systems, offering a promising new paradigm for nonlinear optimal control design.", "doi": "10.7907/4AD2-0T48", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:1917", "collection": "thesis", "collection_id": "1917", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05212007-082553", "primary_object_url": { "basename": "Huang_y_1999.pdf", "content": "final", "filesize": 4460304, "license": "other", "mime_type": "application/pdf", "url": "/1917/1/Huang_y_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Nonlinear optimal control: an enhanced quasi-LPV approach", "author": [ { "family_name": "Huang", "given_name": "Yun", "clpid": "Huang-Yun" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Realistic models of physical systems are often nonlinear. Our objective is to synthesize controllers for nonlinear systems that not only provide stability, but also deliver good closed-loop performance.\r\n\r\nThe frozen Riccati equation approach is thoroughly examined. Although it suffers fundamental deficiencies due to its pointwise nature, it is proven that optimality is always possible under a certain assumption on the optimal value of the performance index. This is a consequence of the non-uniqueness of the pointwise linear model of the nonlinear dynamics. However, one cannot assess a priori the guaranteed global performance for a particular model choice.\r\n\r\nAn alternative to the pointwise design is to treat nonlinear plants as linear parameter varying systems with the underlying parameters being functions of the state variables. By exploiting the variation rate bounds of the parameters, a controller that smoothly schedules on the parameters can be synthesized by solving a convex optimization problem. Depending upon the choice of the variation rate bounds, the resulting controller can range from replicating the pointwise design result, which comes with no guarantee on performance, to providing quadratic stability, in which case it can withstand arbitrarily fast parameter variation.\r\n\r\nUnder the above quasi-LPV framework, we present a new scheme that incorporates the freedom of choosing the state-dependent linear representation into the control design process. It is shown that the L2-gain analysis can be reformulated as an infinite dimensional convex optimization problem, and an approximate solution can be obtained by solving a collection of linear matrix inequalities. The synthesis problem is cast as a minimization over an infinite dimensional bilinear matrix inequality constraint. An iterative algorithm, similar to the \"D - K iteration\" for \u00b5 synthesis, is proposed to compute the best achievable performance. It is demonstrated through several examples that this approach can effectively reduce conservatism of the overall design.", "doi": "10.7907/5VNR-GF60", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:4035", "collection": "thesis", "collection_id": "4035", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10112006-154843", "primary_object_url": { "basename": "Slatkin_ab_1999.pdf", "content": "final", "filesize": 14938610, "license": "other", "mime_type": "application/pdf", "url": "/4035/1/Slatkin_ab_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling and Experiments for a Class of Robotic Endoscopes", "author": [ { "family_name": "Slatkin", "given_name": "Andrew Brett", "clpid": "Slatkin-Andrew-Brett" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Knowles", "given_name": "James K.", "clpid": "Knowles-J-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Grundfest", "given_name": "W.", "clpid": "Grundfest-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Current developments in minimally invasive medical practice motivated this study of self-propelled, robotic endoscopes for deep penetration into curved physiological lumens. The conceptual design of such devices is applicable to endoscopy within a variety of lumens in the human body, e.g., blood vessels, but the initial objective of this technology is to provide access to the interior of the entire small intestine without surgical incisions. The small intestine presents several challenges to endoscopic penetration: it is extremely compliant to applied loading, internally lubricated, easily injured, and contains many tight curves along its length of approximately eighteen feet.
\r\n\r\nThis thesis reports the basic design and locomotion concepts for one class of endoscopic robots that are intended to provide safe and reliable traversal of the small intestine via worm-like actuation. Five generations of proof-of-concept prototype robots have been built to validate the fundamental concepts. Furthermore, these miniaturized robots have incorporated the following features: redundant actuation with computer control, tool-free modular assembly, and on-board videoimaging capability. The prototypes have been tested in rubber tubing, the small intestines of deceased pigs, and in the small intestines of live, anaesthetized pigs.
\r\n\r\nAt the onset of this research, little regarding the elastic properties of small intestine existed in the biomechanics literature that would be applicable to the design of these mechanisms. However, accurate prediction of the small intestine's response to robotic loadings would dramatically improve the research and development process of these machines. Thus, an investigation of the elastic behavior of the small intestine commenced. Finite deformation, nonlinear, anisotropic, incompressible, viscoelastic behavior of the small intestine was studied. This soft tissue biomechanical analysis and experimentation (on living and dissected intestinal specimens) culminated with a numerical model that simulates intestinal response to the actions of a prototypical robotic component. Experiments on living specimens were performed to determine the levels of applied loadings and internal stresses that are likely to injure these fragile tissues, and the biomechanics computer modeling incorporates three distinct measures for injury potential.
", "doi": "10.7907/NG6V-TD44", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:4035", "collection": "thesis", "collection_id": "4035", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10112006-154843", "primary_object_url": { "basename": "Slatkin_ab_1999.pdf", "content": "final", "filesize": 14938610, "license": "other", "mime_type": "application/pdf", "url": "/4035/1/Slatkin_ab_1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Modeling and Experiments for a Class of Robotic Endoscopes", "author": [ { "family_name": "Slatkin", "given_name": "Andrew Brett", "clpid": "Slatkin-Andrew-Brett" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Knowles", "given_name": "James K.", "clpid": "Knowles-J-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Grundfest", "given_name": "W.", "clpid": "Grundfest-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Current developments in minimally invasive medical practice motivated this study of self-propelled, robotic endoscopes for deep penetration into curved physiological lumens. The conceptual design of such devices is applicable to endoscopy within a variety of lumens in the human body, e.g., blood vessels, but the initial objective of this technology is to provide access to the interior of the entire small intestine without surgical incisions. The small intestine presents several challenges to endoscopic penetration: it is extremely compliant to applied loading, internally lubricated, easily injured, and contains many tight curves along its length of approximately eighteen feet.
\r\n\r\nThis thesis reports the basic design and locomotion concepts for one class of endoscopic robots that are intended to provide safe and reliable traversal of the small intestine via worm-like actuation. Five generations of proof-of-concept prototype robots have been built to validate the fundamental concepts. Furthermore, these miniaturized robots have incorporated the following features: redundant actuation with computer control, tool-free modular assembly, and on-board videoimaging capability. The prototypes have been tested in rubber tubing, the small intestines of deceased pigs, and in the small intestines of live, anaesthetized pigs.
\r\n\r\nAt the onset of this research, little regarding the elastic properties of small intestine existed in the biomechanics literature that would be applicable to the design of these mechanisms. However, accurate prediction of the small intestine's response to robotic loadings would dramatically improve the research and development process of these machines. Thus, an investigation of the elastic behavior of the small intestine commenced. Finite deformation, nonlinear, anisotropic, incompressible, viscoelastic behavior of the small intestine was studied. This soft tissue biomechanical analysis and experimentation (on living and dissected intestinal specimens) culminated with a numerical model that simulates intestinal response to the actions of a prototypical robotic component. Experiments on living specimens were performed to determine the levels of applied loadings and internal stresses that are likely to injure these fragile tissues, and the biomechanics computer modeling incorporates three distinct measures for injury potential.
", "doi": "10.7907/NG6V-TD44", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:15018", "collection": "thesis", "collection_id": "15018", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08312022-180047419", "primary_object_url": { "basename": "Grigoriev_RO_1998.pdf", "content": "final", "filesize": 46993645, "license": "other", "mime_type": "application/pdf", "url": "/15018/1/Grigoriev_RO_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Symmetry and Localized Control of Extended Chaotic Systems", "author": [ { "family_name": "Grigoriev", "given_name": "Roman O.", "clpid": "Grigoriev-Roman-O" } ], "thesis_advisor": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" } ], "thesis_committee": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Roukes", "given_name": "Michael Lee", "orcid": "0000-0002-2916-6026", "clpid": "Roukes-M-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The present study is prompted by the failure of conventional chaos control theory to provide a practically sound algorithm for controlling the chaos in general spatially extended experimental systems. The primary reason for this failure is the presence of symmetry, which is a feature of most extended dynamical systems and which violates a number of assumptions of genericity made by conventional control theory. These\r\nassumptions can be relaxed, but at a price that increases with increasing symmetry of the target state. This price includes the larger number of independent control parameters that must be adjusted to steer the system towards the target trajectory, as well as the larger number of independent observables required to reconstruct the dynamics of an experimental system with symmetries.
\r\n\r\nWe show that spatially extended chaotic systems can be controlled by monitoring and perturbing them at multiple spatial locations, or pinning sites, with separations determined by the noise in the system. We show that the arrangement of pinning sites must comply with constraints determined by the symmetry of the system in order to achieve control. We determine how the system can be forced from the spatiotemporally chaotic state into the controllable target state. Finally, we determine the maxim al distance between pinning sites and the maximal level of noise tolerated\r\nby a given arrangement of pinning sites for a model extended system.
", "doi": "10.7907/zxm1-n119", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:306", "collection": "thesis", "collection_id": "306", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01232008-144001", "primary_object_url": { "basename": "Goodwine_jw_1998.pdf", "content": "final", "filesize": 5355401, "license": "other", "mime_type": "application/pdf", "url": "/306/1/Goodwine_jw_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Control of stratified systems with robotic applications", "author": [ { "family_name": "Goodwine", "given_name": "John William", "clpid": "Goodwine-J-W" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Caughey", "given_name": "Thomas Kirk", "clpid": "Caughey-T-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Many interesting and important control systems evolve on stratified configuration spaces. Roughly speaking, a configuration manifold is called \"stratified\" if it contains subspaces (submanifolds) upon which the system had different equations of motion. Robotic systems, in particular, are of this nature. For example, a legged robot has discontinuous equations of motion near points in the configuration space where each of its \"feet\" comes into contact with the ground. In such a case, when the system moves from one submanifold to another, the equations of motion change in a non-smooth, or even discontinuous manner. In such cases, traditional nonlinear control methodologies are inapplicable because they generally rely upon some form of differentiation. Yet, it is precisely the discontinuous nature of such systems that is often their most important characteristic.\n\nThis dissertation presents methods which consider the intrinsic physical geometric structure present in such problems to address nonlinear controllability and motion planning for stratified systems. For both problems, by exploiting this geometric structure of stratified systems, we can extend standard nonlinear control results and methodologies to the stratified case. A related problem addressed by this dissertation is that of controllability of systems where some control inputs are constrained to be non-negative. This problem arises in stratified systems which arise by way of physical contact because the normal force between contacting systems must be nonnegative. For all the results, a basic goal is to generate results which are general. For example, for robotics applications, these results are independent of a particular robot's number of legs, fingers or morphology.\n", "doi": "10.7907/49h9-q898", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:3105", "collection": "thesis", "collection_id": "3105", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08122005-152639", "primary_object_url": { "basename": "Kelly_sd_1998.pdf", "content": "final", "filesize": 17181627, "license": "other", "mime_type": "application/pdf", "url": "/3105/1/Kelly_sd_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The mechanics and control of robotic locomotion with applications to aquatic vehicles", "author": [ { "family_name": "Kelly", "given_name": "Scott D.", "clpid": "Kelly-S-D" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Caughey", "given_name": "Thomas Kirk", "clpid": "Caughey-T-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This work illuminates the utility of a theory of locomotion rooted in geometric mechanics and nonlinear control. We regard the internal configuration of a deformable body, together with its position and orientation in ambient space, as a point in a trivial principal fiber bundle over the manifold of body deformations. We obtain connections on such bundles which describe the nonholonomic constraints, conservation laws, and force balances to which certain propulsors are subject, and contruct and analyze control-affine normal forms for different classes of systems. We examine the applicability of results involving geometric phases to the practical computation of trajectories for systems described by single connections. We propose a model for planar carangiform swimming based on reduced Euler-Lagrange equations for the interaction of a rigid body and an incompressible fluid, accounting for the generation of thrust due to vortex shedding through controlled coupling terms. We investigate the correct form of this coupling experimentally with a robotic propulsor, comparing its observed behavior with that predicted numerically.\r\n", "doi": "10.7907/50M3-1529", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:3100", "collection": "thesis", "collection_id": "3100", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08122005-094404", "primary_object_url": { "basename": "Glavaski_s_1998.pdf", "content": "final", "filesize": 7891628, "license": "other", "mime_type": "application/pdf", "url": "/3100/1/Glavaski_s_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Robust system analysis and nonlinear system model reduction", "author": [ { "family_name": "Glavaski", "given_name": "Sonja", "clpid": "Glavaski-S" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Tierno", "given_name": "Jorge E.", "clpid": "Tierno-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "McEliece", "given_name": "Robert J.", "clpid": "McEliece-R-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe aim of the first part of this thesis is to broaden the classes of linear systems and performance measures that numerical tools for robustness analysis can be used for. First, we consider robustness problems involving uncertain real parameters and present several new approaches to computing an improved structured singular value [...] lower bound. We combine these algorithms to yield a substantially improved power algorithm.\n\nThen, we show that both the worst case [...] performance and the worst case [...] performance of uncertain systems subject to norm bounded structured LTI perturbations can be written exactly in terms of the skewed [...]. The algorithm for the structured singular value lower bound computation, can be extended to computing skewed [...] lower bound without significant loss of performance or accuracy.\n\nWe also demonstrate how a power algorithm can be used to compute a necessary condition for disturbance rejection of both discrete and continuous time nonlinear systems. For the general case of a system with a non-optimal controller this algorithm can provide us with knowledge of the worst case disturbance.\n\nIn the second part of this thesis we explore different approaches to the model reduction of systems. First, we show that the balancing transforma and Galerkin projection commute. We also demonstrate that if the balancing transformation matrix is orthogonal, balanced truncation and Galerkin projection commute.\n\nNext, we pursue model reduction of nonlinear systems with rotational symmetry. We separate the movement of the wave from the evolution of the wave shape using the \"centering procedure,\" and accurately approximate the shape of the wave with just few modes. The method may be viewed as a way of implementing the Karhunen-Loeve expansion on the space of solutions of the given PDE modulo a given symmetry group. The methodology is quite general and therefore should be useful in a variety of problems.", "doi": "10.7907/jh14-eg48", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:493", "collection": "thesis", "collection_id": "493", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02042008-082018", "primary_object_url": { "basename": "Rhodes_ca_1998.pdf", "content": "final", "filesize": 9516625, "license": "other", "mime_type": "application/pdf", "url": "/493/1/Rhodes_ca_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Nonlinear modeling and identification for process control", "author": [ { "family_name": "Rhodes", "given_name": "Carl", "clpid": "Rhodes-Carl" } ], "thesis_advisor": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" } ], "thesis_committee": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Wiggins", "given_name": "Stephen R.", "clpid": "Wiggins-S-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ideally, processes to be controlled would behave in a linear manner so that well-developed methods of linear control could be applied directly. However, environmental regulations and increased competition are forcing these processes to operate in regions where the assumptions of linearity tend to break down. There has been a great deal of recent academic interest in the control of nonlinear systems, but there are relatively few applications of these methods in industry. One major reason may be the lack of tools for developing models suitable for nonlinear control schemes.\r\n\r\nA number of tools that can be used in the modeling of nonlinear systems for process control are presented in this thesis. In the first section, the problem of determining the proper regression vector size for black-box modeling is examined. The false nearest neighbors algorithm (FNN) is suggested as a solution for this problem. Extensions, analysis, and numerous applications of the FNN algorithm are given and the algorithm is seen to be a useful tool in the identification of nonlinear models.\r\n\r\nIn the second section of the thesis, the problem of nonlinear model reduction for systems exhibiting large time-scale separations is examined. A method of determining the reduced order manifold of slow dynamics is outlined and it is proved that this algorithm identifies the proper manifold. Some thoughts on how the results of the algorithm can be used for developing reduced models are presented.\r\n\r\nIn the third section, the concept of data-based control is introduced. This method of control attempts to utilize process data directly through local modeling techniques. Some preliminary work in this area is given for trajectory tracking and computing controllable sets and data-based control is successfully applied to an experimental electrical circuit. Finally, some thoughts on possible future work in this field are presented.\r\n", "doi": "10.7907/96TN-SN45", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:191", "collection": "thesis", "collection_id": "191", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01152008-082733", "primary_object_url": { "basename": "Rathinam_m_1997.pdf", "content": "final", "filesize": 6515859, "license": "other", "mime_type": "application/pdf", "url": "/191/1/Rathinam_m_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Differentially flat nonlinear control systems", "author": [ { "family_name": "Rathinam", "given_name": "Muruhan", "clpid": "Rathinam-M" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Differentially flat systems are underdetermined systems of (nonlinear) ordinary differential equations (ODEs) whose solution curves are in smooth one-one correspondence with arbitrary curves in a space whose dimension equals the number of equations by which the system is underdetermined. For control systems this is the same as the number of inputs. The components of the map from the system space to the smaller dimensional space are referred to as the flat outputs. Flatness allows one to systematically generate feasible trajectories in a relatively simple way. Typically the flat outputs may depend on the original independent and dependent variablesterms of which the ODEs are written as well as finitely many derivatives of the dependent variables. Flatness of systems underdetermined by one equation is completely characterised by Elie Cartan's work. But for general underdetermined systems no complete characterisation of flatness exists.\n\nIn this dissertation we describe two different geometric frameworks for studying flatness and provide constructive methods for deciding the flatness of certain classes of nonlinear systems and for finding these flat outputs if they exist. We first introduce the concept of \"absolute equivalence\" due to Cartan and define flatness in this frame work. We provide a method of testing for the flatness of systems, which involves making a guess for all but one of the flat outputs after which the problem is reduced to the case solved by Cartan. Secondly we present an alternative geometric approach to flatness which uses \"jet bundles\" and present a theorem which partially characterises flat outputs that depend only on the original variables but not on their derivatives, for the case of systems described by two independent one-forms in arbitrary number of variables. Finally, for the class of Lagrangian mechanical systems whose number of control inputs is one less than the number of degrees of freedom, we provide a characterisation of flat outputs that depend only on the configuration variables, but not on their derivatives. This characterisation makes use of the Riemannian metric provided by the kinetic energy of the system.\n", "doi": "10.7907/k7pm-hs13", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:207", "collection": "thesis", "collection_id": "207", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01162008-153136", "primary_object_url": { "basename": "Kothare_mv_1997.pdf", "content": "final", "filesize": 10270567, "license": "other", "mime_type": "application/pdf", "url": "/207/1/Kothare_mv_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Control of Systems Subject to Constraints", "author": [ { "family_name": "Kothare", "given_name": "Mayuresh V.", "clpid": "Kothare-Mayuresh-V" } ], "thesis_advisor": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" } ], "thesis_committee": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Every operating control system must deal with constraints. On the one hand, the range and rate of change of the input or manipulated variable is limited by the physical nature of the actuator (saturation limits). On the other hand, process state variables or outputs (pressures, temperatures, voltages) may not be allowed to exceed certain bounds arising from equipment limitation, safety considerations, or environmental regulations.
\r\n\r\nA rich theory exists for designing controllers - both linear (H2/H\u221e, LQG, LTR, pole-placement) and nonlinear (nonlinear H\u221e, control, feedback linearization, sliding mode control, gain scheduling). However, none of these popular and fashionable controller design techniques account for the presence of input or output constraints. Although occasionally these constraints may be neglected, in general, they lead to design and operating problems unless they are accounted for properly.
\r\n\r\nIn traditional control practice, overrides or mode selection schemes are used to deal with output constraints: they switch between a \"bank\" of controllers, each of which is designed to achieve a specific objective. In both cases (saturation limit and mode selection), a control input nonlinearity is introduced into the operating system.
\r\n\r\nDespite its significance, the study of the constrained control problem has received far less attention than the traditional unconstrained (linear and nonlinear) control theory. With few exceptions, most of the controller design techniques for constrained systems are by-and-large ad-hoc, with very little guarantees of stability, performance and robustness to plant model uncertainty.
\r\n\r\nThe objective of this thesis is to take a broad approach towards the constrained control problem. One part of the thesis is devoted to the development of a systematic and unifying theory for studying the so-called Anti-Windup Bumpless Transfer (AWBT) problem. The other part aims towards the development of a general novel approach for the synthesis of a robust model predictive control (MPC) algorithm.
\r\n", "doi": "10.7907/anhq-xj51", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:94", "collection": "thesis", "collection_id": "94", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01092008-110959", "primary_object_url": { "basename": "D'Andrea_r_1997.pdf", "content": "final", "filesize": 10475677, "license": "other", "mime_type": "application/pdf", "url": "/94/1/D'Andrea_r_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Generalizations of H-infinity optimization. Control of rotating stall", "author": [ { "family_name": "D'Andrea", "given_name": "Raffaello", "clpid": "D'Andrea-Raffaello" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Perona", "given_name": "Pietro", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Smith", "given_name": "Roy", "clpid": "Smith-Roy" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Arguably one of the most significant contributions to the field of optimal control has been the formulation and eventual solution of the H\u221e design problem. Armed with this mathematical tool, designs which are robust to plant uncertainty and insensitive to plant parameters can be performed in a systematic and rigorous fashion.
\r\n\r\nThe H\u221e methodology, however, typically leads to conservative designs. The reasons are twofold. The first is that the plant uncertainty can only be accounted for in an approximate manner, with the result that designs are performed for a set of allowable systems which is larger than what is being modeled; thus the resulting control strategy is forced to guard against non-realizable situations, potentially sacrificing system performance. The second has to do with the physical interpretation of H\u221e optimization: the minimization of a system's power to power gain. Thus it is implicitly assumed in the design process that the worst case disturbance is allowed to be an arbitrary power signal, such as a sinusoid. This is clearly a poor modeling choice for many types of physical disturbances, such as sensor or thermal noise, wind gusts, and impulsive forces.
\r\n\r\nThe main contribution of this dissertation is the extension of H\u221e optimization to allow for general closed loop design objectives which address the two limitations outlined above. In particular, non-conservative, computationally tractable, linear matrix inequality based methods for control design are developed for a certain class of physically motivated uncertain systems. In addition, these new techniques can accommodate constraints on the allowable disturbances, excluding unrealistic disturbances from the design process.
\r\n\r\nAnother contribution of this dissertation is an attempt to view control in the broader context of system design. Typically, a control algorithm is only sought after the system to be controlled has already been designed, and the type and location of the actuators and sensors has been determined. For most applications, however, the level of performance which can be attained by any control strategy is dictated by the dynamics of the plant. Thus from a system level, the above methodology is not optimal, since the control design process is decoupled from the design of the rest of the system. By adopting the behavioral framework for systems, an optimization problem where the given system is not treated as an input-output operator, a natural assumption when considering first principles models, is formulated and solved. The interpretation of the above extension of H\u221e optimization is that of designing optimal systems.
\r\n\r\nIn contrast to the general purpose tools developed in the first part of the dissertation and summarized above, the second part deals with an actual experimental problem, that of controlling rotating stall using pulsed air injection in a low-speed, axial flow compressor. By modeling the injection of air as an unsteady shift in the compressor characteristic, the viability of various air injection orientations are established. A control strategy is developed which controls the pulsing of air in front of the rotor face based on unsteady pressure measurements near the rotor face. Experimental results show that this technique eliminates the hysteresis loop normally associated with rotating stall. A parametric study is used to determine the optimal control parameters for suppression of stall. The resulting control strategy is also shown to suppress surge when a plenum is present. Using a high fidelity model, the main features of the experimental results are duplicated via simulations. The main contributions of this part of the dissertation are a simple control scheme which has the potential of greatly increasing the operability of compressors, and a low-order modeling mechanism which captures the essential features of air injection, facilitating subsequent analyses and control designs which make use of air injectors.
\r\n", "doi": "10.7907/4R8P-RR02", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:28", "collection": "thesis", "collection_id": "28", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01042008-091550", "primary_object_url": { "basename": "Beck_cl_1997.pdf", "content": "final", "filesize": 5530330, "license": "other", "mime_type": "application/pdf", "url": "/28/1/Beck_cl_1997.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Model Reduction and Minimality for Uncertain Systems", "author": [ { "family_name": "Beck", "given_name": "Carolyn Louise", "orcid": "0000-0003-4880-6380", "clpid": "Beck-Carolyn-Louise" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The emphasis of this thesis is on the development of systematic methods for reducing the size and complexity of uncertain system models. Given a model for a large complex system, the objective of these methods is to find a simplified model which accurately describes the physical system, thus facilitating subsequent control design and analysis.
\r\n\r\nModel reduction methods and realization theory are presented for uncertain systems represented by Linear Fractional Transformations (LFTs) on a block diagonal uncertainty structure. A complete generalization of balanced realizations, balanced Gramians and balanced truncation model reduction with guaranteed error bounds is given, which is based on computing solutions to a pair of Linear Matrix Inequalities (LMIs). A necessary and sufficient condition for exact reducibility of uncertain systems, the converse of minimality, is also presented. This condition further generalizes the role of controllability and observability Gramians, and is expressed in terms of singular solutions to the same LMIs. These reduction methods provide a systematic means for both uncertainty simplification and state order reduction in the case of uncertain systems, but also may be interpreted as state order reduction for multi-dimensional systems.
\r\n\r\nLFTs also provide a convenient way of obtaining realizations for systems described by rational functions of several noncommuting indeterminates. Such functions arise naturally in robust control when studying systems with structured uncertainty, but also may be viewed as a particular type of description for a formal power series. This thesis establishes connections between minimal LFT realizations and minimal linear representations of formal power series, which have been studied extensively in a variety of disciplines, including nonlinear system realization theory. The result is a fairly complete development of minimal realization theory for LFT systems.
\r\n\r\nGeneral LMI problems and solutions are discussed with the aim of providing sufficient background and references for the construction of computational procedures to reduce uncertain systems. A simple algorithm for computing balanced reduced models of uncertain systems is presented, followed by a discussion of the application of this procedure to a pressurized water reactor for a nuclear power plant.
\r\n", "doi": "10.7907/MPV7-2Q79", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:206", "collection": "thesis", "collection_id": "206", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01162008-152619", "primary_object_url": { "basename": "Vanelli_ca_1997.pdf", "content": "final", "filesize": 3758809, "license": "other", "mime_type": "application/pdf", "url": "/206/1/Vanelli_ca_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Autonomous Reorientation of a Maneuver-Limited Spacecraft Under Simple Pointing Constraints", "author": [ { "family_name": "Vanelli", "given_name": "Charles Anthony", "clpid": "Vanelli-Charles-Anthony" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This report presents techniques for using discrete finite rotations to reorient a spacecraft from a given initial attitude to a final attitude which satisfies a specified aiming objective. The objective may be a fully specified final orientation or it may require that the spacecraft direct an instrument along a certain direction. Constraints are also imposed on the allowable intermediate orientations that the spacecraft may assume during the course of the maneuver, representing the operational requirements of onboard instrumentation. The algorithms presented consider solutions that will achieve the desired objective with only one or two slew maneuvers, although they may be easily extended to consider more complicated solutions requiring additional maneuvers.", "doi": "10.7907/kap2-6n63", "publication_date": "1997", "thesis_type": "engd", "thesis_year": "1997" }, { "id": "thesis:28", "collection": "thesis", "collection_id": "28", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01042008-091550", "primary_object_url": { "basename": "Beck_cl_1997.pdf", "content": "final", "filesize": 5530330, "license": "other", "mime_type": "application/pdf", "url": "/28/1/Beck_cl_1997.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Model Reduction and Minimality for Uncertain Systems", "author": [ { "family_name": "Beck", "given_name": "Carolyn Louise", "orcid": "0000-0003-4880-6380", "clpid": "Beck-Carolyn-Louise" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The emphasis of this thesis is on the development of systematic methods for reducing the size and complexity of uncertain system models. Given a model for a large complex system, the objective of these methods is to find a simplified model which accurately describes the physical system, thus facilitating subsequent control design and analysis.
\r\n\r\nModel reduction methods and realization theory are presented for uncertain systems represented by Linear Fractional Transformations (LFTs) on a block diagonal uncertainty structure. A complete generalization of balanced realizations, balanced Gramians and balanced truncation model reduction with guaranteed error bounds is given, which is based on computing solutions to a pair of Linear Matrix Inequalities (LMIs). A necessary and sufficient condition for exact reducibility of uncertain systems, the converse of minimality, is also presented. This condition further generalizes the role of controllability and observability Gramians, and is expressed in terms of singular solutions to the same LMIs. These reduction methods provide a systematic means for both uncertainty simplification and state order reduction in the case of uncertain systems, but also may be interpreted as state order reduction for multi-dimensional systems.
\r\n\r\nLFTs also provide a convenient way of obtaining realizations for systems described by rational functions of several noncommuting indeterminates. Such functions arise naturally in robust control when studying systems with structured uncertainty, but also may be viewed as a particular type of description for a formal power series. This thesis establishes connections between minimal LFT realizations and minimal linear representations of formal power series, which have been studied extensively in a variety of disciplines, including nonlinear system realization theory. The result is a fairly complete development of minimal realization theory for LFT systems.
\r\n\r\nGeneral LMI problems and solutions are discussed with the aim of providing sufficient background and references for the construction of computational procedures to reduce uncertain systems. A simple algorithm for computing balanced reduced models of uncertain systems is presented, followed by a discussion of the application of this procedure to a pressurized water reactor for a nuclear power plant.
\r\n", "doi": "10.7907/MPV7-2Q79", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:5048", "collection": "thesis", "collection_id": "5048", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12182007-090504", "primary_object_url": { "basename": "Choset_h_1996.pdf", "content": "final", "filesize": 17313237, "license": "other", "mime_type": "application/pdf", "url": "/5048/1/Choset_h_1996.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Sensor Based Motion Planning: The Hierarchical Generalized Voronoi Graph", "author": [ { "family_name": "Choset", "given_name": "Howard Marc", "orcid": "0000-0002-2266-8744", "clpid": "Choset-Howard-Marc" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Sensor based motion planning incorporates sensor information reflecting the state of a robot's environment into its planning process, whereas traditional approaches assume complete prior knowledge of the robot's environment. Recent research has focused on the development and incremental construction of the hierarchical generalized Voronoi graph (HGVG), which is a concise representation of a robot's environment. The HGVG is advantageous in that it lends itself to sensor based construction in a rigorous and provably correct manner. With this approach, a robot can enter an unknown environment, incrementally construct the HGVG, and then use the HGVG for future excursions in the environment. Simulations and experiments validate this approach.", "doi": "10.7907/49ee-a204", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:5089", "collection": "thesis", "collection_id": "5089", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12202007-115753", "primary_object_url": { "basename": "Morris_jc_1996.pdf", "content": "final", "filesize": 8567172, "license": "other", "mime_type": "application/pdf", "url": "/5089/1/Morris_jc_1996.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Experimental Control: a Helicopter Case Study", "author": [ { "family_name": "Morris", "given_name": "John Christopher", "clpid": "Morris-John-Christopher" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Robust control has not been used as widely as it could because modelling tools have not advanced as far as analysis and synthesis tools. This becomes readily apparent when applying robust control theory to real problems. With this in mind, an experimental platform was designed and built to study the application of robust control. This platform consists of a real-time computer and a radio-controlled model helicopter mounted on a six degree-of-freedom stand. Experimental systems provide the opportunity not only to verify the applicability of new control theory but also to highlight potential deficiencies.
\r\n\r\nTraditional system identification and control techniques were used to construct hover controllers for the model helicopter. These techniques are not suitable for the construction of robust models for a system of this complexity. In particular, there was no systematic way to augment nominal identified models with uncertainty suitable for the construction of robust controllers.
\r\n\r\nTo address this issue, frequency-domain model validation algorithms and software were developed. These algorithms provide a methodology for verifying the applicability and consistency between experimental data and robust models. Additionally, they provide a method whereby nominal model parameters can be tuned in a robust setting. This is the first set of software tools which provide this capability for general linear uncertain systems.
\r\n\r\nUsing these new software tools, a systematic design process was developed which incorporated frequency-domain model validation analysis, \u00b5-analysis and \u00b5-synthesis, simulation, and implementation. This design process proved to be a valuable new tool for constructing robust models and designing robust control systems. In particular, by applying this design process to the helicopter, the size of uncertainty in the robust model was substantially reduced without sacrificing the ability of the model to \"cover\" experimental data and the first controller implemented performed well. This was strikingly different from the results obtained when using standard robust control techniques, where several controllers destabilized the helicopter when implemented, even though they performed well under simulation.
\r\n\r\nThe model validation software and design process provide a consistent methodology and systematic framework which connects system identification, the construction of robust models, and controller synthesis with experimental data. For the first time the control engineer can compute measures on the validity of a robust model, with respect to all observed data on the actual physical system, which are directly related to the robustness measures resulting from \u00b5-analysis and \u00b5-synthesis.
\r\n", "doi": "10.7907/sdad-de68", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:4194", "collection": "thesis", "collection_id": "4194", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10202005-153514", "primary_object_url": { "basename": "Ostrowski_jp_1996.pdf", "content": "final", "filesize": 8656927, "license": "other", "mime_type": "application/pdf", "url": "/4194/1/Ostrowski_jp_1996.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The mechanics and control of undulatory robotic locomotion", "author": [ { "family_name": "Ostrowski", "given_name": "James Patrick", "clpid": "Ostrowski-J-P" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Chirikjian", "given_name": "Gregory S.", "clpid": "Chirikjian-G-S" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Wiggins", "given_name": "Stephen R.", "clpid": "Wiggins-S-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this dissertation, we examine a formulation of problems of undulatory robotic locomotion within the context of mechanical systems with nonholonomic constraints and symmetries. Using tools from geometric mechanics, we study the underlying structure found in general problems of locomotion. In doing so, we decompose locomotion into two basic components: internal shape changes and net changes in position and orientation. This decomposition has a natural mathematical interpretation in which the relationship between shape changes and locomotion can be described using a connection on a trivial principal fiber bundle.\n\nWe begin by reviewing the processes of Lagrangian reduction and reconstruction for unconstrained mechanical systems with Lie group symmetries, and present new formulations of this process which are easily adapted to accommodate external constraints. Additionally, important physical quantities such as the mechanical connection and reduced mass-inertia matrix can be trivially determined using this formulation. The presence of symmetries then allows us to reduce the necessary calculations to simple matrix manipulations.\n\nThe addition of constraints significantly complicates the reduction process; however, we show that for invariant constraints, a meaningful connection can be synthesized by defining a generalized momentum representing the momentum of the system in directions allowed by the constraints. We then prove that the generalized momentum and its governing equation possess certain invariances which allows for a reduction process similar to that found in the unconstrained case. The form of the reduced equations highlights the synthesized connection and the matrix quantities used to calculate these equations.\n\nThe use of connections naturally leads to methods for testing controllability and aids in developing intuition regarding the generation of various locomotive gaits. We present accessibility and controllability tests based on taking derivatives of the connection, and relate these tests to taking Lie brackets of the input vector fields.\n\nThe theory is illustrated using several examples, in particular the examples of the snakeboard and Hirose snake robot. We interpret each of these examples in light of the theory developed in this thesis, and examine the generation of locomotive gaits using sinusoidal inputs and their relationship to the controllability tests based on Lie brackets.\n", "doi": "10.7907/Y1TF-RF86", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:5069", "collection": "thesis", "collection_id": "5069", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12192007-112031", "type": "thesis", "title": "Model Predictive Control (MPC) for Constrained Nonlinear Systems", "author": [ { "family_name": "De Oliveira", "given_name": "Simone Loureiro", "clpid": "DeOliveira-Simone-Loureiro" } ], "thesis_advisor": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" } ], "thesis_committee": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Wiggins", "given_name": "Stephen R.", "clpid": "Wiggins-S-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis addresses the development of stabilizing model predictive control algorithms for nonlinear systems subject to input and state constraints and in the presence of parametric and/or structural uncertainty, disturbances and measurement noise.
\r\n\r\nOur basic model predictive control (MPC) scheme consists of a finite horizon MPC technique with the introduction of an additional state constraint which we have denoted contractive constraint. This is a Lyapunov-based approach in which a Lyapunov function chosen a priori is decreased, not continuously, but discretely; it is allowed to increase at other times (between prediction horizons). We will show \r\nin this work that the implementation of this additional constraint into the on-line optimization makes it possible to prove rather strong stability properties of the closed-loop system. In the nominal case and in the absence of disturbances, it is possible to show that the presence of the contractive constraint renders the closed-loop system exponentially stable. We will also examine how the stability properties weaken as structural and/or parametric model/plant mismatch, disturbances and measurement noise are considered.
\r\n\r\nAnother important aspect considered in this work is the computational efficiency and implement ability of the algorithms proposed. The MPC schemes previously proposed in the literature which are able to guarantee stability of the closed-loop system involve the solution of a nonlinear programming problem at each time step in order to find the optimal (or, at least, feasible) control sequence. Nonlinear programming is the general case in which both the objective and constraint functions may be non-linear, and is the most difficult of the smooth optimization problems.
\r\n\r\nDue to the difficulties inherent to solving nonlinear programming problems and since MPC requires the optimal (or feasible) solution to be computed on-line, it is important that an alternative implementation be found which guarantees that the problem can be solved in a finite number of steps. It is well-known that both linear and quadratic programming (QP) problems satisfy this requirement.
\r\n\r\nIf a standard quadratic objective function is used and the input/state constraints are linear in the decision variables, then the contractive constraint (which is originally a quadratic constraint) can be implemented in such a way that the optimization problem to be solved in the prediction step of the MPC algorithm is reduced to a QP. Having linear input/state constraints means that a linear approximation of the original nonlinear system has to be used in the prediction as well as in the computation of the contractive constraint. Thus, in order to make the algorithm more easily implementable we introduce the difficulty of having to handle the mismatch between the real nonlinear system and its linear approximation which is used for prediction. In other words, we now have a robust MPC control problem at hand. In this case, it is the contractive constraint which comes to the rescue and allows the MPC controller to stabilize the closed-loop system spite of the linear/nonlinear mismatch, for certain choices of the contractive parameter (the parameter which defines how much \"shrinkage\" of the states is required during one prediction horizon).
\r\n\r\nIn summary, this thesis is an application of contractive principles to model predictive control and it is dedicated to robust stability analysis, design and implementation of state and output feedback \"contractive\" MPC schemes.
\r\n", "doi": "10.7907/MXYW-TB71", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:68", "collection": "thesis", "collection_id": "68", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01082008-103705", "primary_object_url": { "basename": "Soatto_s_1996.pdf", "content": "final", "filesize": 11557336, "license": "other", "mime_type": "application/pdf", "url": "/68/1/Soatto_s_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A geometric framework for dynamic vision", "author": [ { "family_name": "Soatto", "given_name": "Stefano", "clpid": "Soatto-Stefano" } ], "thesis_advisor": [ { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" } ], "thesis_committee": [ { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Ponce", "given_name": "Jean", "clpid": "Ponce-J" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Morari", "given_name": "Manfred", "orcid": "0000-0002-7696-5058", "clpid": "Morari-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis explores the problem of inferring information about the three-dimensional world from its projections onto a camera (images). Among all visual cues, we do not address \"pictorial\" ones, such as texture or shading. Instead, we concentrate on \"dynamic\" cues, which are associated with variations of the image over time.\r\n\r\nIn order to eliminate pictorial cues, one may represent the world as a collection of geometric primitives, such as points, curves or surfaces in three-dimensional space. Then, from the two-dimensional motion of the projection of such primitives onto the image, one can infer the three-dimensional structure of the world and its motion relative to the viewer.\r\n\"Three-dimensional structure from two-dimensional images\" has now been a central theme in Computer Vision for over two decades, and tools from Linear Algebra and Projective Geometry have been widely employed to attack the problem as a \"static\" task. It is only in recent years that the role of time has started to be recognized, after the influential work of Dickmanns and his coworkers on vehicle guidance on freeways.\r\n\r\nWe do not impose restrictions on the structure of the environment, and we cast the problem of general three-dimensional structure and motion estimation within the framework of Dynamical Systems. We show how different algebraic constraints on the image projections can be interpreted as nonlinear and implicit dynamical models whose (unknown) parameters live in peculiar differentiable manifolds that encode three-dimensional information. Recovering such three-dimensional information then amounts to identifying dynamical models while taking into account the geometry of the parameter manifolds.", "doi": "10.7907/x87w-t943", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:68", "collection": "thesis", "collection_id": "68", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01082008-103705", "primary_object_url": { "basename": "Soatto_s_1996.pdf", "content": "final", "filesize": 11557336, "license": "other", "mime_type": "application/pdf", "url": "/68/1/Soatto_s_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A geometric framework for dynamic vision", "author": [ { "family_name": "Soatto", "given_name": "Stefano", "clpid": "Soatto-Stefano" } ], "thesis_advisor": [ { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" } ], "thesis_committee": [ { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Koch", "given_name": "Christof", "orcid": "0000-0001-6482-8067", "clpid": "Koch-C" }, { "family_name": "Ponce", "given_name": "Jean", "clpid": "Ponce-J" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Morari", "given_name": "Manfred", "orcid": "0000-0002-7696-5058", "clpid": "Morari-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis explores the problem of inferring information about the three-dimensional world from its projections onto a camera (images). Among all visual cues, we do not address \"pictorial\" ones, such as texture or shading. Instead, we concentrate on \"dynamic\" cues, which are associated with variations of the image over time.\r\n\r\nIn order to eliminate pictorial cues, one may represent the world as a collection of geometric primitives, such as points, curves or surfaces in three-dimensional space. Then, from the two-dimensional motion of the projection of such primitives onto the image, one can infer the three-dimensional structure of the world and its motion relative to the viewer.\r\n\"Three-dimensional structure from two-dimensional images\" has now been a central theme in Computer Vision for over two decades, and tools from Linear Algebra and Projective Geometry have been widely employed to attack the problem as a \"static\" task. It is only in recent years that the role of time has started to be recognized, after the influential work of Dickmanns and his coworkers on vehicle guidance on freeways.\r\n\r\nWe do not impose restrictions on the structure of the environment, and we cast the problem of general three-dimensional structure and motion estimation within the framework of Dynamical Systems. We show how different algebraic constraints on the image projections can be interpreted as nonlinear and implicit dynamical models whose (unknown) parameters live in peculiar differentiable manifolds that encode three-dimensional information. Recovering such three-dimensional information then amounts to identifying dynamical models while taking into account the geometry of the parameter manifolds.", "doi": "10.7907/x87w-t943", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:3582", "collection": "thesis", "collection_id": "3582", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09172007-080812", "primary_object_url": { "basename": "Paganini_f_1996.pdf", "content": "final", "filesize": 9097631, "license": "other", "mime_type": "application/pdf", "url": "/3582/1/Paganini_f_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Sets and Constraints in the Analysis of Uncertain Systems", "author": [ { "family_name": "Paganini-Herrera", "given_name": "Fernando", "clpid": "Paganini-Herrera-Fernando" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Goldsmith", "given_name": "Andrea Jo", "clpid": "Goldsmith-A-J" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "McEliece", "given_name": "Robert J.", "clpid": "McEliece-R-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis is concerned with the analysis of dynamical systems in the presence of model uncertainty. The approach of robust control theory has been to describe uncertainty in terms of a structured set of models, and has proven successful for questions, like stability, which call for a worst-case evaluation over this set. In this respect, a first contribution of this thesis is to provide robust stability tests for the situation of combined time varying, time invariant and parametric uncertainties.
\r\n\r\nThe worst-case setting has not been so attractive for questions of disturbance rejection, since the resulting performance criteria (e.g., H\u221e) treat the disturbance as an adversary and ignore important spectral structure, usually better characterized by the theory of stochastic processes. The main contribution of this thesis is to show that the set-based methodology can indeed be extended to the modeling of white noise, by employing standard statistical tests in order to identify a typical set, and performing subsequent analysis in a worst-case setting. Particularly attractive sets are those described by quadratic signal constraints, which have proven to be very powerful for the characterization of unmodeled dynamics. The combination of white noise and unmodeled dynamics constitutes the Robust H2 performance problem, which is rooted in the origins of robust control theory. By extending the scope of the quadratic constraint methodology we obtain a solution to this problem in terms of a convex condition for robustness analysis, which for the first time places it on an equal footing with the H\u221e performance measure.
\r\n\r\nA separate contribution of this thesis is the development of a framework for analysis of uncertain systems in implicit form, in terms of equations rather than input-output maps. This formulation is motivated from first principles modeling, and provides an extension of the standard input-output robustness theory. In particular, we obtain in this way a standard form for robustness analysis problems with constraints, which also provides a common setting for robustness analysis and questions of model validation and system identification.
", "doi": "10.7907/3X73-5F28", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:16", "collection": "thesis", "collection_id": "16", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01032008-090000", "primary_object_url": { "basename": "Newlin_mp_1996.pdf", "content": "final", "filesize": 5577596, "license": "other", "mime_type": "application/pdf", "url": "/16/1/Newlin_mp_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Model Validation, Control, and Computation", "author": [ { "family_name": "Newlin", "given_name": "Matthew Philip", "clpid": "Newlin-Matthew- Philip" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Smith", "given_name": "Roy", "clpid": "Smith-Roy" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Engineering in general is concerned with controlling and predicting future behavior with some certainty despite having only imperfect information. Although feedback can be an exceptionally effective engineering tool and is often easy to apply, the behavior of a system under feedback can be extremely sensitive to model mismatch, which is always present. The potential for unpredictable behavior is a major drawback to the engineering application of feedback. Robust control theory addresses this difficulty by parametrizing a family of feedback controllers that are less sensitive to model mismatch.
\r\n\r\nDespite encouraging early applications, robust control theory has so far been deficient in analysis of systems, synthesis of controllers, connection to real problems, and applicability to nonlinear problems. Further, results on the computational complexity of robust control problems that necessitate either bounds computation or a restricted class of problems have cast doubts about the potential utility of the area.
\r\n\r\nInitial work in robust control focused on complex uncertainty in the frequency domain. A perceived deficiency is that such model sets are unrealistic: uncertainty in mass, stiffness, aero-coefficients, and the like are naturally modeled as real variations. This thesis includes initial work on practical upper bound computation and substantially improved lower bound computation for moderately large robust control analysis problems that include such real parametric uncertainty, despite the computational complexity of the problems. Although better upper bound computation than that described here is now available for small problems, such is not the case for large problems. The improved lower bound computation chronicled here is desirable because the initial lower bound computation for problems with real parametric uncertainty is not as reliable as in the complex case. Additionally, this thesis shows that branch and bound is a limited but critical tool for better computation, a fact that previously has gone unrecognized.
\r\n\r\nTogether, these contributions allow for the practical computation of robust control problems of engineering interest and provide the basis not only for applications that may ultimately determine the utility of the robust control paradigm but also for the computation of various outgrowths of the [mu] framework, which is the basis for computational robust control.
\r\n\r\nOne such outgrowth is the model validation problem. Model validation tests whether a robust control model in the [mu] framework is consistent with experimentally determined time histories quite a different problem than standard system identification. This thesis shows that the model validation problem is indeed closely related to the standard [mu] problem and its computation.
\r\n\r\nThe practical computation of the model validation problem, which should follow naturally from the work presented here, provides the basis for the connection between robust control theory and practical applications. Future work along these lines should elevate the application of robust control theory from chance and intuition to a standard engineering tool.
\r\n\r\nFurther, the techniques that render the model validation problem similar to the standard [mu] problem are applicable to a great variety of systems analysis and design problems. This newly perceived generality of the [mu] paradigm may ultimately provide a unifying framework for the many seemingly disparate aspects of systems and control design.
", "doi": "10.7907/nvwd-hw47", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:3582", "collection": "thesis", "collection_id": "3582", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09172007-080812", "primary_object_url": { "basename": "Paganini_f_1996.pdf", "content": "final", "filesize": 9097631, "license": "other", "mime_type": "application/pdf", "url": "/3582/1/Paganini_f_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Sets and Constraints in the Analysis of Uncertain Systems", "author": [ { "family_name": "Paganini-Herrera", "given_name": "Fernando", "clpid": "Paganini-Herrera-Fernando" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Goldsmith", "given_name": "Andrea Jo", "clpid": "Goldsmith-A-J" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "McEliece", "given_name": "Robert J.", "clpid": "McEliece-R-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis is concerned with the analysis of dynamical systems in the presence of model uncertainty. The approach of robust control theory has been to describe uncertainty in terms of a structured set of models, and has proven successful for questions, like stability, which call for a worst-case evaluation over this set. In this respect, a first contribution of this thesis is to provide robust stability tests for the situation of combined time varying, time invariant and parametric uncertainties.
\r\n\r\nThe worst-case setting has not been so attractive for questions of disturbance rejection, since the resulting performance criteria (e.g., H\u221e) treat the disturbance as an adversary and ignore important spectral structure, usually better characterized by the theory of stochastic processes. The main contribution of this thesis is to show that the set-based methodology can indeed be extended to the modeling of white noise, by employing standard statistical tests in order to identify a typical set, and performing subsequent analysis in a worst-case setting. Particularly attractive sets are those described by quadratic signal constraints, which have proven to be very powerful for the characterization of unmodeled dynamics. The combination of white noise and unmodeled dynamics constitutes the Robust H2 performance problem, which is rooted in the origins of robust control theory. By extending the scope of the quadratic constraint methodology we obtain a solution to this problem in terms of a convex condition for robustness analysis, which for the first time places it on an equal footing with the H\u221e performance measure.
\r\n\r\nA separate contribution of this thesis is the development of a framework for analysis of uncertain systems in implicit form, in terms of equations rather than input-output maps. This formulation is motivated from first principles modeling, and provides an extension of the standard input-output robustness theory. In particular, we obtain in this way a standard form for robustness analysis problems with constraints, which also provides a common setting for robustness analysis and questions of model validation and system identification.
", "doi": "10.7907/3X73-5F28", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:5048", "collection": "thesis", "collection_id": "5048", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12182007-090504", "primary_object_url": { "basename": "Choset_h_1996.pdf", "content": "final", "filesize": 17313237, "license": "other", "mime_type": "application/pdf", "url": "/5048/1/Choset_h_1996.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Sensor Based Motion Planning: The Hierarchical Generalized Voronoi Graph", "author": [ { "family_name": "Choset", "given_name": "Howard Marc", "orcid": "0000-0002-2266-8744", "clpid": "Choset-Howard-Marc" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Sensor based motion planning incorporates sensor information reflecting the state of a robot's environment into its planning process, whereas traditional approaches assume complete prior knowledge of the robot's environment. Recent research has focused on the development and incremental construction of the hierarchical generalized Voronoi graph (HGVG), which is a concise representation of a robot's environment. The HGVG is advantageous in that it lends itself to sensor based construction in a rigorous and provably correct manner. With this approach, a robot can enter an unknown environment, incrementally construct the HGVG, and then use the HGVG for future excursions in the environment. Simulations and experiments validate this approach.", "doi": "10.7907/49ee-a204", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:3468", "collection": "thesis", "collection_id": "3468", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-080755", "type": "thesis", "title": "The Whirling Blade and the Steaming Cauldron", "author": [ { "family_name": "Bodenheimer", "given_name": "Robert Edward", "orcid": "0000-0002-0616-5936", "clpid": "Bodenheimer-Robert-Edward" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "McEliece", "given_name": "Robert J.", "clpid": "McEliece-R-J" }, { "family_name": "Packard", "given_name": "Andrew K.", "clpid": "Packard-A-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation applies recent theoretical developments in control to two practical examples. The first example is control of the primary circuit of a pressurized water nuclear reactor. This is an interesting example because the plant is complex and its dynamics vary greatly over the operating range of interest. The second example is a thrust-vectored ducted fan engine, a nonlinear flight control experiment at Caltech.
\r\n\r\nThe main part of this dissertation is the application of linear parameter-dependent control techniques to the examples. The synthesis technique is based on the solution of linear matrix inequalities (LMIs) and produces a controller which achieves specified performance against the worst-case time variation of measurable parameters entering the plant in a linear fractional manner. Thus the plant can have widely varying dynamics over the operating range, a quality possessed by both examples. The controllers designed with these methods perform extremely well and are compared to H\u221e, gain-scheduled, and nonlinear controllers.
\r\n\r\nAdditionally, an in-depth examination of the model of the ducted fan is performed, including system identification. From this work, we proceed to apply various techniques to examine what they can tell us in the context of a practical example. The primary technique is LMI-based model validation.
\r\n\r\nThe contribution this dissertation makes is to show that parameter-dependent control techniques can be applied with great effectiveness to practical applications. Moreover, the trade-off between modelling and controller performance is examined in some detail. Finally, we demonstrate the applicability of recent model validation techniques in practice, and discuss stabilizability issues.
", "doi": "10.7907/fmwm-mm97", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:835", "collection": "thesis", "collection_id": "835", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03022006-131646", "primary_object_url": { "basename": "Lu_wm_1995.pdf", "content": "final", "filesize": 13033096, "license": "other", "mime_type": "application/pdf", "url": "/835/1/Lu_wm_1995.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Control of Uncertain Systems: State-Space Characterizations", "author": [ { "family_name": "Lu", "given_name": "Wei-Min", "clpid": "Lu-Wei-Min" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Hou", "given_name": "Thomas Y.", "orcid": "0000-0001-6287-1133", "clpid": "Hou-T-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" }, { "family_name": "Wiggins", "given_name": "Stephen R.", "orcid": "0000-0002-0780-0911", "clpid": "Wiggins-S-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A central issue in control system design has been to deal with uncertainty and nonlinearity in the systems. In this dissertation, an integrated treatment for both uncertainty and nonlinearity is proposed. This dissertation consists of two relatively independent parts. The first part deals with uncertain linear systems, while the second part treats uncertain nonlinear systems.
\r\n\r\nIn the first part, the problem of control synthesis of uncertain linear systems is considered. A linear fractional transformation (LFT) framework is proposed for robust control design of uncertain linear control systems with structured uncertainty. Linear parameter-varying systems whose coefficients depend on some time-invariant unknown parameters are treated in a general algebraic framework; both the stabilization and the H\u221e-control problems are considered. For uncertain linear systems under structured perturbations, robustness synthesis problems are characterized in terms of linear matrix inequalities (LMIs) in the LFT framework. A generalized PBH test is also used to characterize the robustness synthesis problems. Moreover, a separation principle for the control synthesis of uncertain linear systems is revealed. The machinery also streamlines a number of results concerning the analysis and synthesis of multidimensional systems.
\r\n\r\nIn the second part, the problem of control synthesis for nonlinear systems is addressed; stabilization, L1-control, H\u221e-control, robustness analysis, and robustness synthesis problems for nonlinear systems are examined in detail. In particular, locally and globally stabilizing controller parameterizations for nonlinear systems are derived; the formulae generalize the celebrated Youla-parameterization for linear systems. Both nonlinear L1-control and nonlinear H\u221e-control are also considered for dealing with disturbance attenuation problems for nonlinear systems. The L1-performance and L1-control of nonlinear systems are characterized in terms of certain invariance sets of the state space; in addition, the relation between the L1-control of a continuous-time system and the \u21131-control of the related Euler approximated discrete-time systems is established. A systematic treatment for H\u221e-control synthesis of nonlinear systems is provided; the nonlinear H\u221e-control problem is characterized in terms of Hamilton-Jacobi Inequalities (HJIs) and nonlinear matrix inequalities (NLMIs); a class of H\u221e-controllers are parameterized as a fractional transformation of contractive stable parameters. Finally, the problems of stability and performance robustness analysis and synthesis for uncertain nonlinear systems subject to structured perturbations with bounded L2-gains are introduced; they are characterized in terms of HJIs and NLMIs as well. Computational issues are also addressed; it is confirmed that the computation needed for robustness analysis and synthesis of nonlinear systems is of equivalent difficulty to that for checking Lyapunov stability.
", "doi": "10.7907/dnxg-nz58", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4224", "collection": "thesis", "collection_id": "4224", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10232007-141113", "primary_object_url": { "basename": "Zheng_zq_1995.pdf", "content": "final", "filesize": 17648921, "license": "other", "mime_type": "application/pdf", "url": "/4224/1/Zheng_zq_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Robust control of systems subject to constraints", "author": [ { "family_name": "Zheng", "given_name": "Zhi Qiang (Alex)", "clpid": "Zheng-Z-Q-A" } ], "thesis_advisor": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" } ], "thesis_committee": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" }, { "family_name": "Sideris", "given_name": "Athanasios", "clpid": "Sideris-A" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Most practical control problems are dominated by constraints. Although a rich theory has been developed for the robust control of linear systems, very little is known about the robust control of linear systems with constraints. Over the years various model-based algorithms (given a generic term Model Predictive Control) have been used in industry to control complex multivariable systems with operating constraints. The design and tuning of these controllers is difficult for two reasons:\n\n1. Process models are always inaccurate which implies that the controllers must be robust.\n\n2. Even in the simplest case where process models are linear, the overall systems are nonlinear because of the constraints.\n\nDespite Model Predictive Control's considerable practical importance, there is very little theory to guide the design and tuning of these controllers for stability and robustness. It is the goal of this thesis to develop such a theory. Specifically, a general framework based on Model Predictive Control is developed to synthesize controllers for discrete-time linear systems subject to constraints with robust stability and performance guarantees.", "doi": "10.7907/q8vt-s855", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:2875", "collection": "thesis", "collection_id": "2875", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07132006-143133", "primary_object_url": { "basename": "Lewis_ad_1995.pdf", "content": "final", "filesize": 7123017, "license": "other", "mime_type": "application/pdf", "url": "/2875/1/Lewis_ad_1995.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Aspects of geometric mechanics and control of mechanical systems", "author": [ { "family_name": "Lewis", "given_name": "Andrew David", "clpid": "Lewis-A-D" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Marsden", "given_name": "Jerrold E.", "clpid": "Marsden-J-E" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Caughey", "given_name": "Thomas Kirk", "clpid": "Caughey-T-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Many interesting control systems are mechanical control systems. In spite of this, there has not been much effort to develop methods which use the special structure of mechanical systems to obtain analysis tools which are suitable for these systems. In this dissertation we take the first steps towards a methodical treatment of mechanical control systems.\n\nFirst we develop a framework for analysis of certain classes of mechanical control systems. In the Lagrangian formulation we study \"simple mechanical control systems\" whose Lagrangian is \"kinetic energy minus potential energy.\" We propose a new and useful definition of controllability for these systems and obtain a computable set of conditions for this new version of controllability. We also obtain decompositions of simple mechanical systems in the case when they are not controllable. In the Hamiltonian formulation we study systems whose control vector fields are Hamiltonian. We obtain decompositions which describe the controllable and uncontrollable dynamics. In each case, the dynamics are shown to be Hamiltonian in a suitably general sense.\n\nNext we develop intrinsic descriptions of Lagrangian and Hamiltonian mechanics in the presence of external inputs. This development is a first step towards a control theory for general Lagrangian and Hamiltonian control systems. Systems with constraints are also studied. We first give a thorough overview of variational methods including a comparison of the \"nonholonomic\" and \"vakonomic\" methods. We also give a generalised definition for a constraint and, with this more general definition, we are able to give some preliminary controllability results for constrained systems.\n", "doi": "10.7907/CHWF-M421", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4139", "collection": "thesis", "collection_id": "4139", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10172007-104556", "primary_object_url": { "basename": "M'Closkey_rt_1995.pdf", "content": "final", "filesize": 6682073, "license": "other", "mime_type": "application/pdf", "url": "/4139/1/M'Closkey_rt_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Exponential stabilization of driftless nonlinear control systems", "author": [ { "family_name": "M'Closkey", "given_name": "Robert Thomas", "clpid": "M-Closkey-R-R" } ], "thesis_advisor": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" } ], "thesis_committee": [ { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel Wakeman", "clpid": "Burdick-J-W" }, { "family_name": "Doyle", "given_name": "John Comstock", "clpid": "Doyle-J-C" }, { "family_name": "Wiggins", "given_name": "Stephen R.", "clpid": "Wiggins-S-R" }, { "family_name": "Caughey", "given_name": "Thomas Kirk", "clpid": "Caughey-T-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThis dissertation lays the foundation for practical exponential stabilization of driftless control systems. Driftless systems have the form,\n\n[...].\n\nSuch systems arise when modeling mechanical systems with nonholonomic constraints. In engineering applications it is often required to maintain the mechanical system around a desired configuration. This task is treated as a stabilization problem where the desired configuration is made an asymptotically stable equilibrium point. The control design is carried out on an approximate system. The approximation process yields a nilpotent set of input vector fields which, in a special coordinate system, are homogeneous with respect to a non-standard dilation. Even though the approximation can be given a coordinate-free interpretation, the homogeneous structure is useful to exploit. Since implementing a controller requires choosing a coordinate system, there are extra benefits to be gained by choosing coordinates in which the approximation is homogeneous. The feedbacks are required to be homogeneous functions and thus preserve the homogeneous structure in the closed-loop system. The stability achieved is called p-exponential stability. This extended notion of exponential stability is required since the feedback, and hence the closed-loop system, is not Lipschitz. However, it is shown that the convergence rate of a Lipschitz closed-loop driftless system cannot be bounded by an exponential envelope.\n\nThe synthesis methods generate feedbacks which are not smooth on [...]. The solutions of the closed-loop system are proven to be unique in this case. In addition, for many driftless systems the control inputs are often velocities. A more appropriate formulation of the stabilization problem has the control law specifying forces instead of velocities. We have extended the kinematic velocity controllers to controllers which command forces and still p-exponentially stabilize the system. \n\nPerhaps the ultimate justification of the methods proposed in this thesis are the experimental results. The experiments demonstrate the superior convergence performance of the p-exponential stabilizers versus traditional smooth feedbacks. The experiments also highlight the importance of transformation conditioning in the feedbacks. Other design issues, such as scaling the measured states to eliminate hunting, are discussed. The methods and problems in this thesis bring the practical control of strongly nonlinear systems one step closer.\n", "doi": "10.7907/7myb-h217", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4189", "collection": "thesis", "collection_id": "4189", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10202005-090745", "primary_object_url": { "basename": "Chen_im_1994.pdf", "content": "final", "filesize": 9999984, "license": "other", "mime_type": "application/pdf", "url": "/4189/1/Chen_im_1994.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theory and Applications of Modular Reconfigurable Robotic Systems", "author": [ { "family_name": "Chen", "given_name": "I-Ming", "orcid": "0000-0002-4831-3781", "clpid": "Chen-I-Ming" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Rodriguez", "given_name": "Guillermo", "clpid": "Rodriguez-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A modular reconfigurable robotic system consists of various link and joint units with standardized connecting interfaces that can be easily separated and reassembled into different configurations. Compared to a fixed configuration robot, which is usually a compromised design for a limited set of tasks, a modular robot can accomplish a large class of tasks through reconfiguration of a small inventory of modules. This thesis studies how to find an optimal module assembly configuration constructed from a given inventory of module components for a specific task. A set of generalized module models that bear features found in many real implementations is introduced. The modular robot assembly configuration is represented by a novel Assembly Incidence Matrix (AIM). Equivalence relations based on module geometry symmetries and graph isomorphisms are defined on the AIMs. An enumeration algorithm to generate non-isomorphic assembly configurations based on this equivalence relation is proposed. Examples demonstrate that this method is a significant improvement over a brute force enumeration process. Configuration independent kinematic models for modular robots are developed, and they are essential for solving the task-optimal configuration problem. A task-oriented objective function is defined on the set of non-isomorphic module assembly configurations. Task requirements and kinematic constraints on the robot assembly are treated as parameters to this objective function. The task-optimal configuration problem is formulated as a combinatorial optimization problem to which genetic algorithms are employed for solutions. Examples of finding task-optimal serial revolute-jointed robot configurations are demonstrated. In addition, the applications of modular robots to planning multifinger grasping and manipulation are developed. Planning two-finger grasps is done through finding antipodal point grasps on smooth shaped objects. Planning n-finger grasps is achieved by defining a qualitative force-closure test function on the n-finger grasps on an object. Applications of this test function to manipulation task and finger gaiting are illustrated.", "doi": "10.7907/2AAA-RY45", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:4189", "collection": "thesis", "collection_id": "4189", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10202005-090745", "primary_object_url": { "basename": "Chen_im_1994.pdf", "content": "final", "filesize": 9999984, "license": "other", "mime_type": "application/pdf", "url": "/4189/1/Chen_im_1994.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theory and Applications of Modular Reconfigurable Robotic Systems", "author": [ { "family_name": "Chen", "given_name": "I-Ming", "orcid": "0000-0002-4831-3781", "clpid": "Chen-I-Ming" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Rodriguez", "given_name": "Guillermo", "clpid": "Rodriguez-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A modular reconfigurable robotic system consists of various link and joint units with standardized connecting interfaces that can be easily separated and reassembled into different configurations. Compared to a fixed configuration robot, which is usually a compromised design for a limited set of tasks, a modular robot can accomplish a large class of tasks through reconfiguration of a small inventory of modules. This thesis studies how to find an optimal module assembly configuration constructed from a given inventory of module components for a specific task. A set of generalized module models that bear features found in many real implementations is introduced. The modular robot assembly configuration is represented by a novel Assembly Incidence Matrix (AIM). Equivalence relations based on module geometry symmetries and graph isomorphisms are defined on the AIMs. An enumeration algorithm to generate non-isomorphic assembly configurations based on this equivalence relation is proposed. Examples demonstrate that this method is a significant improvement over a brute force enumeration process. Configuration independent kinematic models for modular robots are developed, and they are essential for solving the task-optimal configuration problem. A task-oriented objective function is defined on the set of non-isomorphic module assembly configurations. Task requirements and kinematic constraints on the robot assembly are treated as parameters to this objective function. The task-optimal configuration problem is formulated as a combinatorial optimization problem to which genetic algorithms are employed for solutions. Examples of finding task-optimal serial revolute-jointed robot configurations are demonstrated. In addition, the applications of modular robots to planning multifinger grasping and manipulation are developed. Planning two-finger grasps is done through finding antipodal point grasps on smooth shaped objects. Planning n-finger grasps is achieved by defining a qualitative force-closure test function on the n-finger grasps on an object. Applications of this test function to manipulation task and finger gaiting are illustrated.", "doi": "10.7907/2AAA-RY45", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:818", "collection": "thesis", "collection_id": "818", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03012005-141633", "primary_object_url": { "basename": "Bhattacharyya_a_1994.pdf", "content": "final", "filesize": 6752918, "license": "other", "mime_type": "application/pdf", "url": "/818/1/Bhattacharyya_a_1994.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Internal flows and force matrices in axial flow inducers", "author": [ { "family_name": "Bhattacharyya", "given_name": "Abhijit", "clpid": "Bhattacharyya-A" } ], "thesis_advisor": [ { "family_name": "Acosta", "given_name": "Allan J.", "clpid": "Acosta-A-J" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" } ], "thesis_committee": [ { "family_name": "Acosta", "given_name": "Allan J.", "clpid": "Acosta-A-J" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Murray", "given_name": "Richard M.", "clpid": "Murray-R-M" }, { "family_name": "Caughey", "given_name": "Thomas Kirk", "clpid": "Caughey-T-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Axial flow pump runners known as inducers are subject to complex internal flows and fluid-induced lateral and rotordynamic forces. The internal flows in inducers are three dimensional and are characterized by complicated secondary flows. The current research investigates the boundary layer flows on the blades, hub and housing of unshrouded and shrouded axial flow inducers using flow visualization techniques. Rotordynamic and lateral force data on unshrouded inducers were also obtained under varying conditions of flow and whirl.\n\nStudies on the internal flows showed that the blade boundary layer flow had strong radial components at off-design conditions. The flow remains attached to the blade surface of unshrouded inducers at all flow coefficients tested. The origin of the upstream swirling backflow was found to be at the discharge plane of the inducer. In addition, flow reversal was observed at the suction side blade tip near the leading edge in a shrouded inducer. Re-entry of the hub boundary layer flow (a downstream backflow) into the blade passage area was observed at flow coefficients below design. For unshrouded inducers the radially outward flow near the blade tip mixed with the tip clearance leakage flow to form the upstream backflow. These observations provide a better understanding of the internal flows and the occurrence of upstream backflows in inducers.\n\nThe rotordynamic forces acting on an inducer due to an imposed whirl motion was also investigated. It was found that the rotordynamic force data at various whirl frequency ratios does not allow a normal quadratic fit; consequently the conventional inertial, stiffness and damping coefficients cannot be obtained and a definite whirl ratio describing the instability region does not result. Rotordynamic forces were found to be significantly dependent on the flow coefficient. At flow coefficients below design, these forces are characterized by multiple zero crossings at various whirl frequencies and large destabilizing peeks. Theoretical estimates of the tangential rotordynamic force on a non-whirling inducer using actuator disk theory were significantly different, both in magnitude and direction, from the experimentally measured forces.\n\nThe effect of upstream and downstream flow distortions on the rotordynamic and lateral forces on an inducer were studied. It was found that at flow coefficients below design, large lateral forces occurred in the presence of a downstream asymmetry. The reverse flows occurring downstream which consist of high energy fluid are the possible cause of these large forces. The imposition of a uniform downstream condition reduced these forces to near zero values. Results of inlet distortion experiments show that a strong inlet shear causes a significant increase in the lateral force. However, weak inlet shear flows and the flow asymmetry due to a 180\u00b0 upstream bend did not cause a significant lateral force. It was found that flow distortions upstream or downstream did not cause any significant effect on the rotordynamic forces. Cavitation was found to have important consequences for fluid-induced rotordynamic forces. These forces become destabilizing for both forward and reverse whirl. The magnitudes of the destabilizing forces were found to increase with decreasing cavitation numbers.\n", "doi": "10.7907/Q4ST-4X32", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:4695", "collection": "thesis", "collection_id": "4695", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11302007-075425", "primary_object_url": { "basename": "Young_pm_1993.pdf", "content": "final", "filesize": 23876911, "license": "other", "mime_type": "application/pdf", "url": "/4695/1/Young_pm_1993.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Robustness with Parametric and Dynamic Uncertainty", "author": [ { "family_name": "Young", "given_name": "Peter Michael", "clpid": "Young-Peter-Michael" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Franklin", "given_name": "Joel N.", "clpid": "Franklin-J-N" }, { "family_name": "Morari", "given_name": "Manfred", "orcid": "0000-0002-7696-5058", "clpid": "Morari-M" }, { "family_name": "Dahleh", "given_name": "Munther A.", "orcid": "0000-0002-1470-2148", "clpid": "Dahleh-Munther-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In many disciplines of engineering it is often convenient, for analysis and design purposes, to approximate the real behavior of physical systems by mathematical models. For some applications however, and in particular when one wishes to design a high performance controller, the differences between the behavior of the mathematical model and the physical system can be crucial to the performance of the final design. The theory of robust control attempts to take into account these inherent inaccuracies in the model, and provide systematic analysis and design techniques in the face of this \"uncertainty.\"
\r\n\r\nThese goals can be restated as formal mathematical problems. In order to handle more realistic descriptions of physical systems, one has to allow more sophisticated models, and this leads to more difficult mathematical problems. In this thesis we will consider both the theoretical and computational aspects of such problems. In particular we will consider robustness in the presence of both real (e. g., parametric) and complex (e. g., dynamic) structured uncertainty.
\r\n\r\nThis leads to a consideration of the general mixed \u00b5 analysis and synthesis problems. Some special cases of the analysis problem can be solved exactly, but the general problem is in fact NP hard, so that in order to develop solutions for large problems with reasonable computational requirements, we will adopt a scheme of computing and refining upper and lower bounds. By exploiting the theoretical properties of the problem, we are able to develop practical algorithms, capable of handling mixed \u00b5 analysis problems with tens of parameters, in computation times that are typically of the order of minutes. This is despite the fact that the mixed \u00b5 problem appears to have inherently combinatoric worst-case behavior.
\r\n\r\nFor the synthesis problem a new \"D,G-K iteration\" procedure is developed to design a stabilizing controller which attempts to minimize the peak value across frequency of mixed \u00b5. The scheme utilizes a combination of some new results from the mixed \u00b5 upper bound problem with the H\u221e optimal control solution. The theoretical results developed here have already been successfully applied to a number of real engineering problems, and some of these applications are briefly reviewed, to illustrate the advantages offered by the new analysis and synthesis techniques.
", "doi": "10.7907/HJF8-J281", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:4695", "collection": "thesis", "collection_id": "4695", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11302007-075425", "primary_object_url": { "basename": "Young_pm_1993.pdf", "content": "final", "filesize": 23876911, "license": "other", "mime_type": "application/pdf", "url": "/4695/1/Young_pm_1993.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Robustness with Parametric and Dynamic Uncertainty", "author": [ { "family_name": "Young", "given_name": "Peter Michael", "clpid": "Young-Peter-Michael" } ], "thesis_advisor": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "thesis_committee": [ { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Franklin", "given_name": "Joel N.", "clpid": "Franklin-J-N" }, { "family_name": "Morari", "given_name": "Manfred", "orcid": "0000-0002-7696-5058", "clpid": "Morari-M" }, { "family_name": "Dahleh", "given_name": "Munther A.", "orcid": "0000-0002-1470-2148", "clpid": "Dahleh-Munther-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In many disciplines of engineering it is often convenient, for analysis and design purposes, to approximate the real behavior of physical systems by mathematical models. For some applications however, and in particular when one wishes to design a high performance controller, the differences between the behavior of the mathematical model and the physical system can be crucial to the performance of the final design. The theory of robust control attempts to take into account these inherent inaccuracies in the model, and provide systematic analysis and design techniques in the face of this \"uncertainty.\"
\r\n\r\nThese goals can be restated as formal mathematical problems. In order to handle more realistic descriptions of physical systems, one has to allow more sophisticated models, and this leads to more difficult mathematical problems. In this thesis we will consider both the theoretical and computational aspects of such problems. In particular we will consider robustness in the presence of both real (e. g., parametric) and complex (e. g., dynamic) structured uncertainty.
\r\n\r\nThis leads to a consideration of the general mixed \u00b5 analysis and synthesis problems. Some special cases of the analysis problem can be solved exactly, but the general problem is in fact NP hard, so that in order to develop solutions for large problems with reasonable computational requirements, we will adopt a scheme of computing and refining upper and lower bounds. By exploiting the theoretical properties of the problem, we are able to develop practical algorithms, capable of handling mixed \u00b5 analysis problems with tens of parameters, in computation times that are typically of the order of minutes. This is despite the fact that the mixed \u00b5 problem appears to have inherently combinatoric worst-case behavior.
\r\n\r\nFor the synthesis problem a new \"D,G-K iteration\" procedure is developed to design a stabilizing controller which attempts to minimize the peak value across frequency of mixed \u00b5. The scheme utilizes a combination of some new results from the mixed \u00b5 upper bound problem with the H\u221e optimal control solution. The theoretical results developed here have already been successfully applied to a number of real engineering problems, and some of these applications are briefly reviewed, to illustrate the advantages offered by the new analysis and synthesis techniques.
", "doi": "10.7907/HJF8-J281", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:3245", "collection": "thesis", "collection_id": "3245", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08272007-132407", "primary_object_url": { "basename": "Higgins_cm_1993.pdf", "content": "final", "filesize": 7071731, "license": "other", "mime_type": "application/pdf", "url": "/3245/1/Higgins_cm_1993.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Classification and Approximation with Rule-Based Networks", "author": [ { "family_name": "Higgins", "given_name": "Charles Marion", "clpid": "Higgins-Charles-Marion" } ], "thesis_advisor": [ { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" } ], "thesis_committee": [ { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" }, { "family_name": "Franklin", "given_name": "Joel N.", "clpid": "Franklin-J-N" }, { "family_name": "Posner", "given_name": "Edward C.", "clpid": "Posner-E-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis describes the architecture of learning systems which can explain their decisions through a rule-based knowledge representation. Two problems in learning are addressed: pattern classification and function approximation.
\r\n\r\nIn Part I, a pattern classifier for discrete-valued problems is presented. The system utilizes an information-theoretic algorithm for constructing informative rules from example data. These rules are then used to construct a computational network to perform parallel inference and posterior probability estimation. The network can be extended incrementally; that is, new data can be incorporated without repeating the training on previous data. It is shown that this technique performs comparably with other techniques including the backpropagation network while having unique advantages in incremental learning capability, training efficiency, and knowledge representation. Examples are shown of rule-based classification and explanation.
\r\n\r\nIn Part II, we present a method for the learning of fuzzy logic membership functions and rules to predict a numerical function from examples of the function and its independent variables. This method uses a three-step approach to building a complete function approximation system: first, learning the membership functions and creating a cell-based rule representation; second, simplifying the cell-based rules using an information-theoretic approach for induction of rules from discrete-valued data; and finally, constructing a computational network to compute the function value given its independent variables. Applications of the system to adaptive control are suggested, including a method for learning a complete control system for an unknown plant. Experimental validation of the suggested methods using a ball-and-beam system is shown.
", "doi": "10.7907/4r7r-w573", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:3245", "collection": "thesis", "collection_id": "3245", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08272007-132407", "primary_object_url": { "basename": "Higgins_cm_1993.pdf", "content": "final", "filesize": 7071731, "license": "other", "mime_type": "application/pdf", "url": "/3245/1/Higgins_cm_1993.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Classification and Approximation with Rule-Based Networks", "author": [ { "family_name": "Higgins", "given_name": "Charles Marion", "clpid": "Higgins-Charles-Marion" } ], "thesis_advisor": [ { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" } ], "thesis_committee": [ { "family_name": "Goodman", "given_name": "Rodney M.", "clpid": "Goodman-R-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" }, { "family_name": "Franklin", "given_name": "Joel N.", "clpid": "Franklin-J-N" }, { "family_name": "Posner", "given_name": "Edward C.", "clpid": "Posner-E-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis describes the architecture of learning systems which can explain their decisions through a rule-based knowledge representation. Two problems in learning are addressed: pattern classification and function approximation.
\r\n\r\nIn Part I, a pattern classifier for discrete-valued problems is presented. The system utilizes an information-theoretic algorithm for constructing informative rules from example data. These rules are then used to construct a computational network to perform parallel inference and posterior probability estimation. The network can be extended incrementally; that is, new data can be incorporated without repeating the training on previous data. It is shown that this technique performs comparably with other techniques including the backpropagation network while having unique advantages in incremental learning capability, training efficiency, and knowledge representation. Examples are shown of rule-based classification and explanation.
\r\n\r\nIn Part II, we present a method for the learning of fuzzy logic membership functions and rules to predict a numerical function from examples of the function and its independent variables. This method uses a three-step approach to building a complete function approximation system: first, learning the membership functions and creating a cell-based rule representation; second, simplifying the cell-based rules using an information-theoretic approach for induction of rules from discrete-valued data; and finally, constructing a computational network to compute the function value given its independent variables. Applications of the system to adaptive control are suggested, including a method for learning a complete control system for an unknown plant. Experimental validation of the suggested methods using a ball-and-beam system is shown.
", "doi": "10.7907/4r7r-w573", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:3199", "collection": "thesis", "collection_id": "3199", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08222007-105213", "primary_object_url": { "basename": "Braatz_rd_1993.pdf", "content": "final", "filesize": 7747644, "license": "other", "mime_type": "application/pdf", "url": "/3199/1/Braatz_rd_1993.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Robust Loopshaping for Process Control", "author": [ { "family_name": "Braatz", "given_name": "Richard Dean", "orcid": "0000-0003-4304-3484", "clpid": "Braatz-Richard-Dean" } ], "thesis_advisor": [ { "family_name": "Morari", "given_name": "Manfred", "orcid": "0000-0002-7696-5058", "clpid": "Morari-M" } ], "thesis_committee": [ { "family_name": "Morari", "given_name": "Manfred", "orcid": "0000-0002-7696-5058", "clpid": "Morari-M" }, { "family_name": "Gavalas", "given_name": "George R.", "orcid": "0000-0003-1468-6835", "clpid": "Gavalas-G-R" }, { "family_name": "Doyle", "given_name": "John Comstock", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Strong trends in chemical engineering and plant operation have made the control of processes increasingly difficult and have driven the process industry's demand for improved control techniques. Improved control leads to savings in resources, smaller downtimes, improved safety, and reduced pollution.
\r\n\r\nThough the need for improved process control is clear, advanced control methodologies have had only limited acceptance and application in industrial practice. The reason for this gap between control theory and practice is that existing control methodologies do not adequately address all of the following control system requirements and problems associated with control design:\r\n
A framework is presented to address these control requirements/problems in a general, unified manner. The approach will be demonstrated on adhesive coating processes and distillation columns.
", "doi": "10.7907/vqmv-kw76", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:4458", "collection": "thesis", "collection_id": "4458", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11082006-132210", "primary_object_url": { "basename": "Chirikjian_gs_1992.pdf", "content": "final", "filesize": 6509372, "license": "other", "mime_type": "application/pdf", "url": "/4458/1/Chirikjian_gs_1992.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theory and Applications of Hyper-Redundant Robotic Manipulators", "author": [ { "family_name": "Chirikjian", "given_name": "Gregory Scott", "clpid": "Chirikjian-Gregory-Scott" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Knowles", "given_name": "James K.", "clpid": "Knowles-J-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Hayati", "given_name": "S.", "clpid": "Hayati-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The term \"hyper-redundant\" refers to robotic manipulators and mobile robots with a very large, possibly infinite, number of actuatable degrees of freedom. These robots are analogous in morphology and operation to snakes, worms, elephant trunks, and tentacles. This thesis presents a novel kinematic framework for hyper-redundant manipulator motion planning and task implementation. The basis of this formulation is the use of a \"backbone reference set\" which captures the essential macroscopic geometric features of hyper-redundant robots. In the analytical part of this work, the backbone representation is developed and used to solve problems in obstacle avoidance, locomotion, grasping, and \"optimal\" end effector placement. The latter part of this thesis deals with the design and implementation of a thirty-degree-of-freedom planar hyper-redundant manipulator which is used to demonstrate these novel kinematic and motion planning techniques. Design issues such as robustness with respect to mechanical failure, and design for easy assembly and repair are also addressed. The analytical and design concepts are combined to illustrate tasks for which hyper-redundant robotic mechanisms are well suited.\r\n", "doi": "10.7907/F12D-0X25", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:4458", "collection": "thesis", "collection_id": "4458", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11082006-132210", "primary_object_url": { "basename": "Chirikjian_gs_1992.pdf", "content": "final", "filesize": 6509372, "license": "other", "mime_type": "application/pdf", "url": "/4458/1/Chirikjian_gs_1992.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theory and Applications of Hyper-Redundant Robotic Manipulators", "author": [ { "family_name": "Chirikjian", "given_name": "Gregory Scott", "clpid": "Chirikjian-Gregory-Scott" } ], "thesis_advisor": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" } ], "thesis_committee": [ { "family_name": "Burdick", "given_name": "Joel Wakeman", "orcid": "0000-0002-3091-540X", "clpid": "Burdick-J-W" }, { "family_name": "Antonsson", "given_name": "Erik K.", "clpid": "Antonsson-E-K" }, { "family_name": "Knowles", "given_name": "James K.", "clpid": "Knowles-J-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Hayati", "given_name": "S.", "clpid": "Hayati-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The term \"hyper-redundant\" refers to robotic manipulators and mobile robots with a very large, possibly infinite, number of actuatable degrees of freedom. These robots are analogous in morphology and operation to snakes, worms, elephant trunks, and tentacles. This thesis presents a novel kinematic framework for hyper-redundant manipulator motion planning and task implementation. The basis of this formulation is the use of a \"backbone reference set\" which captures the essential macroscopic geometric features of hyper-redundant robots. In the analytical part of this work, the backbone representation is developed and used to solve problems in obstacle avoidance, locomotion, grasping, and \"optimal\" end effector placement. The latter part of this thesis deals with the design and implementation of a thirty-degree-of-freedom planar hyper-redundant manipulator which is used to demonstrate these novel kinematic and motion planning techniques. Design issues such as robustness with respect to mechanical failure, and design for easy assembly and repair are also addressed. The analytical and design concepts are combined to illustrate tasks for which hyper-redundant robotic mechanisms are well suited.\r\n", "doi": "10.7907/F12D-0X25", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" } ]