Xenorhabdus griffiniae is a bacterium that lives inside the intestine of the entomopathogenic nematode Steinernema hermaphroditum and partners with the nematode to infect and kill insect larvae in soil. The construction of gene circuits, such as reporters, in X. griffiniae would provide tools to study and better understand the symbiotic relationship it has with its host. However, because X. griffiniae is not a model organism, information about gene circuit construction in X. griffiniae is limited. We developed and characterized a DNA part library similar to the CIDAR MoClo extension library for E. coli to allow more efficient construction of genetic circuits in X. griffiniae. TurboRFP expressing strains with different constitutive Anderson promoters and different ribosome binding sites (RBS) were constructed to quantify promoter and RBS strengths in X. griffiniae. Furthermore, two fluorescent proteins sfGFP and sfYFP as well as the bioluminescent luxCDABE operon were added to the part library and successfully expressed in X. griffiniae. We then used the characterized parts of the cell to build and characterize IPTG inducible constructs.
\nIdentifying the cause of a system-level failure in a cyber-physical system (CPS) can be like tracing a needle in a haystack. This paper approaches the problem by assuming that the CPS has been designed compositionally and that each component in the system is associated with an assume-guarantee contract. We exploit recent advances in contract-based design that show how to compute the contract for the entire system using the component-level contracts. When presented with a system-level failure, our approach is able to efficiently identify the components that are responsible for the system-level failure together with the specific predicates in those components' specifications that are involved in the fault. We implemented this approach using Pacti and demonstrate it through illustrative examples inspired by an autonomous vehicle in the DARPA urban challenge.
", "doi": "10.1007/978-3-032-05435-7_24", "issn": "0302-9743", "isbn": "978-3-032-05434-0", "publisher": "Springer Nature Switzerland", "publication": "Lecture Notes in Computer Science", "publication_date": "2025-09-12", "volume": "16087", "pages": "438-456" }, { "id": "authors:gyf3c-y6p16", "collection": "authors", "collection_id": "gyf3c-y6p16", "cite_using_url": "https://authors.library.caltech.edu/records/gyf3c-y6p16", "type": "monograph", "title": "A DNA part library for reliable engineering of the emerging model nematode symbiotic bacterium Xenorhabdus griffiniae HGB2511", "author": [ { "family_name": "Larsson", "given_name": "Elin M.", "orcid": "0000-0003-1341-5937", "clpid": "Larsson-Elin-Maria" }, { "family_name": "Wang", "given_name": "Olivia Y.", "orcid": "0009-0005-8554-5775", "clpid": "Wang-Olivia-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Xenorhabdus griffiniae is a bacterium that lives inside the intestine of the entomopathogenic nematode Steinernema hermaphroditum and partners with the nematode to infect and kill insect larvae in soil. The construction of gene circuits, like reporters, in X. griffiniae would provide tools to study and better understand the symbiotic relationship it has with its host. However, because X. griffiniae is not a model organism, information about gene circuit construction in X. griffiniae is limited. We develop and characterize a DNA part library similar to the CIDAR MoClo extension library for E. coli to allow more efficient construction of genetic circuits in X. griffiniae. TurboRFP expressing strains with different constitutive Anderson promoters and different ribosome binding sites (RBS) were constructed to quantify promoter and RBS strengths in X. griffiniae. Furthermore, two fluorescent proteins sfGFP and sfYFP, as well as the bioluminescent luxCDABE operon were added to the part library and successfully expressed in X. griffiniae. We then used the characterized parts to build and characterize IPTG inducible constructs.
", "doi": "10.1101/2025.06.09.658710", "publisher": "BioRxiv", "publication_date": "2025-06-09" }, { "id": "authors:1xz93-wgt26", "collection": "authors", "collection_id": "1xz93-wgt26", "cite_using_url": "https://authors.library.caltech.edu/records/1xz93-wgt26", "type": "article", "title": "A Portable Arsenic Sensor Integrating Bacillus megaterium with CMOS Technology", "author": [ { "family_name": "Hu", "given_name": "Chelsea Y.", "orcid": "0000-0002-2211-1778", "clpid": "Hu-Chelsea-Y" }, { "family_name": "McManus", "given_name": "John", "orcid": "0009-0007-7077-0624", "clpid": "McManus-John" }, { "family_name": "Aghlmand", "given_name": "Fatemeh", "orcid": "0000-0002-5103-9314", "clpid": "Aghlmand-Fatemeh" }, { "family_name": "Mei", "given_name": "Tracy", "orcid": "0000-0003-2743-0126" }, { "family_name": "Larsson", "given_name": "Elin", "orcid": "0000-0003-1341-5937", "clpid": "Larsson-Elin" }, { "family_name": "Emami", "given_name": "Azita", "orcid": "0000-0002-6945-9958", "clpid": "Emami-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Bacteria innately monitor their environment by dynamically regulating gene expression to respond to fluctuating conditions. Through synthetic biology, we can harness this natural capability to design cell-based sensors. Bacillus megaterium, a soil bacterium, stands out due to its remarkable heavy metal tolerance and sporulation ability, making it an ideal candidate for heavy metal detection with low transportation costs. However, challenges persist: the synthetic biology toolkit for this strain is underdeveloped, and conventional whole-cell sensors necessitate specialized laboratory equipment to read the output. In our study, we have genetically modified B. megaterium for arsenic detection and established a detection threshold below the EPA’s recommendation of 10 ppb for drinking water in both vegetative and spore forms. Additionally, we have integrated both engineered B. megaterium living cells and spores with a complementary metal-oxide-semiconductor (CMOS) chip, providing a proof-of-concept for field-deployable arsenic detection. We show that the limit of detection (LOD) of our integrated sensor is within the range to test arsenic levels in soil and food. As a proof of concept, this work paves the way for the deployment of our sensor in resource-limited settings, ensuring real-time arsenic detection in challenging environments.
", "doi": "10.1021/acssynbio.4c00895", "pmcid": "PMC12090344", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2025-05-16", "series_number": "5", "volume": "14", "issue": "5", "pages": "1615-1624" }, { "id": "authors:n18vd-tcz58", "collection": "authors", "collection_id": "n18vd-tcz58", "cite_using_url": "https://authors.library.caltech.edu/records/n18vd-tcz58", "type": "article", "title": "Optimizing Protein Production in the One-Pot PURE System: Insights into Reaction Composition and Expression Efficiency", "author": [ { "family_name": "Zhang", "given_name": "Yan", "orcid": "0000-0003-0719-5456", "clpid": "Zhang-Yan" }, { "family_name": "Deveikis", "given_name": "Matas", "orcid": "0000-0001-7444-2950" }, { "family_name": "Qiu", "given_name": "Yanping", "orcid": "0000-0003-2948-2173", "clpid": "Qiu-Yanping" }, { "family_name": "Bj\u00f6rn", "given_name": "Lovisa", "orcid": "0009-0007-6983-3341", "clpid": "Bj\u00f6rn-Lovisa" }, { "family_name": "Martinez", "given_name": "Zachary A.", "orcid": "0000-0002-7830-3162", "clpid": "Martinez-Zachary-A" }, { "family_name": "Chou", "given_name": "Tsui-Fen", "orcid": "0000-0003-2410-2186", "clpid": "Chou-Tsui-Fen" }, { "family_name": "Freemont", "given_name": "Paul S.", "orcid": "0000-0002-5658-8486" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The One-Pot PURE (Protein synthesis Using Recombinant Elements) system simplifies the preparation of traditional PURE systems by coculturing and purifying 36 essential proteins for gene expression in a single step, enhancing accessibility and affordability for widespread laboratory adoption and customization. However, replicating this protocol to match the productivity of traditional PURE systems can take considerable time and effort due to uncharacterized variability. In this work, we observed unstable PURE protein expression in the original One-Pot PURE strains, E. coli M15/pREP4 and BL21(DE3), and addressed this issue using glucose-mediated catabolite repression to minimize burdensome background expression. We also identified several limitations making the M15/pREP4 strain unsuitable for PURE protein expression, including coculture incompatibility with BL21(DE3) and uncharacterized proteolytic activity. We showed that consolidating all expression vectors into a protease-deficient BL21(DE3) strain minimized proteolysis, led to more uniform coculture cell growth at the time of induction, and improved the stoichiometry of critical translation initiation factors in the final PURE mixture for efficient cell-free protein production. In addition to optimizing the One-Pot PURE protein composition, we found that variations in commercial energy solution formulations could compensate for suboptimal PURE protein stoichiometry. Notably, altering the source of E. coli tRNAs in the energy solution alone led to significant differences in the expression capacity of cell-free reactions, highlighting the importance of tRNA codon usage in influencing protein expression yield. Taken together, this work systematically investigates the proteome and biochemical factors influencing the One-Pot PURE system productivity, offering insights to enhance its robustness and adaptability across laboratories.
", "doi": "10.1021/acssynbio.4c00779", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2025-05-16", "series_number": "5", "volume": "14", "issue": "5", "pages": "1496-1508" }, { "id": "authors:6rsmy-pph05", "collection": "authors", "collection_id": "6rsmy-pph05", "cite_using_url": "https://authors.library.caltech.edu/records/6rsmy-pph05", "type": "article", "title": "ATMO: an aerially transforming morphobot for dynamic ground-aerial transition", "author": [ { "family_name": "Mandralis", "given_name": "Ioannis", "orcid": "0000-0001-5270-0672", "clpid": "Mandralis-Ioannis-M" }, { "family_name": "Nemovi", "given_name": "Reza" }, { "family_name": "Ramezani", "given_name": "Alireza", "orcid": "0000-0002-3391-5288" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" } ], "abstract": "Designing ground-aerial robots is challenging due to the increased actuation requirements which can lead to added weight and reduced locomotion efficiency. Morphobots mitigate this by combining actuators into multi-functional groups and leveraging ground transformation to achieve different locomotion modes. However, transforming on the ground requires dealing with the complexity of ground-vehicle interactions during morphing, limiting applicability on rough terrain. Mid-air transformation offers a solution to this issue but demands operating near or beyond actuator limits while managing complex aerodynamic forces. We address this problem by introducing the Aerially Transforming Morphobot (ATMO), a robot which transforms near the ground achieving smooth transition between aerial and ground modes. To achieve this, we leverage the near ground aerodynamics, uncovered by experimental load cell testing, and stabilize the system using a model-predictive controller that adapts to ground proximity and body shape. The system is validated through numerous experimental demonstrations. We find that ATMO can land smoothly at body postures past its actuator saturation limits by virtue of the uncovered ground-effect.", "doi": "10.1038/s44172-025-00413-6", "issn": "2731-3395", "publisher": "Nature Publishing Group", "publication": "Communications Engineering", "publication_date": "2025-04-19", "series_number": "1", "volume": "4", "issue": "1", "pages": "74" }, { "id": "authors:5ns21-pn241", "collection": "authors", "collection_id": "5ns21-pn241", "cite_using_url": "https://authors.library.caltech.edu/records/5ns21-pn241", "type": "article", "title": "Barrier-Based Test Synthesis for Safety-Critical Systems Subject to Timed Reach-Avoid Specifications", "author": [ { "family_name": "Akella", "given_name": "Prithvi", "orcid": "0000-0003-4375-0015", "clpid": "Akella-Prithvi" }, { "family_name": "Ahmadi", "given_name": "Mohamadreza", "orcid": "0000-0003-1447-3012", "clpid": "Ahmadi-Mohamadreza" }, { "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" } ], "abstract": "We propose an adversarial, time-varying test-synthesis procedure for safety-critical systems without requiring specific knowledge of the underlying controller steering the system. Specifically, our approach codifies the system objective as a timed reach-avoid specification. Then, by coupling control barrier functions with this class of specifications, we construct an instantaneous difficulty metric whose minimizer corresponds to the most difficult test at that system state. By defining tests as the minimizer of this difficulty metric over the space of allowable tests, we provably identify realizable and maximally difficult tests of system behavior. Finally, we develop this test-synthesis procedure for both continuous and discrete-time systems and showcase our test-synthesis procedure on simulated and hardware examples.
", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2025-04", "series_number": "4", "volume": "70", "issue": "4", "pages": "2180 - 2195" }, { "id": "authors:4kyba-3mm91", "collection": "authors", "collection_id": "4kyba-3mm91", "cite_using_url": "https://authors.library.caltech.edu/records/4kyba-3mm91", "type": "article", "title": "Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation", "author": [ { "family_name": "Merk", "given_name": "Liana N." }, { "family_name": "Shur", "given_name": "Andrey S." }, { "family_name": "Jena", "given_name": "Smrutiti" }, { "family_name": "Munoz", "given_name": "Javier" }, { "family_name": "Brubaker", "given_name": "Douglas K." }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Green", "given_name": "Leopold N.", "orcid": "0000-0001-5479-6970", "clpid": "Green-Leopold-N" } ], "abstract": "Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917 (EcN). Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuit's selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to recombinant cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes driven by logical signal processing. It demonstrates the feasibility of IL-22 derived from probiotic EcN with minimal off-target effects in a gut epithelial context.", "doi": "10.1021/acssynbio.3c00668", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2024-12-20", "series_number": "12", "volume": "13", "issue": "12", "pages": "3885\u20133896" }, { "id": "authors:nwqa7-8hz87", "collection": "authors", "collection_id": "nwqa7-8hz87", "cite_using_url": "https://authors.library.caltech.edu/records/nwqa7-8hz87", "type": "article", "title": "Metabolic Perturbations to an Escherichia coli-based Cell-Free System Reveal a Trade-off between Transcription and Translation", "author": [ { "family_name": "Kapasiawala", "given_name": "Manisha", "orcid": "0000-0002-0302-2921", "clpid": "Kapasiawala-Manisha" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Cell-free transcription-translation (TX-TL) systems have been used for diverse applications, but their performance and scope are limited by variability and poor predictability. To understand the drivers of this variability, we explored the effects of metabolic perturbations to anEscherichia coli (E. coli) Rosetta2 TX-TL system. We targeted three classes of molecules: energy molecules, in the form of nucleotide triphosphates (NTPs); central carbon \"fuel\" molecules, which regenerate NTPs; and magnesium ions (Mg2+). Using malachite green mRNA aptamer (MG aptamer) and destabilized enhanced green fluorescent protein (deGFP) as transcriptional and translational readouts, respectively, we report the presence of a trade-off between optimizing total protein yield and optimizing total mRNA yield, as measured by integrating the area under the curve for mRNA time-course dynamics. We found that a system's position along the trade-off curve is strongly determined by Mg2+ concentration, fuel type and concentration, and cell lysate preparation and that variability can be reduced by modulating these components. Our results further suggest that the trade-off arises from limitations in translation regulation and inefficient energy regeneration. This work advances our understanding of the effects of fuel and energy metabolism on TX-TL in cell-free systems and lays a foundation for improving TX-TL performance, lifetime, standardization, and prediction.", "doi": "10.1021/acssynbio.4c00361", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2024-11-20", "series_number": "12", "volume": "13", "issue": "12", "pages": "3976\u20133990" }, { "id": "authors:hhh1k-q0a16", "collection": "authors", "collection_id": "hhh1k-q0a16", "cite_using_url": "https://authors.library.caltech.edu/records/hhh1k-q0a16", "type": "article", "title": "Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence", "author": [ { "family_name": "Jurado", "given_name": "Zoila", "orcid": "0000-0003-4160-5068", "clpid": "Jurado Quiroga-Zoila-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The malachite green aptamer (MGapt) is known for its utility in RNA measurement in vivo and in lysate-based cell-free protein systems. However, MGapt fluorescence dynamics do not accurately reflect RNA concentration. Our study finds that MGapt fluorescence is unstable in commercial PURE systems. We discovered that the chemical composition of the cell-free reaction strongly influences MGapt fluorescence, which leads to inaccurate RNA calculations. Specific to the commercial system, we posit that MGapt fluorescence is significantly affected by the system’s chemical properties, governed notably by the presence of dithiothreitol (DTT). We propose a model that, on average, accurately predicts MGapt measurement within a 10% margin, leveraging DTT concentration as a critical factor. This model sheds light on the complex dynamics of MGapt in cell-free systems and underscores the importance of considering environmental factors in RNA measurements using aptamers.
", "doi": "10.1021/acssynbio.4c00211", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2024-10-18", "series_number": "10", "volume": "13", "issue": "10", "pages": "3109 - 3118" }, { "id": "authors:hb9x2-t0n76", "collection": "authors", "collection_id": "hb9x2-t0n76", "cite_using_url": "https://authors.library.caltech.edu/records/hb9x2-t0n76", "type": "monograph", "title": "Policy Recommendations for the Regulation of Engineered Microbes for Environmental Release", "author": [ { "family_name": "Marken", "given_name": "John P.", "orcid": "0000-0001-9696-088X", "clpid": "Marken-John-P" }, { "family_name": "Maxon", "given_name": "Mary E." }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Engineered Microbes for Environmental Release (EMERs) are an emerging biotechnology sector that is poised to play a significant role in shaping the global bioeconomy through their ability to address challenges related to climate change, environmental remediation and diagnostics, self-regenerating structural infrastructure, and more. However, the current U.S. regulatory system is not well equipped to efficiently regulate EMERs, leading to a large regulatory burden on EMER developers that may not be commensurate with the level of risk associated with the product. Such burdens impede innovation in the EMER sector. In this report, we identify some of the specific challenges that EMER products face in navigating the federal biotechnology regulatory framework, and present actionable policy recommendations to the federal government, the biotechnology industry, and the wider scientific community about how to address these challenges.
", "doi": "10.57959/bgny-v542", "publisher": "The Linde Center for Science, Society, and Policy, Caltech", "publication_date": "2024-06-28" }, { "id": "authors:y9t9z-32k63", "collection": "authors", "collection_id": "y9t9z-32k63", "cite_using_url": "https://authors.library.caltech.edu/records/y9t9z-32k63", "type": "article", "title": "Layered Control Systems Operating on Multiple Clocks", "author": [ { "family_name": "Incer", "given_name": "Inigo", "orcid": "0000-0001-7933-692X", "clpid": "Incer-Inigo" }, { "family_name": "Csomay-Shanklin", "given_name": "Noel", "orcid": "0000-0002-2361-1694", "clpid": "Csomay-Shanklin-Noel" }, { "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" } ], "abstract": "In vitro transcription–translation (TX–TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX–TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. All three species demonstrated multiple sonication, runoff, and salt conditions producing detectable protein synthesis. One of these new TX–TL systems, P. synxantha, demonstrated a maximum protein yield of 2.5 μM at 125 proteins per DNA template, a maximum protein synthesis rate of 20 nM/min, and a range of DNA concentrations with a linear correspondence with the resulting protein synthesis. A set of different constitutive promoters driving mNeonGreen expression were tested in TX–TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX–TL-derived promoter strength and the in vivo promoter strength indicates that these lysate-based cell-free systems can be used to characterize and engineer biological parts without genomic integration, enabling a faster design–build–test cycle.
\nMicrobial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty in ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2–79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25–100 μM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8–8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter’s performance in shaken liquid culture predicts its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally aware design process provides an example of how laboratory bioengineering efforts can generate microbes with a greater promise to function reliably in their applied contexts.
\nDeep-learning models have been rapidly adopted by many fields, partly due to the deluge of data humanity has amassed. In particular, the petabases of biological sequencing data enable the unsupervised training of protein language models that learn the “language of life.” However, due to their prohibitive size and complexity, contemporary deep-learning models are often unwieldy, especially for scientists with limited machine learning backgrounds. TRILL (TRaining and Inference using the Language of Life) is a platform for creative protein design and discovery. Leveraging several state-of-the-art models such as ESM-2, DiffDock, and RFDiffusion, TRILL allows researchers to generate novel proteins, predict 3-D structures, extract high-dimensional representations of proteins, functionally classify proteins and more. What sets TRILL apart is its ability to enable complex pipelines by chaining together models and effectively merging the capabilities of different models to achieve a sum greater than its individual parts. Whether using Google Colab with one GPU or a supercomputer with hundreds, TRILL allows scientists to effectively utilize models with millions to billions of parameters by using optimized training strategies such as ZeRO-Offload and distributed data parallel. Therefore, TRILL not only bridges the gap between complex deep-learning models and their practical application in the field of biology, but also simplifies the orchestration of these models into comprehensive workflows, democratizing access to powerful methods. Documentation: https://trill.readthedocs.io/en/latest/home.html.
", "doi": "10.1101/2023.10.24.563881", "pmcid": "PMC10659302", "issn": "2692-8205", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "bioRxiv", "publication_date": "2023-11-10", "pages": "2023.10.24.563881" }, { "id": "authors:7sg3b-knb56", "collection": "authors", "collection_id": "7sg3b-knb56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230411-764712100.4", "type": "article", "title": "Rules of the Road: Formal Guarantees for Autonomous Vehicles With Behavioral Contract Design", "author": [ { "family_name": "Cai", "given_name": "Karena X.", "orcid": "0000-0002-8392-4158", "clpid": "Cai-Karena-X" }, { "family_name": "Phan-Minh", "given_name": "Tung", "orcid": "0000-0002-1403-5197", "clpid": "Phan-Minh-Tung" }, { "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" } ], "abstract": "The problem of safe and fair conflict resolution among inertial, distributed agents \u2014 particularly in highly interactive settings \u2014 is of paramount importance to the autonomous vehicles industry. The difficulty of solving this problem can be attributed to the fact that agents have to reason over other agents' complex behaviors. We propose the idea of using a behavioral contract to capture a set of explicitly defined assumptions about how all agents in the environment make decisions. In this article, we present a behavioral contract for a specific class of agents that can guarantee the safety and liveness (i.e., progress) of all agents operating in accordance with it. The behavioral contract has two main components\u2014an ordered behavioral rulebook that the agent uses to select its intended action and some additional constraints that define when an agent has precedence (or not) to take its intended action. If all of the agents act according to this contract, we can guarantee safety under all traffic conditions and liveness for all agents under \"sparse\" traffic conditions. The formalism of the contract also enables assignment of blame. We provide proofs of correctness of the behavioral contract and validate our results in simulation.", "doi": "10.1109/tro.2023.3247951", "issn": "1552-3098", "publisher": "IEEE", "publication": "IEEE Transactions on Robotics", "publication_date": "2023-06", "series_number": "3", "volume": "39", "issue": "3", "pages": "1853-1872" }, { "id": "authors:m2y80-6k516", "collection": "authors", "collection_id": "m2y80-6k516", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230706-731611100.7", "type": "article", "title": "Control education for societal-scale challenges: A community roadmap", "author": [ { "family_name": "Rossiter", "given_name": "John Anthony", "orcid": "0000-0002-1336-0633", "clpid": "Rossiter-John-Anthony" }, { "family_name": "Cassandras", "given_name": "Christos G.", "clpid": "Cassandras-Christos-G" }, { "family_name": "Hespanha", "given_name": "Jo\u00e3o", "orcid": "0000-0003-2809-4718", "clpid": "Hespanha-Jo\u00e3o" }, { "family_name": "Dormido", "given_name": "Sebastian", "orcid": "0000-0002-2405-8771", "clpid": "Dormido-Sebastian" }, { "family_name": "de la Torre", "given_name": "Luis", "orcid": "0000-0002-9648-9597", "clpid": "de-la-Torre-Luis" }, { "family_name": "Ranade", "given_name": "Gireeja", "orcid": "0000-0002-6747-4492", "clpid": "Ranade-Gireeja" }, { "family_name": "Visioli", "given_name": "Antonio", "orcid": "0000-0002-9246-5715", "clpid": "Visioli-Antonio" }, { "family_name": "Hedengren", "given_name": "John", "orcid": "0000-0002-5535-5277", "clpid": "Hedengren-John" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Antsaklis", "given_name": "Panos", "orcid": "0000-0002-6836-5028", "clpid": "Antsaklis-Panos" }, { "family_name": "Lamnabhi-Lagarrigue", "given_name": "Francoise", "orcid": "0000-0003-2512-3587", "clpid": "Lamnabhi-Lagarrigue-Francoise" }, { "family_name": "Parisini", "given_name": "Thomas", "orcid": "0000-0001-5396-9665", "clpid": "Parisini-Thomas" } ], "abstract": "This article focuses on extending, disseminating and interpreting the findings of an IEEE Control Systems Society working group looking at the role of control theory and engineering in solving some of the many current and future societal challenges. The findings are interpreted in a manner designed to give focus and direction to both future education and research work in the general control theory and engineering arena, interpreted in the broadest sense. The paper is intended to promote discussion in the community and also provide a useful starting point for colleagues wishing to re-imagine the design and delivery of control-related topics in our education systems, especially at the tertiary level and beyond.", "doi": "10.1016/j.arcontrol.2023.03.007", "issn": "1367-5788", "publisher": "Elsevier", "publication": "Annual Reviews in Control", "publication_date": "2023-05-29", "volume": "55", "pages": "1-17" }, { "id": "authors:km8n7-d0664", "collection": "authors", "collection_id": "km8n7-d0664", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-332770500.2", "type": "article", "title": "Addressable and adaptable intercellular communication via DNA messaging", "author": [ { "family_name": "Marken", "given_name": "John P.", "orcid": "0000-0001-9696-088X", "clpid": "Marken-John-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains' ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages' dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it using plasmid conjugation in E. coli. Our system can bias the transfer of messages to targeted receiver strains by 100- to 1000-fold, and their recipient lists can be dynamically updated in situ to control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.", "doi": "10.1038/s41467-023-37788-z", "pmcid": "PMC10126159", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2023-04-24", "volume": "14", "pages": "Art. No. 2358" }, { "id": "authors:w1yvb-4bn26", "collection": "authors", "collection_id": "w1yvb-4bn26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230512-807789000.8", "type": "article", "title": "Advances in theoretical and computational nonlinear control \u2014 Dedicated to the 80th birthday of Professor Arthur J. Krener", "author": [ { "family_name": "Kang", "given_name": "Wei", "orcid": "0000-0001-9989-0485", "clpid": "Kang-Wei" }, { "family_name": "Burns", "given_name": "John", "clpid": "Burns-John" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It is with great pleasure that we introduce this special issue of Systems & Control Letters, on \"Advances in Theoretical and Computational Nonlinear Control \u2014 Dedicated to the 80th Birthday of Professor Arthur J. Krener\".", "doi": "10.1016/j.sysconle.2023.105492", "issn": "0167-6911", "publisher": "Elsevier", "publication": "Systems and Control Letters", "publication_date": "2023-04", "volume": "174", "pages": "Art. No. 105492" }, { "id": "authors:0adck-tpr02", "collection": "authors", "collection_id": "0adck-tpr02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230327-442725000.2", "type": "monograph", "title": "Probing metabolism in an E. coli-based cell-free system reveals a trade-off between transcription and translation", "author": [ { "family_name": "Kapasiawala", "given_name": "Manisha", "orcid": "0000-0002-0302-2921", "clpid": "Kapasiawala-Manisha" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Cell-free transcription-translation (TX-TL) systems have been used for diverse applications, from prototyping gene circuits to providing a platform for the development of synthetic life, but their performance is limited by issues such as batch-to-batch variability, poor predictability, and limited lifetime. These issues stem largely from the fact that cell lysate contains an active and complex metabolism whose effect on TX-TL has remained largely uncharacterized. \n\nMotivated by a minimal model of cell-free metabolism, this work explored the effects of energy molecules, which power TX-TL, and fuel molecules, which regenerate energy by harnessing core metabolism, on anE. coli-based TX-TL system. This work reports a compensatory interaction between TX-TL components Mg\u207a\u00b2 and 3-phosphoglyceric acid (3-PGA, used to regenerate ATP), where if one component's concentration is increased, the other's must likewise be increased to maintain optimal translation. Furthermore, maximum total mRNA and protein production occur in different and opposite concentration regimes of Mg\u207a\u00b2 and 3-PGA. To explore the observed phenomenon, transcription and translation were decoupled. Under translation inhibition, transcriptional output was uniform across Mg\u207a\u00b2 and 3-PGA concentrations, but in a translation-only system, maximum protein production occurred in the previously found optimal regime of Mg\u207a\u00b2 and 3-PGA, suggesting a TX-TL trade-off. Using alternative fuels to regenerate energy, this work found that the trade-off is universal across the different fuel sources, and that a system's position along the trade-off is determined strongly by Mg\u207a\u00b2 and DNA concentrations. In systems where additional energy is supplied and where a fuel source is absent, the trade-off is absent, suggesting the trade-off arises from limitations in the regulation of translation and efficient energy regeneration. This work represents a significant advancement in understanding the effects of fuel and energy metabolism on TX-TL in cell-free systems and lays the foundation for improving TX-TL performance, lifetime, standardization, and prediction.", "doi": "10.1101/2023.03.22.533877", "publication_date": "2023-03-24" }, { "id": "authors:kr828-q9993", "collection": "authors", "collection_id": "kr828-q9993", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-366887000.4", "type": "article", "title": "Characterization of Integrase and Excisionase Activity in a Cell-Free Protein Expression System Using a Modeling and Analysis Pipeline", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Rodriguez", "given_name": "Makena L.", "clpid": "Rodriguez-Makena-L" }, { "family_name": "Poole", "given_name": "William", "orcid": "0000-0002-2958-6776", "clpid": "Poole-William" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parametrizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in a cell-free protein expression system. We build on existing Python tools\u2500BioCRNpyler, AutoReduce, and Bioscrape\u2500to create this pipeline. For enzyme-mediated DNA recombination in a cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model; hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parametrization.", "doi": "10.1021/acssynbio.2c00534", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2023-02-17", "series_number": "2", "volume": "12", "issue": "2", "pages": "511-523" }, { "id": "authors:sba98-91065", "collection": "authors", "collection_id": "sba98-91065", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182856000.69", "type": "monograph", "title": "Addressable and adaptable intercellular communication via DNA messaging", "author": [ { "family_name": "Marken", "given_name": "John P.", "orcid": "0000-0001-9696-088X", "clpid": "Marken-John-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains' ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages' dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it in a plasmid conjugation-based communication channel. Our system can bias the transfer of messages to targeted receiver strains by 100-to 1000-fold, and their recipient lists can be dynamically updatedin situto control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.", "doi": "10.1101/2022.11.17.516988", "publication_date": "2022-11-18" }, { "id": "authors:p9rkr-pz990", "collection": "authors", "collection_id": "p9rkr-pz990", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221205-666301600.7", "type": "article", "title": "Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli", "author": [ { "family_name": "Williams", "given_name": "Rory L.", "orcid": "0000-0003-2605-5790", "clpid": "Williams-Rory-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. Here, we show that a strategy of terminal differentiation improves the evolutionary stability of burdensome functions in a general manner by realizing a reproductive and metabolic division of labor. To implement this strategy, we develop a genetic differentiation circuit in Escherichia coli using unidirectional integrase-recombination. With terminal differentiation, differentiated cells uniquely express burdensome functions driven by the orthogonal T7 RNA polymerase, but their capacity to proliferate is limited to prevent the propagation of advantageous loss-of-function mutations that inevitably occur. We demonstrate computationally and experimentally that terminal differentiation increases duration and yield of high-burden expression and that its evolutionary stability can be improved with strategic redundancy. Further, we show this strategy can even be applied to toxic functions. Overall, this study provides an effective, generalizable approach for protecting burdensome engineered functions from evolutionary degradation.", "doi": "10.1038/s41467-022-34361-y", "pmcid": "PMC9649629", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2022-11-10", "volume": "13", "pages": "Art. No. 6822" }, { "id": "authors:pnp9k-akm20", "collection": "authors", "collection_id": "pnp9k-akm20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221219-234102223", "type": "monograph", "title": "Synthesizing Reactive Test Environments for Autonomous Systems: Testing Reach-Avoid Specifications with Multi-Commodity Flows", "author": [ { "family_name": "Badithela", "given_name": "Apurva", "clpid": "Badithela-Apurva" }, { "family_name": "Graebener", "given_name": "Josefine B.", "clpid": "Graebener-Josefine-B" }, { "family_name": "Ubellacker", "given_name": "Wyatt", "orcid": "0000-0002-4732-6185", "clpid": "Ubellacker-Wyatt-L" }, { "family_name": "Mazumdar", "given_name": "Eric V.", "orcid": "0000-0002-1815-269X", "clpid": "Mazumdar-Eric" }, { "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" } ], "abstract": "We study automated test generation for verifying discrete decision-making modules in autonomous systems. We utilize linear temporal logic to encode the requirements on the system under test in the system specification and the behavior that we want to observe during the test is given as the test specification which is unknown to the system. First, we use the specifications and their corresponding non-deterministic B\u00fcchi automata to generate the specification product automaton. Second, a virtual product graph representing the high-level interaction between the system and the test environment is constructed modeling the product automaton encoding the system, the test environment, and specifications. The main result of this paper is an optimization problem, framed as a multi-commodity network flow problem, that solves for constraints on the virtual product graph which can then be projected to the test environment. Therefore, the result of the optimization problem is reactive test synthesis that ensures that the system meets the test specifications along with satisfying the system specifications. This framework is illustrated in simulation on grid world examples, and demonstrated on hardware with the Unitree A1 quadruped, wherein dynamic locomotion behaviors are verified in the context of reactive test environments.", "doi": "10.48550/arXiv.2210.10304", "publisher": "arXiv", "publication_date": "2022-10-19" }, { "id": "authors:0x59b-dhz66", "collection": "authors", "collection_id": "0x59b-dhz66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221219-234021838", "type": "monograph", "title": "Evaluation Metrics for Object Detection for Autonomous Systems", "author": [ { "family_name": "Badithela", "given_name": "Apurva", "clpid": "Badithela-Apurva" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "orcid": "0000-0002-3977-122X", "clpid": "Wongpiromsarn-Tichakorn" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper studies the evaluation of learning-based object detection models in conjunction with model-checking of formal specifications defined on an abstract model of an autonomous system and its environment. In particular, we define two metrics -- \\emph{proposition-labeled} and \\emph{class-labeled} confusion matrices -- for evaluating object detection, and we incorporate these metrics to compute the satisfaction probability of system-level safety requirements. While confusion matrices have been effective for comparative evaluation of classification and object detection models, our framework fills two key gaps. First, we relate the performance of object detection to formal requirements defined over downstream high-level planning tasks. In particular, we provide empirical results that show that the choice of a good object detection algorithm, with respect to formal requirements on the overall system, significantly depends on the downstream planning and control design. Secondly, unlike the traditional confusion matrix, our metrics account for variations in performance with respect to the distance between the ego and the object being detected. We demonstrate this framework on a car-pedestrian example by computing the satisfaction probabilities for safety requirements formalized in Linear Temporal Logic (LTL).", "doi": "10.48550/arXiv.2210.10298", "publisher": "arXiv", "publication_date": "2022-10-19" }, { "id": "authors:4cc39-qh396", "collection": "authors", "collection_id": "4cc39-qh396", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-366884000.3", "type": "monograph", "title": "Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Rodriguez", "given_name": "Makena L.", "clpid": "Rodriguez-Makena-L" }, { "family_name": "Poole", "given_name": "William", "orcid": "0000-0002-2958-6776", "clpid": "Poole-William" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parameterizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in cell-free protein expression system. We build on existing Python tools \u2014 BioCRNpyler, AutoReduce, and Bioscrape \u2014 to create this pipeline. For enzyme-mediated DNA recombination in cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model, hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parameterization.", "doi": "10.1101/2022.10.05.511053", "publication_date": "2022-10-07" }, { "id": "authors:re72y-6h272", "collection": "authors", "collection_id": "re72y-6h272", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221003-756400000.10", "type": "article", "title": "Layered feedback control overcomes performance trade-off in synthetic biomolecular networks", "author": [ { "family_name": "Hu", "given_name": "Chelsea Y.", "orcid": "0000-0002-2211-1778", "clpid": "Hu-Chelsea-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "AbstractLayered feedback is an optimization strategy in feedback control designs widely used in engineering. Control theory suggests that layering multiple feedbacks could overcome the robustness-speed performance trade-off limit. In natural biological networks, genes are often regulated in layers to adapt to environmental perturbations. It is hypothesized layering architecture could also overcome the robustness-speed performance trade-off in genetic networks. In this work, we validate this hypothesis with a synthetic biomolecular network in living E. coli cells. We start with system dynamics analysis using models of various complexities to guide the design of a layered control architecture in living cells. Experimentally, we interrogate system dynamics under three groups of perturbations. We consistently observe that the layered control improves system performance in the robustness-speed domain. This work confirms that layered control could be adopted in synthetic biomolecular networks for performance optimization. It also provides insights into understanding genetic feedback control architectures in nature.", "doi": "10.1038/s41467-022-33058-6", "pmcid": "PMC9474519", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2022-09-14", "volume": "13", "pages": "Art. No. 5393" }, { "id": "authors:c4ba7-6zp34", "collection": "authors", "collection_id": "c4ba7-6zp34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221219-234018464", "type": "monograph", "title": "OUTformation: Distributed Data-Gathering with Feedback under Unknown Environment and Communication Delay Constraints", "author": [ { "family_name": "Han", "given_name": "SooJean", "orcid": "0000-0003-1195-6465", "clpid": "Han-SooJean" }, { "family_name": "Effros", "given_name": "Michelle", "orcid": "0000-0003-3757-0675", "clpid": "Effros-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Towards the informed design of large-scale distributed data-gathering architectures under real-world assumptions such as nonzero communication delays and unknown environment dynamics, this paper considers the effects of allowing feedback communication from the central processor to external sensors. Using simple but representative state-estimation examples, we investigate fundamental tradeoffs between the mean-squared error (MSE) of the central processor's estimate of the environment state, and the total power expenditure per sensor under more conventional architectures without feedback (INformation) versus those with broadcast feedback (OUTformation). The primary advantage of enabling feedback is that each sensor's understanding of the central processor's estimate improves, which enables each sensor to determine when and what parts of its current observations to transmit. We use theory to demonstrate conditions in which OUTformation maintains the same MSE as INformation with less power expended on average, and conditions in which OUTformation obtains less MSE than INformation at additional power cost. These performance tradeoffs are also considered under settings where environments undergo less variation, and sensors implement random backoff times to prevent transmission collisions. Our results are supported via numerical studies, which show that the properties derived in theory still hold even when some of the simplifying assumptions are removed.", "doi": "10.48550/arXiv.2208.06395", "publisher": "arXiv", "publication_date": "2022-08-12" }, { "id": "authors:vzzzx-dqa08", "collection": "authors", "collection_id": "vzzzx-dqa08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220715-744315000", "type": "book_section", "title": "Towards Better Test Coverage: Merging Unit Tests for\u00a0Autonomous Systems", "book_title": "NASA Formal Methods: 14th International Symposium, NFM 2022, Pasadena, CA, USA, May 24\u201327, 2022, Proceedings", "author": [ { "family_name": "Graebener", "given_name": "Josefine B.", "clpid": "Graebener-Josefine-B" }, { "family_name": "Badithela", "given_name": "Apurva", "clpid": "Badithela-Apurva" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Deshmukh", "given_name": "Jyotirmoy V.", "clpid": "Deshmukh-Jyotirmoy-V" }, { "family_name": "Havelund", "given_name": "Klaus", "clpid": "Havelund-Klaus" }, { "family_name": "Perez", "given_name": "Ivan", "clpid": "Perez-Ivan" } ], "abstract": "We present a framework for merging unit tests for autonomous systems. Typically, it is intractable to test an autonomous system for every scenario in its operating environment. The question of whether it is possible to design a single test for multiple requirements of the system motivates this work. First, we formally define three attributes of a test: a test specification that characterizes behaviors observed in a test execution, a test environment, and a test policy. Using the merge operator from contract-based design theory, we provide a formalism to construct a merged test specification from two unit test specifications. Temporal constraints on the merged test specification guarantee that non-trivial satisfaction of both unit test specifications is necessary for a successful merged test execution. We assume that the test environment remains the same across the unit tests and the merged test. Given a test specification and a test environment, we synthesize a test policy filter using a receding horizon approach, and use the test policy filter to guide a search procedure (e.g. Monte-Carlo Tree Search) to find a test policy that is guaranteed to satisfy the test specification. This search procedure finds a test policy that maximizes a pre-defined robustness metric for the test while the filter guarantees a test policy for satisfying the test specification. We prove that our algorithm is sound. Furthermore, the receding horizon approach to synthesizing the filter ensures that our algorithm is scalable. Finally, we show that merging unit tests is impactful for designing efficient test campaigns to achieve similar levels of coverage in fewer test executions. We illustrate our framework on two self-driving examples in a discrete-state setting.", "doi": "10.1007/978-3-031-06773-0_7", "isbn": "9783031067723", "publisher": "Springer", "place_of_publication": "Cham", "publication_date": "2022-05", "pages": "133-155" }, { "id": "authors:1x87p-ed577", "collection": "authors", "collection_id": "1x87p-ed577", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200804-104555959", "type": "article", "title": "BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts", "author": [ { "family_name": "Poole", "given_name": "William", "orcid": "0000-0002-2958-6776", "clpid": "Poole-William" }, { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Shur", "given_name": "Andrey", "orcid": "0000-0001-9372-6713", "clpid": "Shur-Andrey-S" }, { "family_name": "Tuza", "given_name": "Zoltan A.", "orcid": "0000-0003-2896-1527", "clpid": "Tuza-Zoltan-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Biochemical interactions in systems and synthetic biology are often modeled with chemical reaction networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in Python, that compiles high-level design specifications represented using a modular library of biochemical parts, mechanisms, and contexts to CRN implementations. This compilation process offers four advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to be represented succinctly with design choices propagated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later. By using BioCRNpyler, users ranging from expert modelers to novice script-writers can easily build, manage, and explore sophisticated biochemical models using diverse biochemical implementations, environments, and modeling assumptions.", "doi": "10.1371/journal.pcbi.1009987", "pmcid": "PMC9060376", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2022-04-20", "series_number": "4", "volume": "18", "issue": "4", "pages": "Art. No. e1009987" }, { "id": "authors:k02tb-zyr67", "collection": "authors", "collection_id": "k02tb-zyr67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220412-265499000", "type": "monograph", "title": "From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Incer", "given_name": "Inigo", "clpid": "Incer-Inigo" }, { "family_name": "Sangiovanni-Vincentelli", "given_name": "Alberto", "orcid": "0000-0003-1298-8389", "clpid": "Sangiovanni-Vincentelli-Alberto-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We provide a new perspective on using formal methods to model specifications and synthesize implementations for the design of biological circuits. In synthetic biology, design objectives are rarely described formally. We present an assume-guarantee contract framework to describe biological circuit design objectives as formal specifications. In our approach, these formal specifications are implemented by circuits modeled by ordinary differential equations, yielding a design framework that can be used to design complex synthetic biological circuits at scale. We describe our approach using the design of a biological AND gate as a motivating, running example.", "doi": "10.1101/2022.04.08.487709", "publication_date": "2022-04-11" }, { "id": "authors:yc4sr-fb679", "collection": "authors", "collection_id": "yc4sr-fb679", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200909-145940519", "type": "article", "title": "Synthetic mammalian signaling circuits for robust cell population control", "author": [ { "family_name": "Ma", "given_name": "Yitong", "orcid": "0000-0003-4446-7326", "clpid": "Ma-Yitong" }, { "family_name": "Budde", "given_name": "Mark W.", "orcid": "0000-0002-4359-1424", "clpid": "Budde-Mark-W" }, { "family_name": "Mayalu", "given_name": "Micha\u00eblle N.", "orcid": "0000-0002-9678-0157", "clpid": "Mayalu-Micha\u00eblle-N" }, { "family_name": "Zhu", "given_name": "Junqin", "orcid": "0000-0002-8159-6402", "clpid": "Zhu-Junqin" }, { "family_name": "Lu", "given_name": "Andrew C.", "orcid": "0000-0002-7594-6445", "clpid": "Lu-Andrew-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" } ], "abstract": "In multicellular organisms, cells actively sense and control their own population density. Synthetic mammalian quorum-sensing circuits could provide insight into principles of population control and extend cell therapies. However, a key challenge is reducing their inherent sensitivity to \"cheater\" mutations that evade control. Here, we repurposed the plant hormone auxin to enable orthogonal mammalian cell-cell communication and quorum sensing. We designed a paradoxical population control circuit, termed \"Paradaux,\" in which auxin stimulates and inhibits net cell growth at different concentrations. This circuit limited population size over extended timescales of up to 42 days of continuous culture. By contrast, when operating in a non-paradoxical regime, population control became more susceptible to mutational escape. These results establish auxin as a versatile \"private\" communication system and demonstrate that paradoxical circuit architectures can provide robust population control.", "doi": "10.1016/j.cell.2022.01.026", "pmcid": "PMC8995209", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2022-03-17", "series_number": "6", "volume": "185", "issue": "6", "pages": "967-979" }, { "id": "authors:mwtva-41847", "collection": "authors", "collection_id": "mwtva-41847", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140925-085129247", "type": "article", "title": "Synthetic logic circuits using RNA aptamer against T7 RNA polymerase", "author": [ { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Quijano", "given_name": "Juan F.", "orcid": "0000-0002-5803-3935", "clpid": "Quijano-Juan-F" }, { "family_name": "Kim", "given_name": "Jeongwon", "clpid": "Kim-Jeongwon" }, { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. We first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks in vitro. As a step to quickly assess the feasibility of aptamer functions in vivo, we tested the aptamer and its sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. The expression of aptamer in E. coli demonstrated control over GFP expression driven by T7 RNA polymerase, indicating its ability to serve as building blocks for logic circuits and transcriptional cascades. This work elucidates the potential of T7 RNA polymerase aptamer as regulators for synthetic biological circuits and metabolic engineering.", "doi": "10.1002/biot.202000449", "issn": "1860-7314", "publisher": "Wiley", "publication": "Biotechnology Journal", "publication_date": "2022-03", "series_number": "3", "volume": "17", "issue": "3", "pages": "Art. No. 2000449" }, { "id": "authors:8eqsz-zc081", "collection": "authors", "collection_id": "8eqsz-zc081", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220124-747977500", "type": "article", "title": "Robustness guarantees for structured model reduction of\u00a0dynamical systems with applications to biomolecular models", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Model reduction methods usually focus on the error performance analysis; however, in presence of uncertainties, it is important to analyze the robustness properties of the error in model reduction as well. This problem is particularly relevant for engineered biological systems that need to function in a largely unknown and uncertain environment. We give robustness guarantees for structured model reduction of linear and nonlinear dynamical systems under parametric uncertainties. We consider a model reduction problem where the states in the reduced model are a strict subset of the states of the full model, and the dynamics for all of the other states are collapsed to zero (similar to quasi-steady-state approximation). We show two approaches to compute a robustness guarantee metric for any such model reduction\u2014a direct linear analysis method for linear dynamics and a sensitivity analysis based approach that also works for nonlinear dynamics. Using the robustness guarantees with an error metric and an input-output mapping metric, we propose an automated model reduction method to determine the best possible reduced model for a given detailed system model. We apply our method for the (1) design space exploration of a gene expression system that leads to a new mathematical model that accounts for the limited resources in the system and (2) model reduction of a population control circuit in bacterial cells.", "doi": "10.1002/rnc.6013", "issn": "1049-8923", "publisher": "Wiley", "publication": "International Journal of Robust and Nonlinear Control", "publication_date": "2022-01-24" }, { "id": "authors:wdsfr-e5e61", "collection": "authors", "collection_id": "wdsfr-e5e61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220224-200901027", "type": "monograph", "title": "Robust Safe Control Synthesis with Disturbance Observer-Based Control Barrier Functions", "author": [ { "family_name": "Da\u015f", "given_name": "Ersin", "orcid": "0000-0003-1291-3803", "clpid": "Da\u015f-Ersin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In a complex real-time operating environment, external disturbances and uncertainties adversely affect the safety, stability, and performance of dynamical systems. This paper presents a robust stabilizing safety-critical controller synthesis framework with control Lyapunov functions (CLFs) and control barrier functions (CBFs) in the presence of disturbance. A high-gain input observer method is adapted to estimate the time-varying unmodelled dynamics of the CBF with an error bound using the first-order time derivative of the CBF. This approach leads to an easily tunable low order disturbance estimator structure with a design parameter as it utilizes only the CBF constraint. The estimated unknown input and associated error bound are used to ensure robust safety and exponential stability by formulating a CLF-CBF quadratic program. The proposed method is applicable to both relative degree one and higher relative degree CBF constraints. The efficacy of the proposed approach is demonstrated using a numerical simulations of an adaptive cruise control system and a Segway platform with an external disturbance.", "doi": "10.48550/arXiv.2201.05758", "publisher": "arXiv", "publication_date": "2022-01-15" }, { "id": "authors:1e54n-qhj51", "collection": "authors", "collection_id": "1e54n-qhj51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210511-085123358", "type": "book_section", "title": "Time-Optimal Navigation in Uncertain Environments with High-Level Specifications", "book_title": "2021 60th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Rosolia", "given_name": "Ugo", "orcid": "0000-0002-1682-0551", "clpid": "Rosolia-Ugo" }, { "family_name": "Ahmadi", "given_name": "Mohamadreza", "orcid": "0000-0003-1447-3012", "clpid": "Ahmadi-Mohamadreza" }, { "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" } ], "abstract": "Mixed observable Markov decision processes (MOMDPs) are a modeling framework for autonomous systems described by both fully and partially observable states. In this work, we study the problem of synthesizing a control policy for MOMDPs that minimizes the expected time to complete the control task while satisfying syntactically co-safe Linear Temporal Logic (scLTL) specifications. First, we present an exact dynamic programming update to compute the value function. Leveraging this result, we propose a point-based approximation, which allows us to compute a lower bound of the closed-loop probability of satisfying the specifications. The effectiveness of the proposed approach and comparisons with standard strategies are shown on high-fidelity navigation tasks with partially observable static obstacles.", "doi": "10.1109/CDC45484.2021.9683486", "isbn": "978-1-6654-3659-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-12-14", "pages": "4287-4294" }, { "id": "authors:4xqya-s9m89", "collection": "authors", "collection_id": "4xqya-s9m89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220210-721878000", "type": "book_section", "title": "Robustness Guarantees for Structured Model Reduction of Dynamical Systems", "book_title": "2021 60th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Model reduction methods usually focus on the error performance analysis; however, in presence of uncertainties, it is important to analyze the robustness properties of the error in model reduction as well. In this paper, we give robustness guarantees for structured model reduction of linear and nonlinear dynamical systems under parametric uncertainties. In particular, we consider a model reduction where the states in the reduced model are a strict subset of the states of the full model, and the dynamics for all other states are collapsed to zero (similar to quasi-steady state approximation). We show two approaches to compute a robustness metric for any such model reduction \u2014 a direct linear analysis method for linear dynamics and a sensitivity analysis based approach that also works for nonlinear dynamics. We also prove that for linear systems, both methods give equivalent results.", "doi": "10.1109/cdc45484.2021.9683298", "isbn": "978-1-6654-3659-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-12-14", "pages": "6920-6927" }, { "id": "authors:z6t4a-42m57", "collection": "authors", "collection_id": "z6t4a-42m57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220210-721863000", "type": "book_section", "title": "Leveraging Classification Metrics for Quantitative System-Level Analysis with Temporal Logic Specifications", "book_title": "2021 60th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Badithela", "given_name": "Apurva", "clpid": "Badithela-Apurva" }, { "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" } ], "abstract": "In many autonomy applications, performance of perception algorithms is important for effective planning and control. In this paper, we introduce a framework for computing the probability of satisfaction of formal system specifications given a confusion matrix, a statistical average performance measure for multi-class classification. We define the probability of satisfaction of a linear temporal logic formula given a specific initial state of the agent and true state of the environment. Then, we present an algorithm to construct a Markov chain that represents the system behavior under the composition of the perception and control components such that the probability of the temporal logic formula computed over the Markov chain is consistent with the probability that the temporal logic formula is satisfied by our system. We illustrate this approach on a simple example of a car with pedestrian on the sidewalk environment, and compute the probability of satisfaction of safety requirements for varying parameters of the vehicle. We also illustrate how satisfaction probability changes with varied precision and recall derived from the confusion matrix. Based on our results, we identify several opportunities for future work in developing quantitative system-level analysis that incorporates perception models.", "doi": "10.1109/cdc45484.2021.9683611", "isbn": "978-1-6654-3659-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-12-14", "pages": "564-571" }, { "id": "authors:8w47y-2x462", "collection": "authors", "collection_id": "8w47y-2x462", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210929-174530596", "type": "monograph", "title": "How to model DNA replication in stochastic models of synthetic gene circuits (and why)", "author": [ { "family_name": "Clamons", "given_name": "Samuel E.", "orcid": "0000-0002-7993-2278", "clpid": "Clamons-Samuel-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Biocircuit modeling sometimes requires explicit tracking of a self-replicating DNA species. The most obvious, straightforward way to model a replicating DNA is structurally unstable and leads to pathological model behavior. We describe a simple, stable replication mechanism with good model behavior and show how to derive it from a mechanistic model of ColE1 replication.", "doi": "10.1101/2021.09.26.461880", "publisher": "Cold Spring Harbor Laboratory", "publication_date": "2021-09-27" }, { "id": "authors:44ahy-m7y19", "collection": "authors", "collection_id": "44ahy-m7y19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210914-194152756", "type": "monograph", "title": "Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks", "author": [ { "family_name": "Hu", "given_name": "Chelsea Y.", "orcid": "0000-0002-2211-1778", "clpid": "Hu-Chelsea-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Layered feedback is an optimization strategy in feedback control designs widely used in electrical and mechanical engineering. Layered control theory suggests that the performance of controllers is bound by the universal robustness-efficiency tradeoff limit, which could be overcome by layering two or more feedbacks together. In natural biological networks, genes are often regulated with redundancy and layering to adapt to environmental perturbations. Control theory hypothesizes that this layering architecture is also adopted by nature to overcome this performance trade-off. In this work, we validated this property of layered control with a synthetic network in living E. coli cells. We performed system analysis on a node-based design to confirm the tradeoff properties before proceeding to simulations with an effective mechanistic model, which guided us to the best performing design to engineer in cells. Finally, we interrogated its system dynamics experimentally with eight sets of perturbations on chemical signals, nutrient abundance, and growth temperature. For all cases, we consistently observed that the layered control overcomes the robustness-efficiency trade-off limit. This work experimentally confirmed that layered control could be adopted in synthetic biomolecular networks as a performance optimization strategy. It also provided insights in understanding genetic feedback control architectures in nature.", "doi": "10.1101/2021.09.12.459953", "publication_date": "2021-09-14" }, { "id": "authors:gcqax-8a355", "collection": "authors", "collection_id": "gcqax-8a355", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220224-200812106", "type": "monograph", "title": "Risk-Averse Decision Making Under Uncertainty", "author": [ { "family_name": "Ahmadi", "given_name": "Mohamadreza", "orcid": "0000-0003-1447-3012", "clpid": "Ahmadi-Mohamadreza" }, { "family_name": "Rosolia", "given_name": "Ugo", "orcid": "0000-0002-1682-0551", "clpid": "Rosolia-Ugo" }, { "family_name": "Ingham", "given_name": "Michel D.", "orcid": "0000-0001-5893-543X", "clpid": "Ingham-Michel-D" }, { "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" } ], "abstract": "A large class of decision making under uncertainty problems can be described via Markov decision processes (MDPs) or partially observable MDPs (POMDPs), with application to artificial intelligence and operations research, among others. Traditionally, policy synthesis techniques are proposed such that a total expected cost or reward is minimized or maximized. However, optimality in the total expected cost sense is only reasonable if system behavior in the large number of runs is of interest, which has limited the use of such policies in practical mission-critical scenarios, wherein large deviations from the expected behavior may lead to mission failure. In this paper, we consider the problem of designing policies for MDPs and POMDPs with objectives and constraints in terms of dynamic coherent risk measures, which we refer to as the constrained risk-averse problem. For MDPs, we reformulate the problem into a infsup problem via the Lagrangian framework and propose an optimization-based method to synthesize Markovian policies. For MDPs, we demonstrate that the formulated optimization problems are in the form of difference convex programs (DCPs) and can be solved by the disciplined convex-concave programming (DCCP) framework. We show that these results generalize linear programs for constrained MDPs with total discounted expected costs and constraints. For POMDPs, we show that, if the coherent risk measures can be defined as a Markov risk transition mapping, an infinite-dimensional optimization can be used to design Markovian belief-based policies. For stochastic finite-state controllers (FSCs), we show that the latter optimization simplifies to a (finite-dimensional) DCP and can be solved by the DCCP framework. We incorporate these DCPs in a policy iteration algorithm to design risk-averse FSCs for POMDPs.", "doi": "10.48550/arXiv.2109.04082", "publisher": "arXiv", "publication_date": "2021-09-09" }, { "id": "authors:x7d2y-k8b85", "collection": "authors", "collection_id": "x7d2y-k8b85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210311-095327802", "type": "article", "title": "Data-driven network models for genetic circuits from time-series data with incomplete measurements", "author": [ { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Yuan", "given_name": "Ye", "orcid": "0000-0001-8669-7950", "clpid": "Yuan-Ye" }, { "family_name": "Gon\u00e7alves", "given_name": "Jorge", "orcid": "0000-0002-5228-6165", "clpid": "Gon\u00e7alves-Jorge-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Synthetic gene networks are frequently conceptualized and visualized as static graphs. This view of biological programming stands in stark contrast to the transient nature of biomolecular interaction, which is frequently enacted by labile molecules that are often unmeasured. Thus, the network topology and dynamics of synthetic gene networks can be difficult to verify in vivo or in vitro, due to the presence of unmeasured biological states. Here we introduce the dynamical structure function as a new mesoscopic, data-driven class of models to describe gene networks with incomplete measurements of state dynamics. We develop a network reconstruction algorithm and a code base for reconstructing the dynamical structure function from data, to enable discovery and visualization of graphical relationships in a genetic circuit diagram as time-dependent functions rather than static, unknown weights. We prove a theorem, showing that dynamical structure functions can provide a data-driven estimate of the size of crosstalk fluctuations from an idealized model. We illustrate this idea with numerical examples. Finally, we show how data-driven estimation of dynamical structure functions can explain failure modes in two experimentally implemented genetic circuits, a previously reported in vitro genetic circuit and a new E. coli-based transcriptional event detector.", "doi": "10.1098/rsif.2021.0413", "issn": "1742-5689", "publisher": "Royal Society", "publication": "Journal of the Royal Society Interface", "publication_date": "2021-09", "series_number": "182", "volume": "18", "issue": "182", "pages": "Art. No. 20210413" }, { "id": "authors:jdq62-d5n95", "collection": "authors", "collection_id": "jdq62-d5n95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211122-221808622", "type": "article", "title": "Rapid Characterization of Genetic Parts with Cell-free Systems", "author": [ { "family_name": "McManus", "given_name": "John B.", "clpid": "McManus-John-B" }, { "family_name": "Bernhards", "given_name": "Casey B.", "clpid": "Bernhards-Casey-B" }, { "family_name": "Sharpes", "given_name": "Caitlin E.", "clpid": "Sharpes-Caitlin-E" }, { "family_name": "Garcia", "given_name": "David C.", "orcid": "0000-0002-6029-7964", "clpid": "Garcia-David-C" }, { "family_name": "Cole", "given_name": "Stephanie D.", "clpid": "Cole-Stephanie-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Emanuel", "given_name": "Peter A.", "orcid": "0000-0001-5475-7349", "clpid": "Emanuel-Peter-A" }, { "family_name": "Lux", "given_name": "Matthew W.", "orcid": "0000-0002-2773-742X", "clpid": "Lux-Matthew-W" } ], "abstract": "Characterizing and cataloging genetic parts are critical to the design of useful genetic circuits. Having well-characterized parts allows for the fine-tuning of genetic circuits, such that their function results in predictable outcomes. With the growth of synthetic biology as a field, there has been an explosion of genetic circuits that have been implemented in microbes to execute functions pertaining to sensing, metabolic alteration, and cellular computing. Here, we show a rapid and cost-effective method for characterizing genetic parts. Our method utilizes cell-free lysate, prepared in-house as a medium to evaluate parts via the expression of a reporter protein. Template DNA is prepared by PCR amplification using inexpensive primers to add variant parts to the reporter gene, and the template is added to the reaction as linear DNA without cloning. Parts that can be added in this way include promoters, operators, ribosome binding sites, insulators, and terminators. This approach, combined with the incorporation of an acoustic liquid handler and 384-well plates, allows the user to carry out high-throughput evaluations of genetic parts in a single day. By comparison, cell-based screening approaches require time-consuming cloning and have longer testing times due to overnight culture and culture density normalization steps. Further, working in cell-free lysate allows the user to exact tighter control over the expression conditions through the addition of exogenous components and DNA at precise concentrations. Results obtained from cell-free screening can be used directly in applications of cell-free systems or, in some cases, as a way to predict function in whole cells.", "doi": "10.3791/62816", "issn": "1940-087X", "publisher": "JoVE", "publication": "Journal of Visualized Experiments", "publication_date": "2021-08-31", "volume": "174", "pages": "Art. No. e62816" }, { "id": "authors:xjphx-6tc71", "collection": "authors", "collection_id": "xjphx-6tc71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220224-200808616", "type": "monograph", "title": "Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems", "author": [ { "family_name": "Badithela", "given_name": "Apurva", "clpid": "Badithela-Apurva" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we investigate formal test-case generation for high-level mission objectives, specifically reachability, of autonomous systems. We use Kripke structures to represent the high-level decision-making of the agent under test and the abstraction of the test environment. First, we define the notion of a test specification, focusing on a fragment of linear temporal logic represented by sequence temporal logic formulas. Second, we formulate the problem of test graph synthesis to find a test configuration for which the agent must satisfy the test specification to satisfy its mission objectives. We an algorithm, based on network flows, for synthesizing a test graph by restricting transitions, represented by edge deletions, on the original graph induced by the Kripke structures. The algorithm synthesizes the test graph iteratively using an integer linear program. We prove completeness for our algorithm, and we show that the edge deletions in each iteration maintain feasibility of the integer linear program in the subsequent iteration. We formalize the notion of a minimally constrained test graph in terms of maximum flow, and prove the synthesized test graph to be minimally constrained. We demonstrate our algorithm on a simple graph and on gridworlds.", "doi": "10.48550/arXiv.2108.05911", "publisher": "arXiv", "publication_date": "2021-08-12" }, { "id": "authors:2ybkp-8xr65", "collection": "authors", "collection_id": "2ybkp-8xr65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220503-50866100", "type": "book_section", "title": "Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis", "book_title": "2021 European Control Conference (ECC)", "author": [ { "family_name": "Mayalu", "given_name": "Micha\u00eblle N.", "orcid": "0000-0002-9678-0157", "clpid": "Mayalu-Micha\u00eblle-N" }, { "family_name": "Sarma", "given_name": "Anish", "orcid": "0000-0003-1261-0589", "clpid": "Sarma-Anish-A" }, { "family_name": "Xiao", "given_name": "Fangzhou", "orcid": "0000-0002-5001-5644", "clpid": "Xiao-Fangzhou" }, { "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" } ], "abstract": "Intercommunication of the microbiome-gut-brain axis occurs through various signaling pathways including the vagus nerve, immune system, endocrine/paracrine, and bacteria-derived metabolites. But how these pathways integrate to influence cognition remains undefined. In this paper, we create a systems level mathematical framework comprised of interconnected organ-level dynamical subsystems to increase conceptual understanding of how these subsystems contribute to cognitive performance. With this framework we propose that control of hippocampal long-term potentiation (hypothesized to correlate with cognitive performance) is influenced by interorgan signaling with diet as the external control input. Specifically, diet can influence synaptic strength (LTP) homeostatic conditions necessary for learning. The proposed model provides new qualitative information about the functional relationship between diet and output cognitive performance. The results can give insight for optimization of cognitive performance via diet in experimental animal models.", "doi": "10.23919/ecc54610.2021.9655216", "isbn": "978-9-4638-4236-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-07", "pages": "312-318" }, { "id": "authors:g0sev-vq056", "collection": "authors", "collection_id": "g0sev-vq056", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191029-132616005", "type": "book_section", "title": "Contracts of Reactivity", "book_title": "2021 European Control Conference (ECC)", "author": [ { "family_name": "Phan-Minh", "given_name": "Tung", "clpid": "Phan-Minh-Tung" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a theory of contracts that is centered around reacting to failures and explore it from a general assume-guarantee perspective as well as from a concrete context of automated synthesis from linear temporal logic (LTL) specifications, all of which are compatible with a contract metatheory introduced by Benveniste et al. We also provide an automated procedure for synthesizing reactive assume-guarantee contracts and implementations that capture ideas such as optimality and robustness based on assume-guarantee lattices computed from antitone Galois connection fixpoints. Lastly, we provide an example of a reactive GR(1) contract and a simulation of its implementation.", "doi": "10.23919/ECC54610.2021.9654932", "isbn": "978-9-4638-4236-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-06-29", "pages": "2611-2618" }, { "id": "authors:vwgw2-b5q48", "collection": "authors", "collection_id": "vwgw2-b5q48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210511-085543440", "type": "book_section", "title": "Limits of Probabilistic Safety Guarantees when Considering Human Uncertainty", "book_title": "2021 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Cheng", "given_name": "Richard", "orcid": "0000-0001-8301-9169", "clpid": "Cheng-Richard" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" } ], "abstract": "When autonomous robots interact with humans, such as during autonomous driving, explicit safety guarantees are crucial in order to avoid potentially life-threatening accidents. Many data-driven methods have explored learning probabilistic bounds over human agents' trajectories (i.e. confidence tubes that contain trajectories with probability \u03b4), which can then be used to guarantee safety with probability 1\u2212 \u03b4. However, almost all existing works consider \u03b4 \u2265 0.001. The purpose of this paper is to argue that (1) in safety-critical applications, it is necessary to provide safety guarantees with \u03b4 < 10\u207b\u2078, and (2) current learning-based methods are illequipped to compute accurate confidence bounds at such low \u03b4. Using human driving data (from the highD dataset), as well as synthetically generated data, we show that current uncertainty models use inaccurate distributional assumptions to describe human behavior and/or require infeasible amounts of data to accurately learn confidence bounds for \u03b4 \u2264 10\u207b\u2078. These two issues result in unreliable confidence bounds, which can have dangerous implications if deployed on safety-critical systems.", "doi": "10.1109/ICRA48506.2021.9561843", "isbn": "978-1-7281-9077-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-06", "pages": "3182-3189" }, { "id": "authors:4t67z-nxz42", "collection": "authors", "collection_id": "4t67z-nxz42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210513-144618998", "type": "article", "title": "Guiding Ethical Principles in Engineering Biology Research", "author": [ { "family_name": "Mackelprang", "given_name": "Rebecca", "clpid": "Mackelprang-Rebecca" }, { "family_name": "Aurand", "given_name": "Emily R.", "orcid": "0000-0003-4092-8551", "clpid": "Aurand-Emliy-R" }, { "family_name": "Bovenberg", "given_name": "Roel A. L.", "clpid": "Bovenberg-Roel-A-L" }, { "family_name": "Brink", "given_name": "Kathryn R.", "clpid": "Brink-Kathryn-R" }, { "family_name": "Charo", "given_name": "R. Alta", "clpid": "Charo-R-Alta" }, { "family_name": "Delborne", "given_name": "Jason A.", "clpid": "Delborne-James-A" }, { "family_name": "Diggans", "given_name": "James", "clpid": "Diggans-James" }, { "family_name": "Ellington", "given_name": "Andrew D.", "orcid": "0000-0001-6246-5338", "clpid": "Ellington-Andrew-D" }, { "family_name": "Fortman", "given_name": "Jeffrey L. \"Clem\"", "clpid": "Fortman-Jeffrey-L-Clem" }, { "family_name": "Isaacs", "given_name": "Farren J.", "orcid": "0000-0001-8615-8236", "clpid": "Isaacs-Farren-J" }, { "family_name": "Medford", "given_name": "June I.", "orcid": "0000-0002-0599-4863", "clpid": "Medford-June-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-Vincent" }, { "family_name": "Palmer", "given_name": "Megan J.", "clpid": "Palmer-Megan-J" }, { "family_name": "Zoloth", "given_name": "Laurie", "clpid": "Zoloth-Laurie" }, { "family_name": "Friedman", "given_name": "Douglas C.", "orcid": "0000-0001-7234-4943", "clpid": "Friedman-Douglas-C" } ], "abstract": "Engineering biology is being applied toward solving or mitigating some of the greatest challenges facing society. As with many other rapidly advancing technologies, the development of these powerful tools must be considered in the context of ethical uses for personal, societal, and/or environmental advancement. Researchers have a responsibility to consider the diverse outcomes that may result from the knowledge and innovation they contribute to the field. Together, we developed a Statement of Ethics in Engineering Biology Research to guide researchers as they incorporate the consideration of long-term ethical implications of their work into every phase of the research lifecycle. Herein, we present and contextualize this Statement of Ethics and its six guiding principles. Our goal is to facilitate ongoing reflection and collaboration among technical researchers, social scientists, policy makers, and other stakeholders to support best outcomes in engineering biology innovation and development.", "doi": "10.1021/acssynbio.1c00129", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2021-05-21", "series_number": "5", "volume": "10", "issue": "5", "pages": "907-910" }, { "id": "authors:e0ys3-46y11", "collection": "authors", "collection_id": "e0ys3-46y11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210120-165231602", "type": "book_section", "title": "Constrained Risk-Averse Markov Decision Processes", "author": [ { "family_name": "Ahmadi", "given_name": "Mohamadreza", "orcid": "0000-0003-1447-3012", "clpid": "Ahmadi-Mohamadreza" }, { "family_name": "Rosolia", "given_name": "Ugo", "orcid": "0000-0002-1682-0551", "clpid": "Rosolia-Ugo" }, { "family_name": "Ingham", "given_name": "Michel D.", "orcid": "0000-0001-5893-543X", "clpid": "Ingham-Michel-D" }, { "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" } ], "abstract": "We consider the problem of designing policies for Markov decision processes (MDPs) with dynamic coherent risk objectives and constraints. We begin by formulating the problem in a Lagrangian framework. Under the assumption that the risk objectives and constraints can be represented by a Markov risk transition mapping, we propose an optimization-based method to synthesize Markovian policies that lower-bound the constrained risk-averse problem. We demonstrate that the formulated optimization problems are in the form of difference convex programs (DCPs) and can be solved by the disciplined convex-concave programming (DCCP) framework. We show that these results generalize linear programs for constrained MDPs with total discounted expected costs and constraints. Finally, we illustrate the effectiveness of the proposed method with numerical experiments on a rover navigation problem involving conditional-value-at-risk (CVaR) and entropic-value-at-risk (EVaR) coherent risk measures.", "doi": "10.48550/arXiv.2012.02423", "publisher": "Association for the Advancement of Artificial Intelligence", "publication_date": "2021-05-18" }, { "id": "authors:6nghw-ett12", "collection": "authors", "collection_id": "6nghw-ett12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210506-075939102", "type": "monograph", "title": "A Method for Cost-Effective and Rapid Characterization of Genetic Parts", "author": [ { "family_name": "McManus", "given_name": "John B.", "clpid": "McManus-John-B" }, { "family_name": "Bernhards", "given_name": "Casey B.", "clpid": "Bernhards-Casey-B" }, { "family_name": "Sharpes", "given_name": "Caitlin E.", "clpid": "Sharpes-Caitlin-E" }, { "family_name": "Garcia", "given_name": "David C.", "clpid": "Garcia-David-C" }, { "family_name": "Cole", "given_name": "Stephanie D.", "clpid": "Cole-Stephanie-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Emanuel", "given_name": "Peter A.", "orcid": "0000-0001-5475-7349", "clpid": "Emanuel-Peter-A" }, { "family_name": "Lux", "given_name": "Matthew W.", "orcid": "0000-0002-2773-742X", "clpid": "Lux-Matthew-W" } ], "abstract": "Characterizing and cataloging genetic parts are critical to the design of useful genetic circuits. Having well-characterized parts allows for the fine-tuning of genetic circuits, such that their function results in predictable outcomes. With the growth of synthetic biology as a field, there has been an explosion of genetic circuits that have been implemented in microbes to execute functions pertaining to sensing, metabolic alteration, and cellular computing. Here, we show a cost-effective and rapid method for characterizing genetic parts. Our method utilizes cell-free lysate, prepared in-house, as a medium to evaluate parts via the expression of a reporter protein. Template DNA is prepared by PCR-amplification using inexpensive primers to add variant parts to the reporter gene, and the template is added to the reaction as linear DNA without cloning. Parts that can be added in this way include promoters, operators, ribosome binding sites, insulators, and terminators. This approach, combined with the incorporation of an acoustic liquid handler and 384-well plates, allows the user to carry out high-throughput evaluations of genetic parts in a single day. By comparison, cell-based screening approaches require time-consuming cloning and have longer testing times due to overnight culture and culture density normalization steps. Further, working in cell-free lysate allows the user to exact tighter control over the expression conditions through the addition of exogenous components, or by titrating DNA concentrations rather than relying on limited plasmid copy numbers. Because this method retains a cell-like environment, the function of the genetic part will typically mimic its function in whole cells.", "doi": "10.1101/2021.04.30.440836", "publication_date": "2021-05-01" }, { "id": "authors:rpyy3-e3323", "collection": "authors", "collection_id": "rpyy3-e3323", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201111-093413972", "type": "book_section", "title": "Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations", "book_title": "2021 American Control Conference (ACC)", "author": [ { "family_name": "Ren", "given_name": "Xinying", "clpid": "Ren-Xinying" }, { "family_name": "Cuba Samaniego", "given_name": "Christian", "orcid": "0000-0003-1858-2259", "clpid": "Cuba-Samaniego-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-Elisa" } ], "abstract": "Molecular feedback control circuits can improve robustness of gene expression at single cell-level. This achievement can be offset by requirements of rapid protein expression, that may induce cellular stress, known as burden, that reduces colony growth. To begin to address this challenge we take inspiration by 'division-of-labor' in heterogeneous cell populations: we propose to combine bistable switches and quorum sensing systems to coordinate gene expression at population-level. We show that bistable switches in individual cells operating in parallel yield an ultrasensitive response, while cells maintain heterogeneous levels of gene expression. Within a feedback loop, these switches can achieve robust reference tracking and adaptation to disturbances at the population-level. We also demonstrate that molecular sequestration enables tunable hysteresis in individual switches, making it possible to obtain a wide range of stable population-level expressions.", "doi": "10.23919/ACC50511.2021.9482836", "isbn": "978-1-6654-4197-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2021-05", "pages": "652-659" }, { "id": "authors:xgt8b-ptj74", "collection": "authors", "collection_id": "xgt8b-ptj74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210511-092411322", "type": "monograph", "title": "Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture", "author": [ { "family_name": "Graebener", "given_name": "Josefine B.", "clpid": "Graebener-Josefine-B" }, { "family_name": "Phan-Minh", "given_name": "Tung", "clpid": "Phan-Minh-Tung" }, { "family_name": "Yan", "given_name": "Jiaqi", "clpid": "Yan-Jiaqi" }, { "family_name": "Zhao", "given_name": "Qiming", "clpid": "Zhao-Qiming" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Increased complexity in cyber-physical systems calls for modular system design methodologies that guarantee correct and reliable behavior, both in normal operations and in the presence of failures. This paper aims to extend the contract-based design approach using a directive-response architecture to enable reactivity to failure scenarios. The architecture is demonstrated on a modular automated valet parking (AVP) system. The contracts for the different components in the AVP system are explicitly defined, implemented, and validated against a Python implementation.", "doi": "10.48550/arXiv.2103.12919", "publisher": "arXiv", "publication_date": "2021-03-24" }, { "id": "authors:bygwm-0wk74", "collection": "authors", "collection_id": "bygwm-0wk74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200806-153554109", "type": "article", "title": "A MATLAB toolbox for modeling genetic circuits in cell-free systems", "author": [ { "family_name": "Singhal", "given_name": "Vipul", "orcid": "0000-0003-1670-1824", "clpid": "Singhal-Vipul" }, { "family_name": "Tuza", "given_name": "Zoltan A.", "orcid": "0000-0003-2896-1527", "clpid": "Tuza-Zoltan-A" }, { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We introduce a MATLAB-based simulation toolbox, called txtlsim, for an Escherichia coli-based Transcription\u2013Translation (TX\u2013TL) system. This toolbox accounts for several cell-free-related phenomena, such as resource loading, consumption and degradation, and in doing so, models the dynamics of TX\u2013TL reactions for the entire duration of solution phase batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protein-expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.", "doi": "10.1093/synbio/ysab007", "pmcid": "PMC8102020", "issn": "2397-7000", "publisher": "Oxford University Press", "publication": "Synthetic Biology", "publication_date": "2021-02-05", "series_number": "1", "volume": "6", "issue": "1", "pages": "Art. No. ysab007" }, { "id": "authors:2j3nq-z6s90", "collection": "authors", "collection_id": "2j3nq-z6s90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201221-102922403", "type": "monograph", "title": "Analysis of Circuits for Dosage Control in Microbial Populations", "author": [ { "family_name": "Walton", "given_name": "Sophie J.", "orcid": "0000-0003-1320-1525", "clpid": "Walton-Sophie-J" }, { "family_name": "Clamons", "given_name": "Samuel E.", "orcid": "0000-0002-7993-2278", "clpid": "Clamons-Samuel-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Designing genetic circuits to control the behaviors of microbial populations is an ongoing challenge in synthetic biology. Here we analyze circuits which implement dosage control by controlling levels of a global signal in a microbial population in face of varying cell density, growth rate, and environmental dilution. We utilize the Lux quorum sensing system to implement dosage control circuits, and we analyze the dynamics of circuits using both simplified analytical analysis and in silico simulations. We demonstrate that strong negative feedback through inhibiting LuxI synthase expression along with AiiA degradase activity results in circuits with fast response times and robustness to cell density and dilution rate. We find that degradase activity yields robustness to variations in population density for large population sizes, while negative feedback to synthase production decreases sensitivity to dilution rates.", "doi": "10.1101/2020.12.18.423556", "publication_date": "2020-12-20" }, { "id": "authors:dag9k-gv551", "collection": "authors", "collection_id": "dag9k-gv551", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200527-124225030", "type": "book_section", "title": "Formal Test Synthesis for Safety-Critical Autonomous Systems based on Control Barrier Functions", "book_title": "2020 59th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Akella", "given_name": "Prithvi", "clpid": "Akella-Prithvi" }, { "family_name": "Ahmadi", "given_name": "Mohamadreza", "orcid": "0000-0003-1447-3012", "clpid": "Ahmadi-Mohamadreza" }, { "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" } ], "abstract": "The prolific rise in autonomous systems has led to questions regarding their safe instantiation in real-world scenarios. Failures in safety-critical contexts such as humanrobot interactions or even autonomous driving can ultimately lead to loss of life. In this context, this paper aims to provide a method by which one can algorithmically test and evaluate an autonomous system. Given a black-box autonomous system with some operational specifications, we construct a minimax problem based on control barrier functions to generate a family of test parameters designed to optimally evaluate whether the system can satisfy the specifications. To illustrate our results, we utilize the Robotarium as a case study for an autonomous system that claims to satisfy waypoint navigation and obstacle avoidance simultaneously. We demonstrate that the proposed test synthesis framework systematically finds those sequences of events (tests) that identify points of system failure.", "doi": "10.1109/CDC42340.2020.9303776", "isbn": "9781728174471", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2020-12", "pages": "790-795" }, { "id": "authors:rhcjt-68j20", "collection": "authors", "collection_id": "rhcjt-68j20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210120-165255737", "type": "monograph", "title": "Rules of the Road: Towards Safety and Liveness Guarantees for Autonomous Vehicles", "author": [ { "family_name": "Cai", "given_name": "Karena X.", "clpid": "Cai-Karena-X" }, { "family_name": "Phan-Minh", "given_name": "Tung", "clpid": "Phan-Minh-Tung" }, { "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" } ], "abstract": "The ability to guarantee safety and progress for all vehicles is vital to the success of the autonomous vehicle industry. We present a framework for the distributed control of autonomous vehicles that is safe and guarantees progress for all agents. In this paper, we first introduce a new game paradigm which we term the quasi-simultaneous discrete-time game. We then define an Agent Protocol agents must use to make decisions in this quasi-simultaneous discrete-time game setting. According to the protocol, agents first select an intended action and then each agent determines whether it can take its intended action or not, given its proposed intention and the intentions of nearby agents. The protocol so defined will ensure safety under all traffic conditions and liveness for all agents under \"sparse\" traffic conditions. These guarantees, however, are predicated on the premise that all agents are operating with the aforementioned protocol. We provide proofs of correctness of the protocol and validate our results in simulation.", "doi": "10.48550/arXiv.2011.14148", "publisher": "arXiv", "publication_date": "2020-11-28" }, { "id": "authors:btga8-n4d36", "collection": "authors", "collection_id": "btga8-n4d36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201207-130405486", "type": "monograph", "title": "A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We derive phenomenological models of gene expression from a mechanistic description of chemical reactions using an automated model reduction method. Using this method, we get analytical descriptions and computational performance guarantees to compare the reduced dynamics with the full models. We develop a new two-state model with the dynamics of the available free ribosomes in the system and the protein concentration. We show that this new two-state model captures the detailed mass-action kinetics of the chemical reaction network under various biologically plausible conditions on model parameters. On comparing the performance of this model with the commonly used mRNA transcript-protein dynamical model for gene expression, we analytically show that the free ribosome and protein model has superior error and robustness performance.", "doi": "10.1101/2020.11.25.399287", "publication_date": "2020-11-26" }, { "id": "authors:e7x24-c2p56", "collection": "authors", "collection_id": "e7x24-c2p56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201111-100159834", "type": "monograph", "title": "Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions", "author": [ { "family_name": "Merk", "given_name": "Liana N.", "clpid": "Merk-L-N" }, { "family_name": "Shur", "given_name": "Andrey S.", "clpid": "Shur-Andrey-S" }, { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Green", "given_name": "Leopold N.", "orcid": "0000-0001-5479-6970", "clpid": "Green-L-N" } ], "abstract": "The mammalian gut contains trillions of microbes that interact with host cells and monitor changes in the environment. Opportunistic pathogens exploit environmental conditions to stimulate their growth and virulence, leading to a resurgence of chronic disorders such as inflammatory bowel disease (IBD). Current therapies are effective in less than 30% of patients due to the lack of adherence to prescription schedules and overall, off-target effects. Smart microbial therapeutics can be engineered to colonize the gut, providing in situ surveillance and conditional disease modulation. However, many current engineered microbes can only respond to single gut environmental factors, limiting their effectiveness. In this work, we implement the previously characterized split activator AND logic gate in the probiotic E. coli strain Nissle 1917. Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, IPTG. We report 4-6 fold induction with minimal leak when both signals are present. We model the dynamics of the AND gate using chemical reaction networks, and by tuning parameters in silico, we identified perturbations that affect our circuit's selectivity. We anticipate that our results will prove useful for designing living therapeutics for spatial targeting and signal processing in complex environments.", "doi": "10.1101/2020.11.10.377085", "publication_date": "2020-11-11" }, { "id": "authors:48cq5-sqj38", "collection": "authors", "collection_id": "48cq5-sqj38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210120-165252232", "type": "monograph", "title": "Reactive motion planning with probabilistic safety guarantees", "author": [ { "family_name": "Chen", "given_name": "Yuxiao", "orcid": "0000-0001-5276-7156", "clpid": "Chen-Yuxiao" }, { "family_name": "Rosolia", "given_name": "Ugo", "orcid": "0000-0002-1682-0551", "clpid": "Rosolia-Ugo" }, { "family_name": "Fan", "given_name": "Chuchu", "clpid": "Fan-Chuchu" }, { "family_name": "Ames", "given_name": "Aaron D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Motion planning in environments with multiple agents is critical to many important autonomous applications such as autonomous vehicles and assistive robots. This paper considers the problem of motion planning, where the controlled agent shares the environment with multiple uncontrolled agents. First, a predictive model of the uncontrolled agents is trained to predict all possible trajectories within a short horizon based on the scenario. The prediction is then fed to a motion planning module based on model predictive control. We proved generalization bound for the predictive model using three different methods, post-bloating, support vector machine (SVM), and conformal analysis, all capable of generating stochastic guarantees of the correctness of the predictor. The proposed approach is demonstrated in simulation in a scenario emulating autonomous highway driving.", "doi": "10.48550/arXiv.2011.03590", "publisher": "arXiv", "publication_date": "2020-11-06" }, { "id": "authors:e3dmx-5p177", "collection": "authors", "collection_id": "e3dmx-5p177", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200401-104547968", "type": "article", "title": "Guidelines for designing the antithetic feedback motif", "author": [ { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Leong", "given_name": "Yoke Peng", "orcid": "0000-0001-8560-8856", "clpid": "Leong-Yoke-Peng" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Integral feedback control is commonly used in mechanical and electrical systems to achieve zero steady-state error following an external disturbance. Equivalently, in biological systems, a property known as robust perfect adaptation guarantees robustness to environmental perturbations and return to the pre-disturbance state. Previously, Briat et al. proposed a biomolecular design for integral feedback control (robust perfect adaptation) called the antithetic feedback motif. The antithetic feedback controller uses the sequestration binding reaction of two biochemical species to record the integral of the error between the current and the desired output of the network it controls. The antithetic feedback motif has been successfully built using synthetic components in vivo in Escherichia coli and Saccharomyces cerevisiae cells. However, these previous synthetic implementations of antithetic feedback have not produced perfect integral feedback control due to the degradation and dilution of the two controller species. Furthermore, previous theoretical results have cautioned that integral control can only be achieved under stability conditions that not all antithetic feedback motifs necessarily fulfill. In this paper, we study how to design antithetic feedback motifs that simultaneously achieve good stability and small steady-state error properties, even as the controller species are degraded and diluted. We provide simple tuning guidelines to achieve flexible and practical synthetic biological implementations of antithetic feedback control. We use several tools and metrics from control theory to design antithetic feedback networks, paving the path for the systematic design of synthetic biological controllers.", "doi": "10.1088/1478-3975/ab8454", "issn": "1478-3967", "publisher": "IOP", "publication": "Physical Biology", "publication_date": "2020-09", "series_number": "5", "volume": "17", "issue": "5", "pages": "Art. No. 055002" }, { "id": "authors:3vtb4-p9h09", "collection": "authors", "collection_id": "3vtb4-p9h09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190918-100800913", "type": "article", "title": "Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop", "author": [ { "family_name": "Patel", "given_name": "Abhilash", "orcid": "0000-0001-6319-658X", "clpid": "Patel-Abhilash" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" } ], "abstract": "Robustness to temperature variation is an important specification in biomolecular circuit design. While the cancellation of parametric temperature dependencies has been shown to improve the temperature robustness of the period in a synthetic oscillator design, the performance of other biomolecular circuit designs in different temperature conditions is relatively unclear. Using a combination of experimental measurements and mathematical models, we assessed the temperature robustness of two biomolecular circuit motifs\u2014a negative feedback loop and a feedforward loop. We found that the measured responses of both the circuits changed with temperature, both in the amplitude and in the transient response. We also found that, in addition to the cancellation of parametric temperature dependencies, certain parameter regimes could facilitate the temperature robustness of the negative feedback loop, although at a performance cost. We discuss these parameter regimes in the context of the measured data for the negative feedback loop. These results should help develop a framework for assessing and designing temperature robustness in biomolecular circuits.", "doi": "10.1021/acssynbio.0c00023", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2020-07-17", "series_number": "7", "volume": "9", "issue": "7", "pages": "1581-1590" }, { "id": "authors:jz8ya-psz53", "collection": "authors", "collection_id": "jz8ya-psz53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200108-154918519", "type": "book_section", "title": "Learning Pose Estimation for UAV Autonomous Navigation and Landing Using Visual-Inertial Sensor Data", "book_title": "2020 American Control Conference (ACC)", "author": [ { "family_name": "Baldini", "given_name": "Francesca", "clpid": "Baldini-F" }, { "family_name": "Anandkumar", "given_name": "Animashree", "clpid": "Anandkumar-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this work, we propose a robust network-in-the-loop control system for autonomous navigation and landing of an Unmanned-Aerial-Vehicle (UAV). To estimate the UAV's absolute pose, we develop a deep neural network (DNN) architecture for visual-inertial odometry, which provides a robust alternative to traditional methods. We first evaluate the accuracy of the estimation by comparing the prediction of our model to traditional visual-inertial approaches on the publicly available EuRoC MAV dataset. The results indicate a clear improvement in the accuracy of the pose estimation up to 25% over the baseline. Finally, we integrate the data-driven estimator in the closed-loop flight control system of Airsim, a simulator available as a plugin for Unreal Engine, and we provide simulation results for autonomous navigation and landing.", "doi": "10.23919/ACC45564.2020.9147400", "isbn": "9781538682661", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2020-07", "pages": "2961-2966" }, { "id": "authors:9kqpk-fqn13", "collection": "authors", "collection_id": "9kqpk-fqn13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200109-092433424", "type": "book_section", "title": "Risk-Averse Planning Under Uncertainty", "book_title": "2020 American Control Conference (ACC)", "author": [ { "family_name": "Ahmadi", "given_name": "Mohamadreza", "orcid": "0000-0003-1447-3012", "clpid": "Ahmadi-Mohamadreza" }, { "family_name": "Ono", "given_name": "Masahiro", "clpid": "Ono-Masahiro" }, { "family_name": "Ingham", "given_name": "Michel D.", "clpid": "Ingham-M-D" }, { "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" } ], "abstract": "We consider the problem of designing policies for partially observable Markov decision processes (POMDPs) with dynamic coherent risk objectives. Synthesizing risk-averse optimal policies for POMDPs requires infinite memory and thus undecidable. To overcome this difficulty, we propose a method based on bounded policy iteration for designing stochastic but finite state (memory) controllers, which takes advantage of standard convex optimization methods. Given a memory budget and optimality criterion, the proposed method modifies the stochastic finite state controller leading to sub-optimal solutions with lower coherent risk.", "doi": "10.23919/ACC45564.2020.9147792", "isbn": "9781538682661", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2020-07", "pages": "3305-3312" }, { "id": "authors:rhwh9-tfa81", "collection": "authors", "collection_id": "rhwh9-tfa81", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200730-143943975", "type": "book_section", "title": "Invariant Sets for Integrators and Quadrotor Obstacle Avoidance", "book_title": "2020 American Control Conference (ACC)", "author": [ { "family_name": "Doeser", "given_name": "Ludvig", "clpid": "Doeser-Ludvig" }, { "family_name": "Nilsson", "given_name": "Petter", "orcid": "0000-0001-8748-6936", "clpid": "Nilsson-Petter" }, { "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" } ], "abstract": "Ensuring safety through set invariance has proven a useful method in a variety of applications in robotics and control. However, finding analytical expressions for maximal invariant sets, so as to maximize the operational freedom of the system without compromising safety, is notoriously difficult for high-dimensional systems with input constraints. Here we present a generic method for characterizing invariant sets of nth-order integrator systems, based on analyzing roots of univariate polynomials. Additionally, we obtain analytical expressions for the orders n \u2264 4. Using differential flatness we subsequently leverage the results for the n = 4 case to the problem of obstacle avoidance for quadrotor UAVs. The resulting controller has a light computational footprint that showcases the power of finding analytical expressions for control-invariant sets.", "doi": "10.23919/acc45564.2020.9147872", "isbn": "9781538682661", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2020-07", "pages": "3814-3821" }, { "id": "authors:a835q-xhq33", "collection": "authors", "collection_id": "a835q-xhq33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200109-092058249", "type": "book_section", "title": "Intermittent Connectivity for Exploration in Communication-Constrained Multi-Agent Systems", "author": [ { "family_name": "Klaesson", "given_name": "Filip", "clpid": "Klaesson-Filip" }, { "family_name": "Nilsson", "given_name": "Petter", "orcid": "0000-0001-8748-6936", "clpid": "Nilsson-Petter" }, { "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" } ], "abstract": "Motivated by exploration of communication-constrained underground environments using robot teams, we study the problem of planning for intermittent connectivity in multi-agent systems. We propose a novel concept of information-consistency to handle situations where the plan is not initially known by all agents, and suggest an integer linear program for synthesizing information-consistent plans that also achieve auxiliary goals. Furthermore, inspired by network flow problems we propose a novel way to pose connectivity constraints that scales much better than previous methods. In the second part of the paper we apply these results in an exploration setting, and propose a clustering method that separates a large exploration problem into smaller problems that can be solved independently. We demonstrate how the resulting exploration algorithm is able to coordinate a team of ten agents to explore a large environment.", "doi": "10.1109/ICCPS48487.2020.00031", "publisher": "IEEE", "publication_date": "2020-04" }, { "id": "authors:p9w5c-8nc27", "collection": "authors", "collection_id": "p9w5c-8nc27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200327-083242603", "type": "monograph", "title": "Layered Feedback Control Improves Robust Functionality across Heterogeneous Cell Populations", "author": [ { "family_name": "Ren", "given_name": "Xinying", "clpid": "Ren-Xinying" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Realizing homeostatic control of metabolites or proteins is one of the key goals of synthetic circuits. However, if control is only implemented internally in individual cells, cell-cell heterogeneity may break the homeostasis on populationlevel since cells do not contribute equally to the production or regulation. New control structures are needed to achieve robust functionality in heterogeneous cell populations. Quorum sensing(QS) serves as a collective mechanism by releasing and sensing small and diffusible signaling molecules for group decision-making. We propose a layered feedback control structure that includes a global controller using quorum sensing and a local controller via internal signal-receptor systems. We demonstrate with modeling and simulation that the global controller drives contributing cells to compensate for disturbances while the local controller governs the fail-mode performance in non-contributing cells. The layered controller can tolerate a higher portion of non-contributing cells or longer generations of mutant cells while maintaining metabolites or proteins level within a small error range, compared with only internal feedback control. We further discuss the potential of such layered structures in robust control of cell population size,population fraction and other population-dependent functions.", "doi": "10.1101/2020.03.24.006528", "publication_date": "2020-03-25" }, { "id": "authors:f818a-vce67", "collection": "authors", "collection_id": "f818a-vce67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200220-154511531", "type": "monograph", "title": "Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a Python-based software package to automatically obtain phenomenological models of input-controlled synthetic biological circuits from descriptive models. From the parts and mechanism description of a synthetic biological circuit, it is easy to obtain a chemical reaction model of the circuit under the assumptions of mass-action kinetics using various existing tools. However, using these models to guide design decisions during an experiment is difficult due to a large number of reaction rate parameters and species in the model. Hence, phenomenological models are often developed that describe the effective relationships among the circuit inputs, outputs, and only the key states and parameters. In this paper, we present an algorithm to obtain these phenomenological models in an automated manner using a Python package for circuits with inputs that control the desired outputs. This model reduction approach combines the common assumptions of time-scale separation, conservation laws, and species' abundance to obtain the reduced models that can be used for design of synthetic biological circuits. We consider an example of a simple gene expression circuit and another example of a layered genetic feedback control circuit to demonstrate the use of the model reduction procedure.", "doi": "10.1101/2020.02.15.950840", "publication_date": "2020-02-20" }, { "id": "authors:c1whe-kj281", "collection": "authors", "collection_id": "c1whe-kj281", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200220-083645813", "type": "monograph", "title": "A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology", "author": [ { "family_name": "Marken", "given_name": "John P.", "orcid": "0000-0001-9696-088X", "clpid": "Marken-J-P" }, { "family_name": "Xiao", "given_name": "Fangzhou", "orcid": "0000-0002-5001-5644", "clpid": "Xiao-Fangzhou" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system's structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator.", "doi": "10.1101/2020.02.18.953620", "publication_date": "2020-02-17" }, { "id": "authors:d5gv5-t0h14", "collection": "authors", "collection_id": "d5gv5-t0h14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200128-150452496", "type": "monograph", "title": "Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli", "author": [ { "family_name": "Mayalu", "given_name": "Micha\u00eblle N.", "orcid": "0000-0002-9678-0157", "clpid": "Mayalu-M-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We have developed a mathematical framework to analyze the cooperative control of cell population homeostasis via paradoxical signaling in synthetic contexts. Paradoxical signaling functions through quorum sensing (where cells produce and release a chemical signal as a function of cell density). Precisely, the same quorum sensing signal provides both positive (proliferation) and negative (death) feedback in different signal concentration regimes. As a consequence, the relationship between intercellular quorum sensing signal concentration and net growth rate (cell proliferation minus death rates) can be non-monotonic. This relationship is a condition for robustness to certain cell mutational overgrowths and allows for increased stability in the presence of environmental perturbations. Here, we explore stability and robustness of a conceptualized synthetic circuit. Furthermore, we asses possible design principles that could exist among a subset of paradoxical circuit implementations. This analysis sparks the development a bio-molecular control theory to identify ideal underlying characteristics for paradoxical signaling control systems.", "doi": "10.1101/2020.01.27.921734", "publication_date": "2020-01-28" }, { "id": "authors:waevr-jpt88", "collection": "authors", "collection_id": "waevr-jpt88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200402-143200982", "type": "monograph", "title": "Counter-example Guided Learning of Bounds on Environment Behavior", "author": [ { "family_name": "Chen", "given_name": "Yuxiao", "orcid": "0000-0001-5276-7156", "clpid": "Chen-Yuxiao" }, { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Phan-Minh", "given_name": "Tung", "clpid": "Phan-Minh-Tung" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "There is a growing interest in building autonomous systems that interact with complex environments. The difficulty associated with obtaining an accurate model for such environments poses a challenge to the task of assessing and guaranteeing the system's performance. We present a data-driven solution that allows for a system to be evaluated for specification conformance without an accurate model of the environment. Our approach involves learning a conservative reactive bound of the environment's behavior using data and specification of the system's desired behavior. First, the approach begins by learning a conservative reactive bound on the environment's actions that captures its possible behaviors with high probability. This bound is then used to assist verification, and if the verification fails under this bound, the algorithm returns counter-examples to show how failure occurs and then uses these to refine the bound. We demonstrate the applicability of the approach through two case-studies: i) verifying controllers for a toy multi-robot system, and ii) verifying an instance of human-robot interaction during a lane-change maneuver given real-world human driving data.", "doi": "10.48550/arXiv.2001.07233", "publisher": "arXiv", "publication_date": "2020-01-20" }, { "id": "authors:dqnwk-2x543", "collection": "authors", "collection_id": "dqnwk-2x543", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200109-092918089", "type": "book_section", "title": "Towards Assume-Guarantee Profiles for Autonomous Vehicles", "book_title": "2019 IEEE 58th Conference on Decision and Control (CDC)", "author": [ { "family_name": "Phan-Minh", "given_name": "Tung", "clpid": "Phan-Minh-Tung" }, { "family_name": "Cai", "given_name": "Karena X.", "clpid": "Cai-Karena-X" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Rules or specifications for autonomous vehicles are currently formulated on a case-by-case basis, and put together in a rather ad-hoc fashion. As a step towards eliminating this practice, we propose a systematic procedure for generating a set of supervisory specifications for self-driving cars that are 1) associated with a distributed assume-guarantee structure and 2) characterizable by the notion of consistency and completeness. Besides helping autonomous vehicles make better decisions on the road, the assume-guarantee contract structure also helps address the notion of blame when undesirable events occur. We give several game-theoretic examples to demonstrate applicability of our framework.", "doi": "10.1109/CDC40024.2019.9030068", "isbn": "978-1-7281-1398-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-12", "pages": "2788-2795" }, { "id": "authors:drhjw-a6n92", "collection": "authors", "collection_id": "drhjw-a6n92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191202-140340910", "type": "monograph", "title": "Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA", "author": [ { "family_name": "Larsson", "given_name": "Elin M.", "orcid": "0000-0003-1341-5937", "clpid": "Larsson-E-M" }, { "family_name": "McManus", "given_name": "John B.", "clpid": "McManus-John-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Environmental applications of synthetic biology such as water remediation require engineered strains to function robustly in a fluctuating and potentially hostile environment. The construction of synthetic biofilm formation circuits could potentially alleviate this issue by promoting cell survival. Towards this end, we construct a xylose-inducible system for the expression of the functional amyloids CsgA and TasA in the soil bacterium Bacillus megaterium. We find that although both amyloids are expressed, only TasA is successfully exported from the cells. Furthermore, expression of CsgA results in a significant growth penalty for the cells while expression of TasA does not. Finally, we show that TasA expression conveys a small but detectable increase in cells' adhesion to nickel beads. These results suggest that TasA is a promising candidate for future work on synthetic biofilm formation in B. megaterium.", "doi": "10.1101/858266", "publication_date": "2019-11-29" }, { "id": "authors:mcspr-cxm03", "collection": "authors", "collection_id": "mcspr-cxm03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171102-092833279", "type": "book_section", "title": "Parallelizing Synthesis from Temporal Logic Specifications by Identifying Equicontrollable States", "book_title": "Robotics Research: The 18th International Symposium ISRR", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Amato", "given_name": "Nancy M.", "clpid": "Amato-N-M" }, { "family_name": "Hager", "given_name": "Greg", "clpid": "Hager-G" }, { "family_name": "Thomas", "given_name": "Shawna", "clpid": "Thomas-S" }, { "family_name": "Torres-Torriti", "given_name": "Miguel", "clpid": "Torres-Torriti-M" } ], "abstract": "For the synthesis of correct-by-construction control policies from temporal logic specifications the scalability of the synthesis algorithms is often a bottleneck. In this paper, we parallelize synthesis from specifications in the GR(1) fragment of linear temporal logic by introducing a hierarchical procedure that allows decoupling of the fixpoint computations. The state space is partitioned into equicontrollable sets using solutions to parametrized games that arise from decomposing the original GR(1) game into smaller reachability-persistence games. Following the partitioning, another synthesis problem is formulated for composing the strategies from the decomposed reachability games. The formulation guarantees that composing the synthesized controllers ensures satisfaction of the given GR(1) property. Experiments with robot planning problems demonstrate good performance of the approach.", "doi": "10.1007/978-3-030-28619-4_57", "isbn": "978-3-030-28618-7", "publisher": "Springer", "place_of_publication": "Cham", "publication_date": "2019-11-28", "pages": "827-842" }, { "id": "authors:2x9e7-s7y33", "collection": "authors", "collection_id": "2x9e7-s7y33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190422-091140360", "type": "article", "title": "A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression", "author": [ { "family_name": "McManus", "given_name": "John B.", "clpid": "McManus-John-B" }, { "family_name": "Lux", "given_name": "Matthew W.", "clpid": "Lux-Matthew-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Emanuel", "given_name": "Peter A.", "orcid": "0000-0001-5475-7349", "clpid": "Emanuel-Peter-A" } ], "abstract": "The T7 bacteriophage RNA polymerase (T7 RNAP) serves as a model for understanding RNA synthesis, as a tool for protein expression, and as an actuator for synthetic gene circuit design in bacterial cells and cell-free extract. T7 RNAP is an attractive tool for orthogonal protein expression in bacteria owing to its compact single subunit structure and orthogonal promoter specificity. Understanding the mechanisms underlying T7 RNAP regulation is important to the design of engineered T7-based transcription factors, which can be used in gene circuit design. To explore regulatory mechanisms for T7 RNAP-driven expression, we developed a rapid and cost-effective method to characterize engineered T7-based transcription factors using cell-free protein synthesis and an acoustic liquid handler. Using this method, we investigated the effects of the tetracycline operator's proximity to the T7 promoter on the regulation of T7 RNAP-driven expression. Our results reveal a mechanism for regulation that functions by interfering with the transition of T7 RNAP from initiation to elongation and validates the use of the method described here to engineer future T7-based transcription factors.", "doi": "10.1016/j.abb.2019.07.010", "issn": "0003-9861", "publisher": "Elsevier", "publication": "Archives of Biochemistry and Biophysics", "publication_date": "2019-10-15", "volume": "674", "pages": "Art. No. 108045" }, { "id": "authors:8grfs-rnn49", "collection": "authors", "collection_id": "8grfs-rnn49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190731-095458774", "type": "monograph", "title": "Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking", "author": [ { "family_name": "Clamons", "given_name": "Samuel", "orcid": "0000-0002-7993-2278", "clpid": "Clamons-Samuel-E" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Synthetic transcriptional networks built from CRISPR-based repressors (CRISPRi) rely on shared use of a core dCas9 protein. In E. coli, CRISPRi cannot sup- port more than about a dozen simultaneous gRNAs before the fold repression of any individual gRNA drops below 10x. We show with a simple model based on previous characterization of competition in CRISPRi that activation by CRISPR-based activators (CRISPRa) is much less sensitive to dCas9 bottle- necking than CRISPRi. We predict that E. coli should be able to support dozens to hundreds of CRISPRa gRNAs at > 10-fold activation.", "doi": "10.1101/719278", "publication_date": "2019-07-30" }, { "id": "authors:ky3xs-87k68", "collection": "authors", "collection_id": "ky3xs-87k68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190708-153642582", "type": "article", "title": "Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks", "author": [ { "family_name": "Olsman", "given_name": "Noah", "orcid": "0000-0002-4351-3880", "clpid": "Olsman-N" }, { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Xiao", "given_name": "Fangzhou", "orcid": "0000-0002-5001-5644", "clpid": "Xiao-Fangzhou" }, { "family_name": "Leong", "given_name": "Yoke Peng", "orcid": "0000-0001-8560-8856", "clpid": "Leong-Yoke-Peng" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "abstract": "Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism called antithetic integral feedback, which can be implemented using the binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of antithetic integral feedback and contribute to a more general theory of biological control systems.", "doi": "10.1016/j.cels.2019.06.001", "issn": "2405-4712", "publisher": "Elsevier", "publication": "Cell Systems", "publication_date": "2019-07-24", "series_number": "1", "volume": "9", "issue": "1", "pages": "49-63" }, { "id": "authors:9es63-xhk04", "collection": "authors", "collection_id": "9es63-xhk04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190426-090024789", "type": "book_section", "title": "Robust Estimation Framework with Semantic Measurements", "book_title": "2019 American Control Conference (ACC)", "author": [ { "family_name": "Cai", "given_name": "Karena X.", "clpid": "Cai-Karena-X" }, { "family_name": "Harvard", "given_name": "Alexei", "clpid": "Harvard-A" }, { "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" } ], "abstract": "Conventional simultaneous localization and mapping (SLAM) algorithms rely on geometric measurements and require loop-closure detections to correct for drift accumulated over a vehicle trajectory. Semantic measurements can add measurement redundancy and provide an alternative form of loop closure. We propose two different estimation algorithms that incorporate semantic measurements provided by vision-based object classifiers. An a priori map of regions where the objects can be detected is assumed. The first estimation framework is posed as a maximum-likelihood problem, where the likelihood function for semantic measurements is derived from the confusion matrices of the object classifiers. The second estimation framework is comprised of two parts: 1) a continuous-state estimation formulation that includes semantic measurements as a form of state constraints and 2) a discrete-state estimation formulation used to compute the certainty of object detection measurements using a Hidden Markov Model (HMM). The advantages of incorporating semantic measurements in these frameworks are demonstrated in numerical simulations. In particular, the proposed estimation algorithms improve upon the robustness and accuracy of conventional SLAM algorithms.", "doi": "10.23919/ACC.2019.8814793", "isbn": "978-1-5386-7926-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-07", "pages": "3809-3816" }, { "id": "authors:2bnkm-7vf48", "collection": "authors", "collection_id": "2bnkm-7vf48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190905-153443641", "type": "book_section", "title": "Transforming Data Across Environments Despite Structural Non-Identifiability", "book_title": "2019 American Control Conference (ACC)", "author": [ { "family_name": "Singhal", "given_name": "Vipul", "clpid": "Singhal-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The phenomenon of parameter (structural) non-identifiability can pose significant challenges to the use of parametrized dynamical models. We demonstrate that, for the case of models being used to transform data across environments, it is possible to derive conditions under which the presence of structural non-identifiability does not hinder our modeling objective. We also show that when the non-identifiability has a certain structural feature called (thin) covariation, these conditions are violated, and the transformation methodology must be modified. We demonstrate these results on the problem of correcting batch effects in cell extracts, which are used as rapid prototyping platforms in synthetic biology.", "isbn": "978-1-5386-7926-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-07", "pages": "5639-5646" }, { "id": "authors:ptvj6-bm918", "collection": "authors", "collection_id": "ptvj6-bm918", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-124409997", "type": "monograph", "title": "Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability", "author": [ { "family_name": "Singhal", "given_name": "Vipul", "clpid": "Singhal-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The bottom up design of genetic circuits to control cellular behavior is one of the central objectives within Synthetic Biology. Performing design iterations on these circuits in vivo is often a time consuming process, which has led to E. coli cell extracts to be used as simplified circuit prototyping environments. Cell extracts, however, display large batch-to-batch variability in gene expression. In this paper, we develop the theoretical groundwork for a model based calibration methodology for correcting this variability. We also look at the interaction of this methodology with the phenomenon of parameter (structural) non-identifiability, which occurs when the parameter identification inverse problem has multiple solutions. In particular, we show that under certain consistency conditions on the sets of output-indistinguishable parameters, data variability reduction can still be performed, and when the parameter sets have a certain structural feature called covariation, our methodology may be modified in a particular way to still achieve the desired variability reduction.", "publisher": "Caltech Library", "publication_date": "2019-07" }, { "id": "authors:b9r4t-mh539", "collection": "authors", "collection_id": "b9r4t-mh539", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190905-152940342", "type": "book_section", "title": "Risk-aware motion planning for automated vehicle among human-driven cars", "book_title": "2019 American Control Conference (ACC)", "author": [ { "family_name": "Ge", "given_name": "Jin I.", "orcid": "0000-0001-6429-9337", "clpid": "Ge-Jin-I" }, { "family_name": "Sch\u00fcrmann", "given_name": "Bastian", "clpid": "Sch\u00fcrmann-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Althoff", "given_name": "Matthias", "clpid": "Althoff-M" } ], "abstract": "We consider the maneuver planning problem for automated vehicles when they share the road with human-driven cars and interact with each other using a finite set of maneuvers. Each maneuver is calculated considering input constraints, actuator disturbances and sensor noise, so that we can use a maneuver automaton to perform higher-level planning that is robust against lower-level effects. In order to model the behavior of human-driven cars in response to the intent of the automated vehicle, we use control improvisation to build a probabilistic model. To accommodate for potential mismatches between the learned human model and human driving behaviors, we use a conditional value-at-risk objective function to obtain the optimal policy for the automated vehicle. We demonstrate through simulations that our motion planning framework consisting of an interactive human driving model and risk-aware motion planning strategy makes it possible to adapt to different traffic conditions and confidence levels.", "isbn": "978-1-5386-7926-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-07", "pages": "3987-3993" }, { "id": "authors:evm0n-ds358", "collection": "authors", "collection_id": "evm0n-ds358", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190905-144348506", "type": "book_section", "title": "A modal interface contract theory for guarded input/output automata with an application in traffic system design", "book_title": "2019 American Control Conference (ACC)", "author": [ { "family_name": "Phan-Minh", "given_name": "Tung", "clpid": "Phan-Minh-Tung" }, { "family_name": "Guo", "given_name": "Steve", "clpid": "Guo-Steve" }, { "family_name": "Sch\u00fcrmann", "given_name": "Bastian", "clpid": "Sch\u00fcrmann-B" }, { "family_name": "Althoff", "given_name": "Matthias", "clpid": "Althoff-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "As a direct contribution to recent efforts of bringing formal design-by-contract methods to hybrid systems, we introduce a variant of modal interface contract theory based on input/output automata with guarded transitions. We present an algebra of operators for interface composition, contract composition, contract conjunction, contract refinement and some theorems to demonstrate that our contract object has reasonably universal semantics. As an application, we use our framework to aid the design of a networked control system of traffic.", "isbn": "978-1-5386-7926-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-07", "pages": "1704-1711" }, { "id": "authors:st9ft-4kk15", "collection": "authors", "collection_id": "st9ft-4kk15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-125317403", "type": "article", "title": "Analysis of primitive genetic interactions for the design of a genetic signal differentiator", "author": [ { "family_name": "Halter", "given_name": "Wolfgang", "orcid": "0000-0001-9902-5782", "clpid": "Halter-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Allg\u00f6wer", "given_name": "Frank", "clpid": "Allg\u00f6wer-F" } ], "abstract": "We study the dynamic and static input\u2013output behavior of several primitive genetic interactions and their effect on the performance of a genetic signal differentiator. In a simplified design, several requirements for the linearity and time-scales of processes like transcription, translation and competitive promoter binding were introduced. By experimentally probing simple genetic constructs in a cell-free experimental environment and fitting semi-mechanistic models to these data, we show that some of these requirements can be verified, while others are only met with reservations in certain operational regimes. Analyzing the linearized model of the resulting genetic network, we conclude that it approximates a differentiator with relative degree one. Taking also the discovered nonlinearities into account and using a describing function approach, we further determine the particular frequency and amplitude ranges where the genetic differentiator can be expected to behave as such.", "doi": "10.1093/synbio/ysz015", "issn": "2397-7000", "publisher": "Oxford University Press", "publication": "Synthetic Biology", "publication_date": "2019-06-27", "series_number": "1", "volume": "4", "issue": "1", "pages": "Art. No. ysz015" }, { "id": "authors:xtt51-tpg86", "collection": "authors", "collection_id": "xtt51-tpg86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190604-143031841", "type": "monograph", "title": "Bacterial Controller Aided Wound Healing: A Case Study in Dynamical Population Controller Design", "author": [ { "family_name": "Green", "given_name": "Leopold N.", "orcid": "0000-0001-5479-6970", "clpid": "Green-L-N" }, { "family_name": "Hu", "given_name": "Chelsea Y.", "orcid": "0000-0002-2211-1778", "clpid": "Hu-Chelsea-Y" }, { "family_name": "Ren", "given_name": "Xinying Y.", "clpid": "Ren-Xinying-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Wound healing is a complicated biological process consisting of many types of cellular dynamics and functions regulated by chemical and molecular signals. Recent advances in synthetic biology have made it possible to predictably design and build closed-loop controllers that can function appropriately alongside biological species. In this paper we develop a simple dynamical population model mimicking the sequential relay-like dynamics of cellular populations involved in the wound healing process. Our model consists of four nodes and five signals whose parameters we can tune to simulate various chronic healing conditions. We also develop a set of regulator functions based on type-1 incoherent feed forward loops (IFFL) that can sense the change from acute healing to incomplete chronic wounds, improving the system in a timely manner. Both the wound healing and type-1 IFFL controller architectures are compatible with available synthetic biology experimental tools for potential applications.", "doi": "10.1101/659714", "publication_date": "2019-06-04" }, { "id": "authors:jkcy4-68505", "collection": "authors", "collection_id": "jkcy4-68505", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526570", "type": "book_section", "title": "Cooperation Enhances Robustness of Coexistence in Spatially Structured Consortia", "book_title": "2019 18th European Control Conference (ECC)", "author": [ { "family_name": "Ren", "given_name": "Xinying", "clpid": "Ren-Xinying" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Designing synthetic microbial consortia is an emerging area in synthetic biology and a major goal is to realize stable and robust coexistence of multiple species. Cooperation and competition are fundamental intra/interspecies interactions that shape population level behaviors, yet it is not well-understood how these interactions affect the stability and robustness of coexistence. In this paper, we show that communities with cooperative interactions are more robust to population disturbance, e.g., depletion by antibiotics, by forming intermixed spatial patterns. Meanwhile, competition leads to population spatial heterogeneity and more fragile coexistence in communities. Using reaction-diffusion and nonlocal PDE models and simulations of a two-species E. coli consortium, we demonstrate that cooperation is more beneficial than competition in maintaining coexistence in spatially structured consortia, but not in well-mixed environments. This also suggests a tradeoff between constructing heterogeneous communities with localized functions and maintaining robust coexistence. The results provide general strategies for engineering spatially structured consortia by designing interspecies interactions and suggest the importance of cooperation for biodiversity in microbial community.", "doi": "10.23919/ECC.2019.8796069", "isbn": "978-3-907144-00-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-06", "pages": "2651-2656" }, { "id": "authors:3fjyz-v0n76", "collection": "authors", "collection_id": "3fjyz-v0n76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190822-160825121", "type": "book_section", "title": "Model of Paradoxical Signaling Regulated T-Cell Population Control for Design of Synthetic Circuits", "book_title": "2019 18th European Control Conference (ECC)", "author": [ { "family_name": "Mayalu", "given_name": "Micha\u00eblle N.", "orcid": "0000-0002-9678-0157", "clpid": "Mayalu-M-N" }, { "family_name": "Mehta", "given_name": "Harman", "clpid": "Mehta-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Paradoxical signaling occurs when the same signaling molecule can trigger antagonistic cell functions. For example, T-Cells secret cytokine IL-2 which promotes T-Cell proliferation and also affects cell death. It has been shown that cells with this signaling capability have bi-stable population dynamics. Cells can achieve identical levels of population homeostasis for initial cell concentrations within the region of attraction. These capabilities are desirable in the context of synthetic population control circuits designed for application in therapeutic treatment of various diseases. It thus becomes important to understand the dependence of the cell system on the intracellular paradoxical components and to develop accurate models to provide insight into optimal design characteristics. Here, we create a model that integrates three IL-2 driven intracellular mechanisms that trigger 1) T-cell proliferation 2) T-cell apoptosis and 3) IL-2 production. Using this model, we are able to explore the internal mechanisms necessary for paradoxical signaling in T-Cells. It was shown that the intracellular mechanisms considered were sufficient to produce population dynamic characteristics of paradoxical signaling consistent with published systems level models and data. Furthermore, analysis of parameters revealed dependency of population bistability on the production and activation of the specific intracellular proteins considered.", "doi": "10.23919/ECC.2019.8795764", "isbn": "978-3-907144-00-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2019-06", "pages": "2152-2158" }, { "id": "authors:s4jjh-qwf08", "collection": "authors", "collection_id": "s4jjh-qwf08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190528-093001677", "type": "monograph", "title": "Design of a genetic layered feedback controller in synthetic biological circuitry", "author": [ { "family_name": "Hu", "given_name": "Chelsea Y.", "orcid": "0000-0002-2211-1778", "clpid": "Hu-Chelsea-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Feedback control is the key to achieve robust performances for many engineered systems. However, its application in biological contexts is still largely unexplored. In this work, we designed, analyzed and simulated a layered controller functioning at both molecular and populational levels. First, we used a minimal model of three states to represent a system where state A activates state B; state R is a by-product of state B that acts as a negative feedback regulating both state A, B, and sequentially R. We call the feedback applied to state B a cis feedback and the one applied to state A a trans feedback. Through stability analysis via linearization at equilibrium and sensitivity analysis at transient state, we found that the cis feedback attenuates disturbances better but recovers slower; the trans feedback recovers faster but has more dramatic responses to fluctuations; the layered feedback demonstrates both advantageous traits of the two single layers. Then we designed two versions of synthetic genetic circuits to implement the layered controller in living cells. One version with an sRNA as regulator R, the other with a transcription factor protein as the regulator R. The analysis and dynamical simulation of the models confirmed the analytical results from the minimal model. At the same time, we found that the protein regulated feedback controls have faster recovery speed but the RNA version has a stronger disturbance attenuation effect.", "doi": "10.1101/647057", "publication_date": "2019-05-24" }, { "id": "authors:d7326-k9d39", "collection": "authors", "collection_id": "d7326-k9d39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190517-100226134", "type": "monograph", "title": "An automated model reduction tool to guide the design and analysis of synthetic biological circuits", "author": [ { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present an automated model reduction algorithm that uses quasi-steady state approximation to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure robust performance of the reduced model in the presence of parametric uncertainties. We develop the theory for this model reduction algorithm and present the implementation of the algorithm that can be used to perform model reduction of given SBML models. To demonstrate the utility of this algorithm, we consider the design of a synthetic biological circuit to control the population density and composition of a consortium consisting of two different cell strains. We show how the model reduction algorithm can be used to guide the design and analysis of this circuit.", "doi": "10.1101/640276", "publication_date": "2019-05-17" }, { "id": "authors:0s3f2-3dh59", "collection": "authors", "collection_id": "0s3f2-3dh59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-092300001", "type": "monograph", "title": "Control of density and composition in an engineered two-member bacterial community", "author": [ { "family_name": "McCardell", "given_name": "Reed D.", "clpid": "McCardell-R-D" }, { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "As studies continue to demonstrate how our health is related to the status of our various commensal microbiomes, synthetic biologists are developing tools and approaches to control these microbiomes and stabilize healthy states or remediate unhealthy ones. Building on previous work to control bacterial communities, we have constructed a synthetic two-member bacterial consortium engineered to reach population density and composition steady states set by inducer inputs. We detail a screening strategy to search functional parameter space in this high-complexity genetic circuit as well as initial testing of a functional two-member circuit.\n\nWe demonstrate non-independent changes in total population density and composition steady states with a limited set of varying inducer concentrations. After a dilution to perturb the system from its steady state, density and composition steady states are not regained. Modeling and simulation suggest a need for increased degradation of intercellular signals to improve circuit performance. Future experiments will implement increased signal degradation and investigate the robustness of control of each characteristic to perturbations from steady states.", "doi": "10.1101/632174", "publication_date": "2019-05-09" }, { "id": "authors:g25sc-rrr18", "collection": "authors", "collection_id": "g25sc-rrr18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190422-091140053", "type": "monograph", "title": "Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli", "author": [ { "family_name": "Williams", "given_name": "Rory L.", "orcid": "0000-0003-2605-5790", "clpid": "Williams-Rory-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically unnecessary for cellular survival and burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. To improve the evolutionary stability of engineered functions in a general manner, we developed an integrase-recombination-based differentiation gene circuit in Escherichia coli. In this system, differentiated cells uniquely carry out burdensome or toxic engineered functions but have limited capacity to grow (terminal differentiation), preventing the propagation of selectively advantageous loss of function mutations that inevitably arise. To experimentally implement terminal differentiation, we co-opted the R6K plasmid system, using differentiation to simultaneously activate T7 RNAP-driven expression of arbitrary engineered functions, and inactivate expression of \u03c0 protein (an essential factor for R6K plasmid replication), thereby allowing limitation of differentiated cell growth through antibiotic selection. We experimentally demonstrate terminal differentiation increases both duration and magnitude of high-burden T7 RNAP-driven expression, and that its evolutionary stability can be further improved with strategic redundancy. Using burdensome overexpression of a fluorescent protein as a model engineered function, our terminal differentiation circuit results in a ~2.8-fold (single-cassette) and ~4.2-fold (two-cassette) increase of total fluorescent protein produced compared to high-burden naive expression in which all cells inducibly express T7 RNAP. Finally, we demonstrate that differentiation can enable the expression of even toxic functions, a feat not achieved to our knowledge by any other strategy for addressing long-term evolutionary stability. Overall, this study provides an effective generalizable strategy for protecting engineered functions from evolutionary degradation.", "doi": "10.1101/614529", "publication_date": "2019-04-21" }, { "id": "authors:yks7t-y7b17", "collection": "authors", "collection_id": "yks7t-y7b17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190402-080939441", "type": "monograph", "title": "Quantitative characterization of random partitioning in the evolution of plasmid-encoded traits", "author": [ { "family_name": "Halleran", "given_name": "Andrew D.", "orcid": "0000-0001-8720-1451", "clpid": "Halleran-A-D" }, { "family_name": "Flores-Bautista", "given_name": "Emanuel", "clpid": "Flores-Bautista-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Plasmids are found across bacteria, archaea, and eukaryotes and play an important role in evolution. Plasmids exist at different copy numbers, the number of copies of the plasmid per cell, ranging from a single plasmid per cell to hundreds of plasmids per cell. This feature of a copy number greater than one can lead to a population of plasmids within a single cell that are not identical clones of one another, but rather have individual mutations that make a given plasmid unique. During cell division, this population of plasmids is partitioned into the two daughter cells, resulting in a random distribution of different plasmid variants in each daughter. In this study, we use stochastic simulations to investigate how random plasmid partitioning compares to a perfect partitioning model. Our simulation results demonstrate that random plasmid partitioning accelerates mutant allele fixation when the allele is beneficial and the selection is in an additive or recessive regime where increasing the copy number of the beneficial allele results in additional benefit for the host. This effect does not depend on the size of the benefit conferred or the mutation rate, but is magnified by increasing plasmid copy number.", "doi": "10.1101/594879", "publication_date": "2019-03-31" }, { "id": "authors:hmep9-tfs13", "collection": "authors", "collection_id": "hmep9-tfs13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190328-093304845", "type": "monograph", "title": "Addressable, \"Packet-Based\" Intercellular Communication through Plasmid Conjugation", "author": [ { "family_name": "Marken", "given_name": "John P.", "orcid": "0000-0001-9696-088X", "clpid": "Marken-J-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We develop a system for implementing \"packet-based\" intercellular communication in an engineered bacterial population via conjugation. Our system uses gRNA-based identification markers that allow messages to be addressed to specific strains via Cas9-mediated cleavage of messages sent to the wrong recipient, which we show reduces plasmid transfer by four orders of magnitude. Integrase-mediated editing of the address on the message plasmid allows cells to dynamically update the message's recipients in vivo. As a proof-of-concept demonstration of our system, we propose a linear path scheme that would propagate a message sequentially through the strains of a population in a defined order.", "doi": "10.1101/591552", "publication_date": "2019-03-28" }, { "id": "authors:x3d00-g0f42", "collection": "authors", "collection_id": "x3d00-g0f42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190312-134813069", "type": "article", "title": "Construction of Incoherent Feedforward Loop Circuits in a Cell-Free System and in Cells", "author": [ { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Cells utilize transcriptional regulation networks to respond to environmental signals. Network motifs, such as feedforward loops, play essential roles in these regulatory networks. In this work, we construct two different functional and modular incoherent type 1 feedforward loop circuits in a cell-free transcription\u2013translation system and in cells. With the help of mathematical modeling and the cell-free system, we can streamline the design\u2013build\u2013test cycles of the circuits, in which we characterize and optimize these circuits in vitro to confirm that they function as expected before implementing them in vivo. We show that the performance of these circuits from in vitro studies closely recapitulates those from in vivo experiments. We demonstrate that these feedforward loops show dynamic response and pulse-like behavior both in vitro and in vivo. These novel feedforward loop network motifs can be incorporated in more complicated biological circuits as detectors or responders.", "doi": "10.1021/acssynbio.8b00493", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2019-03-15", "series_number": "3", "volume": "8", "issue": "3", "pages": "606-610" }, { "id": "authors:71fsr-jjb78", "collection": "authors", "collection_id": "71fsr-jjb78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190228-112317657", "type": "article", "title": "Synthesizing voluntary lane-change policy using control improvisation", "author": [ { "family_name": "Ge", "given_name": "Jin I.", "orcid": "0000-0001-6429-9337", "clpid": "Ge-Jin-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this work, we propose control improvisation to synthesize voluntary lane-change policy that meets human preferences under given traffic environments. We first train Markov models to describe the lane-change environment for an automated vehicle under assumed traffic patterns. Parameters in the environment model are trained using traffic data and calibrated using control improvisation. Then, based on human lane-change behavior, we train a voluntary lane-change policy using explicit-duration Markov decision process. Parameters in the lane-change policy are calibrated through control improvisation to allow an automated car to voluntarily change lanes while avoiding overly frequent lane-change maneuvers under various traffic environments.", "doi": "10.1016/j.ifacol.2019.01.007", "issn": "2405-8963", "publisher": "Elsevier", "publication": "IFAC-PapersOnLine", "publication_date": "2019-02-08", "series_number": "34", "volume": "51", "issue": "34", "pages": "396-399" }, { "id": "authors:ntk3d-5e996", "collection": "authors", "collection_id": "ntk3d-5e996", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191003-134611922", "type": "book_section", "title": "Inverse Abstraction of Neural Networks Using Symbolic Interpolation", "book_title": "Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Gao", "given_name": "Sicun", "clpid": "Gao-Sicun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Neural networks in real-world applications have to satisfy critical properties such as safety and reliability. The analysis of such properties typically requires extracting information through computing pre-images of the network transformations, but it is well-known that explicit computation of pre-images is intractable. We introduce new methods for computing compact symbolic abstractions of pre-images by computing their overapproximations and underapproximations through all layers. The abstraction of pre-images enables formal analysis and knowledge extraction without affecting standard learning algorithms. We use inverse abstractions to automatically extract simple control laws and compact representations for pre-images corresponding to unsafe outputs. We illustrate that the extracted abstractions are interpretable and can be used for analyzing complex properties.", "doi": "10.1609/aaai.v33i01.33013437", "isbn": "978-1-57735-809-1", "publisher": "Association for the Advancement of Artificial Intelligence (AAAI)", "publication_date": "2019-02", "pages": "3437-3444" }, { "id": "authors:2q00r-v6053", "collection": "authors", "collection_id": "2q00r-v6053", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190410-120654801", "type": "conference_item", "title": "End-to-End Safe Reinforcement Learning through Barrier Functions for Safety-Critical Continuous Control Tasks", "author": [ { "family_name": "Cheng", "given_name": "Richard", "clpid": "Cheng-Richard-P" }, { "family_name": "Orosz", "given_name": "G\u00e1bor", "orcid": "0000-0002-9000-3736", "clpid": "Orosz-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" } ], "abstract": "Reinforcement Learning (RL) algorithms have found limited success beyond simulated applications, and one main reason is the absence of safety guarantees during the learning process. Real world systems would realistically fail or break before an optimal controller can be learned. To address this issue, we propose a controller architecture that combines (1) a model-free RL-based controller with (2) model-based controllers utilizing control barrier functions (CBFs) and (3) on-line learning of the unknown system dynamics, in order to ensure safety during learning. Our general framework leverages the success of RL algorithms to learn high-performance controllers, while the CBF-based controllers both guarantee safety and guide the learning process by constraining the set of explorable polices. We utilize Gaussian Processes (GPs) to model the system dynamics and its uncertainties. \n\nOur novel controller synthesis algorithm, RL-CBF, guarantees safety with high probability during the learning process, regardless of the RL algorithm used, and demonstrates greater policy exploration efficiency. We test our algorithm on (1) control of an inverted pendulum and (2) autonomous car-following with wireless vehicle-to-vehicle communication, and show that our algorithm attains much greater sample efficiency in learning than other state-of-the-art algorithms and maintains safety during the entire learning process.", "doi": "10.48550/arXiv.1903.08792", "publisher": "arXiv", "publication_date": "2019-02" }, { "id": "authors:7pf29-rcc17", "collection": "authors", "collection_id": "7pf29-rcc17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190204-130950357", "type": "book_section", "title": "Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-Free Extracts", "book_title": "2018 IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Halter", "given_name": "Wolfgang", "clpid": "Halter-W" }, { "family_name": "Allg\u00f6wer", "given_name": "Frank", "clpid": "Allg\u00f6wer-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Gyorgy", "given_name": "Andras", "clpid": "Gyorgy-A" } ], "abstract": "The fact that genes compete for shared cellular resources poses a fundamental challenge when identifying parameters of genetic parts. A recently developed model of gene expression tackles this problem by explicitly accounting for resource competition. In addition to accurately describing experimental data, this model only depends on a small number of easily identifiable parameters with clear physical interpretation. Based on this model, we outline a procedure to select the optimal set of experiments to characterize biomolecular parts in synthetic biology. Additionally, we reveal the role competition for shared resources plays, provide guidelines how to minimize its detrimental effects, and how to leverage this phenomenon to extract the most information about unknown parameters. To illustrate the results, we consider the case of part characterization in cell-free extracts, treat plasmid DNA concentrations as decision variables, and demonstrate the significant performance difference between naive and optimal experiment design.", "doi": "10.1109/CDC.2018.8619039", "isbn": "978-1-5386-1395-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2018-12", "pages": "1872-1879" }, { "id": "authors:6ac4p-zrt74", "collection": "authors", "collection_id": "6ac4p-zrt74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190201-143228935", "type": "book_section", "title": "Voluntary lane-change policy synthesis with control improvisation", "book_title": "2018 IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Ge", "given_name": "Jin I.", "orcid": "0000-0001-6429-9337", "clpid": "Ge-Jin-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we use control improvisation to synthesize voluntary lane-change policy that meets human preferences under given traffic environments. We first train Markov models to describe traffic patterns and the motion of vehicles responding to such patterns using traffic data. The trained parameters are calibrated using control improvisation to ensure the traffic scenario assumptions are satisfied. Based on the traffic pattern, vehicle response models, and Bayesian switching rules, the lane-change environment for an automated vehicle is modeled as a Markov decision process. Based on human lane-change behaviors, we train a voluntary lane-change policy using explicit-duration Markov decision process. Parameters in the lane-change policy are calibrated through control improvisation to allow an automated car to pursue faster speed while maintaining desired frequency of lane-change maneuvers in various traffic environments.", "doi": "10.1109/cdc.2018.8619616", "isbn": "9781538613955", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2018-12", "pages": "3640-3647" }, { "id": "authors:ccfjf-a4206", "collection": "authors", "collection_id": "ccfjf-a4206", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224927", "type": "book_section", "title": "Role of interaction network topology in controlling microbial population in consortia", "book_title": "2018 IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Ren", "given_name": "Xinying", "clpid": "Ren-Xinying" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Engineering microbial consortia is an important new frontier for synthetic biology given its efficiency in performing complex tasks and endurance to environmental uncertainty. Most synthetic circuits regulate populational behaviors via cell-to-cell interactions, which are affected by spatially heterogeneous environments. Therefore, it is important to understand the limits on controlling system dynamics and provide a control strategy for engineering consortia under spatial structures. Here, we build a network model for a fractional population control circuit in two-strain consortia, and characterize the cell-to-cell interaction network by topological properties, such as symmetry, locality and connectivity. Using linear network control theory, we relate the network topology to system output's tracking performance. We analytically and numerically demonstrate that the minimum network control cost for good tracking depends on locality difference between two cell population's spatial distributions and how strongly the controller node contributes to interaction strength. To realize a robust consortia, we can manipulate the environment to form a strongly connected network. Our results ground the expected cell population dynamics in its spatially organized interaction network, and inspire directions in cooperative control in microbial consortia.", "doi": "10.1109/CDC.2018.8619704", "isbn": "978-1-5386-1395-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2018-12", "pages": "2691-2697" }, { "id": "authors:40qy9-86d52", "collection": "authors", "collection_id": "40qy9-86d52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191029-152953038", "type": "monograph", "title": "Voluntary lane-change policy synthesis with reactive control\n improvisation", "author": [ { "family_name": "Ge", "given_name": "Jin I.", "orcid": "0000-0001-6429-9337", "clpid": "Ge-Jin-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we propose reactive control improvisation\nto synthesize voluntary lane-change policy that meets\nhuman preferences under given traffic environments. We first\ntrain Markov models to describe traffic patterns and the motion\nof vehicles responding to such patterns using traffic data. The\ntrained parameters are calibrated using control improvisation\nto ensure the traffic scenario assumptions are satisfied. Based\non the traffic pattern, vehicle response models, and Bayesian\nswitching rules, the lane-change environment for an automated\nvehicle is modeled as a Markov decision process. Based on\nhuman lane-change behaviors, we train a voluntary lane-change\npolicy using explicit-duration Markov decision process.\nParameters in the lane-change policy are calibrated through\nreactive control improvisation to allow an automated car to\npursue faster speed while maintaining desired frequency of\nlane-change maneuvers in various traffic environments.", "publisher": "Caltech Library", "publication_date": "2018-12" }, { "id": "authors:zgewf-02c87", "collection": "authors", "collection_id": "zgewf-02c87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181107-093406633", "type": "monograph", "title": "Design Guidelines For Sequestration Feedback Networks", "author": [ { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Leong", "given_name": "Yoke Peng", "orcid": "0000-0001-8560-8856", "clpid": "Leong-Yoke-Peng" }, { "family_name": "Olsman", "given_name": "Noah", "orcid": "0000-0002-4351-3880", "clpid": "Olsman-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Integral control is commonly used in mechanical and electrical systems to ensure perfect adaptation. A proposed design of integral control for synthetic biological systems employs the sequestration of two biochemical controller species. The unbound amount of controller species captures the integral of the error between the current and the desired state of the system. However, implementing integral control inside bacterial cells using sequestration feedback has been challenging due to the controller molecules being degraded and diluted. Furthermore, integral control can only be achieved under stability conditions that not all sequestration feedback networks fulfill. In this work, we give guidelines for ensuring stability and good performance (small steady-state error) in sequestration feedback networks. Our guidelines provide simple tuning options to obtain a flexible and practical biological implementation of sequestration feedback control. Using tools and metrics from control theory, we pave the path for the systematic design of synthetic biological systems.", "doi": "10.1101/455493", "publication_date": "2018-10-30" }, { "id": "authors:cy5e7-6dq47", "collection": "authors", "collection_id": "cy5e7-6dq47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180622-104112749", "type": "article", "title": "On-chip membrane protein cell-free expression enables development of a direct binding assay: A curious case of potassium channel KcsA-Kv1.3", "author": [ { "family_name": "Vaish", "given_name": "Amit", "clpid": "Vaish-A" }, { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Grandsard", "given_name": "Peter J.", "clpid": "Grandsard-P-J" }, { "family_name": "Chen", "given_name": "Qing", "clpid": "Chen-Qing" } ], "abstract": "Despite the significant role integral membrane proteins (IMPs) play in the drug discovery process, it remains extremely challenging to express, purify, and in vitro stabilize them for detailed biophysical analyses. Cell-free transcription-translation systems have emerged as a promising alternative for producing complex proteins, but they are still not a viable option for expressing IMPs due to improper post-translational folding of these proteins. We have studied key factors influencing in vitro folding of cell-free-expressed IMPs, particularly oligomeric proteins (i.e., ion channels). Using a chimeric ion channel, KcsA-Kv1.3 (K-K), as a model IMP, we have investigated several physiochemical determinants including artificial bilayer environments (i.e., lipid, detergent) for K-K in vitro stabilization. We observed that fusion of a 'superfolder' green fluorescent protein (sfGFP) to K-K as a protein expression reporter not only improves the protein yield, but surprisingly facilitates the K-K tetramer formation, probably by enhancing the solubility of monomeric K-K. Additionally, anionic lipids (i.e., DMPG) were found to be essential for the correct folding of cell-free-expressed monomeric K-K into tetramer, underscoring the importance of lipid-protein interaction in maintaining structural-functional integrity of ion channels. We further developed methods to integrate cell-free-expressed IMPs directly onto a biosensor chip. We employed a solid-supported lipid bilayer onto the surface plasmon resonance (SPR) chip to insert nascent K-K in a membrane. In a different approach, an anti-GFP-functionalized surface was used to capture in situ expressed K-K via its sfGFP tag. Interestingly, only the K-K-functionalized capture surface prepared by the latter strategy was able to interact with K-K's small binding partners. This generalizable approach can be further extended to other membrane proteins for developing direct binding assays involving small ligands.", "doi": "10.1016/j.ab.2018.06.018", "issn": "0003-2697", "publisher": "Elsevier", "publication": "Analytical Biochemistry", "publication_date": "2018-09-01", "volume": "556", "pages": "70-77" }, { "id": "authors:r6eba-5m902", "collection": "authors", "collection_id": "r6eba-5m902", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180920-104049492", "type": "article", "title": "Layering Assume-Guarantee Contracts for Hierarchical System Design", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Specifications for complex engineering systems are typically decomposed into specifications for individual subsystems in a manner that ensures they are implementable and simpler to develop further. We describe a method to algorithmically construct component specifications that 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. We parametrize the information flow between components by introducing parameters that select whether each variable is visible to a component. The decomposition algorithm identifies which variables can be hidden while preserving realizability and ensuring correct composition, and these are eliminated from component specifications by quantification and conversion of binary decision diagrams to formulas. The resulting specifications describe component viewpoints with full information with respect to the remaining variables, which is essential for tractable algorithmic synthesis of implementations. The specifications are written in TLA + , with liveness properties restricted to an implication of conjoined recurrence properties, known as GR(1). We define an operator for forming open systems from closed systems, based on a variant of the \"while-plus\" operator. This operator simplifies the writing of specifications that are realizable without being vacuous. To convert the generated specifications from binary decision diagrams to readable formulas over integer variables, we symbolically solve a minimal covering problem. We show with examples how the method can be applied to obtain contracts that formalize the hierarchical structure of system design.", "doi": "10.1109/JPROC.2018.2834926", "issn": "0018-9219", "publisher": "IEEE", "publication": "Proceedings of the IEEE", "publication_date": "2018-09", "series_number": "9", "volume": "106", "issue": "9", "pages": "1616-1654" }, { "id": "authors:wec2t-gmq84", "collection": "authors", "collection_id": "wec2t-gmq84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171103-115106585", "type": "article", "title": "Simulations and bisimulations for analysis of stability with respect to inputs of hybrid systems", "author": [ { "family_name": "Prabhakar", "given_name": "Pavithra", "clpid": "Prabhakar-Pavithra" }, { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Simulation and bisimulation relations define pre-orders on processes which serve as the basis for approximation based verification techniques, and have been extended towards the design of continuous and hybrid systems with complex logic specifications. We study pre-orders between hybrid systems which preserve stability properties with respect to input. We show that these properties are not bisimulation invariant, and hence propose stronger notions which strengthen simulation and bisimulation relations with uniform continuity constraints. We show that uniform continuity is necessary on the relations corresponding to both the state-space and the input-space, and continuity itself does not suffice. Finally, we demonstrate the satisfiability of our definitions by casting the well-known Lyapunov function based techniques for stability analysis as constructing a simple one-dimensional system which is stable and uniformly continuously simulates the original system.", "doi": "10.1007/s10626-017-0262-9", "issn": "0924-6703", "publisher": "Springer", "publication": "Discrete Event Dynamic Systems", "publication_date": "2018-09", "series_number": "3", "volume": "28", "issue": "3", "pages": "349-374" }, { "id": "authors:8652e-1ns11", "collection": "authors", "collection_id": "8652e-1ns11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180912-130453647", "type": "article", "title": "Temporal Logic Control of POMDPs via Label-based Stochastic Simulation Relations", "author": [ { "family_name": "Haesaert", "given_name": "S.", "clpid": "Haesaert-Sofie" }, { "family_name": "Nilsson", "given_name": "P.", "orcid": "0000-0001-8748-6936", "clpid": "Nilsson-Petter" }, { "family_name": "Vasile", "given_name": "C. I.", "clpid": "Vasile-C-I" }, { "family_name": "Thakker", "given_name": "R.", "clpid": "Thakker-Rohan-A" }, { "family_name": "Agha-Mohammadi", "given_name": "A.", "orcid": "0000-0001-5509-1841", "clpid": "Agha-Mohammadi-A-A" }, { "family_name": "Ames", "given_name": "A. D.", "orcid": "0000-0003-0848-3177", "clpid": "Ames-A-D" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The synthesis of controllers guaranteeing linear temporal logic specifications on partially observable Markov decision processes (POMDP) via their belief models causes computational issues due to the continuous spaces. In this work, we construct a finite-state abstraction on which a control policy is synthesized and refined back to the original belief model. We introduce a new notion of label-based approximate stochastic simulation to quantify the deviation between belief models. We develop a robust synthesis methodology that yields a lower bound on the satisfaction probability, by compensating for deviations a priori, and that utilizes a less conservative control refinement.", "doi": "10.1016/j.ifacol.2018.08.046", "issn": "2405-8963", "publisher": "Elsevier", "publication": "IFAC-PapersOnLine", "publication_date": "2018-08-31", "series_number": "16", "volume": "51", "issue": "16", "pages": "271-276" }, { "id": "authors:1efq8-g0238", "collection": "authors", "collection_id": "1efq8-g0238", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181008-162020352", "type": "monograph", "title": "Context Dependence of Biological Circuits", "author": [ { "family_name": "Catanach", "given_name": "Thomas A.", "orcid": "0000-0002-4321-3159", "clpid": "Catanach-T-A" }, { "family_name": "McCardell", "given_name": "Reed", "clpid": "McCardell-R-D" }, { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It has been an ongoing scientific debate whether biological parameters are conserved across experimental setups with different media, pH values, and other experimental conditions. Our work explores this question using Bayesian probability as a rigorous framework to assess the biological context of parameters in a model of the cell growth controller in You et al. When this growth controller is uninduced, the E. coli cell population grows to carrying capacity; however, when the circuit is induced, the cell population growth is regulated to remain well below carrying capacity. This growth control controller regulates the E. coli cell population by cell to cell communication using the signaling molecule AHL and by cell death using the bacterial toxin CcdB. \n\nTo evaluate the context dependence of parameters such as the cell growth rate, the carrying capacity, the AHL degradation rate, the leakiness of AHL, the leakiness of toxin CcdB, and the IPTG induction factor, we collect experimental data from the growth control circuit in two different media, at two different pH values, and with several induction levels. We define a set of possible context dependencies that describe how these parameters may differ with the experimental conditions and we develop mathematical models of the growth controller across the different experimental contexts. We then determine whether these parameters are shared across experimental contexts or whether they are context dependent. For each of these possible context dependencies, we use Bayesian inference to assess its plausibility and to estimate the parameters of the growth controller. Ultimately, we find that there is significant experimental context dependence in this circuit. Moreover, we also find that the estimated parameter values are sensitive to our assumption of a context relationship.", "doi": "10.1101/360040", "publication_date": "2018-07-03" }, { "id": "authors:mwyq5-kby06", "collection": "authors", "collection_id": "mwyq5-kby06", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-093149145", "type": "book_section", "title": "Toward Specification-Guided Active Mars Exploration for Cooperative Robot Teams", "book_title": "Robotics: Science and Systems XIV", "author": [ { "family_name": "Nilsson", "given_name": "Petter", "orcid": "0000-0001-8748-6936", "clpid": "Nilsson-Petter" }, { "family_name": "Haesaert", "given_name": "Sofie", "clpid": "Haesaert-Sofie" }, { "family_name": "Thakker", "given_name": "Rohan", "clpid": "Thakker-Rohan-A" }, { "family_name": "Otsu", "given_name": "Kyohei", "clpid": "Otsu-Kyohei" }, { "family_name": "Vasile", "given_name": "Cristian-Ioan", "clpid": "Vasile-C-I" }, { "family_name": "Agha-Mohammadi", "given_name": "Ali-Akbar", "orcid": "0000-0001-5509-1841", "clpid": "Agha-Mohammadi-A-A" }, { "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" } ], "contributor": [ { "family_name": "Yu", "given_name": "Tianhe", "clpid": "Yu-Tianhe" }, { "family_name": "Finn", "given_name": "Chelsea", "clpid": "Finn-C" }, { "family_name": "Dasari", "given_name": "Sudeep", "clpid": "Dasari-S" }, { "family_name": "Xie", "given_name": "Annie", "clpid": "Xie-Annie" }, { "family_name": "Zhang", "given_name": "Tianhao", "clpid": "Zhang-Tianhao" } ], "abstract": "As a step towards achieving autonomy in space exploration missions, we consider a cooperative robotics system consisting of a copter and a rover. The goal of the copter is to explore an unknown environment so as to maximize knowledge about a science mission expressed in linear temporal logic that is to be executed by the rover. We model environmental uncertainty as a belief space Markov decision process and formulate the problem as a two-step stochastic dynamic program that we solve in a way that leverages the decomposed nature of the overall system. We demonstrate in simulations that the robot team makes intelligent decisions in the face of uncertainty.", "doi": "10.15607/rss.2018.xiv.047", "isbn": "978-0-9923747-4-7", "publisher": "Robotics: Science and Systems Foundation", "publication_date": "2018-06", "pages": "1-9" }, { "id": "authors:rqwpc-d9137", "collection": "authors", "collection_id": "rqwpc-d9137", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180524-091716800", "type": "article", "title": "Control Theory for Synthetic Biology: Recent Advances in System Characterization, Control Design, and Controller Implementation for Synthetic Biology", "author": [ { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Living organisms are differentiated by their genetic material-millions to billions of DNA bases encoding thousands of genes. These genes are translated into a vast array of proteins, many of which have functions that are still unknown. Previously, it was believed that simply knowing the genetic sequence of an organism would be the key to unlocking all understanding. However, as DNA sequencing technology has become affordable, it has become clear that living cells are governed by complex, multilayered networks of gene regulation that cannot be deduced from sequence alone. Synthetic biology as a field might best be characterized as a learn-by-building approach, in which scientists attempt to engineer molecular pathways that do not exist in nature. In doing so, they test the limits of both natural and engineered organisms.", "doi": "10.1109/MCS.2018.2810459", "issn": "0272-1708", "publisher": "IEEE", "publication": "IEEE Control Systems Magazine", "publication_date": "2018-06", "series_number": "3", "volume": "38", "issue": "3", "pages": "32-62" }, { "id": "authors:734vp-ew070", "collection": "authors", "collection_id": "734vp-ew070", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180525-123941302", "type": "article", "title": "Future systems and control research in synthetic biology", "author": [ { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "family_name": "Qian", "given_name": "Yili", "clpid": "Qian-Yili" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sontag", "given_name": "Eduardo D.", "clpid": "Sontag-E-D" } ], "abstract": "Synthetic biology is the application of engineering principles to the fundamental components of biology, with the aim of creating systems with novel functionalities that can be used for energy, environment, and medical applications. While the potential impact of this new technology is enormous, there are challenges that we need to overcome before the impact of synthetic biology can be fully realized. Many of these challenges fall beyond the scope of molecular biology and are indeed \"system-level\" problems, where very little research is being performed. This paper identifies pressing challenges in synthetic biology that can be formulated as systems and control theoretic problems and outlines potentially new systems and control theories/tools that are required to tackle such problems. The aim is to attract more systems and control theorists to collaborate with molecular biologists and biophysicists and help synthetic biology reach its promise. At the same time, engaging the systems and control community more broadly into the rich research opportunities and life-changing applications of synthetic biology may provide added visibility to the field of systems and controls.", "doi": "10.1016/j.arcontrol.2018.04.007", "issn": "1367-5788", "publisher": "Elsevier", "publication": "Annual Reviews in Control", "publication_date": "2018-05-24", "volume": "45", "pages": "5-17" }, { "id": "authors:p4e4h-pkg93", "collection": "authors", "collection_id": "p4e4h-pkg93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180409-133942183", "type": "article", "title": "Single Day Construction of Multigene Circuits with 3G Assembly", "author": [ { "family_name": "Halleran", "given_name": "Andrew D.", "orcid": "0000-0001-8720-1451", "clpid": "Halleran-A-D" }, { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems take different approaches to accelerate DNA construction. We introduce a hybrid method, Golden Gate-Gibson (3G), that takes advantage of modular part libraries introduced by type IIS restriction enzyme systems and isothermal assembly's ability to build large DNA constructs in single pot reactions. Our method is highly efficient and rapid, facilitating construction of entire multigene circuits in a single day. Additionally, 3G allows generation of variant libraries enabling efficient screening of different possible circuit constructions. We characterize the efficiency and accuracy of 3G assembly for various construct sizes, and demonstrate 3G by characterizing variants of an inducible cell-lysis circuit.", "doi": "10.1021/acssynbio.8b00060", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2018-05-18", "series_number": "5", "volume": "7", "issue": "5", "pages": "1477-1480" }, { "id": "authors:gfm8p-cqf85", "collection": "authors", "collection_id": "gfm8p-cqf85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-140537131", "type": "monograph", "title": "Long-distance communication in synthetic bacterial consortia through active signal propagation", "author": [ { "family_name": "Parkin", "given_name": "James M.", "orcid": "0000-0002-4058-2338", "clpid": "Parkin-J-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "A synthetic cell-cell signaling circuit should ideally be (1) metabolically lightweight, (2) insulated from endogenous gene networks, and (3) excitable rather than oscillatory or bistable. To accomplish these three features, we propose a synchronized pulse-generating circuit based on the design of published synchronized oscillators. This communication module employs a pulse generator built using Lux-type quorum sensing components and an IFFL transcriptional circuit. Both the input and output of this module are AHLs, the quorum sensing signaling molecule. Cells bearing this module therefore act as an excitable medium, producing a pulse of AHL when stimulated by exogenous AHL. Using simulation and microscopy, we demonstrate how this circuit enables traveling pulses of AHL production through microcolonies growing in two dimensions. Traveling pulses achieve cell-cell communication at longer distances than can be achieved by diffusion of signal from sender to receiver cells and may permit more sophisticated coordination in synthetic consortia.", "doi": "10.1101/321307", "publication_date": "2018-05-14" }, { "id": "authors:nynqd-29b21", "collection": "authors", "collection_id": "nynqd-29b21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180626-144153512", "type": "article", "title": "Richard M. Murray [People in Control]", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This issue of IEEE Control Systems Magazine speaks with Richard Murray, the recipient of the 2017 IEEE Control Systems Award; Yongxin Chen, the lead author of the paper that received the 2017 George S. Axelby Outstanding Paper Award; and Joseph Bentsman, the chair of the IEEE Control Systems Society (CSS) Technical Committee on Power Generation.", "doi": "10.1109/MCS.2017.2786445", "issn": "1066-033X", "publisher": "IEEE", "publication": "IEEE Control Systems Magazine", "publication_date": "2018-04", "series_number": "2", "volume": "38", "issue": "2", "pages": "38-40" }, { "id": "authors:687er-8c179", "collection": "authors", "collection_id": "687er-8c179", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190205-112328842", "type": "monograph", "title": "Detecting Adversarial Examples via Neural Fingerprinting", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Zheng", "given_name": "Stephan", "clpid": "Zheng-Stephan" }, { "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" } ], "abstract": "Deep neural networks are vulnerable to adversarial examples, which dramatically alter model output using small input changes. We propose Neural Fingerprinting, a simple, yet effective method to detect adversarial examples by verifying whether model behavior is consistent with a set of secret fingerprints, inspired by the use of biometric and cryptographic signatures. The benefits of our method are that 1) it is fast, 2) it is prohibitively expensive for an attacker to reverse-engineer which fingerprints were used, and 3) it does not assume knowledge of the adversary. In this work, we pose a formal framework to analyze fingerprints under various threat models, and characterize Neural Fingerprinting for linear models. For complex neural networks, we empirically demonstrate that Neural Fingerprinting significantly improves on state-of-the-art detection mechanisms by detecting the strongest known adversarial attacks with 98-100% AUC-ROC scores on the MNIST, CIFAR-10 and MiniImagenet (20 classes) datasets. In particular, the detection accuracy of Neural Fingerprinting generalizes well to unseen test-data under various black- and whitebox threat models, and is robust over a wide range of hyperparameters and choices of fingerprints.", "doi": "10.48550/arXiv.1803.03870", "publisher": "arXiv", "publication_date": "2018-03-11" }, { "id": "authors:vkhn5-n9753", "collection": "authors", "collection_id": "vkhn5-n9753", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180706-104554837", "type": "book_section", "title": "Progress towards flight software hybrid controllers from formal specifications", "book_title": "2018 IEEE Aerospace Conference", "author": [ { "family_name": "Haesaert", "given_name": "S.", "clpid": "Haesaert-S" }, { "family_name": "Reder", "given_name": "L. J.", "clpid": "Reder-L-J" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The manual translation of informally defined requirements into statecharts, from which source code can be generated automatically, can be an error-prone, laborintensive process. Design errors sometimes propagate into final implementation code, only to be discovered during testing and verification. However, the requirements that the software needs to satisfy can be formally defined via temporal logics. In this paper, an approach to automatically synthesize flight-software hybrid-controllers for dynamic systems from formal specifications is given. First, specifications for a specific control functionality are defined by a set of linear temporal logic formulas. These, together with a model of the dynamical system, are then used as inputs to the Caltech-developed temporal logic planning toolbox (TuLiP), which searches for a control design. This results in a controller that is hybrid as it combines a finite state controller together with low-level continuous control actions. We map the resulting controller design to UML statecharts, which can be given as input to the Statechart Autocoder (SCA) developed by the Jet Propulsion Laboratory. SCA maps statechart controller designs to software implementation C code suitable for flight applications. By construction, the resulting code will meet the original formal design specifications, thus eliminating latent design errors. This paper describes the new 2nd generation interface developed to specify and convert the TuLiP-produced design to more optimized (e.g., reduced number of states and transitions) input UML (as XML file) for the JPL Statechart Autocoder. By applying intermediate optimization procedures, in which indistinguishable states are merged and transitions are grouped, the size of the statechart and the resulting code is reduced substantially. This is demonstrated by revisiting our 2016 speed-controller example showing reduction by more than 75% of the states synthesized in the original example.", "doi": "10.1109/AERO.2018.8396562", "isbn": "978-1-5386-2014-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2018-03", "pages": "1-17" }, { "id": "authors:rjf0e-4e484", "collection": "authors", "collection_id": "rjf0e-4e484", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171204-081929055", "type": "article", "title": "Cell-Free and In Vivo Characterization of Lux, Las, and Rpa Quorum Activation Systems in E. coli", "author": [ { "family_name": "Halleran", "given_name": "Andrew D.", "orcid": "0000-0001-8720-1451", "clpid": "Halleran-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Synthetic biologists have turned toward quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell-free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry. We take advantage of the transcription\u2013translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtained in vivo. We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observed in vivo.", "doi": "10.1021/acssynbio.7b00376", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2018-02-16", "series_number": "2", "volume": "7", "issue": "2", "pages": "752-755" }, { "id": "authors:cbz07-b2614", "collection": "authors", "collection_id": "cbz07-b2614", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170920-152025463", "type": "book_section", "title": "Decomposing GR(1) Games with Singleton Liveness Guarantees for Efficient Synthesis", "book_title": "2017 IEEE 56th Annual Conference on Decision and Control (CDC)", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Temporal logic based synthesis approaches are often used to find trajectories that are correct-by-construction for systems with complex behavior. However, the scalability of such approaches is of concern and at times a bottleneck when transitioning from theory to practice. In this paper, we identify a class of problems in the GR(1) fragment of linear-time temporal logic (LTL) where the synthesis problem allows for a decomposition that enables easy parallelization. This decomposition also reduces the alternation depth, resulting in more efficient synthesis. A multi-agent robot gridworld example with coordination tasks is presented to demonstrate the application of the developed ideas and also to perform empirical analysis for benchmarking the decomposition-based synthesis approach.", "doi": "10.1109/CDC.2017.8263775", "isbn": "978-1-5090-2873-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2017-12", "pages": "911-917" }, { "id": "authors:0j175-tv586", "collection": "authors", "collection_id": "0j175-tv586", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170925-083417843", "type": "book_section", "title": "Population regulation in microbial consortia using dual feedback control", "book_title": "2017 IEEE 56th Annual Conference on Decision and Control (CDC)", "author": [ { "family_name": "Ren", "given_name": "Xinying", "clpid": "Ren-Xinying" }, { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "An ongoing area of study in synthetic biology has been the design and construction of synthetic circuits that maintain homeostasis at the population level. Here, we are interested in designing a synthetic control circuit that regulates the total cell population and the relative ratio between cell strains in a culture containing two different cell strains. We have developed a dual feedback control strategy that uses two separate control loops to achieve the two functions respectively. By combining both of these control loops, we have created a population regulation circuit where both the total population size and relative cell type ratio can be set by reference signals. The dynamics of the regulation circuit show robustness and adaptation to perturbations in cell growth rate and changes in cell numbers. The control architecture is general and could apply to any organism for which synthetic biology tools for quorum sensing, comparison between outputs, and growth control are available.", "doi": "10.1101/120253", "isbn": "978-1-5090-2874-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2017-12", "pages": "5341-5347" }, { "id": "authors:vr6jb-n3x89", "collection": "authors", "collection_id": "vr6jb-n3x89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-145354147", "type": "monograph", "title": "Hiding variables when decomposing specifications into GR(1) contracts", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose a method for eliminating variables from component specifications during the decomposition of GR(1) properties into contracts. The variables that can be eliminated are identified by parameterizing the communication architecture to investigate the dependence of realizability on the availability of information. We prove that the selected variables can be hidden from other components, while still expressing the resulting specification as a game with full information with respect to the remaining variables. The values of other variables need not be known all the time, so we hide them for part of the time, thus reducing the amount of information that needs to be communicated between components. We improve on our previous results on algorithmic decomposition of GR(1) properties, and prove existence of decompositions in the full information case. We use semantic methods of computation based on binary decision diagrams. To recover the constructed specifications so that humans can read them, we implement exact symbolic minimal covering over the lattice of integer orthotopes, thus deriving minimal formulae in disjunctive normal form over integer variable intervals.", "publisher": "Caltech Library", "publication_date": "2017-12" }, { "id": "authors:3tsrf-23g13", "collection": "authors", "collection_id": "3tsrf-23g13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171128-230807299", "type": "conference_item", "title": "Measuring the Robustness of Neural Networks via Minimal Adversarial Examples", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Zheng", "given_name": "Stephan", "clpid": "Zheng-Stephan" }, { "family_name": "Gao", "given_name": "Sicun", "clpid": "Gao-Sicun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Neural networks are highly sensitive to adversarial examples, which cause large output deviations with only small input perturbations. However, little is known quantitatively about the distribution and prevalence of such adversarial examples. To address this issue, we propose a rigorous search method that provably finds the smallest possible adversarial example. The key benefit of our method is that it gives precise quantitative insight into the distribution of adversarial examples, and guarantees the absence of adversarial examples if they are not found. The primary idea is to consider the nonlinearity exhibited by the network in a small region of the input space, and search exhaustively for adversarial examples in that region. We show that the frequency of adversarial examples and robustness of neural networks is up to twice as large as reported in previous works that use empirical adversarial attacks. In addition, we provide an approach to approximate the nonlinear behavior of neural networks, that makes our search method computationally feasible.", "publisher": "Caltech Library", "publication_date": "2017-11-30" }, { "id": "authors:dme00-2nb41", "collection": "authors", "collection_id": "dme00-2nb41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-100007899", "type": "monograph", "title": "Modeling Dynamic Transcriptional Circuits with CRISPRi", "author": [ { "family_name": "Clamons", "given_name": "Samuel", "orcid": "0000-0002-7993-2278", "clpid": "Clamons-Samuel-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) promises to reproduce the functions of traditional synthetic transcriptional circuits, but with better orthogonality, programmability, and extensibility. However, CRISPRi lacks obvious cooperativity\u2013a feature classically considered critical for several classic gene regulatory circuits. We use a simple dynamical model of CRISPRi to show that it can be used to build repressilators, toggle switches, and incoherent feed-forward loops. We also show that the function some of these circuits are expected to be sensitive to several key parameters, and we provide specifications for those parameters. Our modeling reveals key engineering requirements and considerations for the construction of dynamic CRISPRi circuits, and provides a roadmap for building those circuits.", "doi": "10.1101/225318", "publication_date": "2017-11-27" }, { "id": "authors:q0h9k-f8c44", "collection": "authors", "collection_id": "q0h9k-f8c44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-100430313", "type": "monograph", "title": "Proof of concept continuous event logging in living cells", "author": [ { "family_name": "Shur", "given_name": "Andrey", "clpid": "Shur-Andrey" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Cells must detect and respond to molecular events such as the presence or absence of specific small molecules. To accomplish this, cells have evolved methods to measure the presence and concentration of these small molecules in their environment and enact changes in gene expression or behavior. However, cells don't usually change their DNA in response to outside stimuli. In this work, we have engineered a genetic circuit that can enact specific and controlled genetic changes in response to small molecule stimuli. Known DNA sequences can be repeatedly integrated in a genomic 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. Therefore, through the co-expression of dCas9 and guide RNA, Bxb1 can be directed to integrate one of two engineered plasmids, which correspond to two orthogonal small molecule inducers that can be recorded with this system. We identified the optimal location of guide RNA binding to the Bxb1 attP integrase attachment site, and characterized the detection limits of the system by measuring the minimal small molecule concentration and shortest induction time necessary to produce measurable differences in array composition as read out by Oxford Nanopore sequencing technology.", "doi": "10.1101/225151", "publication_date": "2017-11-25" }, { "id": "authors:yyk8w-71j62", "collection": "authors", "collection_id": "yyk8w-71j62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181029-141247546", "type": "monograph", "title": "Control of bacterial population density with population feedback and molecular sequestration", "author": [ { "family_name": "McCardell", "given_name": "Reed D.", "clpid": "McCardell-R-D" }, { "family_name": "Huang", "given_name": "Shan", "orcid": "0000-0001-5575-4510", "clpid": "Huang-Shan" }, { "family_name": "Green", "given_name": "Leopold N.", "orcid": "0000-0001-5479-6970", "clpid": "Green-L-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Genetic engineering technology has become sophisticated enough to allow precise manipulation of bacterial genetic material. Engineering efforts with these technologies have created modified bacteria for various medical, industrial, and environmental purposes, but organisms designed for specific functions require improvements in stability, longevity, or efficiency of function. Most bacteria live in multispecies communities, whose composition may be closely linked to the effect the community has on the environment. Bacterial engineering efforts will benefit from building communities with regulated compositions, which will enable more stable and powerful community functions. We present a design of a synthetic two member bacterial community capable of maintaining its composition at a defined ratio of [cell type 1] : [cell type 2]. We have constructed the genetic motif that will act in each cell in the two member community, containing an AHL-based negative feedback loop that activates ccdB toxin, which caps population density with increasing feedback strength. It also contains one of two ccdB sequestration modules, either the ccdA protein antitoxin, or an RNA device which prevents transcription and translation of ccdB mRNA, that rescues capped population density with induction. We compare absorbance and colony counting methods of estimating bacterial population density, finding that absorbance-based methods overestimate viable population density when ccdB toxin is used to control population density. Prior modeling results show that two cell types containing this genetic circuit motif that reciprocally activate the other's ccdB sequestration device will establish a steady state ratio of cell types. Experimental testing and tuning the full two member community will help us improve our modeling of multi-member bacterial communities, learn more about the strengths and weaknesses of our design for community composition control, and identify general principles of design of compositionally-regulated microbial communities.", "doi": "10.1101/225045", "publication_date": "2017-11-25" }, { "id": "authors:6vkse-s0298", "collection": "authors", "collection_id": "6vkse-s0298", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114225422", "type": "monograph", "title": "Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems", "author": [ { "family_name": "Olsman", "given_name": "Noah", "orcid": "0000-0002-4351-3880", "clpid": "Olsman-N" }, { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Xiao", "given_name": "Fangzhou", "orcid": "0000-0002-5001-5644", "clpid": "Xiao-Fangzhou" }, { "family_name": "Leong", "given_name": "Yoke Peng", "orcid": "0000-0001-8560-8856", "clpid": "Leong-Yoke-Peng" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "abstract": "Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism implemented using the sequestration binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of sequestration feedback and contribute to a more general theory of biological control systems.", "doi": "10.1101/222042", "publication_date": "2017-11-20" }, { "id": "authors:43g2m-8t676", "collection": "authors", "collection_id": "43g2m-8t676", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-100811065", "type": "monograph", "title": "Length and time scales of cell-cell signaling circuits in agar", "author": [ { "family_name": "Doong", "given_name": "Joy", "orcid": "0000-0001-8987-6903", "clpid": "Doong-Joy" }, { "family_name": "Parkin", "given_name": "James", "orcid": "0000-0002-4058-2338", "clpid": "Parkin-J-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "A community of genetically heterogeneous cells embedded in an unmixed medium allows for sophisticated operations by retaining spatial differentiation and coordinating division-of-labor. To establish the principles of engineering reliable cell-cell communication in a heterogeneous environment, we examined how circuit parameters and spatial placement affect the range of length and time scales over which simple communication circuits interact. We constructed several \"sender\" and \"receiver\" strains with quorum-sensing signaling circuits. The sender cell colony produces acyl homoserine lactones (AHL), which diffuse across the semisolid medium. The receiver cell colony detects these signal molecules and reports by fluorescence. We have found that a single colony of one sender variant is sufficient to induce receiver response at more than 1.5cm separation. Furthermore, AHL degradase expression in receiver colonies produces a signal threshold effect and reduces the response level in subsequent receiver colonies. Finally, our investigation on the spatial placement of colonies gave rise to the design of a multicellular long-range communication array consisting of two alternating colony types. Its signal response successfully propagated colony-by-colony along a six-colony array spanning 4.8cm at a transmission velocity of 12.8 hours per colony or 0.075cm per hour. In addition, we have developed a reaction-diffusion model that recreates the observed behaviors of the many performed experiments using data-informed parameter estimates of signal diffusion, gene expression, and nutrient consumption. These results demonstrate that a mixed community of colonies can enable new patterning programs, and the corresponding model will facilitate the rational design of complex communication networks.", "doi": "10.1101/220244", "publication_date": "2017-11-18" }, { "id": "authors:hvx8c-p7054", "collection": "authors", "collection_id": "hvx8c-p7054", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170807-111733897", "type": "article", "title": "Cell-free extract based optimization of biomolecular circuits with droplet microfluidics", "author": [ { "family_name": "Hori", "given_name": "Yutaka", "orcid": "0000-0002-3253-4985", "clpid": "Hori-Yutaka" }, { "family_name": "Kantak", "given_name": "Chaitanya", "orcid": "0000-0003-1620-7084", "clpid": "Kantak-Chaitanya" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Abate", "given_name": "Adam R.", "orcid": "0000-0001-9614-4831", "clpid": "Abate-Adam-R" } ], "abstract": "Engineering an efficient biomolecular circuit often requires time-consuming iterations of optimization. Cell-free protein expression systems allow rapid testing of biocircuits in vitro, speeding the design\u2013build\u2013test cycle of synthetic biology. In this paper, we combine this with droplet microfluidics to densely scan a transcription\u2013translation biocircuit space. Our system assays millions of parameter combinations per hour, providing a detailed map of function. The ability to comprehensively map biocircuit parameter spaces allows accurate modeling to predict circuit function and identify optimal circuits and conditions.", "doi": "10.1039/C7LC00552K", "issn": "1473-0197", "publisher": "Royal Society of Chemistry", "publication": "Lab on a Chip", "publication_date": "2017-09-21", "series_number": "18", "volume": "17", "issue": "18", "pages": "3037-3042" }, { "id": "authors:7abpr-0jb96", "collection": "authors", "collection_id": "7abpr-0jb96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180119-083614257", "type": "book_section", "title": "Synthesis of correct-by-construction behavior trees", "book_title": "2017 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)", "author": [ { "family_name": "Colledanchise", "given_name": "Michele", "clpid": "Colledanchise-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "\u00d6gren", "given_name": "Petter", "clpid": "\u00d6gren-P" } ], "abstract": "In this paper we study the problem of synthesizing correct-by-construction Behavior Trees (BTs) controlling agents in adversarial environments. The proposed approach combines the modularity and reactivity of BTs with the formal guarantees of Linear Temporal Logic (LTL) methods. Given a set of admissible environment specifications, an agent model in form of a Finite Transition System and the desired task in form of an LTL formula, we synthesize a BT in polynomial time, that is guaranteed to correctly execute the desired task. To illustrate the approach, we present three examples of increasing complexity.", "doi": "10.1109/IROS.2017.8206502", "isbn": "978-1-5386-2683-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2017-09", "pages": "6039-6046" }, { "id": "authors:vrenc-fe819", "collection": "authors", "collection_id": "vrenc-fe819", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170523-230106516", "type": "book_section", "title": "Learning-Based Abstractions for Nonlinear Constraint Solving", "book_title": "Proceedings of the Twenty-Sixth International Joint Conference on Artificial Intelligence", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Ar\u00e9chiga", "given_name": "Nikos", "clpid": "Ar\u00e9chiga-N" }, { "family_name": "Gao", "given_name": "Sicun", "clpid": "Gao-Sicun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Sierra", "given_name": "Carles", "clpid": "Sierra-C" } ], "abstract": "We propose a new abstraction refinement procedure based on machine learning to improve the performance of nonlinear constraint solving algorithms on large-scale problems. The proposed approach decomposes the original set of constraints into smaller subsets, and uses learning algorithms to propose sequences of abstractions that take the form of conjunctions of classifiers. The core procedure is a refinement loop that keeps improving the learned results based on counterexamples that are obtained from partial constraints that are easy to solve. Experiments show that the proposed techniques significantly improved the performance of state-of-the-art constraint solvers on many challenging benchmarks. The mechanism is capable of producing intermediate symbolic abstractions that are also important for many applications and for understanding the internal structures of hard constraint solving problems.", "doi": "10.24963/ijcai.2017/83", "isbn": "978-0-9992411-0-3", "publisher": "International Joint Conferences on Artificial Intelligence", "publication_date": "2017-08-20", "pages": "592-599" }, { "id": "authors:qj7zc-1bp57", "collection": "authors", "collection_id": "qj7zc-1bp57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160516-100511848", "type": "article", "title": "Design of a Toolbox of RNA Thermometers", "author": [ { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" }, { "family_name": "Apurva", "given_name": "Divyansh", "clpid": "Apurva-D" }, { "family_name": "Satija", "given_name": "Rohit", "clpid": "Satija-R" }, { "family_name": "Siegal", "given_name": "Dan", "orcid": "0000-0002-6821-2769", "clpid": "Siegal-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. While RNA-based sensors, called 'thermometers', have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature, differing in sensitivities and thresholds. We address this issue by constructing a library of RNA thermometers, based on thermodynamic computations, and experimentally measuring their activities in cell-free biomolecular 'breadboards'. Using free energies of the minimum free energy structures as well as melt profile computations, we estimated thata diverse set of temperature responses were possible. We experimentally found a wide range of responses to temperature in the temperature range 29 \u25e6C\u201337 \u25e6C, with fold-changes varying over 3-fold around the starting thermometer. The sensitivities of these responses ranged over 10-fold around the starting thermometer. We correlated these measurements with computational expectations, finding that while there was no strong correlation for the individual thermometers, overall trends of diversity, fold-changes, and sensitivities were similar. These results present a toolbox of RNA-based circuit elements with diverse temperature responses.", "doi": "10.1021/acssynbio.6b00301", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2017-08-18", "series_number": "8", "volume": "6", "issue": "8", "pages": "1461-1470" }, { "id": "authors:kc00w-e6x58", "collection": "authors", "collection_id": "kc00w-e6x58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180430-092750634", "type": "monograph", "title": "System-level studies of a cell-free transcription-translation platform for metabolic engineering", "author": [ { "family_name": "Wu", "given_name": "Yong Y.", "clpid": "Wu-Yong-Y" }, { "family_name": "Sato", "given_name": "Hirokazu", "clpid": "Sato-Hirokazu" }, { "family_name": "Huang", "given_name": "Hongjun", "clpid": "Huang-Hongjun" }, { "family_name": "Culler", "given_name": "Stephanie J.", "clpid": "Culler-S-J" }, { "family_name": "Khandurina", "given_name": "Julia", "clpid": "Khandurina-J" }, { "family_name": "Nagarajan", "given_name": "Harish", "clpid": "Nagarajan-H" }, { "family_name": "Yang", "given_name": "Tae Hoon", "clpid": "Yang-Tae-Hoon" }, { "family_name": "Van Dien", "given_name": "Stephen", "clpid": "Van-Dien-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Current 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. We demonstrate the reliability of TX-TL as a platform for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Using TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied to in vivo strain development.", "doi": "10.1101/172007", "publication_date": "2017-08-03" }, { "id": "authors:jx7y1-57e24", "collection": "authors", "collection_id": "jx7y1-57e24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170731-080503943", "type": "article", "title": "Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks", "author": [ { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Dy", "given_name": "Aaron J.", "orcid": "0000-0003-0535-517X", "clpid": "Dy-Aaron-J" }, { "family_name": "Martin", "given_name": "Kyle B.", "clpid": "Martin-K-B" }, { "family_name": "Ng", "given_name": "Andrew H.", "clpid": "Ng-Andrew-H" }, { "family_name": "Del Vecchio", "given_name": "Domitilla", "orcid": "0000-0001-6472-8576", "clpid": "Del-Vecchio-D" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Collins", "given_name": "James J.", "clpid": "Collins-J-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability.", "doi": "10.1016/j.cels.2017.06.001", "issn": "2405-4712", "publisher": "Cell Press", "publication": "Cell Systems", "publication_date": "2017-07-26", "series_number": "1", "volume": "5", "issue": "1", "pages": "11-24" }, { "id": "authors:pdj4p-zcv35", "collection": "authors", "collection_id": "pdj4p-zcv35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-155806564", "type": "book_section", "title": "Connected cruise control design using probabilistic model checking", "book_title": "2017 American Control Conference", "author": [ { "family_name": "Ge", "given_name": "Jin I.", "orcid": "0000-0001-6429-9337", "clpid": "Ge-Jin-I" }, { "family_name": "Orosz", "given_name": "G\u00e1bor", "orcid": "0000-0002-9000-3736", "clpid": "Orosz-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we synthesize a connected cruise controller with performance guarantee using probabilistic model checking, for a vehicle that receives motion information from several vehicles ahead through wireless vehicle-to-vehicle communication. We model the car-following dynamics of the preceding vehicles as Markov chains and synthesize the connected cruise controller as a Markov decision process. We show through simulations that such a design is robust against imperfections in communication.", "doi": "10.23919/ACC.2017.7963724", "isbn": "978-1-5090-5992-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2017-05", "pages": "4964-4970" }, { "id": "authors:zjdnn-bxw82", "collection": "authors", "collection_id": "zjdnn-bxw82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170614-142315589", "type": "article", "title": "Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks", "author": [ { "family_name": "Meng", "given_name": "X. Flora", "clpid": "Meng-X-Flora" }, { "family_name": "Baetica", "given_name": "Ania-Ariadna", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-Ania-Ariadna" }, { "family_name": "Singhal", "given_name": "Vipul", "orcid": "0000-0003-1670-1824", "clpid": "Singhal-Vipul" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. \nWe first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces.", "doi": "10.1098/rsif.2017.0157", "pmcid": "PMC5454304", "issn": "1742-5689", "publisher": "The Royal Society", "publication": "Journal of the Royal Society Interface", "publication_date": "2017-05", "series_number": "130", "volume": "14", "issue": "130", "pages": "Art. No. 20170157" }, { "id": "authors:2vkpx-r9522", "collection": "authors", "collection_id": "2vkpx-r9522", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-152213138", "type": "book_section", "title": "A fast motion planning representation for configuration flat robots with applications to micro air vehicles", "book_title": "2017 American Control Conference", "author": [ { "family_name": "Fragoso", "given_name": "Anthony T.", "orcid": "0000-0002-5805-9668", "clpid": "Fragoso-Anthony-T" }, { "family_name": "Matthies", "given_name": "Larry H.", "clpid": "Matthies-L-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "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-dimensional 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 multiresolution and multi-sensor representation architecture into a single simple and efficient layer.", "doi": "10.23919/ACC.2017.7963600", "isbn": "978-1-5090-5992-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2017-05", "pages": "4195-4202" }, { "id": "authors:myf9p-n3161", "collection": "authors", "collection_id": "myf9p-n3161", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170629-080527577", "type": "article", "title": "Systems & Control for the future of humanity, research agenda: Current and future roles, impact and grand challenges", "author": [ { "family_name": "Lamnabhi-Lagarrigue", "given_name": "Francoise", "clpid": "Lamnabhi-Lagarrigue-F" }, { "family_name": "Annaswamy", "given_name": "Anuradha", "clpid": "Annaswamy-A" }, { "family_name": "Engell", "given_name": "Sebastian", "clpid": "Engell-S" }, { "family_name": "Isaksson", "given_name": "Alf", "clpid": "Isaksson-A" }, { "family_name": "Khargonekar", "given_name": "Pramod", "clpid": "Khargonekar-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Nijmeijer", "given_name": "Henk", "clpid": "Nijmeijer-H" }, { "family_name": "Samad", "given_name": "Tariq", "clpid": "Samad-T" }, { "family_name": "Tilbury", "given_name": "Dawn", "clpid": "Tilbury-D" }, { "family_name": "Van den Hof", "given_name": "Paul", "clpid": "Van-den-Hof-P" } ], "abstract": "Following in the footsteps of the renowned report \"Control in an Information Rich World,\" Report of the Panel on \"Future Directions in Control, Dynamics, and Systems\" chaired by Richard Murray (2002), this paper aims to demonstrate that Systems & Control is at the heart of the Information and Communication Technologies to most application domains. As such, Systems & Control should be acknowledged as a priority by funding agencies and supported at the levels necessary to enable technologies addressing critical societal challenges. A second intention of this paper is to present to the industrials and the young research generation, a global picture of the societal and research challenges where the discipline of Systems & Control will play a key role. Throughout, this paper demonstrates the extremely rich, current and future, cross-fertilization between five critical societal challenges and seven key research and innovation Systems & Control scientific challenges. This paper is authored by members of the IFAC Task Road Map Committee, established following the 19th IFAC World Congress in Cape Town. Other experts who authored specific parts are listed below.", "doi": "10.1016/j.arcontrol.2017.04.001", "issn": "1367-5788", "publisher": "Elsevier", "publication": "Annual Reviews in Control", "publication_date": "2017-04-26", "volume": "43", "pages": "1-64" }, { "id": "authors:njttn-8e877", "collection": "authors", "collection_id": "njttn-8e877", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170303-084805424", "type": "book_section", "title": "Enhancing tolerance to unexpected jumps in GR(1) games", "book_title": "Proceedings of the 8th ACM/IEEE International Conference on Cyber-Physical Systems, Pitssburgh, PA USA, April 2017 (ICCPS)", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "When used as part of a hybrid controller, finite-memory strategies synthesized from linear-time temporal logic (LTL) specifications rely on an accurate dynamics model in order to ensure correctness of trajectories. In the presence of uncertainty about the underlying model, there may exist unexpected trajectories that manifest as unexpected transitions\nunder control of the strategy. While some disturbances can be captured by augmenting the dynamics model, such approaches may be conservative in that bisimulations may fail to exist for\nwhich strategies can be synthesized. In this paper, we consider games of the GR(1) fragment of LTL, and we characterize the tolerance of hybrid controllers to perturbations that appear as unexpected jumps (transitions) to states in the discrete strategy part of the controller. \n\nAs a first step, we show robustness to certain unexpected transitions that occur in a finite manner, i.e., despite a certain number of unexpected jumps, the sequence of states obtained will still meet a stricter specification and hence the original specification. Additionally, we propose algorithms to improve robustness by increasing tolerance to additional disturbances. A robot gridworld example is presented to demonstrate the application of the developed ideas and also to perform empirical analysis.", "doi": "10.1145/3055004.3055014", "isbn": "978-1-4503-4965-9", "publisher": "ACM", "place_of_publication": "New York, NY", "publication_date": "2017-04-18", "pages": "37-47" }, { "id": "authors:69e82-62n69", "collection": "authors", "collection_id": "69e82-62n69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-103731007", "type": "monograph", "title": "Implementation and System Identification of a Phosphorylation-Based Insulator in a Cell-Free Transcription-Translation System", "author": [ { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "An outstanding challenge in the design of synthetic biocircuits is the development of a robust and efficient strategy for interconnecting functional modules. Recent work demonstrated that a phosphorylation-based insulator (PBI) implementing a dual strategy of high gain and strong negative feedback can be used as a device to attenuate retroactivity. This paper describes the implementation of such a biological circuit in a cell-free transcription-translation system and the structural identifiability of the PBI in the system. We first show that the retroactivity also exists in the cell-free system by testing a simple negative regulation circuit. Then we demonstrate that the PBI circuit helps attenuate the retroactivity significantly compared to the control. We consider a complex model that provides an intricate description of all chemical reactions and leveraging specific physiologically plausible assumptions. We derive a rigorous simplified model that captures the output dynamics of the PBI. We performed standard system identification analysis and determined that the model is globally identifiable with respect to three critical parameters. These three parameters are identifiable under specific experimental conditions and we performed these experiments to estimate the parameters. Our experimental results suggest that the functional form of our simplified model is sufficient to describe the reporter dynamics and enable parameter estimation. In general, this research illustrates the utility of the cell-free expression system as an alternate platform for biocircuit implementation and system identification and it can provide interesting insights into future biological circuit designs.", "doi": "10.1101/122606", "publication_date": "2017-04-02" }, { "id": "authors:ckas1-ccx41", "collection": "authors", "collection_id": "ckas1-ccx41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-110144869", "type": "monograph", "title": "Prototyping And Implementation Of A Novel Feedforward Loop In A Cell-Free Transcription-Translation System And Cells", "author": [ { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Building novel synthetic biological devices is a time-consuming task because of the lengthy cell-based testing and optimization processes. Recent progress made in the cell-free field suggests that the utilization of mathematical models and cell-free transcription-translation testing platforms to systematically design and test novel synthetic biocircuits may help streamline some of the processes. Here we present a study of building a novel functional biological network motif from scratch with the aid of the mathematical modeling and the cell-free prototyping. In this work, we demonstrated that we were able to make a 3-promoter feedforward circuit from a concept to a working biocircuit in cells within a month. We started with performing simulations with a cell-free transcription\u2013translation simulation toolbox. After verifying the feasibility of the circuit design, we used a fast assembling method to build the constructs and used the linear DNAs directly in the cell-free system for prototyping. After additional tests and assemblies, we implemented the circuit in plasmid forms in cells and showed that the in vivo results were consistent with the simulations and the outcomes in the cell-free platform. This study showed the usefulness of modeling and prototyping in building synthetic biocircuits and that we can use these tools to help streamline the process of circuit optimizations in future studies.", "doi": "10.1101/123190", "publication_date": "2017-04-02" }, { "id": "authors:xysr9-7pt09", "collection": "authors", "collection_id": "xysr9-7pt09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200131-144053728", "type": "monograph", "title": "Fast Automatic Verification of Large-Scale Systems with Lookup Tables", "author": [ { "family_name": "Arichega", "given_name": "Nikos", "clpid": "Arichega-N" }, { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Vernekar", "given_name": "Shashank", "clpid": "Vernekar-S" }, { "family_name": "Gao", "given_name": "Sicun", "clpid": "Gao-Sicun" }, { "family_name": "Shiraishi", "given_name": "Shin'Ichi", "clpid": "Shiraishi-Shinichi" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Modern safety-critical systems are difficult to formally verify, largely due to their large scale. In particular, the widespread use of lookup tables in embedded systems across diverse industries, such as aeronautics and automotive systems, create a critical obstacle to the scalability of formal verification. This paper presents a novel approach for the formal verification of large-scale systems with lookup tables. We use a learning-based technique to automatically learn abstractions of the lookup tables and use the abstractions to then prove the desired property. If the verification fails, we propose a falsification heuristic to search for a violation of the specification. In contrast with previous work on lookup table verification, our technique is completely automatic, making it ideal for deployment in a production environment. To our knowledge, our approach is the only technique that can automatically verify large-scale systems lookup with tables. \n\nWe illustrate the effectiveness of our technique on a benchmark which cannot be handled by the commercial tool SLDV, and we demonstrate the performance improvement provided by our technique.", "publisher": "Caltech Library", "publication_date": "2017-04" }, { "id": "authors:0xzfx-sm402", "collection": "authors", "collection_id": "0xzfx-sm402", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190410-120622960", "type": "monograph", "title": "Model Predictive Control for Signal Temporal Logic Specification", "author": [ { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "Donz\u00e9", "given_name": "Alexandre", "clpid": "Donz\u00e9-A" }, { "family_name": "Maasoumy", "given_name": "Mehdi", "clpid": "Maasoumy-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sangiovanni-Vincentelli", "given_name": "Alberto", "orcid": "0000-0003-1298-8389", "clpid": "Sangiovanni-Vincentelli-A-L" }, { "family_name": "Seshia", "given_name": "Sanjit A.", "clpid": "Seshia-S-A" } ], "abstract": "We present a mathematical programming-based method for model predictive control of cyber-physical systems subject to signal temporal logic (STL) specifications. We describe the use of STL to specify a wide range of properties of these systems, including safety, response and bounded liveness. For synthesis, we encode STL specifications as mixed integer-linear constraints on the system variables in the optimization problem at each step of a receding horizon control framework. We prove correctness of our algorithms, and present experimental results for controller synthesis for building energy and climate control.", "doi": "10.48550/arXiv.1703.09563", "publisher": "arXiv", "publication_date": "2017-03-28" }, { "id": "authors:pds01-11065", "collection": "authors", "collection_id": "pds01-11065", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190325-142752006", "type": "monograph", "title": "Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape", "author": [ { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Poole", "given_name": "William", "orcid": "0000-0002-2958-6776", "clpid": "Poole-William" }, { "family_name": "Pandey", "given_name": "Ayush", "orcid": "0000-0003-3590-4459", "clpid": "Pandey-Ayush" }, { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In systems and synthetic biology, it is common to build chemical reaction network (CRN) models of biochemical circuits and networks. Although automation and other high-throughput techniques have led to an abundance of data enabling data-driven quantitative modeling and parameter estimation, the intense amount of simulation needed for these methods still frequently results in a computational bottleneck. Here we present bioscrape (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation of highly customizable chemical reaction networks. Specifically, bioscrape supports deterministic and stochastic simulations, which can incorporate delay, cell growth, and cell division. All functionalities - reaction models, simulation algorithms, cell growth models, partioning models, and Bayesian inference - are implemented as interfaces in an easily extensible and modular object-oriented framework. Models can be constructed via Systems Biology Markup Language (SBML) or specified programmatically via a Python API. Simulation run times obtained with the package are comparable to those obtained using C code - this is particularly advantageous for computationally expensive applications such as Bayesian inference or simulation of cell lineages. We first show the package's simulation capabilities on a variety of example simulations of stochastic gene expression. We then further demonstrate the package by using it to do parameter inference on a model of integrase enzyme-mediated DNA recombination dynamics with experimental data. The bioscrape package is publicly available online (https://github.com/biocircuits/bioscrape) along with more detailed documentation and examples.", "doi": "10.1101/121152", "publication_date": "2017-03-27" }, { "id": "authors:8cwyv-jbk14", "collection": "authors", "collection_id": "8cwyv-jbk14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-101737121", "type": "monograph", "title": "Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology", "author": [ { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The recent abundance of high-throughput data for biological circuits enables data-driven quantitative modeling and parameter estimation. Common modeling issues include long computational times during parameter estimation, and the need for many iterations of this cycle to match data. Here, we present BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation for biological circuits. The BioSCRAPE package can be used for deterministic or stochastic simulations and can incorporate delayed reactions, cell growth, and cell division. Simulation run times obtained with the package are comparable to those obtained using C code - this is particularly advantageous for computationally expensive applications such as Bayesian inference or simulation of cell lineages. We first show the package's simulation capabilities on a variety of example simulations of stochastic gene expression. We then further demonstrate the package by using it to do parameter inference for a model of integrase dynamics using experimental data. The BioSCRAPE package is publicly available online along with more detailed documentation and examples.", "doi": "10.1101/121152", "publication_date": "2017-03-27" }, { "id": "authors:x90ch-0e880", "collection": "authors", "collection_id": "x90ch-0e880", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170627-105933916", "type": "monograph", "title": "Engineering pulsatile communication in bacterial consortia", "author": [ { "family_name": "Parkin", "given_name": "James M.", "orcid": "0000-0002-4058-2338", "clpid": "Parkin-J-M" }, { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Lux-type quorum sensing systems enable communication in bacteria with only two protein components: a signal synthase and an inducible transcription activator. The simplicity of these systems makes them a popular choice for engineering collaborative behaviors in synthetic bacterial consortia, such as photographic edge detection and synchronized oscillation. To add to this body of work, we propose a pulsatile communication circuit that enables dynamic patterning and long-distance communication analogous to action potentials traveling through nerve tissue. We employed a model-driven design paradigm involving incremental characterization of in vivo design candidates with increasing circuit complexity. Beginning with a simple inducible reporter system, we screened a small number of circuits varying in their promoter and ribosomal binding site strengths. From this candidate pool, we selected a candidate to be the seed network for the subsequent round of more complex circuit variants, likewise variable in promoter and RBS strengths. The selection criteria at each level of complexity is tailored to optimize a different desirable performance characteristic. By this approach we individually optimized reporter signal-to-background ratio, pulsatile response to induction, and quiescent basal transcription, avoiding large library screens while ensuring robust performance of the composite circuit.", "doi": "10.1101/111906", "publication_date": "2017-02-26" }, { "id": "authors:rta0b-y7810", "collection": "authors", "collection_id": "rta0b-y7810", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170627-105346578", "type": "monograph", "title": "Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli", "author": [ { "family_name": "Shur", "given_name": "Andrey", "clpid": "Shur-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Serine integrases are bacteriophage proteins responsible for integrating the phage genome into that of the host. Synthetic biologists have co-opted these proteins into useful tools for permanent DNA logic, utilizing their specific DNA recombination abilities to build synthetic cell differentiation and genetic memory systems. Each integrase has a specific pair of DNA sequences (attP/attB sites) that it recombines, but multiple identical sites can result in unpredictable recombination. We have developed a way to control integrase activity on identical attP/attB sites by using catalytically dead Cas9 (dCas9) as a programmable binding protein that can compete with integrase for binding to specific attachment sites. Utilizing a plasmid that contains two identical Bxb1 attP sites, integration can be repressed up to 8 fold at either one of the two attP sites when guide RNA and dCas9 are present. Guide RNA sequences that bind specifically to attB, or either of two attP sites, have been developed. Future goals are to utilize this technology to construct larger and more complex integrase logic circuits.", "doi": "10.1101/110254", "publication_date": "2017-02-21" }, { "id": "authors:902cn-7xz30", "collection": "authors", "collection_id": "902cn-7xz30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170202-080959480", "type": "article", "title": "Privacy Preserving Average Consensus", "author": [ { "family_name": "Mo", "given_name": "Yilin", "orcid": "0000-0001-7937-6737", "clpid": "Mo-Yilin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Average consensus is a widely used algorithm for distributed computing and control, where all the agents in the network constantly communicate and update their states in order to achieve an agreement. This approach could result in an undesirable disclosure of information on the initial state of an agent to the other agents. In this paper, we propose a privacy preserving average consensus algorithm to guarantee the privacy of the initial state and asymptotic consensus on the exact average of the initial values, by adding and subtracting random noises to the consensus process. We characterize the mean square convergence rate of our consensus algorithm and derive the covariance matrix of the maximum likelihood estimate on the initial state. Moreover, we prove that our proposed algorithm is optimal in the sense that it does not disclose any information more than necessary to achieve the average consensus. A numerical example is provided to illustrate the effectiveness of the proposed design.", "doi": "10.1109/TAC.2016.2564339", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2017-02", "series_number": "2", "volume": "62", "issue": "2", "pages": "753-765" }, { "id": "authors:a2gp3-q3v71", "collection": "authors", "collection_id": "a2gp3-q3v71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170619-142716206", "type": "monograph", "title": "Expressing Biologically Active Membrane Proteins in a Cell-Free Transcription-Translation Platform", "author": [ { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Vaish", "given_name": "Amit", "clpid": "Vaish-A" }, { "family_name": "Chen", "given_name": "Qing", "clpid": "Chen-Qing" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Cell-free transcription-translation platforms have been widely utilized to express soluble proteins in basic synthetic biological circuit prototyping. From a synthetic biology point of view, it is critical to express membrane proteins in cell-free transcription-translation systems, and use them directly in biocircuits, considering the fact that histidine kinases, G-protein coupled receptors (GPCRs) and other important biosensors are all membrane proteins. Previous studies have expressed membrane proteins in cell-free systems with the help of detergents, liposomes or nanodiscs, but have not demonstrated the ability to prototype circuit behavior for the purpose of testing more complex circuit functions involving membrane-bound proteins. Built on previous efforts, in this work we demonstrated that we could co-translationally express solubilized and active membrane proteins in our cell-free TX-TL platform with membrane-like materials. We first tested the expression of several constructs with \u03b21 and \u03b22 adrenergic receptors in TX-TL and observed significant insoluble membrane protein production. The addition of nanodiscs to the cell free expression system enabled solubilization of membrane proteins. Nanodisc is lipoprotein- based membrane-like material. The activity of \u03b22 adrenergic receptor was tested with both fluorescence and Surface Plasmon Resonance (SPR) binding assays by monitoring the specific binding response of small-molecule binders, carazolol and norepinephrine. Our results suggest that it is promising to use cell-free expression systems to prototype synthetic biocircuits involving single chain membrane proteins without extra procedures. This data made us one step closer to testing complex membrane protein circuits in cell-free environment.", "doi": "10.1101/104455", "publication_date": "2017-01-30" }, { "id": "authors:w8q5t-t4h42", "collection": "authors", "collection_id": "w8q5t-t4h42", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2016.004", "type": "monograph", "title": "Formalizing synthesis in TLA+", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This report proposes a TLA+ definition for the problem of constructing a strategy that implements a temporal property. It is based on a note by Lamport [1] that outlines a formalization of realizability in TLA. The modified definition proposed here is expressed axiomatically in TLA+. Specifying what function is acceptable as a strategy requires care, so that a function with empty domain be avoided, while ensuring that the strategy will not need to have a domain too large to be a set. \n\nWe prove that initial conditions should appear in assumptions only, unless an initial predicate is added to the definition of a realization. We show that a specification should include an assumption about a set of initial values to ensure that realizability does not become unprovable. We discuss what form of open-system properties expressed with the \"while- plus\" operator -+-> are realizable. \n\nWe formalize the notions of interleaving and disjoint-state behaviors, based on definitions given by Lamport and Abadi, and consider the notion of interleaving for an open-system property. We give examples of expressing different forms of games in TLA+ using the proposed definition, including games with partial information.", "publisher": "Caltech Library", "publication_date": "2016-12-23" }, { "id": "authors:gjwhg-3pr04", "collection": "authors", "collection_id": "gjwhg-3pr04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170111-150031011", "type": "book_section", "title": "Constrained autonomous satellite docking via differential flatness and model predictive control", "book_title": "IEEE 55th Conference on Decision and Control (CDC)", "author": [ { "family_name": "Farahani", "given_name": "Samira S.", "clpid": "Farahani-S-S" }, { "family_name": "Papusha", "given_name": "Ivan", "clpid": "Papusha-I" }, { "family_name": "McGhan", "given_name": "Catharine", "clpid": "McGhan-C-L-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We investigate trajectory generation algorithms that allow a satellite to autonomously rendezvous and dock with a target satellite to perform maintenance tasks, or transport the target satellite to a new operational location. We propose different path planning strategies for each of the phases of rendezvous. In the first phase, the satellite navigates to a point in the Line of Sight (LOS) region of the target satellite. We show that the satellite's equations of motion are differentially flat in the relative coordinates, hence the rendezvous trajectory can be found efficiently in the flat output space without a need to integrate the full nonlinear dynamics. In the second phase, we use model predictive control (MPC) with linearized dynamics to navigate the spacecraft to the final docking location within a constrained approach envelope. We demonstrate feasibility of this study by simulating a sample docking mission.", "doi": "10.1109/CDC.2016.7798766", "isbn": "978-1-5090-1837-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-12", "pages": "3306-3311" }, { "id": "authors:57jtz-prh09", "collection": "authors", "collection_id": "57jtz-prh09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170221-080512453", "type": "book_section", "title": "Synthesis of reactive control protocols for switch electrical power systems for commercial application with safety specifications", "book_title": "2016 IEEE Symposium Series on Computational Intelligence (SSCI)", "author": [ { "family_name": "Christalin", "given_name": "Benson", "clpid": "Christalin-B" }, { "family_name": "Colledanchise", "given_name": "Michele", "clpid": "Colledanchise-M" }, { "family_name": "\u00d6gren", "given_name": "Petter", "clpid": "\u00d6gren-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents a method for the reactive synthesis of fault-tolerant optimal control protocols for a finite deterministic discrete event system subject to safety specifications. A Deterministic Finite State Machine (DFSM) and Behavior Tree (BT) were used to model the system. The synthesis procedure involves formulating the policy problem as a shortest path dynamic programming problem. The procedure evaluates all possible states when applied to the DFSM, or over all possible actions when applied to the BT. The resulting strategy minimizes the number of actions performed to meet operational objectives without violating safety conditions. The effectiveness of the procedure on DFSMs and BTs is demonstrated through three examples of switched electrical power systems for commercial application and analyzed using run-time complexity analysis. The results demonstrated that for large order system BTs provided a tractable model to synthesize an optimal control policy.", "doi": "10.1109/SSCI.2016.7849873", "isbn": "978-1-5090-4241-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-12", "pages": "1-8" }, { "id": "authors:2gzmb-ja750", "collection": "authors", "collection_id": "2gzmb-ja750", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200205-073243713", "type": "monograph", "title": "Identifying and exploiting tolerance to unexpected jumps in synthesized strategies for GR(1) specifications", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "When used as part of a hybrid controller, finite-memory strategies synthesized from LTL specifications rely on an accurate dynamics model in order to ensure correctness of trajectories. In the presence of uncertainty about this underlying model, there may exist unexpected trajectories that manifest as unexpected transitions under control of the strategy. \n\nWhile some disturbances can be captured by augmenting the dynamics model, such approaches may be conservative in that bisimulations may fail to exist for which strategies can be synthesized. In this paper, we characterize the tolerance of such hybrid controllers - synthesized for generalized reactivity(1) specifications- to disturbances that appear as unexpected jumps (transitions) to states in the discrete strategy part of the controller. \n\nAs a first step, we show robustness to certain unexpected transitions that occur in a finite-manner, i.e., despite a certain number of unexpected jumps, the sequence of states obtained will still meet a stricter specification and hence the original specification. Additionally, we propose algorithms to improve robustness by increasing tolerance to additional disturbances. \n\nA robot gridworld example is presented to demonstrate the application of the developed ideas and also to obtain empirical computational and memory cost estimates.", "publisher": "Caltech Library", "publication_date": "2016-12" }, { "id": "authors:cmfhw-jcb74", "collection": "authors", "collection_id": "cmfhw-jcb74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170111-150445053", "type": "book_section", "title": "Quantifying resource competition and its effects in the TX-TL system", "book_title": "IEEE 55th Conference on Decision and Control (CDC)", "author": [ { "family_name": "Gyorgy", "given_name": "Andras", "clpid": "Gyorgy-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Without accounting for the limited availability of shared cellular resources, the standard model of gene expression fails to reliably predict experimental data obtained in vitro. To overcome this limitation, we develop a dynamical model of gene expression explicitly modeling competition for scarce resources. In addition to accurately describing the experimental data, this model only depends on a handful of easily identifiable parameters with clear physical interpretation. Based on this model, we then characterize the combinations of protein concentrations that are simultaneously realizable with shared resources. As application examples, we demonstrate how the results can be used to explain similarities/differences among different in vitro extracts, furthermore, we illustrate that accounting for resource usage is essential in circuit design considering the toggle switch.", "doi": "10.1109/CDC.2016.7798775", "isbn": "978-1-5090-1837-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-12", "pages": "3363-3368" }, { "id": "authors:7tkhx-yd005", "collection": "authors", "collection_id": "7tkhx-yd005", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170111-134705561", "type": "book_section", "title": "Automata theory meets approximate dynamic programming: Optimal control with temporal logic constraints", "book_title": "55th Conference on Decision and Control (CDC), 2016", "author": [ { "family_name": "Papusha", "given_name": "Ivan", "clpid": "Papusha-I" }, { "family_name": "Fu", "given_name": "Jie", "clpid": "Fu-Jie" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We investigate the synthesis of optimal controllers for continuous-time and continuous-state systems under temporal logic specifications. The specification is expressed as a deterministic, finite automaton (the specification automaton) with transition costs, and the optimal system behavior is captured by a cost function that is integrated over time. We construct a dynamic programming problem over the product of the underlying continuous-time, continuous-state system and the discrete specification automaton. To solve this dynamic program, we propose controller synthesis algorithms based on approximate dynamic programming (ADP) for both linear and nonlinear systems under temporal logic constraints. We argue that ADP allows treating the synthesis problem directly, without forming expensive discrete abstractions. We show that, for linear systems under co-safe temporal logic constraints, the ADP solution reduces to a single semidefinite program.", "doi": "10.1109/CDC.2016.7798307", "isbn": "978-1-5090-1838-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-12", "pages": "434-440" }, { "id": "authors:5v63h-c7q73", "collection": "authors", "collection_id": "5v63h-c7q73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170313-102144883", "type": "monograph", "title": "The Effect of Compositional Context on Synthetic Gene Networks", "author": [ { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Dy", "given_name": "Aaron J.", "orcid": "0000-0003-0535-517X", "clpid": "Dy-Aaron-J" }, { "family_name": "Martin", "given_name": "Kyle B.", "clpid": "Martin-K-B" }, { "family_name": "Ng", "given_name": "Andrew H.", "clpid": "Ng-Andrew-H" }, { "family_name": "Del Vecchio", "given_name": "Domitilla", "orcid": "0000-0001-6472-8576", "clpid": "Del-Vecchio-D" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" }, { "family_name": "Collins", "given_name": "James J.", "clpid": "Collins-J-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It is well known that synthetic gene expression is highly sensitive to how genetic elements (promoter structure, spacing regions between promoter and coding sequences, ribosome binding sites, etc.) are spatially configured. An important topic that has received far less attention is how the compositional context, or spatial arrangement, of entire genes within a synthetic gene network affects their individual expression levels. In this paper we show, both quantitatively and qualitatively, that compositional context significantly alters transcription levels in synthetic gene networks. We demonstrate that key characteristics of gene induction, such as ultra-sensitivity and dynamic range, strongly depend on compositional context. We postulate that supercoiling can be used to explain this interference and validate this hypothesis through modeling and a series of in vitro supercoiling relaxation experiments. This compositional interference enables a novel form of feedback in synthetic gene networks. We illustrate the use of this feedback by redesigning the toggle switch to incorporate compositional context. We show the context-optimized toggle switch has improved threshold detection and memory properties.", "doi": "10.1101/083329", "publication_date": "2016-11-30" }, { "id": "authors:ecmh2-yw767", "collection": "authors", "collection_id": "ecmh2-yw767", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170206-084448312", "type": "monograph", "title": "A Bayesian approach to inferring chemical signal timing and amplitude in a temporal logic gate using the cell population distributional response", "author": [ { "family_name": "Baetica", "given_name": "Ania A.", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Catanach", "given_name": "Thomas A.", "orcid": "0000-0002-4321-3159", "clpid": "Catanach-T-A" }, { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Beck", "given_name": "James L.", "clpid": "Beck-J-L" } ], "abstract": "Stochastic gene expression poses an important challenge for engineering robust behaviors in a heterogeneous cell population. Cells address this challenge by operating on distributions of cellular responses generated by noisy processes. Similarly, a previously published temporal logic gate considers the distribution of responses across a cell population under chemical inducer pulsing events. The design uses a system of two integrases to engineer an E. coli strain with four DNA states that records the temporal order of two chemical signal events. The heterogeneous cell population response was used to infer the timing and duration of the two chemical signals for a small set of events. Here we use the temporal logic gate system to address the problem of extracting information about chemical signal events. We use the heterogeneous cell population response to infer whether any event has occurred or not and also to infer its properties such as timing and amplitude. Bayesian inference provides a natural framework to answer our questions about chemical signal occurrence, timing, and amplitude. We develop a probabilistic model that incorporates uncertainty in the how well our model captures the cell population and in how well a sample of measured cells represents the entire population. Using our probabilistic model and cell population measurements taken every five minutes on generated data, we ask how likely it was to observe the data for parameter values that describe square-shaped inducer pulses. We compare the likelihood functions associated with the probabilistic models for the event with the chemical signal pulses turned on versus turned off. Hence, we can determine whether an event of chemical induction of integrase expression has occurred or not. Using Markov Chain Monte Carlo, we sample the posterior distribution of chemical pulse parameters to identify likely pulses that produce the data measurements. We implement this method and obtain accurate results for detecting chemical inducer pulse timing, length, and amplitude. We can detect and identify chemical inducer pulses as short as half an hour, as well as all pulse amplitudes that fall under biologically relevant conditions.", "doi": "10.1101/087379", "publication_date": "2016-11-14" }, { "id": "authors:qancn-eky27", "collection": "authors", "collection_id": "qancn-eky27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170202-073327562", "type": "article", "title": "Stability of Systems with Stochastic Delays and Applications to Genetic Regulatory Networks", "author": [ { "family_name": "Gomez", "given_name": "Marcella M.", "clpid": "Gomez-Marcella-M" }, { "family_name": "Sadeghpour", "given_name": "Mehdi", "orcid": "0000-0003-3946-960X", "clpid": "Sadeghpour-Mehdi" }, { "family_name": "Bennett", "given_name": "Matthew R.", "orcid": "0000-0002-4975-8854", "clpid": "Bennett-Mathew-R" }, { "family_name": "Orosz", "given_name": "G\u00e1bor", "orcid": "0000-0002-9000-3736", "clpid": "Orosz-G\u00e1bor" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The dynamics of systems with stochastically varying time delays are investigated in this paper. It is shown that the mean dynamics can be used to derive necessary conditions for the stability of equilibria of the stochastic system. Moreover, the second moment dynamics can be used to derive sufficient conditions for almost sure stability of equilibria. The results are summarized using stability charts that are obtained via semidiscretization. The theoretical methods are applied to simple gene regulatory networks where it is demonstrated that stochasticity in the delay can improve the stability of steady protein production.", "doi": "10.1137/15M1031965", "pmcid": "PMC5603244", "issn": "1536-0040", "publisher": "Society for Industrial and Applied Mathematics", "publication": "SIAM Journal on Applied Dynamical Systems", "publication_date": "2016-10-13", "series_number": "4", "volume": "15", "issue": "4", "pages": "1844-1873" }, { "id": "authors:96j27-syv30", "collection": "authors", "collection_id": "96j27-syv30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-150803580", "type": "article", "title": "The effects of time-varying temperature on delays in genetic networks", "author": [ { "family_name": "Gomez", "given_name": "Marcella M.", "clpid": "Gomez-Marcella-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Bennett", "given_name": "Matthew R.", "orcid": "0000-0002-4975-8854", "clpid": "Bennett-Mathew-R" } ], "abstract": "Delays in gene networks result from the sequential nature of protein assembly. However, it is unclear how models of gene networks that use delays should be modified when considering time-dependent changes in temperature. This is important, as delay is often used in models of genetic oscillators that can be entrained by periodic fluctuations in temperature. Here, we analytically derive the time dependence of delay distributions in response to time-varying temperature changes. We find that the resulting time-varying delay is nonlinearly dependent on parameters of the time-varying temperature such as amplitude and frequency; therefore, applying an Arrhenius scaling may result in erroneous conclusions. We use these results to examine a model of a synthetic gene oscillator with temperature compensation. We show that temperature entrainment follows from the same mechanism that results in temperature compensation. Under a common Arrhenius scaling alone, the frequency of the oscillator is sensitive to changes in the mean temperature but robust to changes in the frequency of a periodically time-varying temperature. When a mechanism for temperature compensation is included in the model, however, we show that the oscillator is entrained by periodically varying temperature even when maintaining insensitivity to the mean temperature.", "doi": "10.1137/15M1040979", "pmcid": "PMC5656297", "issn": "1536-0040", "publisher": "Society for Industrial and Applied Mathematics", "publication": "SIAM Journal on Applied Dynamical Systems", "publication_date": "2016-09-15", "series_number": "3", "volume": "15", "issue": "3", "pages": "1734-1752" }, { "id": "authors:cabp8-4rk89", "collection": "authors", "collection_id": "cabp8-4rk89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190822-084034717", "type": "book_section", "title": "Resilient Spacecraft Executive: An Architecture for Risk-Aware Operations in Uncertain Environments", "book_title": "AIAA SPACE 2016", "author": [ { "family_name": "McGhan", "given_name": "Catharine L. R.", "clpid": "McGhan-C-L-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Vaquero", "given_name": "Tiago", "clpid": "Vaquero-T" }, { "family_name": "Williams", "given_name": "Brian C.", "clpid": "Williams-B-C" }, { "family_name": "Ingham", "given_name": "Michel D.", "clpid": "Ingham-M-D" }, { "family_name": "Ono", "given_name": "Masahiro", "clpid": "Ono-Masahiro" }, { "family_name": "Estlin", "given_name": "Tara", "clpid": "Estlin-T" }, { "family_name": "Lanka", "given_name": "Ravi", "clpid": "Lanka-R" }, { "family_name": "Arslan", "given_name": "Oktay", "clpid": "Arslan-O" }, { "family_name": "Elaasar", "given_name": "Maged E.", "clpid": "Elaasar-M-E" } ], "abstract": "In this paper we discuss the latest results from the Resilient Space Systems project, a joint effort between Caltech, MIT, NASA Jet Propulsion Laboratory (JPL), and the Woods Hole Oceanographic Institution (WHOI). The goal of the project is to define a resilient, risk-aware software architecture for onboard, real-time autonomous operations that can robustly handle uncertainty in spacecraft behavior within hazardous and unconstrained environments, without unnecessarily increasing complexity. The architecture, called the Resilient Spacecraft Executive (RSE), has been designed to support three functions: (1) adapting to component failures to allow graceful degradation, (2) accommodating environments, science observations, and spacecraft capabilities that are not fully known in advance, and (3) making risk-aware decisions without waiting for slow ground-based reactions. In implementation, the bulk of the RSE effort has focused on the parts of the architecture used for goal-directed execution and control, including the deliberative, habitual, and reflexive modules. We specify the capabilities and constraints needed for each module, and discuss how we have extended the current state-of-the-art algorithms so that they can supply the required functionality, such as risk-aware planning in the deliberative module that conforms to mission operator-supplied priorities and constraints. Furthermore, the RSE architecture is modular to enable extension and reconfiguration, as long as the embedded algorithmic components exhibit the required risk-aware behavior in the deliberative module and risk-bounded behavior in the habitual module. To that end, we discuss some feasible, useful RSE configurations and deployments for a Mars rover case and an autonomous underwater vehicle case. We also discuss additional capabilities that the architecture requires to support needed resiliency, such as onboard analysis and learning.", "doi": "10.2514/6.2016-5541", "isbn": "978-1-62410-427-5", "publisher": "American Institute of Aeronautics and Astronautics", "place_of_publication": "Reston, VA", "publication_date": "2016-09-09", "pages": "Art. No. 2016-5541" }, { "id": "authors:py6yc-hy415", "collection": "authors", "collection_id": "py6yc-hy415", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190822-074943945", "type": "book_section", "title": "Risk-aware Planning in Hybrid Domains: An Application to Autonomous Planetary Rovers", "book_title": "AIAA SPACE 2016", "author": [ { "family_name": "Santana", "given_name": "Pedro", "clpid": "Sanatan-P" }, { "family_name": "Vaquero", "given_name": "Tiago", "clpid": "Vaquero-T" }, { "family_name": "Timmons", "given_name": "Eric", "clpid": "Timmons-E" }, { "family_name": "Williams", "given_name": "Brian C.", "clpid": "Williams-B-C" }, { "family_name": "McGhan", "given_name": "Catharine L. R.", "clpid": "McGhan-C-L-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Toledo", "given_name": "Cl\u00e1udio", "clpid": "Toledo-C" } ], "abstract": "Expanding robotic space exploration beyond the immediate vicinity of Earth's orbit can only be achieved by increasingly autonomous agents, given the sometimes insurmountable challenges of teleoperation over great distances. Among the numerous requirements that a fully autonomous robotic space explorer must meet, here we focus on three key mission-enabling technologies: the ability to act under uncertainty and adapt to its environment; the ability to optimize performance while offering hard bounds on the risk of mission failure; and the ability to handle complex hybrid (discrete and continuous) mission planning problems in a provably correct and scalable fashion. In this paper, we show how CLARK, a planner capable of generating risk-bounded, dynamic temporal plans for autonomous agents operating under uncertainty, is able to efficiently generate temporal plans for a challenging planetary rover scenario featuring temporal uncertainty that could not be addressed by previous methods.", "doi": "10.2514/6.2016-5537", "isbn": "978-1-62410-427-5", "publisher": "American Institute of Aeronautics and Astronautics", "place_of_publication": "Reston, VA", "publication_date": "2016-09-09", "pages": "Art. No. 2016-5537" }, { "id": "authors:y50n2-rdm74", "collection": "authors", "collection_id": "y50n2-rdm74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190822-090943975", "type": "book_section", "title": "Towards Architecture-wide Analysis, Verification, and Validation for Total System Stability During Goal-Seeking Space Robotics Operations", "book_title": "AIAA SPACE 2016", "author": [ { "family_name": "McGhan", "given_name": "Catharine L. R.", "clpid": "McGhan-C-L-R" }, { "family_name": "Wang", "given_name": "Yuh-Shyang", "orcid": "0000-0001-7357-7247", "clpid": "Wang-Yuh-Shyang" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Vaquero", "given_name": "Tiago", "clpid": "Vaquero-T" }, { "family_name": "Williams", "given_name": "Brian C.", "clpid": "Williams-B-C" }, { "family_name": "Colledanchise", "given_name": "Michele", "clpid": "Colledanchise-M" }, { "family_name": "\u00d6gren", "given_name": "Petter", "clpid": "\u00d6gren-P" } ], "abstract": "In this paper we discuss the beginnings of an attempt to define and analyze the stability of an entire modular robotic system architecture - one which includes a three-tier (3T) layer breakdown of capabilities, with symbolic, deterministic planning at the highest level. We approach the problem from the standpoint of a control theory outlook, and try to formalize the issues that result from trying to quantitatively characterize the overall performance of a well-defined system without a need for exhaustive testing. We start by discussing the concept of bounded-input bounded-output stability, giving examples where the technique might not be sufficient to guarantee what we term \"total system stability\" due to complications associated with the levels of abstraction between the modules and components that are being chained together in the architecture. We then go on to discuss necessary conditions that may fall out of this naturally as a result. We further try to better-define the input and output constraints needed to guarantee total system stability, using an assumption-guarantee-like contractual framework that sits alongside the architecture; the requirements then may have influence across multiple modules, in order to keep consistency. We also discuss how the structure of the architectural modules may help or hinder the process of capability characterization and performance analysis of each module and a given architecture configuration as a whole. We then discuss two overlapping methods that, combined, should allow us to analyze the effectiveness of the architecture, and help towards verification and validation of both the components and the system as a whole. Demonstrative examples are given using a specific architectural implementation called the Resilient Spacecraft Executive. In future work, we hope to define both necessary and sufficient conditions for total system stability across such a system architecture for robotics\nuse.", "doi": "10.2514/6.2016-5607", "isbn": "978-1-62410-427-5", "publisher": "American Institute of Aeronautics and Astronautics", "place_of_publication": "Reston, VA", "publication_date": "2016-09-09", "pages": "Art. No. 2016-5607" }, { "id": "authors:2k6hk-3fd81", "collection": "authors", "collection_id": "2k6hk-3fd81", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161020-140012994", "type": "book_section", "title": "Control design for hybrid systems with TuLiP: The Temporal Logic Planning toolbox", "book_title": "2016 IEEE Conference on Control Applications (CCA)", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This tutorial describes TuLiP, the Temporal Logic Planning toolbox, a collection of tools for designing controllers for hybrid systems from specifications in temporal logic. The tools support a workflow that starts from a description of desired behavior, and of the system to be controlled. The system can have discrete state, or be a hybrid dynamical system with a mixed discrete and continuous state space. The desired behavior can be represented with temporal logic and discrete transition systems. The system description can include uncontrollable variables that take discrete or continuous values, and represent disturbances and other environmental factors that affect the dynamics, as well as communication signals that affect controller decisions.", "doi": "10.1109/CCA.2016.7587949", "isbn": "978-1-5090-0755-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-09", "pages": "1030-1041" }, { "id": "authors:jqgxb-0tw77", "collection": "authors", "collection_id": "jqgxb-0tw77", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2016.003", "type": "monograph", "title": "Symbolic construction of GR(1) contracts for systems with full information", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This work proposes a symbolic algorithm for the construction of assume-guarantee specifications that allow multiple agents to cooperate. Each agent is assigned goals expressed in a fragment of linear temporal logic known as generalized Streett with one pair, GR(1). These goals may be unrealizable, unless each agent makes additional assumptions, about the behavior of other agents. The algorithm constructs a contract among the agents, in that only the infinite behavior of the given goals is constrained, known as liveness, not the finite one, known as safety. This defers synthesis to a later stage of refinement, modularizing the design process. We prove that there exist GR(1) games that do not admit any refining GR(1) contract. For this reason, we formulate contracts with nested GR(1) properties and auxiliary communication variables, and prove that they always exist. The algorithm's fixpoint structure is similar to GR(1) synthesis, enjoying time complexity polynomial in the number of states, and linear in number of recurrence goals.", "doi": "10.1109/ACC.2016.7525009", "publisher": "California Institute of Technology", "publication_date": "2016-07-06" }, { "id": "authors:fgb0j-90y51", "collection": "authors", "collection_id": "fgb0j-90y51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160801-165143151", "type": "book_section", "title": "Symbolic construction of GR(1) contracts for systems with full information", "book_title": "2016 American Control Conference (ACC)", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This work proposes a symbolic algorithm for the construction of assume-guarantee specifications that allow multiple agents to cooperate. Each agent is assigned goals expressed in a fragment of linear temporal logic known as generalized Streett with one pair, GR(1). These goals may be unrealizable, unless each agent makes additional assumptions, about the behavior of other agents. The algorithm constructs a contract among the agents, in that only the infinite behavior of the given goals is constrained, known as liveness, not the finite one, known as safety. This defers synthesis to a later stage of refinement, modularizing the design process. We prove that there exist GR(1) games that do not admit any refining GR(1) contract. For this reason, we formulate contracts with nested GR(1) properties and auxiliary communication variables, and prove that they always exist. The algorithm's fixpoint structure is similar to GR(1) synthesis, enjoying time complexity polynomial in the number of states, and linear in number of recurrence goals.", "doi": "10.1109/ACC.2016.7525009", "isbn": "978-1-4673-8680-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-07", "pages": "782-789" }, { "id": "authors:8fw99-47959", "collection": "authors", "collection_id": "8fw99-47959", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160802-094940806", "type": "book_section", "title": "Linear System Identifiability from Distributional and Time Series Data", "book_title": "2016 American Control Conference (ACC)", "author": [ { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider identifiability of linear systems driven by white noise using a combination of distributional and time series measurements. Specifically, we assume that the system has no control inputs available and can only be observed at stationarity. The user is able to measure the full stationary state distribution as well as observe time correlations for small subsets of the state. We formulate theoretical conditions on identifiability of parameters from distributional information alone. We then give a sufficient condition and an effective necessary condition for identifiability using a combination of distributional and time series measurements. We illustrate the ideas with some simple examples as well as a biologically inspired example of a transcription and degradation process.", "doi": "10.1109/ACC.2016.7524946", "isbn": "978-1-4673-8680-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-07", "pages": "392-399" }, { "id": "authors:8snkc-0z872", "collection": "authors", "collection_id": "8snkc-0z872", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200205-074759124", "type": "monograph", "title": "Stochastic Gene Expression in Single Gene Oscillator Variants", "author": [ { "family_name": "Swaminathan", "given_name": "Anandh", "orcid": "0000-0001-9935-6530", "clpid": "Swaminathan-A" }, { "family_name": "Gomez", "given_name": "Marcella M.", "clpid": "Gomez-M-M" }, { "family_name": "Shis", "given_name": "David L.", "clpid": "Shis-D-L" }, { "family_name": "Bennett", "given_name": "Matthew R.", "clpid": "Bennett-M-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It is infeasible to understand all dynamics in cell, but we can aim to understand the impact of design choices under our control. Here we consider a single gene oscillator as a case study to understand the influence of DNA copy number and repressor choice on the resulting dynamics. We first switch the repressor in the oscillator from the originally published lacI to treRL, a chimeric repressor with a lacI DNA binding domain that is inducible by trehalose. This slightly modified system produces faster and more regular oscillations than the original lacI oscillator. We then compare the treRL oscillator at three different DNA copy numbers. The period and amplitude of oscillations increases as the copy number is decreased. We cannot explain the change in period with differential equation models without changing delays or degradation rates. The correlation and phase coherence between daughter cells after cell division also tend to fall off faster for the lower copy oscillator variants. These results suggest that lower copy number variants of our single gene oscillator produce more synchronized oscillations.", "publisher": "Caltech Library", "publication_date": "2016-07" }, { "id": "authors:j3k2e-3vf46", "collection": "authors", "collection_id": "j3k2e-3vf46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170118-094026442", "type": "book_section", "title": "Robust model predictive control for an uncertain smart thermal grid", "book_title": "2016 European Control Conference (ECC)", "author": [ { "family_name": "Farahani", "given_name": "Samira S.", "clpid": "Farahani-S-S" }, { "family_name": "Lukszo", "given_name": "Zofia", "clpid": "Lukszo-Z" }, { "family_name": "Keviczky", "given_name": "Tam\u00e1s", "clpid": "Keviczky-T" }, { "family_name": "De Schutter", "given_name": "Bart", "clpid": "De-Schutter-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The focus of this paper is on modeling and control of Smart Thermal Grids (STGs) in which the uncertainties in the demand and/or supply are included. We solve the corresponding robust model predictive control (MPC) optimization problem using mixed-integer-linear programming techniques to provide a day-ahead prediction for the heat production in the grid. In an example, we compare the robust MPC approach with the robust optimal control approach, in which the day-ahead production plan is obtained by optimizing the objective function for entire day at once. There, we show that the robust MPC approach successfully keeps the supply-demand balance in the STG while satisfying the constraints of the production units in the presence of uncertainties in the heat demand. Moreover, we see that despite the longer computation time, the performance of the robust MPC controller is considerably better than the one of the robust optimal controller.", "doi": "10.1109/ECC.2016.7810452", "isbn": "978-1-5090-2591-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2016-07", "pages": "1195-1200" }, { "id": "authors:w8vjc-rwm94", "collection": "authors", "collection_id": "w8vjc-rwm94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160706-081948550", "type": "monograph", "title": "The role of single occupancy effects on integrase dynamics in a cell-free system", "author": [ { "family_name": "Artavanis", "given_name": "Georgios", "clpid": "Artavanis-G" }, { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Hayes", "given_name": "Clarmyra A.", "clpid": "Hayes-C-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Phage integrase-based circuits are an alternative approach to relying on transcriptional and translational repression for biomolecular circuits. Previous research has shown that circuits based on integrases can perform a variety of functions, including counters, Boolean logic operators, memory modules and temporal event detectors. It is therefore essential to develop a principled theoretical and experimental framework for the design, implementation and study of such circuits. One of the fundamental questions that such a framework should address concerns the functionality limitations and temporal dynamics of the integrases as regulatory elements. Here, we test the functionality of several large serine integrases from a recently published library in a cell-free transcription-translation (TX-TL) platform. Additionally, we use a combination of experimental data and models to investigate integrase dynamics as a function of enzyme concentration and number of binding sites.\nWe report that sequestration of integrase molecules, either in the form of monomers or dimers, by the integrase's own binding sites dominates integrase dynamics, and that the delay in the activation of the reporter is negatively correlated with integrase plasmid concentration. We have validated our sequestration hypothesis by building a model with MATLAB's SimBiology toolbox, and running simulations with various integrase and binding sites concentrations. The simulation results qualitatively match the experimental results, and offer further insights into the system.", "doi": "10.1101/059675", "publication_date": "2016-06-18" }, { "id": "authors:hxd5m-m8p20", "collection": "authors", "collection_id": "hxd5m-m8p20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151116-095719395", "type": "article", "title": "A population-based temporal logic gate for timing and recording chemical events", "author": [ { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Hori", "given_name": "Yutaka", "orcid": "0000-0002-3253-4985", "clpid": "Hori-Yutaka" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "orcid": "0000-0002-1653-3202", "clpid": "Rothemund-P-W-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two\u2010input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single\u2010cell responses that translated into analog population responses. Furthermore, when single\u2010cell genetic states were aggregated into population\u2010level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub\u2010populations could be used to deduce order, timing, and duration of transient chemical events.", "doi": "10.15252/msb.20156663", "pmcid": "PMC5289221", "issn": "1744-4292", "publisher": "Nature Publishing Group", "publication": "Molecular Systems Biology", "publication_date": "2016-05", "series_number": "5", "volume": "12", "issue": "5", "pages": "Art. No. 869" }, { "id": "authors:am445-nq820", "collection": "authors", "collection_id": "am445-nq820", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161116-150409481", "type": "book_section", "title": "Optimal Control of Nonlinear Systems with Temporal Logic Specifications", "book_title": "Robotics Research", "author": [ { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Inaba", "given_name": "Masayuki", "clpid": "Inaba-M" }, { "family_name": "Corke", "given_name": "Peter", "clpid": "Corke-P" } ], "abstract": "We present a mathematical programming-based method for optimal control of nonlinear systems subject to temporal logic task specifications. We specify tasks using a fragment of linear temporal logic (LTL) that allows both finite- and infinite-horizon properties to be specified, including tasks such as surveillance, periodic motion, repeated assembly, and environmental monitoring. Our method directly encodes an LTL formula as mixed-integer linear constraints on the system variables, avoiding the computationally expensive process of creating a finite abstraction. Our approach is efficient; for common tasks our formulation uses significantly fewer binary variables than related approaches and gives the tightest possible convex relaxation. We apply our method on piecewise affine systems and certain classes of differentially flat systems. In numerical experiments, we solve temporal logic motion planning tasks for high-dimensional (10+ \n+\n continuous state) systems.", "doi": "10.1007/978-3-319-28872-7_2", "isbn": "978-3-319-28870-3", "publisher": "Springer", "place_of_publication": "Cham", "publication_date": "2016-04-23", "pages": "21-37" }, { "id": "authors:rs15w-xt215", "collection": "authors", "collection_id": "rs15w-xt215", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150303-123633257", "type": "article", "title": "Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor", "author": [ { "family_name": "de los Santos", "given_name": "Emmanuel L. C.", "clpid": "de-los-Santos-E-L-C" }, { "family_name": "Meyerowitz", "given_name": "Joseph T.", "clpid": "Meyerowitz-J-T" }, { "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" } ], "abstract": "The pursuit of circuits and metabolic pathways of increasing complexity and robustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, variants of qacR, a tetR family repressor, were generated by computational protein design and screened in a cell-free transcription\u2013translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from the in vitro screen were further characterized in vitro and in vivo in a gene circuit. The screen yielded two qacR mutants that respond to vanillin both in vitro and in vivo. While the mutants exhibit some toxicity to cells, presumably due to off-target effects, they are prime starting points for directed evolution toward vanillin sensors with the specifications required for use in a dynamic control loop. We believe this process, a combination of the generation of variants coupled with in vitro screening, can serve as a framework for designing new sensors for other target compounds.", "doi": "10.1021/acssynbio.5b00090", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2016-04-15", "series_number": "4", "volume": "5", "issue": "4", "pages": "287-295" }, { "id": "authors:r390p-tb835", "collection": "authors", "collection_id": "r390p-tb835", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160502-104806241", "type": "monograph", "title": "Development of prokaryotic cell-free systems for synthetic biology", "author": [ { "family_name": "Chiao", "given_name": "Abel C.", "clpid": "Chiao-Abel-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" } ], "abstract": "Prokaryotic cell-free systems are currently heavily used for the production of protein that can be otherwise challenging to produce in cells. However, historically cell-free systems were used to explore natural phenomena before the advent of genetic modification and transformation technology. Recently, synthetic biology has seen a resurgence of this historical use of cell-free systems as a prototyping tool of synthetic and natural genetic circuits. For these cell-free systems to be effective prototyping tools, an understanding of cell-free system mechanics must be established that is not purely protein-expression driven. Here we discuss the development of E. coli-based cell-free systems, with an emphasis on documenting published extract and energy preparation methods into a uniform format. We also discuss additional considerations when applying cell-free systems to synthetic biology.", "doi": "10.1101/048710", "publication_date": "2016-04-15" }, { "id": "authors:s6ncb-46094", "collection": "authors", "collection_id": "s6ncb-46094", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160404-092715239", "type": "book_section", "title": "Application of Correct-by-Construction Principles for a Resilient Risk-Aware Architecture", "book_title": "AIAA SPACE 2015 Conference and Exposition", "author": [ { "family_name": "McGhan", "given_name": "Catharine L. R.", "clpid": "McGhan-C-L-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we discuss the application of correct-by-construction techniques to a resilient,\nrisk-aware software architecture for onboard, real-time autonomous operations. We\nmean to combat complexity and the accidental introduction of bugs through the use of\nverifiable auto-coding software and correct-by-construction techniques, and discuss the use\nof a toolbox for correct-by-construction Temporal Logic Planning (TuLiP) for such a purpose.\nWe describe some of TuLiP's current functionality, specifically its ability to model\nsymbolic discrete systems and synthesize software controllers and control policies that are\ncorrect-by-construction. We then move on to discuss the use of these techniques to define a\ndeliberative goal-directed executive capability that performs risk-informed action-planning\n\u2013 to satisfy the mission goals (specified by mission control) within the specified priorities\nand constraints. Finally, we discuss an application of the TuLiP process to a simple rover\nresilience scenario.", "doi": "10.2514/6.2015-4527", "isbn": "978-1-62410-334-6", "publisher": "AIAA", "place_of_publication": "Reston, VA", "publication_date": "2016-04-04" }, { "id": "authors:23z2y-ypm37", "collection": "authors", "collection_id": "23z2y-ypm37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200205-075449007", "type": "monograph", "title": "Design and application of stationary phase combinatorial promoters", "author": [ { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Cheng", "given_name": "Aileen", "clpid": "Cheng-Aileen" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Current bacterial synthetic circuits rely on the fast dilution and high protein expression that occurs during exponential phase. However, constant exponential phase is both difficult to ensure in a lab environment and almost certainly impractical in any natural setting. Here, we characterize the performance of 13 E. coli native \u03c338 promoters, as well as a previously identified \u03c338 consensus promoter. We then make tetO combinatorial versions of the three strongest promoters to allow for inducible delayed expression. The design of these combinatorial promoters allows for design of circuits with inducible stationary phase activity that can be used for phase-dependent delays in dynamic circuits or spatial partitioning of biofilms.", "publisher": "Caltech Library", "publication_date": "2016-03-29" }, { "id": "authors:k3yy2-xjd16", "collection": "authors", "collection_id": "k3yy2-xjd16", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2016.001", "type": "monograph", "title": "Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Reder", "given_name": "Leonard J.", "clpid": "Reder-L-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes the implementation of an interface connecting the two tools : the JPL SCA (Statechart Autocoder) and TuLiP (Temporal Logic Planning Toolbox) to enable the automatic synthesis of low level implementation code directly from formal specifications. With system dynamics, bounds on uncertainty and formal specifications as inputs, TuLiP synthesizes Mealy machines that are correct-by-construction. An interface is built that automatically translates these Mealy machines into UML statecharts. The SCA accepts the UML statecharts (as XML files) to synthesize flight-certified implementation code. The functionality of the interface is demonstrated through three example systems of varying complexity a) a simple thermostat b) a simple speed controller for an autonomous vehicle and c) a more complex speed controller for an autonomous vehicle with a map-element. In the thermostat controller, there is a specification regarding the desired temperature range that has to be met despite disturbance from the environment. Similarly, in the speed-controllers there are specifications about safe driving speeds depending on sensor health (sensors fail unpredictably) and the map-location. The significance of these demonstrations is the potential circumventing of some of the manual design of statecharts for flight software/controllers. As a result, we expect that less testing and validation will be necessary. In applications where the products of synthesis are used alongside manually designed components, extensive testing or new certificates of correctness of the composition may still be required.", "publisher": "California Institute of Technology", "publication_date": "2016-03-08" }, { "id": "authors:n2t51-awx04", "collection": "authors", "collection_id": "n2t51-awx04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160725-112209526", "type": "book_section", "title": "Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications", "author": [ { "family_name": "Dathathri", "given_name": "Sumanth", "clpid": "Dathathri-S" }, { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Reder", "given_name": "Leonard J.", "clpid": "Reder-L-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes the implementation of an interface\nconnecting the two tools : the JPL SCA (Statechart\nAutocoder) and TuLiP (Temporal Logic Planning Toolbox) to\nenable the automatic synthesis of low level implementation\ncode directly from formal specifications. With system dynamics, bounds on uncertainty and formal specifications as\ninputs, TuLiP synthesizes Mealy machines that are correct-by-construction. An interface is built that automatically translates these Mealy machines into UML statecharts. The SCA accepts the UML statecharts (as XML files) to synthesize flight-certified implementation code. The functionality of the interface is demonstrated through three example systems of varying complexity\na) a simple thermostat b) a simple speed controller for\nan autonomous vehicle and c) a more complex speed controller\nfor an autonomous vehicle with a map-element. In the thermostat controller, there is a specification regarding the desired temperature range that has to be met despite disturbance from the environment. Similarly, in the speed-controllers there are specifications about safe driving speeds depending on sensor health (sensors fail unpredictably) and the map-location. The\nsignificance of these demonstrations is the potential circumventing of some of the manual design of statecharts for flight software/controllers. As a result, we expect that less testing and validation will be necessary. In applications where the products of synthesis are used alongside manually designed components, extensive testing or new certificates of correctness of the composition may still be required.", "doi": "10.1109/AERO.2016.7500557", "publisher": "IEEE", "publication_date": "2016-03" }, { "id": "authors:q8cvf-zyk68", "collection": "authors", "collection_id": "q8cvf-zyk68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190410-120619515", "type": "article", "title": "A multi-paradigm language for reactive synthesis", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" } ], "abstract": "This paper proposes a language for describing reactive synthesis problems that integrates imperative and declarative elements. The semantics is defined in terms of two-player turn-based infinite games with full information. Currently, synthesis tools accept linear temporal logic (LTL) as input, but this description is less structured and does not facilitate the expression of sequential constraints. This motivates the use of a structured programming language to specify synthesis problems. Transition systems and guarded commands serve as imperative constructs, expressed in a syntax based on that of the modeling language Promela. The syntax allows defining which player controls data and control flow, and separating a program into assumptions and guarantees. These notions are necessary for input to game solvers. The integration of imperative and declarative paradigms allows using the paradigm that is most appropriate for expressing each requirement. The declarative part is expressed in the LTL fragment of generalized reactivity(1), which admits efficient synthesis algorithms, extended with past LTL. The implementation translates Promela to input for the Slugs synthesizer and is written in Python. The AMBA AHB bus case study is revisited and synthesized efficiently, identifying the need to reorder binary decision diagrams during strategy construction, in order to prevent the exponential blowup observed in previous work.", "doi": "10.4204/EPTCS.202.6", "issn": "2075-2180", "publisher": "Open Publishing Association", "publication": "Electronic Proceedings in Theoretical Computer Science (EPTCS)", "publication_date": "2016-02-02", "volume": "202", "pages": "73-97" }, { "id": "authors:pktsg-xey74", "collection": "authors", "collection_id": "pktsg-xey74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160120-104956130", "type": "book_section", "title": "Synthesis of reactive controllers for hybrid systems (keynote)", "book_title": "Proceedings of the 43rd Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Decision-making logic in hybrid systems is responsible for selecting modes of operation for the underlying (continuous) control system, reacting to external events and failures in the system, and insuring that the overall control system is satisfying safety and performance specifications. Tools from computer science, such as model-checking and logic synthesis, combined with design patterns from feedback control theory provide new approaches to solving these problems. A major shift is the move from \"design then verify'' to \"specify then synthesize'' approaches to controller design that allow simultaneous synthesis of high-performance, robust control laws and correct-by-construction decision-making logic.", "doi": "10.1145/2837614.2843894", "isbn": "978-1-4503-3549-2", "publisher": "Association for Computing Machinery", "place_of_publication": "New York, NY", "publication_date": "2016-01", "pages": "3" }, { "id": "authors:rtm9d-fbz53", "collection": "authors", "collection_id": "rtm9d-fbz53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160217-085432492", "type": "book_section", "title": "A stochastic framework for the design of transient and steady state behavior of biochemical reaction networks", "book_title": "54th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Baetica", "given_name": "Ania A.", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Yuan", "given_name": "Ye", "orcid": "0000-0001-7858-0437", "clpid": "Yuan-Ye" }, { "family_name": "Gon\u00e7alves", "given_name": "Jorge", "clpid": "Gon\u00e7alves-J-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Stochasticity plays an essential role in the dynamics of biochemical systems. Stochastic behaviors of bimodality, excitability, and fluctuations are present in biochemical reaction networks at low molecular numbers. These stochastic dynamics can be captured by modeling the system using a forward Kolmogorov equation known in the biochemical literature as the chemical master equation. The chemical master equation describes the time evolution of probability distributions of molecule species in the system. We develop a stochastic framework for the design of these time evolving probability distributions. Our design specifications include their uni-/multi-modality, the locations of their modes, and their rate of convergence to the stationary distribution. We formulate these specifications as constraints in an optimization program that determines the desired reaction rate values. We apply our design framework to examples of biochemical reaction networks to illustrate its strengths and limitations.", "doi": "10.1109/CDC.2015.7402699", "isbn": "978-1-4799-7884-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-12", "pages": "3199-3205" }, { "id": "authors:jgasm-tg452", "collection": "authors", "collection_id": "jgasm-tg452", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160216-132738380", "type": "book_section", "title": "Analysis of Control Systems on Symmetric Cones", "book_title": "54th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Papusha", "given_name": "Ivan", "clpid": "Papusha-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It is well known that exploiting special structure is a powerful way to extend the reach of current optimization tools to higher dimensions. While many linear control systems can be treated satisfactorily with linear matrix inequalities (LMI) and semidefinite programming (SDP), practical considerations can still restrict scalability of general methods. Thus, we wish to work with high dimensional systems without explicitly forming SDPs. To that end, we exploit a particular kind of structure in the dynamics matrix, paving the way for a more efficient treatment of a certain class of linear systems. We show how second order cone programming (SOCP) can be used instead of SDP to find Lyapunov functions that certify stability. This framework reduces to a famous linear program (LP) when the system is internally positive, and to a semidefinite program (SDP) when the system has no special structure.", "doi": "10.1109/CDC.2015.7402836", "isbn": "978-1-4799-7884-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-12", "pages": "3971-3976" }, { "id": "authors:sm57v-ryc97", "collection": "authors", "collection_id": "sm57v-ryc97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200205-074505122", "type": "monograph", "title": "Quantitative Performance Bounds in Biomolecular Circuits due to Temperature Uncertainty", "author": [ { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Performance of biomolecular circuits is affected by changes in temperature, due to its influence on underlying reaction rate parameters. While these performance variations have been estimated using Monte Carlo simulations, how to analytically bound them is generally unclear. To address this, we apply control-theoretic representations of uncertainty to examples of different biomolecular circuits, developing a framework to represent uncertainty due to temperature. We estimate bounds on the steady-state performance of these circuits due to temperature uncertainty. Through an analysis of the linearised dynamics, we represent this uncertainty as a feedback uncertainty and bound the variation in the magnitude of the input-output transfer function, providing a estimate of the variation in frequency-domain properties. Finally, we bound the variation in the time trajectories, providing an estimate of variation in time-domain properties. These results should enable a framework for analytical characterisation of uncertainty in biomolecular circuit performance due to temperature variation and may help in estimating relative performance of different controllers.", "publisher": "Caltech Library", "publication_date": "2015-12" }, { "id": "authors:7kc93-tpm90", "collection": "authors", "collection_id": "7kc93-tpm90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200205-081111268", "type": "monograph", "title": "Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks", "author": [ { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Gon\u00e7alves", "given_name": "Jorge M.", "orcid": "0000-0002-5228-6165", "clpid": "Gon\u00e7alves-J-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider the problem of network reconstruction, with applications to biochemical reaction networks. In particular, we consider the problem of global network reconstruction when there are a limited number of sensors that can be used to simultaneously measure state information. We introduce dynamical structure functions as a way to formulate the network reconstruction problem and motivate their usage with an example physical system from synthetic biology. In particular, we argue that in synthetic biology research, network verification is paramount to robust circuit operation and thus, network reconstruction is an invaluable tool. Nonetheless, we argue that existing approaches for reconstruction are hampered by limited numbers of biological sensors with high temporal resolution. In this way, we motivate the global network reconstruction problem using partial network information and prove that by performing a series of reconstruction experiments, where each experiment reconstructs a subnetwork dynamical structure function, the global dynamical structure function can be recovered in most cases. We illustrate these reconstruction techniques on a recently developed four gene biocircuit, an event detector, and show that it is capable of differentiating the temporal order of input events.", "publisher": "Caltech Library", "publication_date": "2015-12" }, { "id": "authors:f2kgh-jdv95", "collection": "authors", "collection_id": "f2kgh-jdv95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161208-102939866", "type": "book_section", "title": "An Iterative Abstraction Algorithm for Reactive Correct-by-Construction Controller Synthesis", "book_title": "54th IEEE Conference on Decision and Control (CDC), 2015", "author": [ { "family_name": "Mattila", "given_name": "Robert", "clpid": "Mattila-R" }, { "family_name": "Mo", "given_name": "Yilin", "orcid": "0000-0001-7937-6737", "clpid": "Mo-Yilin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider the problem of synthesizing correct-by-construction controllers for discrete-time dynamical systems. A commonly adopted approach in the literature is to abstract the dynamical system into a Finite Transition System (FTS) and thus convert the problem into a two player game between the environment and the system on the FTS. The controller design problem can then be solved using synthesis tools for general linear temporal logic or generalized reactivity(1) specifications. In this article, we propose a new abstraction algorithm. Instead of generating a single FTS to represent the system, we generate two FTSs, which are under- and over-approximations of the original dynamical system. We further develop an iterative abstraction scheme by exploiting the concept of winning sets, i.e., the sets of states for which there exists a winning strategy for the system. Finally, the efficiency of the new abstraction algorithm is illustrated by numerical examples.", "doi": "10.1109/CDC.2015.740318671", "isbn": "978-1-4799-7886-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-12", "pages": "6147-6152" }, { "id": "authors:hvrf3-g6n29", "collection": "authors", "collection_id": "hvrf3-g6n29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160217-083025676", "type": "book_section", "title": "Engineering principles of synthetic biochemical oscillators with negative cyclic feedback", "book_title": "54th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Hori", "given_name": "Yutaka", "orcid": "0000-0002-3253-4985", "clpid": "Hori-Yutaka" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper analyzes oscillatory dynamics of a class of cyclic gene regulatory networks and provides engineering principles for the synthesis of biochemical oscillators. We first review previous results that the oscillatory parameter regime of the gene regulatory circuits can be rigorously explored by the local stability analysis of a unique equilibrium. The local stability analysis then leads to the first engineering principle that the circuit components, or genes, should be chosen so that the kinetic profiles of the circuit components are similar to each other. Using a homogeneous oscillator model, we further discuss design strategies to reduce the cell-to-cell variability of the oscillators that is caused by intrinsic noise.", "doi": "10.1109/CDC.2015.7402292", "isbn": "978-1-4799-7884-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-12", "pages": "584-589" }, { "id": "authors:tern8-9md37", "collection": "authors", "collection_id": "tern8-9md37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200204-162407534", "type": "monograph", "title": "Synthesis of Distributed Longitudinal Control Protocols for a Platoon of Autonomous Vehicles", "author": [ { "family_name": "Han", "given_name": "Duo", "clpid": "Han-Duo" }, { "family_name": "Mo", "given_name": "Yilin", "orcid": "0000-0001-7937-6737", "clpid": "Mo-Yilin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We develop a framework for control protocol synthesis for a platoon of autonomous vehicles subject to temporal logic specifications. We describe the desired behavior of the platoon in a set of linear temporal logic formulas, such as collision avoidance, close spacing or comfortability. The problem of decomposing a global specification for the platoon into distributed specification for each pair of adjacent vehicles is hard to solve. We use the invariant specifications to tackle this problem and the decomposition is proved to be scalable.. Based on the specifications in Assumption/Guarantee form, we can construct a two-player game (between the vehicle and its closest leader) locally to automatically synthesize a controller protocol for each vehicle. Simulation example for a distributed vehicles control problem is also shown.", "publisher": "Caltech Library", "publication_date": "2015-12" }, { "id": "authors:dsxn4-zbq65", "collection": "authors", "collection_id": "dsxn4-zbq65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200205-080035495", "type": "monograph", "title": "Finding stationary solutions to the chemical master equation by gluing state spaces at one or two states recursively", "author": [ { "family_name": "Meng", "given_name": "Xianglin", "clpid": "Meng-Xianglin" }, { "family_name": "Baetica", "given_name": "Ania A.", "orcid": "0000-0003-0421-8181", "clpid": "Baetica-A-A" }, { "family_name": "Singhal", "given_name": "Vipul", "clpid": "Singhal-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Noise is indispensible to key cellular activities, including gene expression coordination and probabilistic differentiation. Stochastic models, such as the chemical master equation (CME), are essential to model noise in the levels of cellular components. In the CME framework, each state is associated with the molecular counts of all component species, and specifies the probability for the system to have that set of molecular counts. Analytic solutions to the CME are rarely known but can bring exciting benefits. For instance, simulations of biochemical reaction networks that are multiscale in time can be sped up tremendously by incorporating analytic solutions of the slow time-scale dynamics. Analytic solutions also enable the design of stationary distributions with properties such as the modality of the distribution, the mean expression level, and the level of noise. One way to derive the analytic steady state response of a biochemical reaction network was recently proposed by (M\u00e9lyk\u00fati et al. 2014). The paper recursively glues simple state spaces together, for which we have analytic solutions, at one or two states. \n\nIn this work, we explore the benefits and limitations of the gluing technique proposed by M\u00e9lyk\u00fati et al., and introduce recursive algorithms that use the technique to solve for the analytic steady state response of stochastic biochemical reaction networks. We give formal characterizations of the set of reaction networks whose state spaces can be obtained by carrying out single-point gluing of paths, cycles or both sequentially. We find that the dimension of the state space of a reaction network equals the maximum number of linearly independent reactions in the system. We then characterize the complete set of stochastic biochemical reaction networks that have elementary reactions and two-dimensional state spaces. As an example, we propose a recursive algorithm that uses the gluing technique to solve for the steady state response of a mass-conserving system with two connected monomolecular reversible reactions. Even though the gluing technique can only construct finite state spaces, we find that, by taking the size of a finite state space to infinity, the steady state response can converge to the analytic solution on the resulting infinite state space. \n\nFinally, we illustrate the aforementioned ideas with the example of two interconnected transcriptional components, which was first studied by (Ghaemi and Del Vecchio 2012).", "publisher": "Caltech Library", "publication_date": "2015-11-24" }, { "id": "authors:9nr6z-ggz73", "collection": "authors", "collection_id": "9nr6z-ggz73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151013-090251954", "type": "article", "title": "Rapid cell-free forward engineering of novel genetic ring oscillators", "author": [ { "family_name": "Niederholtmeyer", "given_name": "Henrike", "orcid": "0000-0002-1375-0287", "clpid": "Niederholtmeyer-H" }, { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Hori", "given_name": "Yutaka", "orcid": "0000-0002-3253-4985", "clpid": "Hori-Yutaka" }, { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Verpoorte", "given_name": "Amanda", "clpid": "Verpoorte-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Maerkl", "given_name": "Sebastian J.", "orcid": "0000-0003-1917-5268", "clpid": "Maerkl-S-J" } ], "abstract": "While complex dynamic biological networks control gene expression in all living organisms, the forward engineering of comparable synthetic networks remains challenging. The current paradigm of characterizing synthetic networks in cells results in lengthy design-build-test cycles, minimal data collection, and poor quantitative characterization. Cell-free systems are appealing alternative environments, but it remains questionable whether biological networks behave similarly in cell-free systems and in cells. We characterized in a cell-free system the 'repressilator,' a three-node synthetic oscillator. We then engineered novel three, four, and five-gene ring architectures, from characterization of circuit components to rapid analysis of complete networks. When implemented in cells, our novel 3-node networks produced population-wide oscillations and 95% of 5-node oscillator cells oscillated for up to 72 hours. Oscillation periods in cells matched the cell-free system results for all networks tested. An alternate forward engineering paradigm using cell-free systems can thus accurately capture cellular behavior.", "doi": "10.7554/eLife.09771", "pmcid": "PMC4714972", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2015-10-02", "volume": "4", "pages": "Art. No. e09771" }, { "id": "authors:55fn6-eyd49", "collection": "authors", "collection_id": "55fn6-eyd49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170404-101550871", "type": "article", "title": "Methodology and Tools for Next Generation Cyber-Physical Systems: The iCyPhy Approach", "author": [ { "family_name": "Nuzzo", "given_name": "Pierluigi", "clpid": "Nuzzo-P" }, { "family_name": "Sangiovanni-Vincentelli", "given_name": "Alberto L.", "orcid": "0000-0003-1298-8389", "clpid": "Sangiovanni-Vincentelli-A-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The realization of complex, cyber-physical \"systems of systems\" can substantially benefit from model-based hierarchical and compositional methodologies to make their design possible let alone optimal. In this paper, we introduce the methodology being developed within the industrial Cyber-Physical (iCyPhy) research consortium, which addresses the complexity and heterogeneity of cyber-physical systems by formalizing the design process in a hierarchical and compositional way, and provides a unifying framework where different modeling, analysis and synthesis tools can seamlessly interconnect. We use assume-guarantee contracts and their algebra (e.g. composition, conjunction, refinement) to provide formal support to the entire design flow. The design is carried out as a sequence of refinement steps from a high-level specification (top-down phase) to an implementation built out of a library of components at the lower level (bottom-up phase). At each step, the design is refined by combining synthesis from requirements, optimization and simulation-based design space exploration methods. We illustrate our approach on design examples of embedded controllers for aircraft power distribution and air management systems.", "doi": "10.1002/j.2334-5837.2015.00060.x", "issn": "2334-5837", "publisher": "Wiley", "publication": "INCOSE International Symposium", "publication_date": "2015-10", "series_number": "1", "volume": "25", "issue": "1", "pages": "235-249" }, { "id": "authors:w6fa6-hw749", "collection": "authors", "collection_id": "w6fa6-hw749", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200214-151424905", "type": "monograph", "title": "Robust Model Predictive Control for Signal Temporal Logic Synthesis", "author": [ { "family_name": "Farahani", "given_name": "Samira S.", "clpid": "Farahani-S-S" }, { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Most automated systems operate in uncertain or adversarial conditions, and have to be capable of reliably reacting to changes in the environment. The focus of this paper is on automatically synthesizing reactive controllers for cyber-physical systems subject to signal temporal logic (STL) specifications. We build on recent work that encodes STL specifications as mixed integer linear constraints on the variables of a discrete-time model of the system and environment dynamics. To obtain a reactive controller, we present solutions to the worst-case model predictive control (MPC) problem using a suite of mixed integer linear programming techniques. We demonstrate the comparative effectiveness of several existing worst-case MPC techniques, when applied to the problem of control subject to temporal logic specifications; our empirical results emphasize the need to develop specialized solutions for this domain.", "publisher": "Caltech Library", "publication_date": "2015-10" }, { "id": "authors:4t6ga-7hh74", "collection": "authors", "collection_id": "4t6ga-7hh74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160412-095801286", "type": "book_section", "title": "Online Horizon Selection in Receding Horizon Temporal Logic Planning", "book_title": "2015 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)", "author": [ { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "F\u00e4lt", "given_name": "Mattias", "clpid": "F\u00e4lt-M" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Temporal logics have proven effective for correct-by-construction synthesis of controllers for a wide range of robotic applications. Receding horizon frameworks mitigate the computational intractability of reactive synthesis for temporal logic, but have thus far been limited by pursuing a single sequence of short horizon problems to the goal. We propose a receding horizon algorithm for reactive synthesis that automatically determines a path to the currently pursued goal at runtime, responding as needed to nondeterministic environment behavior. This is achieved by allowing each short horizon to have multiple local goals, and determining which local goal to pursue based on the current global goal, the currently perceived environment and a pre-computed invariant dependent on the global goal. We demonstrate the utility of this additional flexibility in grant-response tasks, using a search-and-rescue example. Moreover, we show that these goal-dependent invariants mitigate the conservativeness of the receding horizon approach.", "doi": "10.1109/IROS.2015.7353864", "isbn": "978-1-4799-9994-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-10", "pages": "3493-3499" }, { "id": "authors:ef26x-91m95", "collection": "authors", "collection_id": "ef26x-91m95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181029-112222224", "type": "monograph", "title": "Design Space Exploration of the Violacein Pathway in Escherichia coli Based Transcription Translation Cell-Free System (TX-TL)", "author": [ { "family_name": "Nguyen", "given_name": "Phuc H. B.", "clpid": "Nguyen-Phuc-H-B" }, { "family_name": "Wu", "given_name": "Yong Y.", "clpid": "Wu-Yong-Y" }, { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this study, an Escherichia coli (E. coli) based transcription translation cell-free system (TX-TL) was employed to sample various enzyme expression levels of the violacein pathway. The pathway was successfully reconstructed in TX-TL. Its variation produced different metabolites as evident from the extracts assorted colors. Analysis of the violacein product via UV-Vis absorption and liquid chromatography-mass spectrometry (LC-MS) detected 68 nanograms of violacein per 10 microliters reaction volume. Significant buildup of prodeoxyviolacein intermediate was also detected in the equimolar TX-TL reaction. Finally, design space exploration experiments suggested an improvement in violacein production at high VioC and VioD DNA concentrations.", "doi": "10.1101/027656", "publication_date": "2015-09-27" }, { "id": "authors:paryp-fqz66", "collection": "authors", "collection_id": "paryp-fqz66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150608-135213453", "type": "article", "title": "Characterizing and prototyping genetic networks with cell-free transcription\u2013translation reactions", "author": [ { "family_name": "Takahashi", "given_name": "Melissa K.", "orcid": "0000-0003-4937-2924", "clpid": "Takahashi-Melissa-K" }, { "family_name": "Hayes", "given_name": "Clarmyra A.", "clpid": "Hayes-C-A" }, { "family_name": "Chappell", "given_name": "James", "clpid": "Chappell-J" }, { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-V" }, { "family_name": "Lucks", "given_name": "Julius B.", "clpid": "Lucks-J-B" } ], "abstract": "A central goal of synthetic biology is to engineer cellular behavior by engineering synthetic gene networks for a variety of biotechnology and medical applications. The process of engineering gene networks often involves an iterative 'design\u2013build\u2013test' cycle, whereby the parts and connections that make up the network are built, characterized and varied until the desired network function is reached. Many advances have been made in the design and build portions of this cycle. However, the slow process of in vivo characterization of network function often limits the timescale of the testing step. Cell-free transcription\u2013translation (TX\u2013TL) systems offer a simple and fast alternative to performing these characterizations in cells. Here we provide an overview of a cell-free TX\u2013TL system that utilizes the native Escherichia coli TX\u2013TL machinery, thereby allowing a large repertoire of parts and networks to be characterized. As a way to demonstrate the utility of cell-free TX\u2013TL, we illustrate the characterization of two genetic networks: an RNA transcriptional cascade and a protein regulated incoherent feed-forward loop. We also provide guidelines for designing TX\u2013TL experiments to characterize new genetic networks. We end with a discussion of current and emerging applications of cell free systems.", "doi": "10.1016/j.ymeth.2015.05.020", "issn": "1046-2023", "publisher": "Elsevier", "publication": "Methods", "publication_date": "2015-09-15", "volume": "86", "pages": "60-72" }, { "id": "authors:bj557-86f87", "collection": "authors", "collection_id": "bj557-86f87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151030-084615377", "type": "article", "title": "Convex Optimal Uncertainty Quantification", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Tao", "given_name": "Molei", "clpid": "Tao-Molei" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Owhadi", "given_name": "Houman", "orcid": "0000-0002-5677-1600", "clpid": "Owhadi-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Optimal uncertainty quantification (OUQ) is a framework for numerical extreme-case analysis of stochastic systems with imperfect knowledge of the underlying probability distribution. This paper presents sufficient conditions under which an OUQ problem can be reformulated as a finite-dimensional convex optimization problem, for which efficient numerical solutions can be obtained. The sufficient conditions include that the objective function is piecewise concave and the constraints are piecewise convex. In particular, we show that piecewise concave objective functions may appear in applications where the objective is defined by the optimal value of a parameterized linear program.", "doi": "10.1137/13094712X", "issn": "1052-6234", "publisher": "Society for Industrial and Applied Mathematics", "publication": "SIAM Journal of Optimization", "publication_date": "2015-07-14", "series_number": "3", "volume": "25", "issue": "3", "pages": "1368-1387" }, { "id": "authors:pdgxh-9gh88", "collection": "authors", "collection_id": "pdgxh-9gh88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150903-084342383", "type": "article", "title": "An analytical approach to bistable biological circuit discrimination using real algebraic geometry", "author": [ { "family_name": "Siegal-Gaskins", "given_name": "Dan", "clpid": "Siegal-Gaskins-D" }, { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Zhou", "given_name": "Tiffany", "clpid": "Zhou-Tiffany" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem\u2014a tool from nineteenth-century real algebraic geometry\u2014to comparing 'functionally equivalent' bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh\u2013Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.", "doi": "10.1098/rsif.2015.0288", "issn": "1742-5689", "publisher": "The Royal Society", "publication": "Journal of the Royal Society Interface", "publication_date": "2015-07-06", "series_number": "108", "volume": "12", "issue": "108", "pages": "Art. No. 20150288" }, { "id": "authors:v5qp9-11a46", "collection": "authors", "collection_id": "v5qp9-11a46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151124-114616357", "type": "book_section", "title": "A state-space realization approach to set identification of biochemical kinetic parameters", "author": [ { "family_name": "Hori", "given_name": "Yutaka", "orcid": "0000-0002-3253-4985", "clpid": "Hori-Yutaka" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper proposes a set-based parameter identification method for biochemical systems. The developed method identifies not a single parameter but a set of parameters that all explain time-series experimental data, enabling the systematic characterization of the uncertainty of identified parameters. Our key idea is to use a state-space realization that has the same input-output behavior as experimental data instead of the experimental data itself for the identification. This allows us to relax the originally nonlinear identification problem to an LMI feasibility problem validating the norm bound of an error system. We show that regions of parameters can be efficiently classified into consistent and inconsistent parameter sets by combining the LMI feasibility problems and a generalized bisection algorithm.", "doi": "10.1109/ECC.2015.7330878", "publisher": "IEEE", "publication_date": "2015-07" }, { "id": "authors:dy79n-kgr93", "collection": "authors", "collection_id": "dy79n-kgr93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160318-094020866", "type": "book_section", "title": "Variable elimination for scalable receding horizon temporal logic planning", "book_title": "2015 American Control Conference (ACC)", "author": [ { "family_name": "F\u00e4lt", "given_name": "Mattias", "clpid": "F\u00e4lt-M" }, { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Correct-by-construction synthesis of high-level reactive control relies on the use of formal methods to generate controllers with provable guarantees on their behavior. While this approach has been successfully applied to a wide range of systems and environments, it scales poorly. A receding horizon framework mitigates this computational blowup, by decomposing the global control problem into several tractable subproblems. The existence of a global controller is ensured through symbolic checks of the specification, and local controllers are synthesized when needed. This reduces the size of the synthesized strategy, but still scales poorly for problems with dynamic environments because of the large number of environment strategies in each subproblem. Ad-hoc methods to locally restrict the environment come with the risk of losing correctness. We present a method for reducing the size of these subproblems by eliminating locally redundant variables, while maintaining correctness of the local (and thus global) controllers. We demonstrate the method using an autonomous car example, on problem sizes that were previously unsolvable due to the number of variables in the environment. We also demonstrate how the reduced specifications can be used to identify opportunities for reusing the synthesized local controllers.", "doi": "10.1109/ACC.2015.7171013", "isbn": "978-1-4799-8685-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-07", "pages": "1917-1922" }, { "id": "authors:vhjq4-x1k88", "collection": "authors", "collection_id": "vhjq4-x1k88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150813-145738981", "type": "article", "title": "Bootstrapping bilinear models of Simple Vehicles", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Learning and adaptivity will play a large role in robotics in the future. Two questions are open: (1) in principle, how much it is possible to learn; and (2) in practice, how much should an agent be able to learn. The bootstrapping scenario describes the extreme case in which agents need to learn \"everything\" from scratch, including a torque-to-pixels model for its robotic body. This paper considers the bootstrapping problem for a subset of the set of all robots. The Simple Vehicles are an idealization of mobile robots equipped with a set of \"canonical\" exteroceptive sensors: the camera, the range finder and the field sampler. The sensorimotor dynamics of these sensors are derived and shown to be surprising similar. These sensorimotor dynamics are well approximated by a class of nonlinear systems that assume an instantaneous bilinear relation among observations, commands, and changes in the observations. The bilinear approximation is sufficient to guarantee success in the task of generalized \"servoing\": driving the observations to a given goal snapshot. Simulations and experiments substantiate the theoretical results. This is the first instance of a bootstrapping agent that can learn the model of the dynamics of a relatively large universe of systems and use the models to solve well-defined tasks, with no parameter tuning or hand-designed features.", "doi": "10.1177/0278364914557708", "issn": "0278-3649", "publisher": "Sage", "publication": "International Journal of Robotics Research", "publication_date": "2015-07", "series_number": "8", "volume": "34", "issue": "8", "pages": "1087-1113" }, { "id": "authors:cgc8r-zpc45", "collection": "authors", "collection_id": "cgc8r-zpc45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150915-083424809", "type": "book_section", "title": "Multi-dimensional state estimation in adversarial environment", "book_title": "34th Chinese Control Conference (CCC)", "author": [ { "family_name": "Mo", "given_name": "Yilin", "orcid": "0000-0001-7937-6737", "clpid": "Mo-Yilin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the estimation of a vector state based on m measurements that can be potentially manipulated by an adversary. The attacker is assumed to have limited resources and can only manipulate up to l of the m measurements. However, it can the compromise measurements arbitrarily. The problem is formulated as a minimax optimization, where one seeks to construct an optimal estimator that minimizes the \"worst-case\" error against all possible manipulations by the attacker and all possible sensor noises. We show that if the system is not observable after removing 2l sensors, then the worst-case error is infinite, regardless of the estimation strategy. If the system remains observable after removing arbitrary set of 2l sensor, we prove that the optimal state estimation can be computed by solving a semidefinite programming problem. A numerical example is provided to illustrate the effectiveness of the proposed state estimator.", "doi": "10.1109/ChiCC.2015.7260376", "isbn": "978-9-8815-6389-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-07", "pages": "4761-4766" }, { "id": "authors:03zew-2r462", "collection": "authors", "collection_id": "03zew-2r462", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190327-154909216", "type": "article", "title": "Specification and Synthesis of Reactive Protocols for Aircraft Electric Power Distribution", "author": [ { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-Huan" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The increasing complexity of electric power systems leads to challenges in integration and verification. We consider the problem of designing a control protocol for an aircraft electric power system that meets a set of requirements describing the correct behaviors of the system and reacts dynamically to changes in internal system states. We formalize the requirements by translating them into a temporal logic specification language and apply game-based, temporal logic formal methods to automatically synthesize a controller protocol that satisfies these overall properties and requirements. Through a case study, we perform a design exploration to show the benefits and tradeoffs between centralized and distributed control architectures.", "doi": "10.1109/TCNS.2015.2401174", "issn": "2325-5870", "publisher": "IEEE", "publication": "IEEE Transactions on Control of Network Systems", "publication_date": "2015-06", "series_number": "2", "volume": "2", "issue": "2", "pages": "193-203" }, { "id": "authors:xz021-mf017", "collection": "authors", "collection_id": "xz021-mf017", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150608-094354039", "type": "monograph", "title": "Protein degradation in a TX-TL cell-free expression system using ClpXP protease", "author": [ { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Singhal", "given_name": "Vipul", "orcid": "0000-0003-1670-1824", "clpid": "Singhal-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "An in vitro S30-based Escherichia coli expression system (\"Transcription-Translation\", or \"TX-TL\") has been developed as an alternative prototyping environment to the cell for synthetic circuits [1-5]. Basic circuit elements, such as switches and cascades, have been shown to function in TX-TL, as well as bacteriophage assembly [2, 6]. Circuits can also be prototyped from basic parts within 8 hours, avoiding cloning and transformation steps [7]. However, most published results have been obtained in a \"batch mode\" reaction, where factors that play an important role for in vivo circuit dynamics \u2013 namely protein degradation and protein dilution \u2013 are severely hindered or are not present. This limits the complexity of circuits built in TX-TL without steady-state or continuous-flow solutions [8-10]. However, alternate methods that enable dilution either require extra equipment and expertise or demand lower reaction throughput. We explored the possibility of supplementing TX-TL with ClpXP, an AAA+ protease pair that selectively degrades tagged proteins [11], to provide finely-tuned degradation. The mechanism of ClpXP degradation has been extensively studied both in vitro and in vivo [12-15]. However, it has not been characterized for use in synthetic circuits \u2013 metrics such as toxicity, ATP usage, degradation variation over time, and cellular loading need to be determined. In particular, TX-TL in batch mode is known to be resource limited [16], and ClpXP is known to require significant amounts of ATP to unfold different protein targets [17, 18]. We find that ClpXP's protein degradation dynamics is dependent on protein identity, but can be determined experimentally. Degradation follows Michaels-Menten kinetics, and can be fine tuned by ClpX or ClpP concentration. Added purified ClpX is also not toxic to TX-TL reactions. Therefore, ClpXP provides a controllable way to introduce protein degradation and dynamics into synthetic circuits in TX-TL.", "doi": "10.1101/019695", "publication_date": "2015-05-21" }, { "id": "authors:2gpv1-mjt24", "collection": "authors", "collection_id": "2gpv1-mjt24", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2015.004", "type": "monograph", "title": "Revisiting the AMBA AHB bus case study", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This report describes a number of changes to the ARM AMBA bus case study from Bloem et al. that lead to significant reduction in synthesis time. In addition, it identifies the reason of blowup for the synthesized strategies in earlier studies as lack of binary decision diagram (BDD) reordering during strategy construction. Enabling dynamic BDD reordering with the group sifting algorithm, we synthesized strategies for as many as 18 masters, with both the original and revised specifications. This conclusion is based on detailed experimental measurements that show the changes of BDD sizes over time for the fixpoint and other variables during the nested fixed point computation, including the cumulative time spent on BDD reordering and the total number of BDD nodes. The measurements were obtained for eight different cases, allowing to compare the original with the revised specifications, with strategy reordering enabled or not, and conjoining the weak fairness guarantees or merging them into a single B\u00fcchi automaton. The revised specification proposed here is expressed using the open Promela language.", "publisher": "California Institute of Technology", "publication_date": "2015-05-12" }, { "id": "authors:tds42-yk640", "collection": "authors", "collection_id": "tds42-yk640", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150612-140758750", "type": "article", "title": "Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription Translation (TX-TL) Systems", "author": [ { "family_name": "Takahashi", "given_name": "Melissa K.", "orcid": "0000-0003-4937-2924", "clpid": "Takahashi-Melissa-K" }, { "family_name": "Chappell", "given_name": "James", "clpid": "Chappell-J" }, { "family_name": "Hayes", "given_name": "Clarmyra A.", "clpid": "Hayes-C-A" }, { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Singhal", "given_name": "Vipul", "orcid": "0000-0003-1670-1824", "clpid": "Singhal-V" }, { "family_name": "Spring", "given_name": "Kevin J.", "clpid": "Spring-K-J" }, { "family_name": "Al-Khabouri", "given_name": "Shaima", "orcid": "0000-0002-5147-9627", "clpid": "Al-Khabouri-S" }, { "family_name": "Fall", "given_name": "Christopher P.", "clpid": "Fall-C-P" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Lucks", "given_name": "Julius B.", "clpid": "Lucks-J-B" } ], "abstract": "RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on time scales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of evaluating these networks in vivo. Here, we adapt an Escherichia coli-based cell-free transcription-translation (TX-TL) system for rapidly prototyping RNA networks. We used this system to measure the response time of an RNA transcription cascade to be approximately five minutes per step of the cascade. We also show that this response time can be adjusted with temperature and regulator threshold tuning. Finally, we use TX-TL to prototype a new RNA network, an RNA single input module, and show that this network temporally stages the expression of two genes in vivo.", "doi": "10.1021/sb400206c", "pmcid": "PMC4487224", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2015-05", "series_number": "5", "volume": "4", "issue": "5", "pages": "503-515" }, { "id": "authors:f2hsj-f1v61", "collection": "authors", "collection_id": "f2hsj-f1v61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150428-075140716", "type": "monograph", "title": "Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system", "author": [ { "family_name": "Wu", "given_name": "Yong Y.", "clpid": "Wu-Yong-Y" }, { "family_name": "Culler", "given_name": "Stephanie", "clpid": "Culler-S-J" }, { "family_name": "Khandurina", "given_name": "Julia", "clpid": "Khandurina-J" }, { "family_name": "Van Dien", "given_name": "Stephen", "clpid": "Van-Dien-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Current methods for assembling metabolic pathways require a process of repeated trial and error and have a long design-build-test cycle. Further, it remains a challenge to precisely tune enzyme expression levels for maximizing target metabolite production. Recently it was shown that a cell-free transcriptional-translation system (TX-TL) can be used to rapidly prototype novel complex biocircuits as well as metabolic pathways. TX-TL systems allow protein expression from multiple DNA pieces, opening up the possibility of modulating concentrations of DNA encoding individual pathway enzymes and testing the related effect on metabolite production. In this work, we demonstrate TX-TL as a platform for exploring the design space of metabolic pathways using a 1,4-BDO biosynthesis pathway as an example. Using TX-TL, we verified enzyme expression and enzyme activity and identified the conversion of 4-hydroxybutyrate to downstream metabolites as a limiting step of the 1,4-BDO pathway. We further tested combinations of various enzyme expression levels and found increasing downstream enzyme expression levels improved 1,4-BDO production.", "doi": "10.1101/017814", "publication_date": "2015-04-09" }, { "id": "authors:958cd-6r359", "collection": "authors", "collection_id": "958cd-6r359", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161128-165454738", "type": "book_section", "title": "Cross-entropy temporal logic motion planning", "book_title": "HSCC '15 Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Girard", "given_name": "Antoine", "clpid": "Girard-A" }, { "family_name": "Sankaranarayanan", "given_name": "Sriram", "clpid": "Sankaranarayanan-S" } ], "abstract": "This paper presents a method for optimal trajectory generation for discrete-time nonlinear systems with linear temporal logic (LTL) task specifications. Our approach is based on recent advances in stochastic optimization algorithms for optimal trajectory generation. These methods rely on estimation of the rare event of sampling optimal trajectories, which is achieved by incrementally improving a sampling distribution so as to minimize the cross-entropy. A key component of these stochastic optimization algorithms is determining whether or not a trajectory is collision-free. We generalize this collision checking to efficiently verify whether or not a trajectory satisfies a LTL formula. Interestingly, this verification can be done in time polynomial in the length of the LTL formula and the trajectory. We also propose a method for efficiently re-using parts of trajectories that only partially satisfy the specification, instead of simply discarding the entire sample. Our approach is demonstrated through numerical experiments involving Dubins car and a generic point-mass model subject to complex temporal logic task specifications.", "doi": "10.1145/2728606.2728635", "isbn": "978-1-4503-3433-4", "publisher": "ACM", "place_of_publication": "New York, NY", "publication_date": "2015-04", "pages": "269-278" }, { "id": "authors:53ztk-tph58", "collection": "authors", "collection_id": "53ztk-tph58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150514-135540768", "type": "book_section", "title": "Reactive Synthesis from Signal Temporal Logic Specifications", "book_title": "Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control", "author": [ { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "Donz\u00e9", "given_name": "Alexandre", "clpid": "Donz\u00e9-A" }, { "family_name": "Sadigh", "given_name": "Dorsa", "clpid": "Sadigh-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Seshia", "given_name": "Sanjit A.", "clpid": "Seshia-S-A" } ], "abstract": "We present a counterexample-guided inductive synthesis approach to controller synthesis for cyber-physical systems subject to signal temporal logic (STL) specifications, operating in potentially adversarial nondeterministic environments. We encode STL specifications as mixed integer-linear constraints on the variables of a discrete-time model of the system and environment dynamics, and solve a series of optimization problems to yield a satisfying control sequence. We demonstrate how the scheme can be used in a receding horizon fashion to fulfill properties over unbounded horizons, and present experimental results for reactive controller synthesis for case studies in building climate control and autonomous driving.", "doi": "10.1145/2728606.2728628", "isbn": "978-1-4503-3433-4", "publisher": "Association for Computing Machinery", "place_of_publication": "New York, NY", "publication_date": "2015-04", "pages": "239-248" }, { "id": "authors:fdsg6-fgh34", "collection": "authors", "collection_id": "fdsg6-fgh34", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2015.003", "type": "monograph", "title": "Synthesis from multi-paradigm specifications", "author": [ { "family_name": "Filippidis", "given_name": "Ioannis", "orcid": "0000-0003-4704-3334", "clpid": "Filippidis-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Holzmann", "given_name": "Gerard J.", "clpid": "Holzmann-G-J" } ], "abstract": "This work proposes a language for describing reactive synthesis problems that integrates imperative and declarative elements. The semantics is defined in terms of two-player turn-based infinite games with full information. Currently, synthesis tools accept linear temporal logic (LTL) as input, but this description is less structured and does not facilitate the expression of sequential constraints. This motivates the use of a structured programming language to specify synthesis problems. Transition systems and guarded commands serve as imperative constructs, expressed in a syntax based on that of the modeling language Promela. The syntax allows defining which player controls data and control flow, and separating a program into assumptions and guarantees. These notions are necessary for input to game solvers. The integration of imperative and declarative paradigms allows using the paradigm that is most appropriate for expressing each requirement. The declarative part is expressed in the LTL fragment of generalized reactivity(1), which admits efficient synthesis algorithms. The implementation translates Promela to input for the Slugs synthesizer and is written in Python.", "publisher": "California Institute of Technology", "publication_date": "2015-03-09" }, { "id": "authors:64682-sx438", "collection": "authors", "collection_id": "64682-sx438", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150316-104657793", "type": "article", "title": "Robot navigation in dense human crowds: Statistical models and experimental studies of human\u2013robot cooperation", "author": [ { "family_name": "Trautman", "given_name": "Pete", "clpid": "Trautman-P" }, { "family_name": "Ma", "given_name": "Jeremy", "clpid": "Ma-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Krause", "given_name": "Andreas", "orcid": "0000-0001-7260-9673", "clpid": "Krause-A" } ], "abstract": "We consider the problem of navigating a mobile robot through dense human crowds. We begin by exploring a fundamental impediment to classical motion planning algorithms called the \"freezing robot problem\": once the environment surpasses a certain level of dynamic complexity, the planner decides that all forward paths are unsafe, and the robot freezes in place (or performs unnecessary maneuvers) to avoid collisions. We argue that this problem can be avoided if the robot anticipates human cooperation, and accordingly we 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. We validate this model with an empirical study of robot navigation in dense human crowds (488 runs), specifically testing how cooperation models effect navigation performance. The multiple goal interacting Gaussian processes algorithm performs comparably with human teleoperators in crowd densities nearing 0.8 humans/m^2, while a state-of-the-art non-cooperative planner exhibits unsafe behavior more than three 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/m^2. We also show that our non-cooperative planner or our reactive planner capture the salient characteristics of nearly any 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.", "doi": "10.1177/0278364914557874", "issn": "0278-3649", "publisher": "Sage", "publication": "International Journal of Robotics Research", "publication_date": "2015-03", "series_number": "3", "volume": "34", "issue": "3", "pages": "335-356" }, { "id": "authors:w9mbv-7zb84", "collection": "authors", "collection_id": "w9mbv-7zb84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150818-140635950", "type": "book_section", "title": "A risk-aware architecture for resilient spacecraft operations", "book_title": "2015 IEEE Aerospace Conference", "author": [ { "family_name": "McGhan", "given_name": "Catharine L. R.", "clpid": "McGhan-C-L-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Serra", "given_name": "Romain", "clpid": "Serra-R" }, { "family_name": "Ingham", "given_name": "Michel D.", "clpid": "Ingham-M-D" }, { "family_name": "Ono", "given_name": "Masahiro", "clpid": "Ono-Masahiro" }, { "family_name": "Estlin", "given_name": "Tara", "clpid": "Estlin-T" }, { "family_name": "Williams", "given_name": "Brian C.", "clpid": "Williams-B-C" } ], "abstract": "In this paper we discuss a resilient, risk-aware software architecture for onboard, real-time autonomous operations that is intended to robustly handle uncertainty in space-craft behavior within hazardous and unconstrained environments, without unnecessarily increasing complexity. This architecture, the Resilient Spacecraft Executive (RSE), serves three main functions: (1) adapting to component failures to allow graceful degradation, (2) accommodating environments, science observations, and spacecraft capabilities that are not fully known in advance, and (3) making risk-aware decisions without waiting for slow ground-based reactions. This RSE is made up of four main parts: deliberative, habitual, and reflexive layers, and a state estimator that interfaces with all three. We use a risk-aware goal-directed executive within the deliberative layer to perform risk-informed planning, to satisfy the mission goals (specified by mission control) within the specified priorities and constraints. Other state-of-the-art algorithms to be integrated into the RSE include correct-by-construction control synthesis and model-based estimation and diagnosis. We demonstrate the feasibility of the architecture in a simple implementation of the RSE for a simulated Mars rover scenario.", "doi": "10.1109/AERO.2015.7119035", "isbn": "978-1-4799-5379-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2015-03", "pages": "1-15" }, { "id": "authors:2bajj-bcd11", "collection": "authors", "collection_id": "2bajj-bcd11", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2015.002", "type": "monograph", "title": "Cross-entropy Temporal Logic Motion Planning", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents a method for optimal trajectory generation for discrete-time nonlinear systems with linear temporal logic (LTL) task specifications. Our approach is based on recent advances in stochastic optimization algorithms for optimal trajectory generation. These methods rely on estimation of the rare event of sampling optimal trajectories, which is achieved by incrementally improving a sampling distribution so as to minimize the cross-entropy. A key component of these stochastic optimization algorithms is determining whether or not a trajectory is collision-free. We generalize this collision checking to efficiently verify whether or not a trajectory satisfies a LTL formula. Interestingly, this verification can be done in time polynomial in the length of the LTL formula and the trajectory. We also propose a method for efficiently re-using parts of trajectories that only partially satisfy the specification, instead of simply discarding the entire sample. Our approach is demonstrated through numerical experiments involving Dubins car and a generic point-mass model subject to complex temporal logic task specifications.", "doi": "10.1145/2728606.2728635", "publisher": "California Institute of Technology", "publication_date": "2015-02-27" }, { "id": "authors:18ykk-gy939", "collection": "authors", "collection_id": "18ykk-gy939", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140424-150617268", "type": "article", "title": "Design and implementation of a synthetic biomolecular concentration tracker", "author": [ { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "de los Santos", "given_name": "Emmanuel L. C.", "clpid": "de-los-Santos-E-L-C" }, { "family_name": "Whitaker", "given_name": "Weston R.", "clpid": "Whitaker-W-R" }, { "family_name": "Dueber", "given_name": "John E.", "clpid": "Dueber-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.", "doi": "10.1021/sb500024b", "pmcid": "PMC4384833", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2015-02", "series_number": "2", "volume": "4", "issue": "2", "pages": "150-161" }, { "id": "authors:mmfek-s3154", "collection": "authors", "collection_id": "mmfek-s3154", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2015.001", "type": "monograph", "title": "Online Horizon Selection in Receding Horizon Temporal Logic Planning", "author": [ { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "F\u00e4lt", "given_name": "Mattias", "clpid": "F\u00e4lt-M" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Temporal logics have proven effective for correct-by-construction synthesis of controllers for a wide range of applications. Receding horizon frameworks mitigate the computational intractability of reactive synthesis for temporal logic, but have thus far been limited by pursuing a single sequence of short horizon problems to the current goal. We propose a receding horizon algorithm for reactive synthesis that automatically determines a path to the currently pursued goal at runtime, in response to a nondeterministic environment. This is achieved by allowing each short horizon to have multiple local goals, and determining which local goal to pursue based on the current global goal, currently perceived environment and a pre-computed invariant dependent on each global goal. We demonstrate the utility of this additional flexibility in grant-response tasks, using a search-and-rescue example. Moreover, we show that these goal-dependent invariants mitigate the conservativeness of the receding horizon approach.", "publisher": "California Institute of Technology", "publication_date": "2015-02" }, { "id": "authors:14zdd-4sy64", "collection": "authors", "collection_id": "14zdd-4sy64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200214-103858802", "type": "monograph", "title": "Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo", "author": [ { "family_name": "Guo", "given_name": "Shaobin", "orcid": "0000-0001-9736-4078", "clpid": "Guo-Shaobin" }, { "family_name": "Hori", "given_name": "Yutaka", "orcid": "0000-0002-3253-4985", "clpid": "Hori-Yutaka" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Biological signaling systems not only detect the absolute levels of the signals, but are also able to sense the fold-changes of the signals. The ability to detect fold-changes provides a powerful tool for biological organisms to adapt to the changes in environment. Here we present the first novel synthetic fold-change detector (FCD) circuit built from ground up in vivo. We systematically designed the FCD circuit in silico, prototyped it in cell-free transcription-translation platform (TX-TL), and eventually implemented it in E. coli cells. We were able to show that the FCD circuit can not only generate pulse-like behavior in response to input, but also produce the same pulse response with inputs of the same fold-change, despite of different absolute signal levels.", "publisher": "Caltech Library", "publication_date": "2015-02" }, { "id": "authors:86hnb-3n106", "collection": "authors", "collection_id": "86hnb-3n106", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150302-124651398", "type": "article", "title": "Editorial for SEED 2014 Special Issue", "author": [ { "family_name": "Jackson", "given_name": "Alicia", "clpid": "Jackson-A" }, { "family_name": "Voigt", "given_name": "Chris", "clpid": "Voigt-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This issue of ACS Synthetic Biology contains articles that\nwere originally submitted as part of the inaugural\nSynthetic Biology: Engineering, Evolution, and Design\n(SEED) conference, held July, 2014, in Manhattan Beach,\nCA. SEED is an annual technical conference dedicated to the\nbroad set of technologies that make up the discipline of\nSynthetic Biology. SEED will be a regularly held meeting, the\nnext iteration of which will be held in Boston in the summer of\n2015.", "doi": "10.1021/acssynbio.5b00001", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2015-01", "series_number": "1", "volume": "4", "issue": "1", "pages": "1" }, { "id": "authors:qd0w7-9ss70", "collection": "authors", "collection_id": "qd0w7-9ss70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150313-113120630", "type": "article", "title": "Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts", "author": [ { "family_name": "Venturelli", "given_name": "Ophelia S.", "clpid": "Venturelli-O-S" }, { "family_name": "Zuleta", "given_name": "Ignacio", "clpid": "Zuleta-I" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "El-Samad", "given_name": "Hana", "orcid": "0000-0001-6239-9916", "clpid": "El-Samad-H" } ], "abstract": "Delineating the strategies by which cells contend with combinatorial changing environments is crucial for understanding cellular regulatory organization. When presented with two carbon sources, microorganisms first consume the carbon substrate that supports the highest growth rate (e.g., glucose) and then switch to the secondary carbon source (e.g., galactose), a paradigm known as the Monod model. Sequential sugar utilization has been attributed to transcriptional repression of the secondary metabolic pathway, followed by activation of this pathway upon depletion of the preferred carbon source. In this work, we demonstrate that although Saccharomyces cerevisiae cells consume glucose before galactose, the galactose regulatory pathway is activated in a fraction of the cell population hours before glucose is fully consumed. This early activation reduces the time required for the population to transition between the two metabolic programs and provides a fitness advantage that might be crucial in competitive environments.", "doi": "10.1101/002907", "pmcid": "PMC4307983", "issn": "1544-9173", "publisher": "Public Library of Science", "publication": "PLoS Biology", "publication_date": "2015-01", "series_number": "1", "volume": "13", "issue": "1", "pages": "Art. No. e1002042" }, { "id": "authors:05jmq-v7j52", "collection": "authors", "collection_id": "05jmq-v7j52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170124-175050123", "type": "book_section", "title": "Model predictive control with signal temporal logic specifications", "book_title": "53rd IEEE Conference on Decision and Control", "author": [ { "family_name": "Raman", "given_name": "Vasumathi", "clpid": "Raman-V" }, { "family_name": "Donz\u00e9", "given_name": "Alexandre", "clpid": "Donz\u00e9-A" }, { "family_name": "Maasoumy", "given_name": "Mehdi", "clpid": "Maasoumy-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sangiovanni-Vincentelli", "given_name": "Alberto", "orcid": "0000-0003-1298-8389", "clpid": "Sangiovanni-Vincentelli-A-L" }, { "family_name": "Seshia", "given_name": "Sanjit A.", "clpid": "Seshia-S-A" } ], "abstract": "We present a mathematical programming-based method for model predictive control of discrete-time cyber-physical systems subject to signal temporal logic (STL) specifications. We describe the use of STL to specify a wide range of properties of these systems, including safety, response and bounded liveness. For synthesis, we encode STL specifications as mixed integer-linear constraints on the system variables in the optimization problem at each step of a model predictive control framework. We present experimental results for controller synthesis for building energy and climate control.", "doi": "10.1109/CDC.2014.7039363", "isbn": "978-1-4673-6090-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-12", "pages": "81-87" }, { "id": "authors:cnxbm-2a321", "collection": "authors", "collection_id": "cnxbm-2a321", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140424-145318619", "type": "book_section", "title": "Designing Robustness to Temperature in a Feedforward Loop Circuit", "book_title": "53rd IEEE Conference on Decision and Control", "author": [ { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "'Incoherent feedforward loops' represent important biomolecular circuit elements capable of a rich set of dynamic behavior including adaptation and pulsed responses. Temperature can modulate some of these properties through its effect on the underlying reaction rate parameters. It is generally unclear how to design a circuit where these properties are robust to variations in temperature. Here, we address this issue using a combination of tools from control and dynamical systems theory as well as preliminary experimental measurements towards such a design. Using a structured uncertainty representation, we analyze a standard incoherent feedforward loop circuit, noting mechanisms that intrinsically confer temperature robustness to some of its properties. Further, we study design variants that can enhance this robustness to temperature, including different negative feedback configurations as well as conditions for perfect temperature compensation. Finally, we find that the response of an incoherent feedforward loop circuit in cells can change with temperature. These results present groundwork for the design of a temperature-robust incoherent feedforward loop circuit.", "doi": "10.1109/CDC.2014.7040112", "isbn": "978-1-4799-7746-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-12", "pages": "4629-4634" }, { "id": "authors:2zcm1-61z65", "collection": "authors", "collection_id": "2zcm1-61z65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170123-170431903", "type": "book_section", "title": "Modeling the effects of compositional context on promoter activity in an E. coli extract based transcription-translation system", "book_title": "53rd IEEE Conference on Decision and Control", "author": [ { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Ng", "given_name": "Andrew", "clpid": "Ng-Andrew-H" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "One of the fundamental challenges in implementing complex biocircuits is understanding how the spatial arrangement of biological parts impacts biocircuit behavior. We develop a set of synthetic biology parts for systematically probing the effects of spatial arrangement on levels of transcription. Our initial experimental assays prove that even the rearrangement of two biocircuit parts (comprised of a promoter, coding sequence, and terminator) into three spatially distinct orientations (convergent, divergent, and tandem orientation) can exhibit significantly different levels of transcription. These findings motivate the need for mathematical models to describe these spatial context effects. We pose a novel nonlinear massaction kinetics based model that enables the integration of knowledge about spatial or compositional context and canonical descriptions of transcriptional dynamics. Our findings suggest that compositional context plays a role in biocircuit part performance and comprise an important piece of biocircuit interconnection theory.", "doi": "10.1109/CDC.2014.7040234", "isbn": "978-1-4673-6090-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-12", "pages": "5405-5412" }, { "id": "authors:d57b5-jw847", "collection": "authors", "collection_id": "d57b5-jw847", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150202-112319257", "type": "article", "title": "Control Software Synthesis and Validation for a Vehicular\n Electric Power Distribution Testbed", "author": [ { "family_name": "Rogersten", "given_name": "Robert", "clpid": "Rogersten-R" }, { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-Huan" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Modern aircraft increasingly rely on electric power, resulting in high safety criticality and complexity in their electric power generation and distribution systems. Motivated by the resulting rapid increase in the costs and duration of the design cycles for such systems, the use of formal specification and automated correct-by-construction control protocols synthesis for primary distribution in vehicular electric power networks is investigated. A design workflow is discussed that aims to transition from the traditional \"design and verify\" approach to a \"specify and synthesize\" approach. An overview is given of a subset of the recent advances in the synthesis of reactive control protocols. These techniques are applied in the context of reconfiguration of the networks in reaction to the changes in their operating environment. These automatically synthesized control protocols are also validated on high-fidelity simulation models and on an academic-scale hardware testbed.", "doi": "10.2514/1.I010167", "issn": "1940-3151", "publisher": "American Institute of Aeronautics and Astronautics", "publication": "Journal of Aerospace Information Systems", "publication_date": "2014-10", "series_number": "10", "volume": "11", "issue": "10", "pages": "665-678" }, { "id": "authors:6yhyr-vne94", "collection": "authors", "collection_id": "6yhyr-vne94", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2014.001", "type": "monograph", "title": "Hot-swapping robot task goals in reactive formal synthesis", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of synthesizing robot controllers to realize a task that unpredictably changes with time. Tasks are formally expressed in the GR(1) fragment of temporal logic, in which some of the variables are set by an\nadversary. The task changes by the addition or removal of goals, which occurs online (i.e., at run-time). We present an algorithm for mending control\nstrategies to realize tasks after the addition of goals, while avoiding global\nre-synthesis of the strategy. Experiments are presented for a planar\nsurveillance task in which new regions of interest are incrementally added.\nRun-times are empirically shown to be favorable compared to re-synthesizing from scratch. We also present an algorithm for mending control strategies for the removal of goals. While in this setting the original strategy is still\nfeasible, our algorithm provides a more satisfying solution by \"tightening\nloose ends.'' Both algorithms are shown to yield so-called reach annotations,\nand thus the control strategies are easily amenable to other algorithms\nconcerning incremental synthesis, e.g., as in previous work by the authors for\nnavigation in uncertain environments.", "publisher": "California Institute of Technology", "publication_date": "2014-09-22" }, { "id": "authors:ypc43-0k255", "collection": "authors", "collection_id": "ypc43-0k255", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150402-125326775", "type": "book_section", "title": "A Compositional Approach to Stochastic Optimal Control with Co-safe Temporal Logic Specifications", "book_title": "2014 IEEE/RSJ International Conference on Intelligent Robots and Systems", "author": [ { "family_name": "Horowitz", "given_name": "Matanya B.", "clpid": "Horowitz-M-B" }, { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We introduce an algorithm for the optimal control of stochastic nonlinear systems subject to temporal logic constraints on their behavior. We compute directly on the state space of the system, avoiding the expensive pre-computation of a discrete abstraction. An automaton that corresponds to the temporal logic specification guides the computation of a control policy that maximizes the probability that the system satisfies the specification. This reduces controller synthesis to solving a sequence of stochastic constrained reachability problems. Each individual reachability problem is solved via the Hamilton-Jacobi-Bellman (HJB) partial differential equation of stochastic optimal control theory. To increase the efficiency of our approach, we exploit a class of systems where the HJB equation is linear due to structural assumptions on the noise. The linearity of the partial differential equation allows us to pre-compute control policy primitives and then compose them, at essentially zero cost, to conservatively satisfy a complex temporal logic specification.", "doi": "10.1109/IROS.2014.6942750", "isbn": "978-1-4799-6934-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-09", "pages": "1466-1473" }, { "id": "authors:jy3xk-15609", "collection": "authors", "collection_id": "jy3xk-15609", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140424-151429285", "type": "article", "title": "Negative autoregulation matches production and demand in synthetic transcriptional networks", "author": [ { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Giordano", "given_name": "Giulia", "clpid": "Giordano-G" }, { "family_name": "Forsberg", "given_name": "Per-Ola", "clpid": "Forsberg-O-O" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose a negative feedback architecture that regulates activity of artificial genes, or \"genelets\", to meet their output downstream demand, achieving robustness with respect to uncertain open-loop output production rates. In particular, we consider the case where the outputs of two genelets interact to form a single assembled product. We show with analysis and experiments that negative autoregulation matches the production and demand of the outputs: the magnitude of the regulatory signal is proportional to the \"error\" between the circuit output concentration and its actual demand. This two-device system is experimentally implemented using in vitro transcriptional networks, where reactions are systematically designed by optimizing nucleic acid sequences with publicly available software packages. We build a predictive ordinary differential equation (ODE) model that captures the dynamics of the system and can be used to numerically assess the scalability of this architecture to larger sets of interconnected genes. Finally, with numerical simulations we contrast our negative autoregulation scheme with a cross-activation architecture, which is less scalable and results in slower response times.", "doi": "10.1101/000430", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2014-08", "series_number": "8", "volume": "3", "issue": "8", "pages": "589-599" }, { "id": "authors:vnbt3-mh588", "collection": "authors", "collection_id": "vnbt3-mh588", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141113-140158076", "type": "article", "title": "The Swarm at the Edge of the Cloud", "author": [ { "family_name": "Lee", "given_name": "Edward A.", "clpid": "Lee-E-A" }, { "family_name": "Rabaey", "given_name": "Jan", "clpid": "Rabaey-J" }, { "family_name": "Hartmann", "given_name": "Bj\u00f6rn", "clpid": "Hartmann-B" }, { "family_name": "Kubiatowics", "given_name": "John", "clpid": "Kubiatowics-J" }, { "family_name": "Pister", "given_name": "Kris", "clpid": "Pister-K" }, { "family_name": "Sangiovanni-Vincentelli", "given_name": "Alberto", "orcid": "0000-0003-1298-8389", "clpid": "Sangiovanni-Vincentelli-A-L" }, { "family_name": "Seshia", "given_name": "Sanjit A.", "clpid": "Seshia-S-A" }, { "family_name": "Wawrzynek", "given_name": "John", "clpid": "Wawrzynek-J" }, { "family_name": "Wessel", "given_name": "David", "clpid": "Wessel-D" }, { "family_name": "Rosing", "given_name": "Tajana Simunic", "clpid": "Rosing-T-S" }, { "family_name": "Blaauw", "given_name": "David", "clpid": "Blaauw-D" }, { "family_name": "Dutta", "given_name": "Prabal", "clpid": "Dutta-P" }, { "family_name": "Fu", "given_name": "Kevin", "clpid": "Fu-K" }, { "family_name": "Guestrin", "given_name": "Carlos", "clpid": "Guestrin-C" }, { "family_name": "Taskar", "given_name": "Ben", "clpid": "Taskar-B" }, { "family_name": "Jafari", "given_name": "Roozbeh", "clpid": "Jafari-R" }, { "family_name": "Jones", "given_name": "Douglas", "clpid": "Jones-D" }, { "family_name": "Kumar", "given_name": "Vijay", "orcid": "0000-0002-3902-9391", "clpid": "Kumar-Vijay" }, { "family_name": "Mangharam", "given_name": "Raul", "clpid": "Mangharam-R" }, { "family_name": "Pappas", "given_name": "George J.", "clpid": "Pappas-G-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Rowe", "given_name": "Anthony", "clpid": "Rowe-A" } ], "abstract": "The paper explains how to use sensors as the eyes, ears, hands, and feet for the cloud. This paper describes the opportunities and challenges when integrating sensors and cloud computing.", "doi": "10.1109/MDAT.2014.2314600", "issn": "2168-2356", "publisher": "IEEE", "publication": "IEEE Design & Test", "publication_date": "2014-07-23", "series_number": "3", "volume": "31", "issue": "3", "pages": "8-20" }, { "id": "authors:5wjdk-gha54", "collection": "authors", "collection_id": "5wjdk-gha54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160513-141535201", "type": "monograph", "title": "Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics", "author": [ { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Temporal dynamics in many biomolecular circuits can change with temperature because\nof the temperature dependence of underlying reaction rate parameters. It is generally unclear what\ncircuit mechanisms can inherently facilitate robustness in the dynamics to variations in temperature.\nHere, we address this issue using a combination of mathematical models and experimental measurements\nin a cell-free transcription-translation system. We find that negative transcriptional feedback\ncan reduce the effect of temperature variation on circuit dynamics. Further, we find that effective\nnegative feedback due to first-order degradation mechanisms can also enable such a temperature\nrobustness effect. Finally, we estimate temperature dependence of key parameters mediating such\nnegative feedback mechanisms. These results should be useful in the design of temperature robust\ncircuit dynamics.", "doi": "10.1101/007385", "publication_date": "2014-07-22" }, { "id": "authors:gryp7-0z868", "collection": "authors", "collection_id": "gryp7-0z868", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140724-160305011", "type": "article", "title": "Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System", "author": [ { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Yeung", "given_name": "Enoch", "orcid": "0000-0001-7630-7429", "clpid": "Yeung-Enoch" }, { "family_name": "Hayes", "given_name": "Clarmyra A.", "clpid": "Hayes-C-A" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In this work, we first characterized methods to protect linear DNA strands from exonuclease degradation in an Escherichia coli based transcription-translation cell-free system (TX-TL), as well as mechanisms of degradation. This enabled the use of linear DNA PCR products in TX-TL. We then compared expression levels and binding dynamics of different promoters on linear DNA and plasmid DNA. We also demonstrated assembly technology to rapidly build circuits entirely in vitro from separate parts. Using this strategy, we prototyped a four component genetic switch in under 8 h entirely in vitro. Rapid in vitro assembly has future applications for prototyping multiple component circuits if combined with predictive computational models.", "doi": "10.1021/sb400131a", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2014-06-20", "series_number": "6", "volume": "3", "issue": "6", "pages": "387-397" }, { "id": "authors:aag12-q0f24", "collection": "authors", "collection_id": "aag12-q0f24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140414-094313495", "type": "article", "title": "Gene Circuit Performance Characterization and Resource Usage in a Cell-Free \"Breadboard\"", "author": [ { "family_name": "Siegal-Gaskins", "given_name": "Dan", "clpid": "Siegal-Gaskins-D" }, { "family_name": "Tuza", "given_name": "Zoltan A.", "orcid": "0000-0003-2896-1527", "clpid": "Tuza-Zoltan-A" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as the complexity of synthetic circuits increases, the benefits\u2014in cost savings and design cycle time\u2014of a more traditional engineering approach can be significant. We have recently developed an in vitro \"breadboard\" prototyping platform based on E. coli cell extract that allows biocircuits to operate in an environment considerably simpler than, but functionally similar to, in vivo. The simplicity of this system makes it a promising tool for rapid biocircuit design and testing, as well as for probing fundamental aspects of gene circuit operation normally masked by cellular complexity. In this work, we characterize the cell-free breadboard using real-time and simultaneous measurements of transcriptional and translational activities of a small set of reporter genes and a transcriptional activation cascade. We determine the effects of promoter strength, gene concentration, and nucleoside triphosphate concentration on biocircuit properties, and we isolate the specific contributions of essential biomolecular resources\u2014core RNA polymerase and ribosomes\u2014to overall performance. Importantly, we show how limits on resources, particularly those involved in translation, are manifested as reduced expression in the presence of orthogonal genes that serve as additional loads on the system.", "doi": "10.1021/sb400203p", "issn": "2161-5063", "publisher": "American Chemical Society", "publication": "ACS Synthetic Biology", "publication_date": "2014-06", "series_number": "6", "volume": "3", "issue": "6", "pages": "416-425" }, { "id": "authors:kagek-80764", "collection": "authors", "collection_id": "kagek-80764", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150320-093857002", "type": "book_section", "title": "Collaborative System Identification via Parameter Consensus", "book_title": "2014 American Control Conference", "author": [ { "family_name": "Papusha", "given_name": "Ivan", "clpid": "Papusha-I" }, { "family_name": "Lavretsky", "given_name": "Eugene", "clpid": "Lavretsky-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Classical schemes in system identification and adaptive control often rely on persistence of excitation to guarantee parameter convergence, which may be difficult to achieve with a single agent and a single input. Inspired by consensus systems, we extend classical parameter adaptation to the multi agent setting by combining an adaptive gradient law with consensus dynamics. The gradient law represents the main learning signal, while consensus dynamics attract each agent's parameter estimates toward those of its neighbors. We show that the resulting decentralized online parameter estimator can be used to identify the true parameters of all agents, even if no single agent employs a persistently exciting input.", "doi": "10.1109/ACC.2014.6858938", "isbn": "978-1-4799-3272-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-06", "pages": "13-19" }, { "id": "authors:ff18x-hpc96", "collection": "authors", "collection_id": "ff18x-hpc96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150320-085455694", "type": "book_section", "title": "Exact Stability Analysis of Discrete-Time Linear Systems with Stochastic Delays", "book_title": "2014 American Control Conference", "author": [ { "family_name": "Gomez", "given_name": "Marcella M.", "clpid": "Gomez-M-M" }, { "family_name": "Qin", "given_name": "Wubing B.", "clpid": "Qin-W-B" }, { "family_name": "Orosz", "given_name": "G\u00e1bor", "orcid": "0000-0002-9000-3736", "clpid": "Orosz-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper provides analytical results regarding the stability of linear discrete-time systems with stochastic delays. Necessary and sufficient stability conditions are derived by using the second moment dynamics which can be used to draw stability charts. The results are applied to a simple connected vehicle system where the stability regions are compared to those given by the mean dynamics. Our results reveal some fundamental limitations of connected cruise control which becomes more significant as the packet drop ratio increases.", "doi": "10.1109/ACC.2014.6859470", "isbn": "978-1-4799-3272-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-06", "pages": "5534-5539" }, { "id": "authors:6bdnw-8b104", "collection": "authors", "collection_id": "6bdnw-8b104", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150320-090407457", "type": "book_section", "title": "A scalable formulation for engineering combination therapies for evolutionary dynamics of disease", "book_title": "2014 American Control Conference", "author": [ { "family_name": "Jonsson", "given_name": "Vanessa", "clpid": "Jonsson-V-D" }, { "family_name": "Rantzer", "given_name": "Anders", "clpid": "Rantzer-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It has been shown that optimal controller synthesis for positive systems can be formulated as a linear program. Leveraging these results, we propose a scalable iterative algorithm for the systematic design of sparse, small gain feedback strategies that stabilize the evolutionary dynamics of a generic disease model. We achieve the desired feedback structure by augmenting the optimization problems with \u2113_1 and \u2113_2 regularization terms, and illustrate our method on an example inspired by an experimental study aimed at finding appropriate HIV neutralizing antibody therapy combinations in the presence of escape mutants.", "doi": "10.1109/ACC.2014.6859452", "isbn": "978-1-4799-3272-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2014-06", "pages": "2771-2778" }, { "id": "authors:pv91t-rnn26", "collection": "authors", "collection_id": "pv91t-rnn26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140421-101928940", "type": "article", "title": "Synthetic circuit for exact adaptation and fold-change detection", "author": [ { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Khetarpal", "given_name": "Ishan", "clpid": "Khetarpal-I" }, { "family_name": "Sen", "given_name": "Shaunak", "orcid": "0000-0002-1412-8633", "clpid": "Sen-Shaunak" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Biological organisms use their sensory systems to\ndetect changes in their environment. The ability of\nsensory systems to adapt to static inputs allows wide\ndynamic range as well as sensitivity to input changes\nincluding fold-change detection, a response that depends\nonly on fold changes in input, and not on absolute\nchanges. This input scale invariance underlies\nan important strategy for search that depends solely\non the spatial profile of the input. Synthetic efforts\nto reproduce the architecture and response of cellular\ncircuits provide an important step to foster understanding\nat themolecular level. We report the bottom-up\nassembly of biochemical systems that show exact\nadaptation and fold-change detection. Using a malachite\ngreen aptamer as the output, a synthetic transcriptional\ncircuit with the connectivity of an incoherent\nfeed-forward loop motif exhibits pulse generation\nand exact adaptation. A simple mathematical model\nwas used to assess the amplitude and duration of\npulse response as well as the parameter regimes\nrequired for fold-change detection. Upon parameter\ntuning, this synthetic circuit exhibits fold-change detection\nfor four successive rounds of two-fold input\nchanges. The experimental realization of fold-change\ndetection circuit highlights the programmability of\ntranscriptional switches and the ability to obtain predictive\ndynamical systems in a cell-free environment\nfor technological applications.", "doi": "10.1093/nar/gku233", "pmcid": "PMC4027175", "issn": "0305-1048", "publisher": "Oxford University Press", "publication": "Nucleic Acids Research", "publication_date": "2014-04-11", "series_number": "9", "volume": "42", "issue": "9", "pages": "6078-6089" }, { "id": "authors:1hbxc-n8d57", "collection": "authors", "collection_id": "1hbxc-n8d57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140502-103349067", "type": "article", "title": "Flying Drosophila stabilize their vision-based velocity controller by sensing wind with their antennae", "author": [ { "family_name": "Fuller", "given_name": "Sawyer Buckminster", "clpid": "Fuller-S-B" }, { "family_name": "Straw", "given_name": "Andrew D.", "orcid": "0000-0001-8381-0858", "clpid": "Straw-A-D" }, { "family_name": "Peek", "given_name": "Martin Y.", "clpid": "Peek-M-Y" }, { "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" } ], "abstract": "Flies and other insects use vision to regulate their groundspeed in flight, enabling them to fly in varying wind conditions. Compared with mechanosensory modalities, however, vision requires a long processing delay (~100 ms) that might introduce instability if operated at high gain. Flies also sense air motion with their antennae, but how this is used in flight control is unknown. We manipulated the antennal function of fruit flies by ablating their aristae, forcing them to rely on vision alone to regulate groundspeed. Arista-ablated flies in flight exhibited significantly greater groundspeed variability than intact flies. We then subjected them to a series of controlled impulsive wind gusts delivered by an air piston and experimentally manipulated antennae and visual feedback. The results show that an antenna-mediated response alters wing motion to cause flies to accelerate in the same direction as the gust. This response opposes flying into a headwind, but flies regularly fly upwind. To resolve this discrepancy, we obtained a dynamic model of the fly's velocity regulator by fitting parameters of candidate models to our experimental data. The model suggests that the groundspeed variability of arista-ablated flies is the result of unstable feedback oscillations caused by the delay and high gain of visual feedback. The antenna response drives active damping with a shorter delay (~20 ms) to stabilize this regulator, in exchange for increasing the effect of rapid wind disturbances. This provides insight into flies' multimodal sensory feedback architecture and constitutes a previously unknown role for the antennae.", "doi": "10.1073/pnas.1323529111", "pmcid": "PMC3977237", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2014-04-01", "series_number": "13", "volume": "111", "issue": "13", "pages": "E1182-E1191" }, { "id": "authors:v1qcn-rhw28", "collection": "authors", "collection_id": "v1qcn-rhw28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170524-161850962", "type": "article", "title": "A Contract-Based Methodology for Aircraft Electric Power System Design", "author": [ { "family_name": "Nuzzo", "given_name": "Pierluigi", "clpid": "Nuzzo-P" }, { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-Huan" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Finn", "given_name": "John B.", "clpid": "Finn-J-B" }, { "family_name": "Sangiovanni-Vincentelli", "given_name": "Alberto L.", "orcid": "0000-0003-1298-8389", "clpid": "Sangiovanni-Vincentelli-A-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Donz\u00e9", "given_name": "Alexandre", "clpid": "Donz\u00e9-A" }, { "family_name": "Seshia", "given_name": "Sanjit A.", "clpid": "Seshia-S-A" } ], "abstract": "In an aircraft electric power system, one or more supervisory control units actuate a set of electromechanical switches to dynamically distribute power from generators to loads, while satisfying safety, reliability, and real-time performance requirements. To reduce expensive redesign steps, this control problem is generally addressed by minor incremental changes on top of consolidated solutions. A more systematic approach is hindered by a lack of rigorous design methodologies that allow estimating the impact of earlier design decisions on the final implementation. To achieve an optimal implementation that satisfies a set of requirements, we propose a platform-based methodology for electric power system design, which enables independent implementation of system topology (i.e., interconnection among elements) and control protocol by using a compositional approach. In our flow, design space exploration is carried out as a sequence of refinement steps from the initial specification toward a final implementation by mapping higher level behavioral and performance models into a set of either existing or virtual library components at the lower level of abstraction. Specifications are first expressed using the formalisms of linear temporal logic, signal temporal logic, and arithmetic constraints on Boolean variables. To reason about different requirements, we use specialized analysis and synthesis frameworks and formulate assume guarantee contracts at the articulation points in the design flow. We show the effectiveness of our approach on a proof-of-concept electric power system design.", "doi": "10.1109/ACCESS.2013.2295764", "issn": "2169-3536", "publisher": "IEEE", "publication": "IEEE Access", "publication_date": "2014-01-07", "volume": "2", "pages": "1-25" }, { "id": "authors:gs7qf-dws25", "collection": "authors", "collection_id": "gs7qf-dws25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190327-160859814", "type": "book_section", "title": "Dynamic state estimation in distributed aircraft electric control systems via adaptive submodularity", "book_title": "52nd IEEE Conference on Decision and Control", "author": [ { "family_name": "Maillet", "given_name": "Quentin", "clpid": "Maillet-Q" }, { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-Huan" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of estimating the discrete state of an aircraft electric system under a distributed control architecture through active sensing. The main idea is to use a set of controllable switches to reconfigure the system in order to gather more information about the unknown state. By adaptively making a sequence of reconfiguration decisions with uncertain outcome, then correlating measurements and prior information to make the next decision, we aim to reduce the uncertainty. A greedy strategy is developed that maximizes the one-step expected uncertainty reduction. By exploiting recent results on adaptive submodularity, we give theoretical guarantees on the worst-case performance of the greedy strategy. We apply the proposed method in a fault detection scenario where the discrete state captures possible faults in various circuit components. In addition, simple abstraction rules are proposed to alleviate state space explosion and to scale up the strategy. Finally, the efficiency of the proposed method is demonstrated empirically on different circuits.", "doi": "10.1109/CDC.2013.6760755", "isbn": "978-1-4673-5714-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-12", "pages": "5497-5503" }, { "id": "authors:111zc-hgm46", "collection": "authors", "collection_id": "111zc-hgm46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190329-155946621", "type": "book_section", "title": "Reverse engineering combination therapies for evolutionary dynamics of disease: An H\u221e approach", "book_title": "52nd IEEE Conference on Decision and Control", "author": [ { "family_name": "Jonsson", "given_name": "Vanessa", "clpid": "Jonsson-V-D" }, { "family_name": "Matni", "given_name": "Nikolai", "orcid": "0000-0003-4936-3921", "clpid": "Matni-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose a general algorithm for the systematic design of feedback strategies to stabilize the evolutionary dynamics of a generic disease model using an H\u221e approach. We show that designing therapy concentrations can be cast as an H\u221e state feedback synthesis problem, where the feedback gain is constrained to not only be strictly diagonal, but also that its diagonal elements satisfy an overdetermined set of linear equations. Leveraging recent results in positive systems, we develop an algorithm that always yields a stabilizing controller.", "doi": "10.1109/CDC.2013.6760185", "isbn": "978-1-4673-5714-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-12", "pages": "2060-2065" }, { "id": "authors:jae6g-jks92", "collection": "authors", "collection_id": "jae6g-jks92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140411-072530586", "type": "book_section", "title": "Automaton-Guided Controller Synthesis for Nonlinear Systems with Temporal Logic", "book_title": "2013 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)", "author": [ { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Amato", "given_name": "N.", "clpid": "Amato-N" } ], "abstract": "We develop a method for the control of discrete-time nonlinear systems subject to temporal logic specifications. Our approach uses a coarse abstraction of the system and an automaton representing the temporal logic specification to guide the search for a feasible trajectory. This decomposes the search for a feasible trajectory into a series of constrained reachability problems. Thus, one can create controllers for any system for which techniques exist to compute (approximate) solutions to constrained reachability problems. Representative techniques include sampling-based methods for motion planning, reachable set computations for linear systems, and graph search for finite discrete systems. Our approach avoids the expensive computation of a discrete abstraction, and its implementation is amenable to parallel computing. We demonstrate our approach with numerical experiments on temporal logic motion planning problems with high-dimensional (10+ states) continuous systems.", "doi": "10.1109/IROS.2013.6696978", "isbn": "978-1-4673-6358-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-11", "pages": "4332-4339" }, { "id": "authors:mh42m-yaw59", "collection": "authors", "collection_id": "mh42m-yaw59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190403-103445318", "type": "book_section", "title": "Pre-orders for reasoning about stability properties with respect to input of hybrid systems", "book_title": "2013 Proceedings of the International Conference on Embedded Software (EMSOFT)", "author": [ { "family_name": "Prabhakar", "given_name": "Pavithra", "clpid": "Prabhakar-P" }, { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Pre-orders on systems are the basis for abstraction based verification of systems. In this paper, we investigate pre-orders for reasoning about stability with respect to inputs of hybrid systems. First, we present a superposition type theorem which gives a characterization of the classical incremental input-to-state stability of continuous systems in terms of the traditional \u03b5-\u03b4 definition of stability. We use this as the basis for defining a notion of incremental input-to-state stability of hybrid systems. Next, we present a pre-order on hybrid systems which preserves incremental input-to-state stability, by extending the classical definitions of bisimulation relations on systems with input, with uniform continuity constraints. We show that the uniform continuity is a necessary requirement by exhibiting counter-examples to show that weaker notions of input bisimulation with just continuity requirements do not suffice to preserve stability. Finally, we demonstrate that the definitions are useful, by exhibiting concrete abstraction functions which satisfy the definitions of pre-orders.", "doi": "10.1109/EMSOFT.2013.6658602", "isbn": "978-1-4799-1443-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-10", "pages": "1-10" }, { "id": "authors:tmd2n-8ka09", "collection": "authors", "collection_id": "tmd2n-8ka09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190213-141617926", "type": "monograph", "title": "Engineering Resilient Space Systems", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Day", "given_name": "John C.", "clpid": "Day-J-C" }, { "family_name": "Ingham", "given_name": "Michel D.", "clpid": "Ingham-M-D" }, { "family_name": "Reder", "given_name": "Leonard J.", "clpid": "Reder-L-J" }, { "family_name": "Williams", "given_name": "Brian C.", "clpid": "Williams-B-C" } ], "abstract": "Several distinct trends will influence space exploration missions in the next decade. Destinations are\nbecoming more remote and mysterious, science questions more sophisticated, and, as mission experience\naccumulates, the most accessible targets are visited, advancing the knowledge frontier to more difficult,\nharsh, and inaccessible environments. This leads to new challenges including: hazardous conditions that\nlimit mission lifetime, such as high radiation levels surrounding interesting destinations like Europa or\ntoxic atmospheres of planetary bodies like Venus; unconstrained environments with navigation hazards,\nsuch as free-floating active small bodies; multielement missions required to answer more sophisticated\nquestions, such as Mars Sample Return (MSR); and long-range missions, such as Kuiper belt exploration,\nthat must survive equipment failures over the span of decades. These missions will need to be successful\nwithout a priori knowledge of the most efficient data collection techniques for optimum science return.\nScience objectives will have to be revised 'on the fly', with new data collection and navigation decisions\non short timescales.\nYet, even as science objectives are becoming more ambitious, several critical resources remain\nunchanged. Since physics imposes insurmountable light-time delays, anticipated improvements to the\nDeep Space Network (DSN) will only marginally improve the bandwidth and communications cadence to\nremote spacecraft. Fiscal resources are increasingly limited, resulting in fewer flagship missions, smaller\nspacecraft, and less subsystem redundancy. As missions visit more distant and formidable locations, the\njob of the operations team becomes more challenging, seemingly inconsistent with the trend of shrinking\nmission budgets for operations support. How can we continue to explore challenging new locations\nwithout increasing risk or system complexity?\nThese challenges are present, to some degree, for the entire Decadal Survey mission portfolio, as\ndocumented in Vision and Voyages for Planetary Science in the Decade 2013\u20132022 (National Research\nCouncil, 2011), but are especially acute for the following mission examples, identified in our recently\ncompleted KISS Engineering Resilient Space Systems (ERSS) study:\n1. A Venus lander, designed to sample the atmosphere and surface of Venus, would have to perform\nscience operations as components and subsystems degrade and fail;\n2. A Trojan asteroid tour spacecraft would spend significant time cruising to its ultimate destination\n(essentially hibernating to save on operations costs), then upon arrival, would have to act as its\nown surveyor, finding new objects and targets of opportunity as it approaches each asteroid,\nrequiring response on short notice; and\n3. A MSR campaign would not only be required to perform fast reconnaissance over long distances\non the surface of Mars, interact with an unknown physical surface, and handle degradations and\nfaults, but would also contain multiple components (launch vehicle, cruise stage, entry and\nlanding vehicle, surface rover, ascent vehicle, orbiting cache, and Earth return vehicle) that\ndramatically increase the need for resilience to failure across the complex system.\nThe concept of resilience and its relevance and application in various domains was a focus during the\nstudy, with several definitions of resilience proposed and discussed. While there was substantial variation\nin the specifics, there was a common conceptual core that emerged\u2014adaptation in the presence of\nchanging circumstances. These changes were couched in various ways\u2014anomalies, disruptions,\ndiscoveries\u2014but they all ultimately had to do with changes in underlying assumptions. Invalid\nassumptions, whether due to unexpected changes in the environment, or an inadequate understanding of\ninteractions within the system, may cause unexpected or unintended system behavior. A system is\nresilient if it continues to perform the intended functions in the presence of invalid assumptions.\nOur study focused on areas of resilience that we felt needed additional exploration and integration,\nnamely system and software architectures and capabilities, and autonomy technologies. (While also an\nimportant consideration, resilience in hardware is being addressed in multiple other venues, including\n2\nother KISS studies.) The study consisted of two workshops, separated by a seven-month focused study\nperiod. The first workshop (Workshop #1) explored the 'problem space' as an organizing theme, and the\nsecond workshop (Workshop #2) explored the 'solution space'. In each workshop, focused discussions\nand exercises were interspersed with presentations from participants and invited speakers.\nThe study period between the two workshops was organized as part of the synthesis activity during the\nfirst workshop. The study participants, after spending the initial days of the first workshop discussing the\nnature of resilience and its impact on future science missions, decided to split into three focus groups,\neach with a particular thrust, to explore specific ideas further and develop material needed for the second\nworkshop. The three focus groups and areas of exploration were:\n1. Reference missions: address/refine the resilience needs by exploring a set of reference missions\n2. Capability survey: collect, document, and assess current efforts to develop capabilities and\ntechnology that could be used to address the documented needs, both inside and outside NASA\n3. Architecture: analyze the impact of architecture on system resilience, and provide principles and\nguidance for architecting greater resilience in our future systems\nThe key product of the second workshop was a set of capability roadmaps pertaining to the three\nreference missions selected for their representative coverage of the types of space missions envisioned for\nthe future. From these three roadmaps, we have extracted several common capability patterns that would\nbe appropriate targets for near-term technical development: one focused on graceful degradation of\nsystem functionality, a second focused on data understanding for science and engineering applications,\nand a third focused on hazard avoidance and environmental uncertainty. Continuing work is extending\nthese roadmaps to identify candidate enablers of the capabilities from the following three categories:\narchitecture solutions, technology solutions, and process solutions.\nThe KISS study allowed a collection of diverse and engaged engineers, researchers, and scientists to think\ndeeply about the theory, approaches, and technical issues involved in developing and applying resilience\ncapabilities. The conclusions summarize the varied and disparate discussions that occurred during the\nstudy, and include new insights about the nature of the challenge and potential solutions:\n1. There is a clear and definitive need for more resilient space systems. During our study period,\nthe key scientists/engineers we engaged to understand potential future missions confirmed the\nscientific and risk reduction value of greater resilience in the systems used to perform these\nmissions.\n2. Resilience can be quantified in measurable terms\u2014project cost, mission risk, and quality of\nscience return. In order to consider resilience properly in the set of engineering trades performed\nduring the design, integration, and operation of space systems, the benefits and costs of resilience\nneed to be quantified. We believe, based on the work done during the study, that appropriate\nmetrics to measure resilience must relate to risk, cost, and science quality/opportunity. Additional\nwork is required to explicitly tie design decisions to these first-order concerns.\n3. There are many existing basic technologies that can be applied to engineering resilient space\nsystems. Through the discussions during the study, we found many varied approaches and\nresearch that address the various facets of resilience, some within NASA, and many more\nbeyond. Examples from civil architecture, Department of Defense (DoD) / Defense Advanced\nResearch Projects Agency (DARPA) initiatives, 'smart' power grid control, cyber-physical\nsystems, software architecture, and application of formal verification methods for software were\nidentified and discussed. The variety and scope of related efforts is encouraging and presents\nmany opportunities for collaboration and development, and we expect many collaborative\nproposals and joint research as a result of the study.\n4. Use of principled architectural approaches is key to managing complexity and integrating\ndisparate technologies. The main challenge inherent in considering highly resilient space\nsystems is that the increase in capability can result in an increase in complexity with all of the\n3\nrisks and costs associated with more complex systems. What is needed is a better way of\nconceiving space systems that enables incorporation of capabilities without increasing\ncomplexity. We believe principled architecting approaches provide the needed means to convey a\nunified understanding of the system to primary stakeholders, thereby controlling complexity in\nthe conception and development of resilient systems, and enabling the integration of disparate\napproaches and technologies. A representative architectural example is included in Appendix F.\n5. Developing trusted resilience capabilities will require a diverse yet strategically directed\nresearch program. Despite the interest in, and benefits of, deploying resilience space systems, to\ndate, there has been a notable lack of meaningful demonstrated progress in systems capable of\nworking in hazardous uncertain situations. The roadmaps completed during the study, and\ndocumented in this report, provide the basis for a real funded plan that considers the required\nfundamental work and evolution of needed capabilities.\nExploring space is a challenging and difficult endeavor. Future space missions will require more\nresilience in order to perform the desired science in new environments under constraints of development\nand operations cost, acceptable risk, and communications delays. Development of space systems with\nresilient capabilities has the potential to expand the limits of possibility, revolutionizing space science by\nenabling as yet unforeseen missions and breakthrough science observations.\nOur KISS study provided an essential venue for the consideration of these challenges and goals.\nAdditional work and future steps are needed to realize the potential of resilient systems\u2014this study\nprovided the necessary catalyst to begin this process.", "doi": "10.26206/WDX7-K192", "publication_date": "2013-09-27" }, { "id": "authors:030yt-mda27", "collection": "authors", "collection_id": "030yt-mda27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131031-134823487", "type": "article", "title": "Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology", "author": [ { "family_name": "Sun", "given_name": "Zachary Z.", "orcid": "0000-0002-9425-2924", "clpid": "Sun-Zachary-Z" }, { "family_name": "Hayes", "given_name": "Clarmyra A.", "clpid": "Hayes-C-A" }, { "family_name": "Shin", "given_name": "Jonghyeon", "clpid": "Shin-Jonghyeon" }, { "family_name": "Caschera", "given_name": "Filippo", "clpid": "Caschera-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-V" } ], "abstract": "Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform. This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology. To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems. The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.6 Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted. The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters. Accompanying mathematical models are available. The resulting system has unique applications in synthetic biology as a prototyping environment, or \"TX-TL biomolecular breadboard.\"", "doi": "10.3791/50762", "issn": "1940-087X", "publisher": "JoVE", "publication": "Journal of Visualized Experiments", "publication_date": "2013-09", "volume": "79", "pages": "Art. No. e50762" }, { "id": "authors:yvrq3-5bn64", "collection": "authors", "collection_id": "yvrq3-5bn64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130916-113727132", "type": "article", "title": "Verifying Cyber-Physical Interactions in Safety-Critical Systems", "author": [ { "family_name": "Mitra", "given_name": "Sayan", "clpid": "Mitra-Sayan" }, { "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" } ], "abstract": "Safety-compromising bugs in software-controlled systems are often hard to detect. In a 2007 DARPA Urban Challenge vehicle, such a defect remained hidden during more than 300 miles of test-driving, manifesting for the first time during the competition. With this incident as an example, the authors discuss formalisms and techniques available for safety analysis of cyber-physical systems.", "doi": "10.1109/MSP.2013.77", "issn": "1540-7993", "publisher": "IEEE", "publication": "IEEE Security and Privacy", "publication_date": "2013-07", "series_number": "4", "volume": "11", "issue": "4", "pages": "28-37" }, { "id": "authors:c2n5c-etp30", "collection": "authors", "collection_id": "c2n5c-etp30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130812-094851124", "type": "article", "title": "Optimization of convergence rate and stability margin of information flow in cooperative systems", "author": [ { "family_name": "Zabarankin", "given_name": "Michael", "clpid": "Zabarankin-M" }, { "family_name": "Murphey", "given_name": "Robert", "clpid": "Murphey-R" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The interplay between the convergence rate and stability margin (e.g. ability to reject disturbances) for a discrete-time information flow filter in cooperative systems is analyzed. For a given communication graph, the convergence rate is defined as the absolute value of the largest nonunit characteristic root of a matrix associated with the filter. The maximal convergence rate, obtained by \"tuning\" the control gains, is highly correlated to the number of distinct eigenvalues of the graph Laplacian (it is 1 for the complete graph). A stability margin is introduced for multiple-input\u2013multiple-output (MIMO) systems and is then maximized with respect to the control gains subject to a constraint on the convergence rate. The optimal stability margin as a function of the convergence rate is bounded above for any order of the filter, and the bound is attained for the complete graph. For the zero-order filter and all strongly connected communication graphs, the optimal stability margin is found analytically, whereas for the first-order filter and undirected communication graphs, it is evaluated numerically. The results demonstrate the ability to distinguish graph topologies that dominate others in their ability to reject disturbances and converge rapidly to a consensus.", "doi": "10.1016/j.automatica.2013.03.018", "issn": "0005-1098", "publisher": "Elsevier", "publication": "Automatica", "publication_date": "2013-07", "series_number": "7", "volume": "49", "issue": "7", "pages": "2030-2038" }, { "id": "authors:bphqk-1yj72", "collection": "authors", "collection_id": "bphqk-1yj72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130802-112333498", "type": "article", "title": "Synthesis of Reactive Switching Protocols From Temporal Logic Specifications", "author": [ { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose formal means for synthesizing switching protocols that determine the sequence in which the modes of a switched system are activated to satisfy certain high-level specifications in linear temporal logic (LTL). The synthesized protocols are robust against exogenous disturbances on the continuous dynamics and can react to possibly adversarial events (both external and internal). Finite-state approximations that abstract the behavior of the underlying continuous dynamics are defined using finite transition systems. Such approximations allow us to transform the continuous switching synthesis problem into a discrete synthesis problem in the form of a two-player game between the system and the environment, where the winning conditions represent the high-level temporal logic specifications. Restricting to an expressive subclass of LTL formulas, these temporal logic games are amenable to solutions with polynomial-time complexity. By construction, existence of a discrete switching strategy for the discrete synthesis problem guarantees the existence of a switching protocol that can be implemented at the continuous level to ensure the correctness of the nonlinear switched system and to react to the environment at run time.", "doi": "10.1109/TAC.2013.2246095", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2013-07", "series_number": "7", "volume": "58", "issue": "7", "pages": "1771-1785" }, { "id": "authors:7yptp-9wj25", "collection": "authors", "collection_id": "7yptp-9wj25", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2013.001", "type": "monograph", "title": "Optimal Control of Mixed Logical Dynamical Systems with Long-Term Temporal Logic Specifications", "author": [ { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a mathematical programming-based method for control of large a class of nonlinear systems subject to temporal logic task specifications. We consider Mixed Logical Dynamical (MLD) systems, which include linear hybrid automata, constrained linear systems, and piecewise affine systems. We specify tasks using a fragment of linear temporal logic (LTL) that allows both finite- and infinite-horizon properties to be specified, including tasks such as surveillance, periodic walking, repeated assembly, and environmental monitoring. Our method directly encodes an LTL formula as mixed-integer linear constraints on the MLD system, instead of computing a finite abstraction. This approach is efficient; for common tasks the formulation may use significantly fewer binary variables than related approaches. In simulation, we solve non-trivial temporal logic motion planning tasks for high-dimensional continuous systems using our approach.", "publisher": "California Institute of Technology", "publication_date": "2013-06-24" }, { "id": "authors:wnk27-54p79", "collection": "authors", "collection_id": "wnk27-54p79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131219-094019593", "type": "book_section", "title": "Computing augmented finite transition systems to synthesize switching protocols for polynomial switched systems", "book_title": "2013 American Control Conference (ACC)", "author": [ { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Prabhakar", "given_name": "Pavithra", "clpid": "Prabhakar-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This work is motivated by the problem of synthesizing mode sequences for continuous-time polynomial switched systems in order to guarantee that the trajectories of the system satisfy certain high-level specifications expressed in linear temporal logic. We use augmented finite transition systems as abstract models of continuous switched systems. Augmented finite transition systems are equipped with liveness properties that can be used to enforce progress in accordance with the underlying dynamics. We then introduce abstraction and refinement relations that induce a preorder on this class of finite transition systems. By construction, the resulting preorder respects the feasibility (i.e., realizability) of the synthesis problem. Hence, existence of a discrete switching strategy for one of these abstract finite transition systems guarantees the existence of a mode sequence for the continuous system such that all of its trajectories satisfy the specification. We also present an algorithm, which can be implemented using sum-of-squares based relaxations, to compute such high fidelity abstract models in a computationally tractable way. Finally, these ideas are illustrated on an example.", "isbn": "978-1-4799-0177-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-06", "pages": "6237-6244" }, { "id": "authors:c08vv-wpk47", "collection": "authors", "collection_id": "c08vv-wpk47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130715-075915746", "type": "book_section", "title": "Biomolecular resource utilization in elementary cell-free gene circuits", "book_title": "2013 American Control Conference (ACC)", "author": [ { "family_name": "Siegal-Gaskins", "given_name": "Dan", "clpid": "Siegal-Gaskins-D" }, { "family_name": "Noireaux", "given_name": "Vincent", "orcid": "0000-0002-5213-273X", "clpid": "Noireaux-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a detailed dynamical model of the behavior of transcription-translation circuits in vitro that makes explicit the roles played by essential molecular resources. A set of simple two-gene test circuits operating in a cell-free biochemical 'breadboard' validate this model and highlight the consequences of limited resource availability. In particular, we are able to confirm the existence of biomolecular 'crosstalk' and isolate its individual sources. The implications of crosstalk for biomolecular circuit design and function are discussed.", "doi": "10.1109/ACC.2013.6580053", "isbn": "978-1-4799-0177-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-06", "pages": "1531-1536" }, { "id": "authors:a4g6k-46g65", "collection": "authors", "collection_id": "a4g6k-46g65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190403-105326642", "type": "book_section", "title": "Feedback architectures to regulate flux of components in artificial gene networks", "book_title": "2013 American Control Conference", "author": [ { "family_name": "Giordano", "given_name": "Giulia", "clpid": "Giordano-G" }, { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper focuses on the regulation of RNA production for in vitro synthetic gene networks. We consider the problem of matching the production rate of several RNA species concurrently transcribed to form RNA complexes. We design regulatory feedback loops based on two schemes: negative auto-regulation (which can minimize the potentially harmful amount of molecules not used to form products) and cross-activation (which can maximize the overall output flux). We analyze numerically the performance of these schemes: in both cases, transcription rate matching can be achieved through proper feedback constants; negative feedback is faster and maintains stability. A possible experimental implementation of a three and four genes negative feedback architecture is also numerically studied.", "doi": "10.1109/ACC.2013.6580572", "isbn": "978-1-4799-0177-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-06", "pages": "4747-4752" }, { "id": "authors:d30r8-zpb47", "collection": "authors", "collection_id": "d30r8-zpb47", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2012.002", "type": "book_section", "title": "Convex optimal uncertainty quantification: Algorithms and a case study in energy storage placement for power grids", "book_title": "2013 American Control Conference (ACC)", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Tao", "given_name": "Molei", "clpid": "Tao-Molei" }, { "family_name": "Owhadi", "given_name": "Houman", "orcid": "0000-0002-5677-1600", "clpid": "Owhadi-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "How does one evaluate the performance of a stochastic system in the absence of a perfect model (i.e. probability distribution)? We address this question under the framework of optimal uncertainty quantification (OUQ), which is an information-based approach for worst-case analysis of stochastic systems. We are able to generalize previous results and show that the OUQ problem can be solved using convex optimization when the function under evaluation can be expressed in a polytopic canonical form (PCF). We also propose iterative methods for scaling the convex formulation to larger systems. As an application, we study the problem of storage placement in power grids with renewable generation. Numerical simulation results for simple artificial examples as well as an example using the IEEE 14-bus test case with real wind generation data are presented to demonstrate the usage of OUQ analysis.", "isbn": "978-1-4799-0177-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-06", "pages": "1130-1137" }, { "id": "authors:32w4c-kan37", "collection": "authors", "collection_id": "32w4c-kan37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131219-095517199", "type": "book_section", "title": "Design and implementation of a biomolecular circuit for tracking protein concentration", "book_title": "2013 American Control Conference (ACC)", "author": [ { "family_name": "de los Santos", "given_name": "Emmanuel L. C.", "clpid": "de-los-Santos-E-L-C" }, { "family_name": "Hsiao", "given_name": "Victoria", "orcid": "0000-0001-9297-1522", "clpid": "Hsiao-Victoria" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes the design, modeling, synthesis and preliminary validation of a protein concentration regulator circuit. The circuit is designed to maintain the level of a target protein to a reference level, specified by the amount of another protein. This is implemented using a single negative feedback loop that inhibits the production of the target protein once its concentration is equal to the reference amount. A mathematical model consisting of a set of ODEs is derived from mass action laws and Hill function approximations of protein production. Steady-state analysis of the model is used to predict parameter sensitivity and experimental behavior. We implemented this circuit in E. coli using scaffold-based sequestration and transcriptional activation. Preliminary experimental results show the system matching predictions from our model and performing the expected task.", "doi": "10.1109/ACC.2013.6580175", "isbn": "978-1-4799-0177-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-06", "pages": "2290-2294" }, { "id": "authors:n2y0r-e1e51", "collection": "authors", "collection_id": "n2y0r-e1e51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140724-105809953", "type": "book_section", "title": "Just-in-time synthesis for reactive motion planning with temporal logic", "book_title": "2013 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The cost of the great expressivity of motion planning subject to temporal logic formulae is intractability. Recent advances in sampling-based methods seem to be only applicable to \"low-level\" control. The problem of realizing \"high-level\" controllers that satisfy a temporal logic specification does not readily admit approximations, unless the notion of correctness is relaxed as might be achieved with probabilistic variants of temporal logics. In this paper, we argue that not all possible environment (uncontrolled) behaviors need to be explicitly planned for, but rather short-time strategies can be generated online while maintaining global correctness. We achieve this by separating feasibility from controller synthesis, using metrics from the underlying continuous state space to ensure short-time strategies chained together provide globally correct behavior.", "doi": "10.1109/ICRA.2013.6631298", "isbn": "978-1-4673-5641-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-05", "pages": "5048-5053" }, { "id": "authors:1dmyy-1cj34", "collection": "authors", "collection_id": "1dmyy-1cj34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140724-125512319", "type": "book_section", "title": "Motion planning in observations space with learned diffeomorphism models", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Nilsson", "given_name": "Adam", "clpid": "Nilsson-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of planning motions in observations space, based on learned models of the dynamics that associate to each action a diffeomorphism of the observations domain. For an arbitrary set of diffeomorphisms, this problem must be formulated as a generic search problem. We adapt established algorithms of the graph search family. In this scenario, node expansion is very costly, as each node in the graph is associated to an uncertain diffeomorphism and corresponding predicted observations. We describe several improvements that ameliorate performance: the introduction of better image similarities to use as heuristics; a method to reduce the number of expanded nodes by preliminarily identifying redundant plans; and a method to pre-compute composite actions that make the search efficient in all directions.", "doi": "10.1109/ICRA.2013.6630973", "publisher": "IEEE", "publication_date": "2013-05" }, { "id": "authors:czn3c-e7a25", "collection": "authors", "collection_id": "czn3c-e7a25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140724-094726571", "type": "book_section", "title": "Efficient reactive controller synthesis for a fragment of linear temporal logic", "book_title": "2013 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Motivated by robotic motion planning, we develop a framework for control policy synthesis for both non-deterministic transition systems and Markov decision processes that are subject to temporal logic task specifications. We introduce a fragment of linear temporal logic that can be used to specify common motion planning tasks such as safe navigation, response to the environment, persistent coverage, and surveillance. This fragment is computationally efficient; the complexity of control policy synthesis is a doubly-exponential improvement over standard linear temporal logic for both non-deterministic transition systems and Markov decision processes. This improvement is possible because we compute directly on the original system, as opposed to the automata-based approach commonly used. We give simulation results for representative motion planning tasks and compare to generalized reactivity.", "doi": "10.1109/ICRA.2013.6631296", "isbn": "978-1-4673-5641-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-05", "pages": "5033-5040" }, { "id": "authors:e9n8z-nmk20", "collection": "authors", "collection_id": "e9n8z-nmk20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130709-103021335", "type": "article", "title": "A robust model predictive control algorithm augmented with a reactive safety mode", "author": [ { "family_name": "Carson", "given_name": "John M., III", "clpid": "Carson-J-M-III" }, { "family_name": "A\u00e7\u0131kme\u015fe", "given_name": "Beh\u00e7et", "clpid": "A\u00e7\u0131kme\u015fe-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "MacMartin", "given_name": "Douglas G.", "orcid": "0000-0003-1987-9417", "clpid": "MacMartin-D-G" } ], "abstract": "A reactive safety mode is built into a robust model predictive control algorithm for uncertain nonlinear systems with bounded disturbances. The algorithm enforces state and control constraints and blends two modes: (I) standard, guarantees re-solvability and asymptotic convergence in a robust receding-horizon manner; (II) safety, if activated, guarantees containment within an invariant set about a reference. The reactive safety mode provides robustness to unexpected, but real-time anticipated, state-constraint changes during standard mode operation. The safety-mode control policy is designed offline and can be activated at any arbitrary time. The standard-mode control has feedforward and feedback components: feedforward is from online solution of a finite-horizon optimal control problem; feedback is designed offline to provide robustness to system uncertainty and disturbances and to establish an invariant \"state tube\" that guarantees standard-mode re-solvability at any time. The algorithm design is shown for a class of systems with incrementally-conic uncertain/nonlinear terms and bounded disturbances.", "doi": "10.1016/j.automatica.2013.02.025", "issn": "0005-1098", "publisher": "Elsevier", "publication": "Automatica", "publication_date": "2013-05", "series_number": "5", "volume": "49", "issue": "5", "pages": "1251-1260" }, { "id": "authors:ms5d0-vmm67", "collection": "authors", "collection_id": "ms5d0-vmm67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140724-090815397", "type": "book_section", "title": "Robot navigation in dense human crowds: the case for cooperation", "book_title": "2013 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Trautman", "given_name": "Peter", "clpid": "Trautman-P" }, { "family_name": "Ma", "given_name": "Jeremy", "clpid": "Ma-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Krause", "given_name": "Andreas", "orcid": "0000-0001-7260-9673", "clpid": "Krause-A" } ], "abstract": "We consider mobile robot navigation in dense human crowds. In particular, we explore two questions. Can we design a navigation algorithm that encourages humans to cooperate with a robot? Would such cooperation improve navigation performance? We address the first question by developing a probabilistic predictive model of cooperative collision avoidance and goal-oriented behavior by extending the interacting Gaussian processes approach to include multiple goals and stochastic movement duration. We answer the second question with an extensive quantitative study of robot navigation in dense human crowds (488 runs completed), specifically testing how cooperation models effect navigation performance. We find that the \"multiple goal\" interacting Gaussian processes algorithm performs comparably with human teleoperators in crowd densities near 1 person/m^2, while a state of the art noncooperative planner exhibits unsafe behavior more than 3 times as often as this multiple goal extension, and more than twice as often as the basic interacting Gaussian processes. Furthermore, a reactive planner based on the widely used \"dynamic window\" approach fails for crowd densities above 0.55 people/m^2. Based on these experimental results, and previous theoretical observations, we conclude that a cooperation model is important for safe and efficient robot navigation in dense human crowds.", "doi": "10.1109/ICRA.2013.6630866", "isbn": "978-1-4673-5641-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-05", "pages": "2153-2160" }, { "id": "authors:twfm3-zjr81", "collection": "authors", "collection_id": "twfm3-zjr81", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140724-131326509", "type": "book_section", "title": "Patching task-level robot controllers based on a local \u00b5-calculus formula", "book_title": "2013 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Prabhakar", "given_name": "Pavithra", "clpid": "Prabhakar-P" }, { "family_name": "Jose", "given_name": "Alex B.", "clpid": "Jose-A-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a method for mending strategies for GR(1) specifications. Given the addition or removal of edges from the game graph describing a problem (essentially transition rules in a GR(1) specification), we apply a \u03bc-calculus formula to a neighborhood of states to obtain a \"local strategy\" that navigates around the invalidated parts of an original synthesized strategy. Our method may thus avoid global resynthesis while recovering correctness with respect to the new specification. We illustrate the results both in simulation and on physical hardware for a planar robot surveillance task.", "doi": "10.1109/ICRA.2013.6631229", "isbn": "978-1-4673-5643-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-05", "pages": "4588-4595" }, { "id": "authors:926s7-aa297", "collection": "authors", "collection_id": "926s7-aa297", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130719-105708428", "type": "book_section", "title": "An aircraft electric power testbed for validating automatically synthesized reactive control protocols", "book_title": "Proceedings of the 16th international conference on Hybrid systems: computation and control", "author": [ { "family_name": "Rogersten", "given_name": "Robert", "clpid": "Rogersten-R" }, { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-H" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Belta", "given_name": "Calin", "clpid": "Belta-C" }, { "family_name": "Ivan\u010di\u0107", "given_name": "Franjo", "clpid": "Ivan\u010di\u0107-F" } ], "abstract": "Modern aircraft increasingly rely on electric power for subsystems that have traditionally run on mechanical power. The complexity and safety-criticality of aircraft electric power systems have therefore increased, rendering the design of these systems more challenging. This work is motivated by the potential that correct-by-construction reactive controller synthesis tools may have in increasing the effectiveness of the electric power system design cycle. In particular, we have built an experimental hardware platform that captures some key elements of aircraft electric power systems within a simplified setting. We intend to use this platform for validating the applicability of theoretical advances in correct-by-construction control synthesis and for studying implementation-related challenges. We demonstrate a simple design workflow from formal specifications to auto-generated code that can run on software models and be used in hardware implementation. We show some preliminary results with different control architectures on the developed hardware testbed.", "doi": "10.1145/2461328.2461344", "isbn": "978-1-4503-1567-8", "publisher": "Association for Computing Machinery", "place_of_publication": "New York, NY", "publication_date": "2013-04", "pages": "89-94" }, { "id": "authors:f5rz8-ts294", "collection": "authors", "collection_id": "f5rz8-ts294", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151124-141949989", "type": "article", "title": "Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Straw", "given_name": "Andrew D.", "orcid": "0000-0001-8381-0858", "clpid": "Straw-A-D" }, { "family_name": "Sayaman", "given_name": "Rosalyn W.", "clpid": "Sayaman-R-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" } ], "abstract": "As animals move through the world in search of resources, they change course in reaction to both external sensory cues and internally-generated programs. Elucidating the functional logic of complex search algorithms is challenging because the observable actions of the animal cannot be unambiguously assigned to externally- or internally-triggered events. We present a technique that addresses this challenge by assessing quantitatively the contribution of external stimuli and internal processes. We apply this technique to the analysis of rapid turns (\"saccades\") of freely flying Drosophila melanogaster. We show that a single scalar feature computed from the visual stimulus experienced by the animal is sufficient to explain a majority (93%) of the turning decisions. We automatically estimate this scalar value from the observable trajectory, without any assumption regarding the sensory processing. A posteriori, we show that the estimated feature field is consistent with previous results measured in other experimental conditions. The remaining turning decisions, not explained by this feature of the visual input, may be attributed to a combination of deterministic processes based on unobservable internal states and purely stochastic behavior. We cannot distinguish these contributions using external observations alone, but we are able to provide a quantitative bound of their relative importance with respect to stimulus-triggered decisions. Our results suggest that comparatively few saccades in free-flying conditions are a result of an intrinsic spontaneous process, contrary to previous suggestions. We discuss how this technique could be generalized for use in other systems and employed as a tool for classifying effects into sensory, decision, and motor categories when used to analyze data from genetic behavioral screens.", "doi": "10.1371/journal.pcbi.1002891", "pmcid": "PMC3585425", "issn": "1553-7358", "publisher": "Public Library of Science", "publication": "PLOS Computational Biology", "publication_date": "2013-02", "series_number": "2", "volume": "9", "issue": "2", "pages": "Art. No. e1002891" }, { "id": "authors:qgpd8-25z64", "collection": "authors", "collection_id": "qgpd8-25z64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130115-094546873", "type": "monograph", "title": "An Aircraft Electric Power Testbed for Validating Automatically Synthesized Reactive Control Protocols", "author": [ { "family_name": "Rogersten", "given_name": "Robert", "clpid": "Rogersten-R" }, { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-H" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Modern aircraft increasingly rely on electric power for subsystems that have traditionally run on mechanical power. The complexity and safety-criticality of aircraft electric power systems have therefore increased, rendering the design of these systems more challenging. This work is motivated by the potential that correct-by-construction reactive controller synthesis tools may have in increasing the effectiveness of the electric power system design cycle. In particular, we have built an experimental hardware platform that captures some key elements of aircraft electric power systems within a simplified setting. We intend to use this platform for validating the applicability of theoretical advances in correct-by-construction control synthesis and for studying implementation-related challenges. We demonstrate a simple design workflow from formal specifications to auto-generated code that can run on software models and be used in hardware implementation. We show some preliminary results with different control architectures on the developed hardware testbed.", "publisher": "Caltech Library", "publication_date": "2013-01-15" }, { "id": "authors:3tvb6-9pv80", "collection": "authors", "collection_id": "3tvb6-9pv80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140425-112422202", "type": "book_section", "title": "Stability of Discrete-Time Systems with Stochastically Delayed Feedback", "book_title": "Control Conference (ECC), 2013 European", "author": [ { "family_name": "Gomez", "given_name": "Marcella M.", "clpid": "Gomez-M-M" }, { "family_name": "Orosz", "given_name": "G\u00e1bor", "orcid": "0000-0002-9000-3736", "clpid": "Orosz-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper investigates the stability of linear systems with stochastic delay in discrete time. Stability of the\nmean and second moment of the non-deterministic system is\ndetermined by a set of deterministic discrete-time equations\nwith distributed delay. A theorem is provided that guarantees convergence of the state with convergence of the second moment, assuming that delays are identically independently distributed. The theorem is applied to a scalar equation where the stability of the equilibrium is determined.", "isbn": "978-3-033-03962-9", "publisher": "IEEE", "place_of_publication": "New York, NY", "publication_date": "2013", "pages": "2609-2614" }, { "id": "authors:faxkf-vwq98", "collection": "authors", "collection_id": "faxkf-vwq98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131220-132617887", "type": "book_section", "title": "Robust control of uncertain Markov Decision Processes with temporal logic specifications", "book_title": "51st IEEE Conference on Decision and Control", "author": [ { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a method for designing a robust control policy for an uncertain system subject to temporal logic specifications. The system is modeled as a finite Markov Decision Process (MDP) whose transition probabilities are not exactly known but are known to belong to a given uncertainty set. A robust control policy is generated for the MDP that maximizes the worst-case probability of satisfying the specification over all transition probabilities in this uncertainty set. To this end, we use a procedure from probabilistic model checking to combine the system model with an automaton representing the specification. This new MDP is then transformed into an equivalent form that satisfies assumptions for stochastic shortest path dynamic programming. A robust version of dynamic programming solves for a \u03b5-suboptimal robust control policy with time complexity O(log1/\u03b5) times that for the non-robust case.", "doi": "10.1109/CDC.2012.6426174", "isbn": "978-1-4673-2065-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-12", "pages": "3372-3379" }, { "id": "authors:0pm1d-xhn91", "collection": "authors", "collection_id": "0pm1d-xhn91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170201-163148693", "type": "book_section", "title": "Reactive controllers for differentially flat systems with temporal logic constraints", "book_title": "2012 IEEE 51st IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose a procedure for the synthesis of control protocols for systems governed by nonlinear differential equations and constrained by temporal logic specifications. This procedure relies on a particular finite-state abstraction of the underlying continuous dynamics and a discrete representation of the external environmental signals. A two-player game formulation provides computationally efficient means to construct a discrete strategy based on the finite-state model. We focus on systems with differentially flat outputs, which, in a straightforward manner, allows the construction of continuous control signals from the discrete transitions dictated by the discrete strategy. The resulting continuous-time output trajectories are provably guaranteed to robustly satisfy the original specifications.", "doi": "10.1109/CDC.2012.6425981", "isbn": "978-1-4673-2066-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-12", "pages": "7664-7670" }, { "id": "authors:h6wj9-cb014", "collection": "authors", "collection_id": "h6wj9-cb014", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131219-103750003", "type": "book_section", "title": "A case study on reactive protocols for aircraft electric power distribution", "book_title": "51st IEEE Conference on Decision and Control", "author": [ { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-Huan" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of designing a control protocol for the aircraft electric power system that meets system requirements and reacts dynamically to changes in internal system states. We formalize these requirements by translating them into a temporal logic specification language describing the correct behaviors of the system, and apply formal methods to automatically synthesize a controller protocol that satisfies system properties and requirements. Through an example, we perform a design exploration to show the benefits and tradeoffs between centralized and distributed control architectures.", "doi": "10.1109/CDC.2012.6426175", "isbn": "978-1-4673-2065-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-12", "pages": "1124-1129" }, { "id": "authors:we9eb-z1346", "collection": "authors", "collection_id": "we9eb-z1346", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130110-104823261", "type": "article", "title": "Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response", "author": [ { "family_name": "Venturelli", "given_name": "Ophelia S.", "clpid": "Venturelli-O-S" }, { "family_name": "El-Samad", "given_name": "Hana", "orcid": "0000-0001-6239-9916", "clpid": "El-Samad-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Feedback loops are ubiquitous features of biological networks and can produce significant phenotypic heterogeneity, including a bimodal distribution of gene expression across an isogenic cell population. In this work, a combination of experiments and computational modeling was used to explore the roles of multiple feedback loops in the bimodal, switch-like response of the Saccharomyces cerevisiae galactose regulatory network. Here, we show that bistability underlies the observed bimodality, as opposed to stochastic effects, and that two unique positive feedback loops established by Gal1p and Gal3p, which both regulate network activity by molecular sequestration of Gal80p, induce this bimodality. Indeed, systematically scanning through different single and multiple feedback loop knockouts, we demonstrate that there is always a concentration regime that preserves the system's bimodality, except for the double deletion of GAL1 and the GAL3 feedback loop, which exhibits a graded response for all conditions tested. The constitutive production rates of Gal1p and Gal3p operate as bifurcation parameters because variations in these rates can also abolish the system's bimodal response. Our model indicates that this second loss of bistability ensues from the inactivation of the remaining feedback loop by the overexpressed regulatory component. More broadly, we show that the sequestration binding affinity is a critical parameter that can tune the range of conditions for bistability in a circuit with positive feedback established by molecular sequestration. In this system, two positive feedback loops can significantly enhance the region of bistability and the dynamic response time.", "doi": "10.1073/pnas.1211902109", "pmcid": "PMC3511703", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2012-11-27", "series_number": "48", "volume": "109", "issue": "48", "pages": "E3324-E3333" }, { "id": "authors:t8589-smq26", "collection": "authors", "collection_id": "t8589-smq26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121220-142113975", "type": "article", "title": "Receding Horizon Temporal Logic Planning", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a methodology for automatic synthesis of embedded control software that incorporates a class of linear temporal logic (LTL) specifications sufficient to describe a wide range of properties including safety, stability, progress, obligation, response and guarantee. To alleviate the associated computational complexity of LTL synthesis, we propose a receding horizon framework that effectively reduces the synthesis problem into a set of smaller problems. The proposed control structure consists of a goal generator, a trajectory planner, and a continuous controller. The goal generator reduces the trajectory generation problem into a sequence of smaller problems of short horizon while preserving the desired system-level temporal properties. Subsequently, in each iteration, the trajectory planner solves the corresponding short-horizon problem with the currently observed state as the initial state and generates a feasible trajectory to be implemented by the continuous controller. Based on the simulation property, we show that the composition of the goal generator, trajectory planner and continuous controller and the corresponding receding horizon framework guarantee the correctness of the system with respect to its specification regardless of the environment in which the system operates. In addition, we present a response mechanism to handle failures that may occur due to a mismatch between the actual system and its model. The effectiveness of the proposed technique is demonstrated through an example of an autonomous vehicle navigating an urban environment. This example also illustrates that the system is not only robust with respect to exogenous disturbances but is also capable of properly handling violation of the environment assumption that is explicitly stated as part of the system specification.", "doi": "10.1109/TAC.2012.2195811", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2012-11", "series_number": "11", "volume": "57", "issue": "11", "pages": "2817-2830" }, { "id": "authors:43wc9-11598", "collection": "authors", "collection_id": "43wc9-11598", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190410-120612586", "type": "monograph", "title": "Synthesis of Reactive Protocols for Vehicle-to-Vehicle Communication", "author": [ { "family_name": "Wiltsche", "given_name": "Clemens", "clpid": "Wiltsche-C" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a synthesis method for communication protocols for active safety applications that satisfy certain formal specifications on quality of service requirements. The protocols are developed to provide reliable communication services for automobile active safety applications. The synthesis method transforms a specification into a distributed implementation of senders and receivers that together satisfy the quality of service requirements by transmitting messages over an unreliable medium. We develop a specification language and an execution model for the implementations, and demonstrate the viability of our method by developing a protocol for a traffic scenario in which a car runs a red light at a busy intersection.", "doi": "10.48550/arXiv.1210.2035", "publisher": "arXiv", "publication_date": "2012-10-07" }, { "id": "authors:gz1wr-jzx39", "collection": "authors", "collection_id": "gz1wr-jzx39", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2012.004", "type": "monograph", "title": "Motion planning in observations space with learned diffeomorphism models", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Nilsson", "given_name": "Adam", "clpid": "Nilsson-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of planning motions in observations\n space, based on learned models of the dynamics that\n associate to each action a diffeomorphism of the\n observations domain. For an arbitrary set of\n diffeomorphisms, this problem must be formulated as a\n generic search problem. We adapt established algorithms of\n the graph search family. In this scenario, node expansion\n is very costly, as each node in the graph is associated to\n an uncertain diffeomorphism and corresponding predicted\n observations. We describe several improvements that\n ameliorate performance: the introduction of better image\n similarities to use as heuristics; a method to reduce the\n number of expanded nodes by preliminarily identifying\n redundant plans; and a method to pre-compute composite\n actions that make the search efficient in all directions.", "publisher": "Caltech Library", "publication_date": "2012-09-27" }, { "id": "authors:4ced0-apw23", "collection": "authors", "collection_id": "4ced0-apw23", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2012.003", "type": "monograph", "title": "Patching task-level robot controllers based on a local \u00b5-calculus formula", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Prabhakar", "given_name": "Pavithra", "clpid": "Prabhakar-P" }, { "family_name": "Jose", "given_name": "Alex B.", "clpid": "Jose-A-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a method for mending strategies for\nGR(1) specifications. Given the addition or removal of edges\nfrom the game graph describing a problem (essentially transition\nrules in a GR(1) specification), we apply a \u00b5-calculus\nformula to a neighborhood of states to obtain a \"local strategy\"\nthat navigates around the invalidated parts of an original\nsynthesized strategy. Our method may thus avoid global resynthesis\nwhile recovering correctness with respect to the new\nspecification. We illustrate the results both in simulation and\non physical hardware for a planar robot surveillance task.", "publisher": "Caltech Library", "publication_date": "2012-09-20" }, { "id": "authors:7ecg9-nwz14", "collection": "authors", "collection_id": "7ecg9-nwz14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121026-084418812", "type": "article", "title": "Verification of Periodically Controlled Hybrid Systems: Application to an Autonomous Vehicle", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Mitra", "given_name": "Sayan", "clpid": "Mitra-S" }, { "family_name": "Lamperski", "given_name": "Andrew", "clpid": "Lamperski-A-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This article introduces Periodically Controlled Hybrid Automata (PCHA) for modular specification of embedded\ncontrol systems. In a PCHA, control actions that change the control input to the plant occur roughly\nperiodically, while other actions that update the state of the controller may occur in the interim. Such actions\ncould model, for example, sensor updates and information received from higher-level planning modules that\nchange the set point of the controller. Based on periodicity and subtangential conditions, a new sufficient\ncondition for verifying invariant properties of PCHAs is presented. For PCHAs with polynomial continuous\nvector fields, it is possible to check these conditions automatically using, for example, quantifier elimination\nor sum of squares decomposition. We examine the feasibility of this automatic approach on a small example.\nThe proposed technique is also used to manually verify safety and progress properties of a fairly complex\nplanner-controller subsystem of an autonomous ground vehicle. Geometric properties of planner-generated\npaths are derived which guarantee that such paths can be safely followed by the controller.", "doi": "10.1145/2331147.2331163", "issn": "1539-9087", "publisher": "Association for Computing Machinery", "publication": "ACM Transactions in Embedded Computing Systems", "publication_date": "2012-08", "series_number": "S2", "volume": "11", "issue": "S2", "pages": "Art. No. 53" }, { "id": "authors:62t20-g3539", "collection": "authors", "collection_id": "62t20-g3539", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247070", "type": "book_section", "title": "Decentralised minimal-time dynamic consensus", "book_title": "2012 American Control Conference (ACC)", "author": [ { "family_name": "Yuan", "given_name": "Ye", "orcid": "0000-0001-7858-0437", "clpid": "Yuan-Ye" }, { "family_name": "Liu", "given_name": "Jun", "orcid": "0000-0002-2504-3651", "clpid": "Liu-Jun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Gon\u00e7alves", "given_name": "Jorge", "clpid": "Gon\u00e7alves-J-M" } ], "abstract": "This paper considers a group of agents that aim to reach an agreement on individually received time-varying signals by local communication. In contrast to static network averaging problem, the consensus considered in this paper is reached in a dynamic sense. A discrete-time dynamic average consensus protocol can be designed to allow all the agents tracking the average of their reference inputs asymptotically. We propose a minimal-time dynamic consensus algorithm, which only utilises a minimal number of local observations of a randomly picked node in a network to compute the final consensus signal. Our results illustrate that with memory and computational ability, the running time of distributed averaging algorithms can be indeed improved dramatically as suggested by Olshevsky and Tsitsiklis.", "doi": "10.1109/acc.2012.6315298", "isbn": "9781457710964", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-06", "pages": "800-805" }, { "id": "authors:zt6xz-ma385", "collection": "authors", "collection_id": "zt6xz-ma385", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121009-105532954", "type": "book_section", "title": "Switching protocol synthesis for temporal logic specifications", "book_title": "2012 American Control Conference (ACC)", "author": [ { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of synthesizing a robust switching controller for nonlinear hybrid systems to guarantee that the trajectories of the system satisfy a high level specification expressed in linear temporal logic. Two different types of finite transition systems, namely under-approximations and over-approximations, that abstract the behavior of the underlying continuous dynamical system are defined. Using these finite abstractions, it is possible to leverage tools from logic and automata theory to synthesize discrete mode sequences or strategies. In particular, we show that the discrete synthesis problem for an under-approximation can be reformulated as a model checking problem and that for an over-approximation can be transformed into a two-player game, which can then be solved by using off-the-shelf tools. By construction, existence of a discrete switching strategy for the discrete synthesis problem guarantees the existence of a continuous switching protocol for the continuous synthesis problem, which can be implemented at the continuous level to ensure the correctness of the trajectories for the nonlinear hybrid system. Moreover, in the case of over-approximations, it is shown that one can easily accommodate specifications that require reacting to possibly adversarial external events within the same framework.", "doi": "10.1109/ACC.2012.6315040", "isbn": "978-1-4577-1095-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-06", "pages": "727-734" }, { "id": "authors:c93vh-gnf56", "collection": "authors", "collection_id": "c93vh-gnf56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247242", "type": "book_section", "title": "Temporal logic control of switched affine systems with an application in fuel balancing", "book_title": "2012 American Control Conference (ACC)", "author": [ { "family_name": "Nilsson", "given_name": "Petter", "orcid": "0000-0001-8748-6936", "clpid": "Nilsson-Petter" }, { "family_name": "\u00d6zay", "given_name": "Necmiye", "orcid": "0000-0002-5552-4392", "clpid": "\u00d6zay-Necmiye" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of synthesizing hierarchical controllers for discrete-time switched affine systems subject to exogenous disturbances that guarantee that the trajectories of the system satisfy a high-level specification expressed as a linear temporal logic formula. Our method builds upon recent results on temporal logic planning and embedded controller synthesis. First, the control problem is lifted to a discrete level by constructing a finite transition system that abstracts the behavior of the underlying switched system. At the discrete level, we recast the problem as a two player temporal logic game by treating the environment driven switches as adversaries. The solution strategy for the game (i.e. the discrete plan) is then implemented at the continuous level by solving finite-horizon optimal control problems that establish reachability between discrete states and that compensate the effects of continuous disturbances. We also extend the earlier work by making efficient use of propositions in the temporal logic formula to drive the abstraction procedure and to facilitate the computation of continuous input at implementation time. An aircraft fuel system example is formulated; and solved using the proposed method. This sample problem demonstrates the applicability of the abstraction procedure and correct-by-construction controllers to regulate the fuel levels in multiple tanks during interesting operations like aerial refueling.", "doi": "10.1109/acc.2012.6315141", "isbn": "9781457710964", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-06", "pages": "5302-5309" }, { "id": "authors:6mrfh-9jd54", "collection": "authors", "collection_id": "6mrfh-9jd54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120703-085636525", "type": "book_section", "title": "Towards formal synthesis of reactive controllers for dexterous robotic manipulation", "book_title": "2012 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Chinchali", "given_name": "Sandeep", "clpid": "Chinchali-S" }, { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In robotic finger gaiting, fingers continuously manipulate an object until joint limitations or mechanical limitations periodically force a switch of grasp. Current approaches to gait planning and control are slow, lack formal guarantees on correctness, and are generally not reactive to changes in object geometry. To address these issues, we apply advances in formal methods to model a gait subject to external perturbations as a two-player game between a finger controller and its adversarial environment. High-level specifications are expressed in linear temporal logic (LTL) and low-level control primitives are designed for continuous kinematics. Simulations of planar manipulation with our synthesized correct-by-construction gait controller demonstrate the benefits of this approach.", "doi": "10.1109/ICRA.2012.6225257", "isbn": "978-1-4673-1403-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-05", "pages": "5183-5189" }, { "id": "authors:t91fz-aeh12", "collection": "authors", "collection_id": "t91fz-aeh12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120703-110333250", "type": "book_section", "title": "Learning diffeomorphism models of robotic sensorimotor cascades", "book_title": "2012 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The problem of bootstrapping consists in designing agents that can learn from scratch the model of their sensorimotor cascade (the series of robot actuators, the external world, and the robot sensors) and use it to achieve useful tasks. In principle, we would want to design agents that can work for any robot dynamics and any robot sensor(s). One of the difficulties of this problem is the fact that the observations are very high dimensional, the dynamics is nonlinear, and there is a wide range of \"representation nuisances\" to which we would want the agent to be robust. In this paper, we model the dynamics of sensorimotor cascades using diffeomorphisms of the sensel space. We show that this model captures the dynamics of camera and range-finder data, that it can be used for long-term predictions, and that it can capture nonlinear phenomena such as a limited field of view. Moreover, by analyzing the learned diffeomorphisms it is possible to recover the \"linear structure\" of the dynamics independently of the commands representation.", "doi": "10.1109/ICRA.2012.6225318", "isbn": "978-1-4673-1403-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-05", "pages": "3657-3664" }, { "id": "authors:vg71z-za941", "collection": "authors", "collection_id": "vg71z-za941", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120703-084401806", "type": "book_section", "title": "Backtracking temporal logic synthesis for uncertain environments", "book_title": "2012 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Livingston", "given_name": "Scott C.", "clpid": "Livingston-S-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" } ], "abstract": "This paper considers the problem of synthesizing correct-by-construction robotic controllers in environments with uncertain but fixed structure. \"Environment\" has two notions in this work: a map or \"world\" in which some controlled agent must operate and navigate (i.e., evolve in a configuration space with obstacles); and an adversarial player that selects continuous and discrete variables to try to make the agent fail (as in a game). Both the robot and the environment are subjected to behavioral specifications expressed as an assume-guarantee linear temporal logic (LTL) formula. We then consider how to efficiently modify the synthesized controller when the robot encounters unexpected changes in its environment. The crucial insight is that a portion of this problem takes place in a metric space, which provides a notion of nearness. Thus if a nominal plan fails, we need not resynthesize it entirely, but instead can \"patch\" it locally. We present an algorithm for doing this, prove soundness (correctness of output), and demonstrate it on an example gridworld.", "doi": "10.1109/ICRA.2012.6225208", "isbn": "978-1-4673-1403-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-05", "pages": "5163-5170" }, { "id": "authors:n0ybp-psz75", "collection": "authors", "collection_id": "n0ybp-psz75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120703-105934140", "type": "book_section", "title": "Fault detection and isolation from uninterpreted data in robotic sensorimotor cascades", "book_title": "2012 IEEE International Conference on Robotics and Automation (ICRA)", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "H\u00e5kansson", "given_name": "Magnus", "clpid": "H\u00e5kansson-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "One of the challenges in designing the next generation of robots operating in non-engineered environments is that there seems to be an infinite amount of causes that make the sensor data unreliable or actuators ineffective. In this paper, we discuss what faults are possible to detect using zero modeling effort: we start from uninterpreted streams of observations and commands, and without a prior knowledge of a model of the world. We show that in sensorimotor cascades it is possible to define static faults independently of a nominal model. We define an information-theoretic usefulness of a sensor reading and we show that it captures several kind of sensorimotor faults frequently encountered in practice. We particularize these ideas to models proposed in previous work as suitable candidates for describing generic sensorimotor cascades. We show several examples with camera and range-finder data, and we discuss a possible way to integrate these techniques in an existing robot software architecture.", "doi": "10.1109/ICRA.2012.6225311", "isbn": "978-1-4673-1403-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2012-05", "pages": "229-236" }, { "id": "authors:6av5c-ej686", "collection": "authors", "collection_id": "6av5c-ej686", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120620-095640251", "type": "book_section", "title": "On synthesizing robust discrete controllers under modeling uncertainty", "book_title": "Proceedings of the 15th ACM international conference on Hybrid Systems: Computation and Control", "author": [ { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We investigate the robustness of reactive control protocols\nsynthesized to guarantee system's correctness with respect\nto given temporal logic specifications. We consider uncertainties in open finite transition systems due to unmodeled transitions. The resulting robust synthesis problem is formulated as a temporal logic game. In particular, if the specification is in the so-called generalized reactivity [1] fragment of linear temporal logic, so is the augmented specification in the resulting robust synthesis problem. Hence, the robust synthesis problem belongs to the same complexity class with the nominal synthesis problem, and is amenable to polynomial\ntime solvers. Additionally, we discuss reasoning about\nthe effects of different levels of uncertainties on robust synthesizability and demonstrate the results on a simple robot motion planning scenario.", "doi": "10.1145/2185632.2185648", "isbn": "978-1-4503-1220-2", "publisher": "Association for Computing Machinery", "place_of_publication": "New York, NY", "publication_date": "2012-04", "pages": "85-94" }, { "id": "authors:sc7fe-hs832", "collection": "authors", "collection_id": "sc7fe-hs832", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120207-074159029", "type": "article", "title": "Quantized Consensus by Means of Gossip Algorithm", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper deals with the distributed averaging problem over a connected network of agents, subject to a quantization constraint. It is assumed that at each time update, only a pair of agents can update their own states in terms of the quantized data being exchanged. The agents are also required to communicate with one another in a stochastic fashion. It is shown that a quantized consensus is reached for an arbitrary quantizer by means of the stochastic gossip algorithm proposed in a recent paper. The expected value of the time at which a quantized consensus is reached is lower and upper bounded in terms of the topology of the graph for a uniform quantizer. In particular, it is shown that these bounds are related to the principal submatrices of the weighted Laplacian matrix. A convex optimization is also proposed to determine a set of probabilities used to pick a pair of agents that leads to a fast convergence of the gossip algorithm.", "doi": "10.1109/TAC.2011.2160593", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2012-01", "series_number": "1", "volume": "57", "issue": "1", "pages": "19-32" }, { "id": "authors:33kzg-9ca08", "collection": "authors", "collection_id": "33kzg-9ca08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247340", "type": "book_section", "title": "A hovercraft robot that uses insect-inspired visual autocorrelation for motion control in a corridor", "book_title": "2011 IEEE International Conference on Robotics and Biomimetics", "author": [ { "family_name": "Fuller", "given_name": "Sawyer B.", "clpid": "Fuller-S-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we are concerned with the challenge of flight control of computationally-constrained micro-aerial vehicles that must rely primarily on vision to navigate confined spaces. We turn to insects for inspiration. We demonstrate that it is possible to control a robot with inertial, flight-like dynamics in the plane using insect-inspired visual autocor-relators or \"elementary motion detectors\" (EMDs) to detect patterns of visual optic flow. The controller, which requires minimal computation, receives visual information from a small omnidirectional array of visual sensors and computes thrust outputs for a fan pair to stabilize motion along the centerline of a corridor. To design the controller, we provide a frequency-domain analysis of the response of an array of correlators to a flat moving wall. The model incorporates the effects of motion parallax and perspective and provides a means for computing appropriate inter-sensor angular spacing and visual blurring. The controller estimates the state of robot motion by decomposing the correlator response into harmonics, an analogous operation to that performed by tangential cells in the fly. This work constitutes the first-known demonstration of control of non-kinematic inertial dynamics using purely correlators.", "doi": "10.1109/robio.2011.6181498", "isbn": "9781457721380", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-12", "pages": "1474-1481" }, { "id": "authors:pg1xs-af021", "collection": "authors", "collection_id": "pg1xs-af021", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247417", "type": "book_section", "title": "Distributed power allocation for vehicle management systems", "book_title": "2011 50th IEEE Conference on Decision and Control and European Control Conference", "author": [ { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of designing distributed control protocols -for aircraft vehicle management systems-that cooperatively allocate electric power while meeting certain higher level goals and requirements, and dynamically reacting to the changes in the internal system state and external environment. A decentralized control problem is posed where each power distribution unit is equipped with a controller that implements a local protocol to allocate power to a certain subset of loads. We use linear temporal logic as the specification language for describing correct behaviors of the system (e.g., safe operating conditions) as well as the admissible dynamic behavior of the environment due to, for example, wind gusts and changes in system health. We start with a global specification and decompose it into local ones. These decompositions allow the protocols for each local controller to be separately synthesized and locally implemented while guaranteeing the global specifications to hold. Through a design example, we show that by refining the interface rules between power distribution units, it is possible to reduce the total power requirement.", "doi": "10.1109/cdc.2011.6161470", "isbn": "9781612848013", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-12", "pages": "4841-4848" }, { "id": "authors:2t7h1-ngn42", "collection": "authors", "collection_id": "2t7h1-ngn42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247494", "type": "book_section", "title": "Analysis and design of a synthetic transcriptional network for exact adaptation", "book_title": "2011 IEEE Biomedical Circuits and Systems Conference (BioCAS)", "author": [ { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents a mathematical model for a synthetic transcriptional regulatory network in vitro. This circuit design resembles one of the well-known network motifs, the incoherent feed-forward loop, in which an activator regulates both a gene and a repressor of the gene. Through mathematical analysis, we show how the circuit can be controlled to demonstrate exact adaptation to input signals.", "doi": "10.1109/biocas.2011.6107798", "isbn": "9781457714702", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-11", "pages": "345-348" }, { "id": "authors:3xw46-ycg28", "collection": "authors", "collection_id": "3xw46-ycg28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111020-091851903", "type": "article", "title": "Timing molecular motion and production with a synthetic transcriptional clock", "author": [ { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Friedrichs", "given_name": "Eike", "clpid": "Friedrichs-Eike" }, { "family_name": "Kim", "given_name": "Jongmin", "orcid": "0000-0002-2713-1006", "clpid": "Kim-Jongmin" }, { "family_name": "Jungmann", "given_name": "Ralf", "clpid": "Jungmann-R" }, { "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": "Simmel", "given_name": "Friedrich C.", "orcid": "0000-0003-3829-3446", "clpid": "Simmel-F-C" } ], "abstract": "The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of \"load\" processes such as the operation of a DNA-based nanomechanical device (\"DNA tweezers\") or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an \"insulator circuit\" was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems.", "doi": "10.1073/pnas.1100060108", "pmcid": "PMC3189071", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2011-10-04", "series_number": "40", "volume": "108", "issue": "40", "pages": "E784-E793" }, { "id": "authors:wyqv1-6c387", "collection": "authors", "collection_id": "wyqv1-6c387", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2011.008", "type": "monograph", "title": "Robust Control of Uncertain Markov Decision Processes with Temporal Logic Specifications", "author": [ { "family_name": "Wolff", "given_name": "Eric M.", "clpid": "Wolff-E-M" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a method for designing robust controllers for dynamical systems with linear temporal logic specifications. We abstract the original system by a finite Markov Decision Process (MDP) that has transition probabilities in a specified uncertainty set. A robust control policy for the MDP is generated that maximizes the worst-case probability of satisfying the specification over all transition probabilities in the uncertainty set. To do this, we use a procedure from probabilistic model checking to combine the system model with an automaton representing the specification. This new MDP is then transformed into an equivalent form that satisfies assumptions for stochastic shortest path dynamic programming. A robust version of dynamic programming allows us to solve for a $\\epsilon$-suboptimal robust control policy with time complexity $O(\\log 1/\\epsilon)$ times that for the non-robust case. We then implement this control policy on the original dynamical system.", "publisher": "California Institute of Technology", "publication_date": "2011-09-25" }, { "id": "authors:wwb40-h3k92", "collection": "authors", "collection_id": "wwb40-h3k92", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2011.006", "type": "monograph", "title": "Synthesis of Switching Protocols from Temporal Logic Specifications", "author": [ { "family_name": "Liu", "given_name": "Jun", "clpid": "Liu-Jun" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose formal means for synthesizing switching protocols that determine the sequence in which the modes of a switched system are activated to satisfy certain high-level specifications in linear temporal logic. The synthesized protocols are robust against exogenous disturbances on the continuous dynamics. Two types of finite transition systems, namely under- and over-approximations, that abstract the behavior of the underlying continuous dynamics are defined. In particular, we show that the discrete synthesis problem for an under-approximation can be formulated as a model checking problem, whereas that for an over-approximation can be transformed into a two-player game. Both of these formulations are amenable to efficient, off-the-shelf software tools. By construction, existence of a discrete switching strategy for the discrete synthesis problem guarantees the existence of a continuous switching protocol for the continuous synthesis problem, which can be implemented at the continuous level to ensure the correctness of the nonlinear switched system. Moreover, the proposed framework can be straightforwardly extended to accommodate specifications that require reacting to possibly adversarial external events. Finally, these results are illustrated using three examples from different application domains.", "publisher": "California Institute of Technology", "publication_date": "2011-09-16" }, { "id": "authors:88sp6-3am82", "collection": "authors", "collection_id": "88sp6-3am82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120406-140547979", "type": "book_section", "title": "Bootstrapping sensorimotor cascades: a group-theoretic perspective", "book_title": "2011 IEEE/RSJ International Conference on Intelligent Robots and Systems", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The bootstrapping problem consists in designing agents that learn a model of themselves and the world, and utilize it to achieve useful tasks. It is different from other learning problems as the agent starts with uninterpreted observations and commands, and with minimal prior information about the world. in this paper, we give a mathematical formalization of this aspect of the problem. We argue that the vague constrain of having \"no prior information\" can be recast as a precise algebraic condition on the agent: that its behavior is invariant to particular classes of nuisances on the world, which we show can be well represented by actions of groups (diffeomorphisms, permutations, linear transformations) on observations and commans. We then introduce the class of bilinear gradient dynamics sensors (BGDS) as a candidate for learning generic robotic sensorimotor cascades. We show how framing the problem as rejection of group nuisances allows a compact and modular analysis of typical preprocessing stages, such as learning the topology of the sensors. We demonstrate learning and using such models on real-word range-finder and camera date from publicly available datasets.", "doi": "10.1109/IROS.2011.6095151", "isbn": "978-1-61284-454-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-09", "pages": "2056-2063" }, { "id": "authors:qakh7-t5114", "collection": "authors", "collection_id": "qakh7-t5114", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120406-141618413", "type": "book_section", "title": "Containment indicator function construction via numerical conformal mapping", "book_title": "2011 IEEE/RSJ International Conference on Intelligent Robots and Systems", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In optimal-control-based motion planning, it is often desired to obtain a proper (preferably smooth) function, referred to as the containment indicator function in this paper, that describes the shape of the free space. The paper studies the use of numerical conformal mapping for constructing the containment indicator function for an arbitrary two-dimensional geometry. The idea of using conformal mapping is to transform the original shape of interest into a simpler target shape (e.g. disk, rectangle), which can then be characterized by elementary functions. Computational methods for finding the desired conformal maps are also studied. The procedure can be formulated as a convex optimization problem and computed efficiently.", "doi": "10.1109/IROS.2011.6095037", "isbn": "978-1-61284-454-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-09", "pages": "3017-3022" }, { "id": "authors:44s34-p8q13", "collection": "authors", "collection_id": "44s34-p8q13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120330-135848739", "type": "book_section", "title": "Uncertain semantics, representation nuisances, and necessary invariance properties of bootstrapping agents", "book_title": "2011 IEEE International Conference on Development and Learning", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In the problem of bootstrapping, an agent must learn to use an unknown body, in an unknown world, starting from zero information about the world, its sensors, and its actuators. So far, this fascinating problem has not; been given a proper normalization. In this paper, we provide a possible rigorous definition of one of the key aspects of bootstrapping, namely the fact that an agent must be able to use \"uninterpreted\" observations and commands. We show that this can be formalized by positing the existence of representation nuisances that act on the data, and which must be tolerated by an agent. The classes of nuisances tolerate d in directly encode the assumptions needed about the world, and therefore the agent's ability to solve smaller or larger classes of bootstrapping problem instances. Moreover, we argue that the behavior of an agent that claims optimality must actually be invariant to the representation nuisances, and we discuss several design principles to obtain such invariance.", "doi": "10.1109/DEVLRN.2011.6037313", "isbn": "978-1-61284-989-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-08", "pages": "1-8" }, { "id": "authors:5ntw2-66g34", "collection": "authors", "collection_id": "5ntw2-66g34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247572", "type": "book_section", "title": "Fault-tolerant controller design with applications in power systems and synthetic biology", "book_title": "Proceedings of the 2011 American Control Conference", "author": [ { "family_name": "Sojoudi", "given_name": "Somayeh", "clpid": "Sojoudi-S" }, { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper deals with fault-tolerant controller design for linear time-invariant (LTI) systems with multiple actuators. Given some critical subsets of the actuators, it is assumed that every combination of actuators can fail as long as the set of the remaining actuators includes one of these subsets. Motivated by electric power systems and biological systems, the goal is to design a controller so that the closed-loop system satisfies two properties: (i) stability under all permissible sets of faults and (ii) better performance after clearing every subset of the existing faults in the system. It is shown that a state-feedback controller satisfying these properties exists if and only if a linear matrix inequality (LMI) problem is feasible. This LMI condition is then transformed into an optimal-control condition, which has a useful interpretation. The results are also generalized to output-feedback and decentralized control cases. The efficacy of this work is demonstrated by designing fault-tolerant speed governors for a power system. The results developed here can be extended to more general types of faults, where each fault can possibly affect all state-space matrices of the system.", "doi": "10.1109/acc.2011.5991381", "isbn": "9781457700811", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-07", "pages": "4135-4142" }, { "id": "authors:sv45d-h1e68", "collection": "authors", "collection_id": "sv45d-h1e68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247658", "type": "book_section", "title": "Bootstrapping bilinear models of robotic sensorimotor cascades", "book_title": "2011 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the bootstrapping problem, which consists in learning a model of the agent's sensors and actuators starting from zero prior information, and we take the problem of servoing as a cross-modal task to validate the learned models. We study the class of sensors with bilinear dynamics, for which the derivative of the observations is a bilinear form of the control commands and the observations themselves. This class of models is simple, yet general enough to represent the main phenomena of three representative sensors (field sampler, camera, and range-finder), apparently very different from one another. It also allows a bootstrapping algorithm based on Hebbian learning, and a simple bioplausible control strategy. The convergence properties of learning and control are demonstrated with extensive simulations and by analytical arguments.", "doi": "10.1109/icra.2011.5979844", "isbn": "9781612843865", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-05", "pages": "4318-4325" }, { "id": "authors:r4rgt-jkx31", "collection": "authors", "collection_id": "r4rgt-jkx31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190410-120609095", "type": "monograph", "title": "Extremal Properties of Complex Networks", "author": [ { "family_name": "Barmpoutis", "given_name": "Dionysios", "clpid": "Barmpoutis-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We describe the structure of connected graphs with the minimum and maximum average distance, radius, diameter, betweenness centrality, efficiency and resistance distance, given their order and size. We find tight bounds on these graph qualities for any arbitrary number of nodes and edges and analytically derive the form and properties of such networks.", "doi": "10.48550/arXiv.1104.5532", "publisher": "arXiv", "publication_date": "2011-04-29" }, { "id": "authors:ehtwx-efc37", "collection": "authors", "collection_id": "ehtwx-efc37", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2011.005", "type": "monograph", "title": "A group-theoretic approach to formalizing bootstrapping problems", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The bootstrapping problem consists in designing agents that learn a model of themselves and the world, and utilize it to achieve useful tasks. It is different from other learning problems as the agent starts with uninterpreted observations and commands, and with minimal prior information about the world. In this paper, we give a mathematical formalization of this aspect of the problem. We argue that the vague constraint of having \"no prior information\" can be recast as a precise algebraic condition on the agent: that its behavior is invariant to particular classes of nuisances on the world, which we show can be well represented by actions of groups (diffeomorphisms, permutations, linear transformations) on observations and commands. We then introduce the class of bilinear gradient dynamics sensors (BGDS) as a candidate for learning generic robotic sensorimotor cascades. We show how framing the problem as rejection of group nuisances allows a compact and modular analysis of typical preprocessing stages, such as learning the topology of the sensors. We demonstrate learning and using such models on real-world range-finder and camera data from publicly available datasets.", "publisher": "Caltech", "publication_date": "2011-04" }, { "id": "authors:w4996-zsc77", "collection": "authors", "collection_id": "w4996-zsc77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247744", "type": "book_section", "title": "Distributed Synthesis of Control Protocols for Smart Camera Networks", "book_title": "2011 IEEE/ACM Second International Conference on Cyber-Physical Systems", "author": [ { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" } ], "abstract": "We considered the problem of designing control protocols for pan-tilt-zoom (PTZ) cameras within a smart camera network where the goal is to guarantee certain temporal logic specifications related to a given surveillance task. We first present a centralized control architecture for assigning PTZ cameras to targets so that the specification is met for any admissible behavior of the targets. Then, in order to alleviate the computational complexity associated with LTL synthesis and to enable implementation of local control protocols on individual PTZ cameras, we propose a distributed synthesis methodology. The main idea is to decompose the global specification into local specifications for each PTZ camera. These decompositions allow the protocols for each camera to be separately synthesized and locally implemented while guaranteeing the global specifications to hold. A thorough design example is presented to illustrate the steps of the proposed procedure.", "doi": "10.1109/iccps.2011.22", "isbn": "9781612846408", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2011-04", "pages": "45-54" }, { "id": "authors:0e1gw-z2s85", "collection": "authors", "collection_id": "0e1gw-z2s85", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120522-084524685", "type": "book_section", "title": "TuLiP: a software toolbox for receding horizon temporal logic planning", "book_title": "Proceedings of the 14th international conference on Hybrid systems: computation and control", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Ozay", "given_name": "Necmiye", "clpid": "Ozay-N" }, { "family_name": "Xu", "given_name": "Huan", "clpid": "Xu-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes TuLiP, a Python-based software toolbox for the synthesis of embedded control software that is provably correct with respect to an expressive subset of linear temporal logic (LTL) specifications. TuLiP combines routines for (1) finite state abstraction of control systems, (2) digital design synthesis from LTL specifications, and (3) receding horizon planning. The underlying digital design synthesis routine treats the environment as adversary; hence, the resulting controller is guaranteed to be correct for any admissible environment profile. TuLiP applies the receding horizon framework, allowing the synthesis problem to be broken into a set of smaller problems, and consequently alleviating the computational complexity of the synthesis procedure, while preserving the correctness guarantee.", "doi": "10.1145/1967701.1967747", "isbn": "978-1-4503-0629-4", "publisher": "Association for Computing Machinery (ACM)", "place_of_publication": "New York, NY", "publication_date": "2011-04", "pages": "313-314" }, { "id": "authors:r3tvy-yjv64", "collection": "authors", "collection_id": "r3tvy-yjv64", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2011.004", "type": "monograph", "title": "Bootstrapping, uncertain semantics, and invariance", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In the problem of bootstrapping, an agent learns to use an unknown body, in an unknown world, starting from zero information about the models involved. This is a fascinating problem, which so far has not been given a proper formalization. In this paper, we give a rigorous definition of what it means for an agent to be able to use \"uninterpreted\" observations and commands: there are some disturbances, represented by group actions, that modify what we call \"semantic maps\". The range of disturbances tolerated by an agent indirectly encode the assumptions needed by the agent. We argue that the behavior of agent which claims optimality (in any sense) must actually be invariant to such disturbances, and we discuss several design principles which allow to obtain this invariance for observations nuisances.", "publisher": "Caltech", "publication_date": "2011-04" }, { "id": "authors:vve9t-shm11", "collection": "authors", "collection_id": "vve9t-shm11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190930-110459012", "type": "book_section", "title": "Formal Synthesis of Embedded Control Software: Application to Vehicle Management Systems", "book_title": "Infotech@Aerospace 2011", "author": [ { "family_name": "Wongpiromsarn", "given_name": "T.", "clpid": "Wongpiromsarn-T" }, { "family_name": "Topcu", "given_name": "U.", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Motivated by the transition from federated to integrated architectures in aerial vehicles, we propose an automated methodology for the synthesis of correct-by-construction control protocols for vehicle management systems. We use linear temporal logic as the specification language for precisely describing correct behaviors of the system as well as the admissible dynamic behavior of the environment due to, for example, wind gusts and changes in the flight conditions. We apply the method in the context of dynamic power allocation among a number of subsystems of varying flight-criticality. The resulting power management protocol is guaranteed to be correct, with respect to the overall system specification, for all admissible environment profiles. This approach also enables reasoning about design tradeoffs such as between efficiency (imposed through formal specifications) and system weight (characterized by the amount of required power generation and energy storage). We present our preliminary results in a simple setting and discuss extensions of the methodology to capture more realistic system and environment models and specifications.", "doi": "10.2514/6.2011-1506", "isbn": "9781600869440", "publisher": "AIAA", "place_of_publication": "Reston, VA", "publication_date": "2011-03-29", "pages": "Art. No. 2011-1506" }, { "id": "authors:cawcc-d0n69", "collection": "authors", "collection_id": "cawcc-d0n69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110308-123056956", "type": "article", "title": "Bisimulation conversion and verification procedure for goal-based control systems", "author": [ { "family_name": "Braman", "given_name": "Julia M. B.", "clpid": "Braman-J-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Fault tolerance and safety verification of control systems are essential for the success of autonomous robotic systems. A control architecture called Mission Data System\n(MDS), developed at the Jet Propulsion Laboratory, addresses these needs with a goal-based control approach. In this paper, a software algorithm for converting goal network control systems into linear hybrid systems is described. The conversion process is a bisimulation; the\nresulting linear hybrid system can be verified for safety in the presence of failures using existing symbolic model checkers, and thus the original goal network is verified. A moderately complex example goal network control system is converted to a linear hybrid system using the automatic conversion software that is based on the bisimulation and then is verified.", "doi": "10.1007/s10703-010-0109-6", "issn": "0925-9856", "publisher": "Springer", "publication": "Formal Methods in System Design", "publication_date": "2011-02", "series_number": "1", "volume": "38", "issue": "1", "pages": "62-95" }, { "id": "authors:b0vry-krq46", "collection": "authors", "collection_id": "b0vry-krq46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111031-100248775", "type": "article", "title": "Dynamics and Stability of Low-Reynolds-Number Swimming Near a Wall", "author": [ { "family_name": "Or", "given_name": "Yizhar", "orcid": "0000-0002-9091-9357", "clpid": "Or-Y" }, { "family_name": "Zhang", "given_name": "Sebastian", "clpid": "Zhang-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The locomotion of microorganisms and tiny artificial swimmers is governed by low-Reynolds-number\nhydrodynamics, where viscous effects dominate and inertial effects are negligible. While the theory\nof low-Reynolds-number locomotion is well studied for unbounded fluid domains, the presence of a\nboundary has a significant influence on the swimmer's trajectories and poses problems of dynamic\nstability of its motion. In this paper we consider a simple theoretical model of a microswimmer near\na wall, study its dynamics, and analyze the stability of its motion. We highlight the underlying\ngeometric structure of the dynamics, and establish a relation between the reversing symmetry of\nthe system and existence and stability of periodic and steady solutions of motion near the wall.\nThe results are demonstrated by numerical simulations and validated by motion experiments with\nmacroscale robotic swimmer prototypes.", "doi": "10.1137/100808745", "issn": "1536-0040", "publisher": "Society for Industrial and Applied Mathematics", "publication": "SIAM Journal on Applied Dynamical Systems", "publication_date": "2011", "series_number": "3", "volume": "10", "issue": "3", "pages": "1013-1041" }, { "id": "authors:detxd-fy181", "collection": "authors", "collection_id": "detxd-fy181", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190410-120605649", "type": "monograph", "title": "Quantification and Minimization of Crosstalk Sensitivity in Networks", "author": [ { "family_name": "Barmpoutis", "given_name": "Dionysios", "clpid": "Barmpoutis-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Crosstalk is defined as the set of unwanted interactions among the different entities of a network. Crosstalk is present in various degrees in every system where information is transmitted through a means that is accessible by all the individual units of the network. Using concepts from graph theory, we introduce a quantifiable measure for sensitivity to crosstalk, and analytically derive the structure of the networks in which it is minimized. It is shown that networks with an inhomogeneous degree distribution are more robust to crosstalk than corresponding homogeneous networks. We provide a method to construct the graph with the minimum possible sensitivity to crosstalk, given its order and size. Finally, for networks with a fixed degree sequence, we present an algorithm to find the optimal interconnection structure among their vertices.", "doi": "10.48550/arXiv.1012.0606", "publisher": "arXiv", "publication_date": "2010-12-02" }, { "id": "authors:9m19t-eaz28", "collection": "authors", "collection_id": "9m19t-eaz28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247830", "type": "book_section", "title": "Tuning a synthetic in vitro oscillator using control-theoretic tools", "book_title": "49th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Sturk", "given_name": "Christopher", "clpid": "Sturk-C" }, { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper demonstrates the effectiveness of simple control-theoretic tools in generating simulation-guided experiments on a synthetic in vitro oscillator. A theoretical analysis of the behavior of such system is motivated by high cost, time consuming experiments, together with the excessive number of tuning parameters. A simplified model of the synthetic oscillator is chosen to capture only its essential features. The model is analyzed using the small gain theorem and the theory of describing functions. Such analysis reveals what are the parameters that primarily determine when the system can admit stable oscillations. Experimental verification of the theoretical and numerical findings is carried out and confirms the predicted results regarding the role of production and degradation rates.", "doi": "10.1109/cdc.2010.5718111", "isbn": "9781424477456", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-12", "pages": "2554-2559" }, { "id": "authors:shvbe-rf064", "collection": "authors", "collection_id": "shvbe-rf064", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141247920", "type": "book_section", "title": "Synthesis of embedded control systems with high sampling frequencies", "book_title": "49th IEEE Conference on Decision and Control (CDC)", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Sojoudi", "given_name": "Somayeh", "clpid": "Sojoudi-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Motivated by current technological advances in the design of real-time embedded systems, this work deals with the digital control of a continuous-time linear time-invariant (LTI) system whose output can be sampled at a high frequency. Since a typical sampled-data controller operating at a high sampling frequency needs heavy (high-precision) computation to alleviate its sensitivity to measurement and computational errors, the objective is to design a robust hybrid controller for high-frequency applications with limited computational power. To this end, we exploit our recent results on delay-based controller design and propose a digital-control scheme that can implement every continuous-time stabilizing (LTI) controller. This robust hybrid controller, which consists of an ideal sampler, a digital controller, a number of modified second-order holds and possibly a unity feedback, can operate at arbitrarily high sampling frequencies without requiring expensive, high-precision computation. We also discuss how to find a continuous-time LTI controller satisfying prescribed design specifications so that its corresponding digital controller requires the least processing time.", "doi": "10.1109/cdc.2010.5718118", "isbn": "9781424477456", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-12", "pages": "7606-7612" }, { "id": "authors:2zzeq-nvb04", "collection": "authors", "collection_id": "2zzeq-nvb04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101029-082222753", "type": "article", "title": "Autonomous driving in urban environments: approaches, lessons and challenges", "author": [ { "family_name": "Campbell", "given_name": "Mark", "clpid": "Campbell-M" }, { "family_name": "Egerstedt", "given_name": "Magnus", "clpid": "Egerstedt-M" }, { "family_name": "How", "given_name": "Jonathan P.", "clpid": "How-J-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The development of autonomous vehicles for urban driving has seen rapid progress in the past 30 years. This paper provides a summary of the current state of the art in autonomous driving in urban environments, based primarily on the experiences of the authors in the 2007 DARPA Urban Challenge (DUC). The paper briefly summarizes the approaches that different teams used in the DUC, with the goal of describing some of the challenges that the teams faced in driving in urban environments. The paper also highlights the long-term research challenges that must be overcome in order to enable autonomous driving and points to opportunities for new technologies to be applied in improving vehicle safety, exploiting intelligent road infrastructure and enabling robotic vehicles operating in human environments.", "doi": "10.1098/rsta.2010.0110", "issn": "1364-503X", "publisher": "Royal Society of London", "publication": "Philosophical Transactions A: Mathematical, Physical and Engineering Sciences", "publication_date": "2010-10-13", "series_number": "1928", "volume": "368", "issue": "1928", "pages": "4649-4672" }, { "id": "authors:1zx0x-m7q59", "collection": "authors", "collection_id": "1zx0x-m7q59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141248010", "type": "book_section", "title": "A bio-plausible design for visual pose stabilization", "book_title": "2010 IEEE/RSJ International Conference on Intelligent Robots and Systems", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Straw", "given_name": "Andrew D.", "orcid": "0000-0001-8381-0858", "clpid": "Straw-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of purely visual pose stabilization (also known as servoing) of a second-order rigid-body system with six degrees of freedom: how to choose forces and torques, based on the current view and a memorized goal image, to steer the pose towards a desired one. Emphasis has been given to the bio-plausibility of the computation, in the sense that the control laws could be in principle implemented on the neural substrate of simple insects. We show that stabilizing laws can be realized by bilinear/quadratic operations on the visual input. This particular computational structure has several numerically favorable characteristics (sparse, local, and parallel), and thus permits an efficient engineering implementation. We show results of the control law tested on an indoor helicopter platform.", "doi": "10.1109/iros.2010.5652857", "isbn": "9781424466740", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-10", "pages": "5679-5686" }, { "id": "authors:zrbdx-3es81", "collection": "authors", "collection_id": "zrbdx-3es81", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2010.003a", "type": "monograph", "title": "Bootstrapping bilinear models of robotic sensorimotor cascades", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the bootstrapping problem, which consists in learning a model of the agent's sensors and actuators starting from zero prior information, and we take the problem of servoing as a cross-modal task to validate the learned models. We study the class of bilinear dynamics sensors, in which the derivative of the observations are a bilinear form of the control commands and the observations themselves. This class of models is simple yet general enough to represent the main phenomena of three representative robotics sensors (field sampler, camera, and range-finder), apparently very different from one another. It also allows a bootstrapping algorithm based on hebbian learning, and that leads to a simple and bioplausible control strategy. The convergence properties of learning and control are demonstrated with extensive simulations and by analytical arguments.", "publisher": "California Institute of Technology", "publication_date": "2010-07-15" }, { "id": "authors:rcvk6-crh09", "collection": "authors", "collection_id": "rcvk6-crh09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-102831203", "type": "book_section", "title": "Experimental demonstration of the dynamics and stability of a low Reynolds number swimmer near a plane wall", "book_title": "Proceedings of the 2010 American Control Conference", "author": [ { "family_name": "Zhang", "given_name": "Sebastian", "clpid": "Zhang-Sebastian" }, { "family_name": "Or", "given_name": "Yizhar", "orcid": "0000-0002-9091-9357", "clpid": "Or-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The motion of microorganisms as well as of tiny robotic swimmers for biomedical applications is governed by low Reynolds number (Re) hydrodynamics, where viscous effects dominate and inertial effects are negligible. This paper presents experimental results that verify theoretical predictions of our recent work which analyzed the dynamics and stability of a low-Re swimmer near a plane wall. The experimental setup uses macro-scale swimmer prototypes which are propelled by rotating cylinders in highly viscous silicone oil. The motion is recorded by a video camera and position measurements are taken by an optical tracking system. The results show good qualitative agreement with our recent theoretical predictions.", "doi": "10.1109/ACC.2010.5530846", "isbn": "978-1-4244-7426-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-07", "pages": "4205-4210" }, { "id": "authors:4xasg-ds893", "collection": "authors", "collection_id": "4xasg-ds893", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110412-152921583", "type": "book_section", "title": "Simple delay-based implementation of continuous-time controllers", "book_title": "2010 American Control Conference (ACC)", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Sojoudi", "given_name": "Somayeh", "clpid": "Sojoudi-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The objective of this work is to study the benefits that delay can provide in simplifying the control process of large-scale systems, motivated by the availability of different types of delays in man-made and biological systems. We show that a continuous-time linear time-invariant (LTI) controller can be approximated by a simple controller that mainly uses delay blocks instead of integrators. More specifically, three methods are proposed to approximate a pre-designed stabilizing LTI controller arbitrarily precisely by a simple delay-based controller composed of delay blocks, a few integrators and possibly a unity feedback. Different problems associated with the developed approximation procedures, such as finding the optimal number of delay blocks or studying the robustness of the designed controller with respect to delay values, are then addressed.", "doi": "10.1109/ACC.2010.5530439", "isbn": "978-1-4244-7426-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-07", "pages": "5781-5788" }, { "id": "authors:y7zqq-asy15", "collection": "authors", "collection_id": "y7zqq-asy15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100709-164812328", "type": "article", "title": "Reply to \"Comments on \"Consensus and Cooperation in Networked Multi-Agent Systems\"\"", "author": [ { "family_name": "Olfati-Saber", "given_name": "R.", "clpid": "Olfati-Saber-R" }, { "family_name": "Fax", "given_name": "J. A.", "clpid": "Fax-J-A" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "[No abstract]", "doi": "10.1109/JPROC.2010.2049912", "issn": "0018-9219", "publisher": "IEEE", "publication": "Proceedings of the IEEE", "publication_date": "2010-07", "series_number": "7", "volume": "98", "issue": "7", "pages": "1354-1355" }, { "id": "authors:k1s3p-pcf59", "collection": "authors", "collection_id": "k1s3p-pcf59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190326-141248096", "type": "book_section", "title": "Limits on the network sensitivity function for homogeneous multi-agent systems on a graph", "book_title": "Proceedings of the 2010 American Control Conference", "author": [ { "family_name": "Tonetti", "given_name": "Stefania", "clpid": "Tonetti-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper explores some tradeoffs and limits of performance in feedback control of interconnected multi-agent systems, focused on the network sensitivity functions. We consider the interaction topology described by a directed graph and we prove that the sensitivity transfer functions between every pair of agents, arbitrarily connected, can be derived using a version of Mason's direct rule. An analysis of the role of cycles shows that these structures influence and considerably limit the behavior of the system. We also derive a networked version of Bode's integral formula, showing that it still holds for multi-agent systems.", "doi": "10.1109/acc.2010.5530753", "isbn": "9781424474271", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2010-07", "pages": "3217-3222" }, { "id": "authors:ex3fk-5kt19", "collection": "authors", "collection_id": "ex3fk-5kt19", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2010.002", "type": "monograph", "title": "Delay-Based Controller Design for Continuous-Time and Hybrid Applications", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Sojoudi", "given_name": "Somayeh", "clpid": "Sojoudi-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Motivated by the availability of different types of delays in embedded systems and biological circuits, the objective of this work is to study the benefits that delay can provide in simplifying the implementation of controllers for continuous-time systems. Given a continuous-time linear time-invariant (LTI) controller, we propose three methods to approximate this controller arbitrarily precisely by a simple controller composed of delay blocks, a few integrators and possibly a unity feedback. Different problems associated with the approximation procedures, such as finding the optimal number of delay blocks or studying the robustness of the designed controller with respect to delay values, are then investigated. We also study the design of an LTI continuous-time controller satisfying given control objectives whose delay-based implementation needs the least number of delay blocks. A direct application of this work is in the sampled-data control of a real-time embedded system, where the sampling frequency is relatively high and/or the output of the system is sampled irregularly. Based on our results on delay-based controller design, we propose a digital-control scheme that can implement every continuous-time stabilizing (LTI)\ncontroller. Unlike a typical sampled-data controller, the hybrid controller introduced here -\u2014 consisting of an ideal sampler, a digital controller, a number of modified second-order holds and possibly a unity feedback -\u2014 is robust to sampling jitter and can operate at arbitrarily high sampling frequencies without requiring expensive, high-precision computation.", "publisher": "California Institute of Technology", "publication_date": "2010-06-12" }, { "id": "authors:2ddzn-26g38", "collection": "authors", "collection_id": "2ddzn-26g38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161213-153527627", "type": "book_section", "title": "Joint DAC/IWBDA Special Session Engineering Biology: Fundamentals and Applications", "book_title": "DAC '10 Proceedings of the 47th Design Automation Conference", "author": [ { "family_name": "Riedel", "given_name": "Marc", "orcid": "0000-0002-3318-346X", "clpid": "Riedel-M-D" }, { "family_name": "Hassoun", "given_name": "Soha", "clpid": "Hassoun-S" }, { "family_name": "Weiss", "given_name": "Ron", "clpid": "Weiss-R" }, { "family_name": "Silver", "given_name": "Pamela", "clpid": "Silver-P" }, { "family_name": "Anderson", "given_name": "J. Christopher", "clpid": "Anderson-J-C" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Sapatnekar", "given_name": "S.", "clpid": "Sapatnekar-S" } ], "abstract": "In the nascent field of synthetic biology, researchers are striving to create biological systems with functionality not seen in nature. This special session features talks that emphasize the fundamental engineering principles underlying this endeavor, highlighting possible synergies with electronic design automation (EDA). Pamela Silver will describe designing and constructing proteins and cells with predictable biological properties. These serve as potential therapeutics, cell-based sensors, factories for generating bio-energy, and bio-remediation. J. Christopher Anderson will demonstrate how complex biological functions can be decomposed into modular devices. He will describe the construction of therapeutic organisms and new tools for building complex systems. Richard Murray will discuss the use of concepts from control and dynamical systems in the analysis and design of biological feedback circuits at the molecular level.", "doi": "10.1145/1837274.1837330", "isbn": "978-1-4503-0002-5", "publisher": "ACM", "place_of_publication": "New York, NY", "publication_date": "2010-06", "pages": "220-221" }, { "id": "authors:ph80z-k8g73", "collection": "authors", "collection_id": "ph80z-k8g73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100712-154830591", "type": "article", "title": "Resource optimisation in a wireless sensor network with guaranteed estimator performance", "author": [ { "family_name": "Shi", "given_name": "L.", "clpid": "Shi-Ling" }, { "family_name": "Capponi", "given_name": "A.", "clpid": "Capponi-A" }, { "family_name": "Johansson", "given_name": "K. H.", "clpid": "Johansson-K-H" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "New control paradigms are needed for large networks of wireless sensors and actuators in order to\nefficiently utilise system resources. In this study, the authors consider the problem of discrete-time state\nestimation over a wireless sensor network. Given a tree that represents the sensor communications with the\nfusion centre, the authors derive the optimal estimation algorithm at the fusion centre, and provide a closedform\nexpression for the steady-state error covariance matrix. They then present a tree reconfiguration\nalgorithm that produces a sensor tree that has low overall energy consumption and guarantees a desired\nlevel of estimation quality at the fusion centre. The authors further propose a sensor tree construction and\nscheduling algorithm that leads to a longer network lifetime than the tree reconfiguration algorithm.\nExamples are provided throughout the paper to demonstrate the algorithms and theory developed.", "doi": "10.1049/iet-cta.2009.0104", "issn": "1751-8644", "publisher": "Institution of Engineering and Technology", "publication": "IET Control Theory and Applications", "publication_date": "2010-05", "series_number": "5", "volume": "4", "issue": "5", "pages": "710-723" }, { "id": "authors:0as71-fjz76", "collection": "authors", "collection_id": "0as71-fjz76", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2010.001", "type": "monograph", "title": "A bio-plausible design for visual pose stabilization", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-S" }, { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Straw", "given_name": "Andrew D.", "orcid": "0000-0001-8381-0858", "clpid": "Straw-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of purely visual pose stabilization (also known as servoing) of a second-order rigid-body system with six degrees of freedom: how to choose forces and torques, based on the current view and a memorized goal image, to steer the pose towards a desired one. Emphasis has been given to the bio-plausibility of the computation, in the sense that the control laws could be in principle implemented on the neural substrate of simple insects. We show that stabilizing laws can be realized by bilinear/quadratic operations on the visual input. This particular computational structure has several numerically favorable characteristics (sparse, local, and parallel), and thus permits an efficient engineering implementation. We show results of the control law tested on an indoor helicopter platform.", "publisher": "California Institute of Technology", "publication_date": "2010-03-10" }, { "id": "authors:q8212-xtv70", "collection": "authors", "collection_id": "q8212-xtv70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100407-095207612", "type": "article", "title": "Kalman Filtering Over a Packet-Dropping Network: A Probabilistic Perspective", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of state estimation of a discrete time process over a packet-dropping network. Previous work on Kalman filtering with intermittent observations is concerned with the asymptotic behavior of E[P_k], i.e., the expected value of the error covariance, for a given packet arrival rate. We consider a different performance metric, Pr[P_k \u2264 M], i.e., the probability that P_k is bounded by a given M. We consider two scenarios in the paper. In the first scenario, when the sensor sends its measurement data to the remote estimator via a packet-dropping network, we derive lower and upper bounds on Pr[P_k \u2264 M]. In the second scenario, when the sensor preprocesses the measurement data and sends its local state estimate to the estimator, we show that the previously derived lower and upper bounds are equal to each other, hence we are able to provide a closed form expression for Pr[P_k \u2264 M]. We also recover the results in the literature when using Pr[P_k \u2264 M] as a metric for scalar systems. Examples are provided to illustrate the theory developed in the paper.", "doi": "10.1109/TAC.2009.2039236", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2010-03", "series_number": "3", "volume": "55", "issue": "3", "pages": "594-604" }, { "id": "authors:9dhrr-zwq55", "collection": "authors", "collection_id": "9dhrr-zwq55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100120-105437457", "type": "article", "title": "Controlling biological networks by time-delayed signals", "author": [ { "family_name": "Orosz", "given_name": "G\u00e1bor", "orcid": "0000-0002-9000-3736", "clpid": "Orosz-G" }, { "family_name": "Moehlis", "given_name": "Jeff", "clpid": "Moehlis-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes the use of time-delayed feedback to regulate the behaviour of biological networks. The general ideas on specific transcriptional regulatory and neural networks are demonstrated. It is shown that robust yet tunable controllers can be constructed that provide the biological systems with model-engineered inputs. The results indicate that time delay modulation may serve as an efficient biocompatible control tool.", "doi": "10.1098/rsta.2009.0242", "issn": "1364-503X", "publisher": "Royal Society of London", "publication": "Philosophical Transactions A: Mathematical, Physical and Engineering Sciences", "publication_date": "2010-01-28", "series_number": "1911", "volume": "368", "issue": "1911", "pages": "439-454" }, { "id": "authors:b4rgf-whm32", "collection": "authors", "collection_id": "b4rgf-whm32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100701-112021323", "type": "book_section", "title": "Receding Horizon Control for Temporal Logic Specifications", "book_title": "HSSC 10: Proceedings of the 13th ACM International Conference on Hybrid Systems: Computation and Control", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we describe a receding horizon framework that\nsatisfies a class of linear temporal logic specifications sufficient to describe a wide range of properties including safety,\nstability, progress, obligation, response and guarantee. The\nresulting embedded control software consists of a goal generator, a trajectory planner, and a continuous controller.\nThe goal generator essentially reduces the trajectory generation problem to a sequence of smaller problems of short\nhorizon while preserving the desired system-level temporal\nproperties. Subsequently, in each iteration, the trajectory\nplanner solves the corresponding short-horizon problem with\nthe currently observed state as the initial state and generates a feasible trajectory to be implemented by the continuous controller. Based on the simulation property, we\nshow that the composition of the goal generator, trajectory\nplanner and continuous controller and the corresponding receding horizon framework guarantee the correctness of the\nsystem. To handle failures that may occur due to a mismatch between the actual system and its model, we propose\na response mechanism and illustrate, through an example,\nhow the system is capable of responding to certain failures\nand continues to exhibit a correct behavior.", "isbn": "978-1-60558-955-8", "publisher": "ACM", "publication_date": "2010", "pages": "101-110" }, { "id": "authors:rf1mb-aga48", "collection": "authors", "collection_id": "rf1mb-aga48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-104610564", "type": "book_section", "title": "Compositional stability analysis based on dual decomposition", "book_title": "Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference", "author": [ { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Packard", "given_name": "Andrew K.", "clpid": "Packard-A-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We propose a compositional stability analysis framework for verifying properties of systems that are interconnections of multiple subsystems. The proposed method assembles stability certificates for the interconnected system based on the certificates for the input-output properties of the subsystems. The decomposition in the analysis is achieved by utilizing dual decomposition ideas from optimization. Decoupled subproblems establish subsystem level input-output properties whereas the \"master\" problem imposes and updates the conditions on the subproblems toward ensuring interconnected system level stability properties. Both global stability analysis and region-of-attraction analysis are discussed.", "doi": "10.1109/CDC.2009.5400309", "isbn": "978-1-4244-3871-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-12", "pages": "1175-1180" }, { "id": "authors:wt3pj-rbq43", "collection": "authors", "collection_id": "wt3pj-rbq43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100121-153456533", "type": "article", "title": "Kalman filtering over wireless fading channels\u2014How to handle\n packet drop", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider estimation of dynamical systems over wireless fading communication channels using a Kalman filter. We show the impact of the stochastic communication noise on the estimation process. We furthermore show how noisy packets should be handled in the receiver. More specifically, we illustrate the impact of the availability of a cross-layer information path on the optimum receiver design. In the absence of a cross-layer information path, it was shown that packet drop should be designed to balance information loss and communication noise in order to optimize the performance. In the presence of a cross-layer path, we show that keeping all the packets will minimize the average estimation error covariance. We also derive the stability condition in the presence of noisy packets and show that it is independent of the shape of the communication noise variance or availability of a cross-layer information path.", "doi": "10.1002/rnc.1398", "issn": "1049-8923", "publisher": "Wiley", "publication": "International Journal of Robust and Nonlinear Control", "publication_date": "2009-12", "series_number": "18", "volume": "19", "issue": "18", "pages": "1993-2015" }, { "id": "authors:3ks9k-x4k11", "collection": "authors", "collection_id": "3ks9k-x4k11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-132458437", "type": "book_section", "title": "A bio-plausible design for visual attitude stabilization", "book_title": "Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Fuller", "given_name": "Sawyer B.", "clpid": "Fuller-S-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of attitude stabilization using exclusively visual sensory input, and we look for a solution which can satisfy the constraints of a \"bio-plausible\" computation. We obtain a PD controller which is a bilinear form of the goal image, and the current and delayed visual input. Moreover, this controller can be learned using classic neural networks algorithms. The structure of the resulting computation, derived from general principles by imposing a bilinear computation, has striking resemblances with existing models for visual information processing in insects (Reichardt Correlators and lobula plate tangential cells). We validate the algorithms using faithful simulations of the fruit fly visual input.", "doi": "10.1109/CDC.2009.5400408", "isbn": "978-1-4244-3871-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-12", "pages": "3513-3520" }, { "id": "authors:kkgh6-cjt58", "collection": "authors", "collection_id": "kkgh6-cjt58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-110325145", "type": "book_section", "title": "Receding horizon temporal logic planning for dynamical systems", "book_title": "Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Topcu", "given_name": "Ufuk", "clpid": "Topcu-U" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper bridges the advances in computer science and control to allow automatic synthesis of control strategies for complex dynamical systems which are guaranteed, by construction, to satisfy the desired properties even in the presence of adversary. The desired properties are expressed in the language of temporal logic. With its expressive power, a wider class of properties than safety and stability can be specified. The resulting system consists of a discrete planner that plans, in the abstracted discrete domain, a set of transitions of the system to ensure the correct behaviors and a continuous controller that continuously implements the plan. To address the computational difficulties in the synthesis of a discrete planner, we present a receding horizon based scheme for executing finite state automata that essentially reduces the synthesis problem to a set of smaller problems.", "doi": "10.1109/CDC.2009.5399536", "isbn": "978-1-4244-3871-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-12", "pages": "5997-6004" }, { "id": "authors:1r5ay-1kt71", "collection": "authors", "collection_id": "1r5ay-1kt71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-103804228", "type": "book_section", "title": "Design of insulating devices for in vitro synthetic circuits", "book_title": "Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference", "author": [ { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes a synthetic in vitro genetic circuit programmed to work as an insulating device. This circuit is composed of nucleic acids, which can be designed to interact according to user defined rules, and of few proteins that perform catalytic functions. A model of the circuit is derived from first principle biochemical laws. This model is shown to exhibit time-scale separation that makes its output insensitive to downstream time varying loads. Simulation results show the circuit effectiveness and represent the starting point for future experimental testing of the device.", "doi": "10.1109/CDC.2009.5400523", "isbn": "978-1-4244-3871-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-12", "pages": "4584-4589" }, { "id": "authors:r120s-4ch11", "collection": "authors", "collection_id": "r120s-4ch11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-105229020", "type": "book_section", "title": "Quantized consensus via adaptive stochastic gossip algorithm", "book_title": "Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper is concerned with the distributed averaging problem over a given undirected graph. To enable every vertex to compute the average of the initial numbers sitting on the vertices of the graph, the policy is to pick an edge at random and update the values on its ending vertices based on some rules, but only in terms of the quantized data being exchanged between them. Our recent paper showed that the quantized consensus is reached under a simple updating protocol which deploys a fixed tuning factor. The current paper allows the tuning factor to be time-dependent in order to achieve two goals. First, this makes it possible to study the numerical stability of the protocol with a fixed tuning factor under a small perturbation of this parameter. Furthermore, exploiting a time-varying tuning factor facilitates the implementation of the consensus protocol and pushes the steady state of the system towards an equilibrium point, as opposed to making it oscillatory. The current paper is an important extension of our recent work, which generalizes a finite-dimensional problem to an infinite-dimensional one that is more challenging in nature.", "doi": "10.1109/CDC.2009.5400005", "isbn": "978-1-4244-3871-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-12", "pages": "5756-5762" }, { "id": "authors:0pcte-k2z58", "collection": "authors", "collection_id": "0pcte-k2z58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-111541230", "type": "book_section", "title": "Geometric control of particle manipulation in a two-dimensional fluid", "book_title": "Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference", "author": [ { "family_name": "Or", "given_name": "Yizhar", "orcid": "0000-0002-9091-9357", "clpid": "Or-Y" }, { "family_name": "Vankerschaver", "given_name": "Joris", "clpid": "Vankerschaver-J" }, { "family_name": "Kelly", "given_name": "Scott D.", "clpid": "Kelly-S-D" }, { "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" } ], "abstract": "Manipulation of particles suspended in fluids is crucial for many applications, such as precision machining, chemical processes, bio-engineering, and self-feeding of microorganisms. In this paper, we study the problem of particle manipulation by cyclic fluid boundary excitations from a geometric-control viewpoint. We focus on the simplified problem of manipulating a single particle by generating controlled cyclic motion of a circular rigid body in a two-dimensional perfect fluid. We show that the drift in the particle location after one cyclic motion of the body can be interpreted as the geometric phase of a connection induced by the system's hydrodynamics. We then formulate the problem as a control system, and derive a geometric criterion for its nonlinear controllability. Moreover, by exploiting the geometric structure of the system, we explicitly construct a feedback-based gait that results in attraction of the particle towards the rigid body. We argue that our gait is robust and model-independent, and demonstrate it in both perfect fluid and Stokes fluid.", "doi": "10.1109/CDC.2009.5399499", "isbn": "978-1-4244-3871-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-12", "pages": "19-26" }, { "id": "authors:rxhzq-sat22", "collection": "authors", "collection_id": "rxhzq-sat22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090828-100125867", "type": "article", "title": "Flight Dynamics and Control of Evasive Maneuvers: The Fruit Fly's Takeoff", "author": [ { "family_name": "Zabala", "given_name": "Francisco A.", "clpid": "Zabala-F-A" }, { "family_name": "Card", "given_name": "Gwyneth M.", "orcid": "0000-0002-7679-3639", "clpid": "Card-G-M" }, { "family_name": "Fontaine", "given_name": "Ebraheem I.", "clpid": "Fontaine-E-I" }, { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We have approached the problem of reverse-engineering the flight control mechanism of the fruit fly by studying the dynamics of the responses to a visual stimulus during takeoff. Building upon a prior framework [G. Card and M. Dickinson, J. Exp. Biol., vol. 211, pp. 341\u2013353, 2008], we seek to understand the strategies employed by the animal to stabilize attitude and orientation during these evasive, highly dynamical maneuvers. As a first step, we consider the dynamics from a gray-box perspective: examining lumped forces produced by the insect's legs and wings. The reconstruction of the flight initiation dynamics, based on the unconstrained motion formulation for a rigid body, allows us to assess the fly's responses to a variety of initial conditions induced by its jump. Such assessment permits refinement by using a visual tracking algorithm to extract the kinematic envelope of the wings [E. I. Fontaine, F. Zabala, M. Dickinson, and J. Burdick, \"Wing and body motion during flight initiation in Drosophila revealed by automated visual tracking,\" submitted for publication] in order to estimate lift and drag forces [F. Zabala, M. Dickinson, and R. Murray, \"Control and stability of insect flight during highly dynamical maneuvers,\" submitted for publication], and recording actual leg-joint kinematics and using them to estimate jump forces [F. Zabala, \"A bio-inspired model for directionality control of flight initiation,\" to be published.]. In this paper, we present the details of our approach in a comprehensive manner, including the salient results.", "doi": "10.1109/TBME.2009.2027606", "issn": "0018-9294", "publisher": "IEEE", "publication": "IEEE Transactions on Biomedical Engineering", "publication_date": "2009-09", "series_number": "9, par", "volume": "56", "issue": "9, par", "pages": "2295-2298" }, { "id": "authors:rvc0y-vad65", "collection": "authors", "collection_id": "rvc0y-vad65", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2009.001", "type": "monograph", "title": "Limits on the Network Sensitivity Function for Multi-Agent Systems on a Graph", "author": [ { "family_name": "Tonetti", "given_name": "Stefania", "clpid": "Tonetti-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This report explores the tradeoffs and limits of performance in feedback control of interconnected multi-agent systems, focused on the network sensitivity functions. We consider the interaction topology described by a directed graph and we prove that the sensitivity transfer functions between every pair of agents, arbitrarily connected, can be derived using a version of the Mason's Direct Rule. Explicit forms for special types of graphs are presented. An analysis of the role of cycles points out that these structures influence and limit considerably the performance of the system. The more the cycles are equally distributed among the formation, the better performance the system can achieve, but they are always worse than the single agent case. We also prove the networked version of Bode's integral formula, showing that it still holds for multi-agent systems.", "publisher": "California Institute of Technology", "publication_date": "2009-09" }, { "id": "authors:fpk3r-2n729", "collection": "authors", "collection_id": "fpk3r-2n729", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091106-154852106", "type": "article", "title": "Cone invariance and rendezvous of multiple agents", "author": [ { "family_name": "Bhattacharya", "given_name": "R.", "clpid": "Bhattacharya-R" }, { "family_name": "Tiwari", "given_name": "A.", "clpid": "Tiwari-A" }, { "family_name": "Fung", "given_name": "J.", "clpid": "Fung-J" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this article is presented a dynamical systems framework for analysing multi-agent rendezvous problems and characterize the dynamical behaviour of the collective system. Recently, the problem of rendezvous has been addressed considerably in the graph theoretic framework, which is strongly based on the communication aspects of the problem. The proposed approach is based on the set invariance theory and focusses on how to generate feedback between the vehicles, a key part of the rendezvous problem. The rendezvous problem is defined on the positions of the agents and the dynamics is modelled as linear first-order systems. These algorithms have also been applied to non-linear first-order systems.\n\nThe rendezvous problem in the framework of cooperative and competitive dynamical systems is analysed that has had some remarkable applications to biological sciences. Cooperative and competitive dynamical systems are shown to generate monotone flows by the classical Muller\u2013Kamke theorem, which is analysed using the set invariance theory. In this article, equivalence between the rendezvous problem and invariance of an appropriately defined cone is established. The problem of rendezvous is cast as a stabilization problem, with a the set of constraints on the trajectories of the agents defined on the phase plane. The n-agent rendezvous problem is formulated as an ellipsoidal cone invariance problem in the n-dimensional phase space. Theoretical results based on set invariance theory and monotone dynamical systems are developed. The necessary and sufficient conditions for rendezvous of linear systems are presented in the form of linear matrix inequalities. These conditions are also interpreted in the Lyapunov framework using multiple Lyapunov functions. Numerical examples that demonstrate application are also presented.", "doi": "10.1243/09544100JAERO443", "issn": "0954-4100", "publisher": "Professional Engineering Publishing", "publication": "Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering", "publication_date": "2009-09", "series_number": "6", "volume": "223", "issue": "6", "pages": "779-789" }, { "id": "authors:cmvck-g9104", "collection": "authors", "collection_id": "cmvck-g9104", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090930-152710419", "type": "article", "title": "Kalman filtering over a packet-delaying network: A probabilistic approach", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Xie", "given_name": "Linhua", "clpid": "Xie-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider Kalman filtering over a packet-delaying network. Given the probability distribution of the delay, we can characterize the filter performance via a probabilistic approach. We assume that the estimator maintains a buffer of length D so that at each time k, the estimator is able to retrieve all available data packets up to time k\u2212D+1. Both the cases of sensor with and without necessary computation capability for filter updates are considered. When the sensor has no computation capability, for a given D, we give lower and upper bounds on the probability for which the estimation error covariance is within a prescribed bound. When the sensor has computation capability, we show that the previously derived lower and upper bounds are equal to each other. An approach for determining the minimum buffer length for a required performance in probability is given and an evaluation on the number of expected filter updates is provided. Examples are provided to demonstrate the theory developed in the paper.", "doi": "10.1016/j.automatica.2009.05.018", "issn": "0005-1098", "publisher": "Elsevier", "publication": "Automatica", "publication_date": "2009-09", "series_number": "9", "volume": "45", "issue": "9", "pages": "2134-2140" }, { "id": "authors:1gnam-v4926", "collection": "authors", "collection_id": "1gnam-v4926", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090826-112853239", "type": "article", "title": "Data Transmission Over Networks for Estimation and Control", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Dana", "given_name": "Amir F.", "clpid": "Dana-A-F" }, { "family_name": "Hespanha", "given_name": "Joao P.", "clpid": "Hespanha-J-P" }, { "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" } ], "abstract": "We consider the problem of controlling a linear time invariant process when the controller is located at a location remote from where the sensor measurements are being generated. The communication from the sensor to the controller is supported by a communication network with arbitrary topology composed of analog erasure channels. Using a separation principle, we prove that the optimal linear-quadratic-Gaussian (LQG) controller consists of an LQ optimal regulator along with an estimator that estimates the state of the process across the communication network. We then determine the optimal information processing strategy that should be followed by each node in the network so that the estimator is able to compute the best possible estimate in the minimum mean squared error sense. The algorithm is optimal for any packet-dropping process and at every time step, even though it is recursive and hence requires a constant amount of memory, processing and transmission at every node in the network per time step. For the case when the packet drop processes are memoryless and independent across links, we analyze the stability properties and the performance of the closed loop system. The algorithm is an attempt to escape the viewpoint of treating a network of communication links as a single end-to-end link with the probability of successful transmission determined by some measure of the reliability of the network.", "doi": "10.1109/TAC.2009.2024567", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2009-08", "series_number": "8", "volume": "54", "issue": "8", "pages": "1807-1819" }, { "id": "authors:1g2sa-ap737", "collection": "authors", "collection_id": "1g2sa-ap737", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100507-094244165", "type": "book_section", "title": "On quantized consensus by means of gossip algorithm - Part I: Convergence proof", "book_title": "American Control Conference, 2009", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper is concerned with the distributed\naveraging problem subject to a quantization constraint. Given\na group of agents associated with scalar numbers, it is assumed\nthat each pair of agents can communicate with a prescribed\nprobability, and that the data being exchanged between them\nis quantized. In this part of the paper, it is proved that the\nstochastic gossip algorithm proposed in a recent paper leads\nto reaching the quantized consensus. Some important steady-state properties of the system (after reaching the consensus)\nare also derived. The results developed here hold true for any\narbitrary quantization, provided that the tuning parameter of\nthe gossip algorithm is chosen properly. The expected value of\nthe convergence time is lower and upper bounded in the second\npart of the paper.", "doi": "10.1109/ACC.2009.5160485", "isbn": "978-1-4244-4523-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-06", "pages": "394-401" }, { "id": "authors:kwb3m-7e641", "collection": "authors", "collection_id": "kwb3m-7e641", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100507-091712132", "type": "book_section", "title": "On quantized consensus by means of gossip algorithm - Part II: Convergence time", "book_title": "2009 American Control Conference", "author": [ { "family_name": "Lavaei", "given_name": "Javad", "clpid": "Lavaei-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper deals with the distributed averaging problem over a connected network of agents, subject to a quantization constraint. It is assumed that at each time update, only a pair of agents can update their own numbers in terms of the quantized data being exchanged. The agents are also required to communicate with one another in a stochastic fashion. In the first part of the paper, it was shown that the quantized consensus is reached by means of a stochastic gossip algorithm proposed in a recent paper, for any arbitrary quantization. The current part of the paper considers the expected value of the time at which the quantized consensus is reached. This quantity (corresponding to the worst case) is lower and upper bounded in terms of the topology of the graph, for uniform quantization. In particular, it is shown that the upper bound is related to the principal minors of the weighted Laplacian matrix. A convex optimization is also proposed to determine the set of probabilities (used to pick a pair of agents) which leads to the fast convergence of the gossip algorithm.", "doi": "10.1109/ACC.2009.5160568", "isbn": "978-1-4244-4523-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-06", "pages": "2958-2965" }, { "id": "authors:7a5hx-t6a79", "collection": "authors", "collection_id": "7a5hx-t6a79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100507-133036019", "type": "book_section", "title": "Real-valued average consensus over noisy quantized channels", "book_title": "American Control Conference, 2009", "author": [ { "family_name": "Censi", "given_name": "Andrea", "orcid": "0000-0001-5162-0398", "clpid": "Censi-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper concerns the average consensus problem\nwith the constraint of quantized communication between\nnodes. A broad class of algorithms is analyzed, in which the\ntransmission strategy, which decides what value to communicate\nto the neighbours, can include various kinds of rounding, probabilistic\nquantization, and bounded noise. The arbitrariness\nof the transmission strategy is compensated by a feedback\nmechanism which can be interpreted as a self-inhibitory action.\nThe result is that the average of the nodes state is not conserved\nacross iterations, and the nodes do not converge to a consensus;\nhowever, we show that both errors can be made as small\nas desired. Bounds on these quantities involve the spectral\nproperties of the graph and can be proved by employing\nelementary techniques of LTI systems analysis.", "doi": "10.1109/ACC.2009.5159872", "isbn": "978-1-4244-4523-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-06", "pages": "4361-4366" }, { "id": "authors:tg97z-p0j72", "collection": "authors", "collection_id": "tg97z-p0j72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-135204769", "type": "book_section", "title": "A real-time helicopter testbed for insect-inspired visual flight control", "book_title": "2009 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Han", "given_name": "Shuo", "clpid": "Han-Shuo" }, { "family_name": "Straw", "given_name": "Andrew D.", "orcid": "0000-0001-8381-0858", "clpid": "Straw-A-D" }, { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The paper describes an indoor helicopter testbed that allows implementing and testing of bio-inspired control algorithms developed from scientific studies on insects. The helicopter receives and is controlled by simulated sensory inputs (e.g. visual stimuli) generated in a virtual 3D environment, where the connection between the physical world and the virtual world is provided by a video camera tracking system. The virtual environment is specified by a 3D computer model and is relatively simple to modify compared to realistic scenes. This enables rapid examinations of whether a certain control law is robust under various environments, an important feature of insect behavior. As a first attempt, flight stabilization and yaw rate control near hover are demonstrated, utilizing biologically realistic visual stimuli as in the fruit fly Drosophila melanogaster.", "doi": "10.1109/ROBOT.2009.5152667", "isbn": "978-1-4244-2788-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2009-05", "pages": "3055-3060" }, { "id": "authors:mda6j-hbv93", "collection": "authors", "collection_id": "mda6j-hbv93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091006-094144123", "type": "article", "title": "Model reduction of interconnected linear systems", "author": [ { "family_name": "Sandberg", "given_name": "H.", "clpid": "Sandberg-H" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The problem of model reduction of linear systems with certain interconnection structure is considered in this paper. To preserve the interconnection structure between subsystems in the reduction, special care needs to be taken. This problem is important and timely because of the recent focus on complex networked systems in control engineering. Two different model reduction methods are introduced and compared in this paper. Both methods are extensions to the well-known balanced truncation method. Compared with earlier work in the area these methods use a more general linear fractional transformation framework, and utilize linear matrix inequalities. Furthermore, new approximation error bounds that reduce to classical bounds in special cases are derived. The so-called structured Hankel singular values are used in the methods, and indicate how important states in the subsystems are with respect to a chosen input-output map for the entire interconnected system. It is shown how these structured Hankel singular values can be used to select an approximation order. Finally, the two methods are applied to a model of a mechanical device.", "doi": "10.1002/oca.854", "issn": "0143-2087", "publisher": "Wiley Interscience", "publication": "Optimal Control Applications and Methods", "publication_date": "2009-05", "series_number": "3", "volume": "30", "issue": "3", "pages": "225-245" }, { "id": "authors:v69bs-h3b78", "collection": "authors", "collection_id": "v69bs-h3b78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090708-083134251", "type": "article", "title": "Dynamics and stability of a class of low Reynolds number swimmers near a wall", "author": [ { "family_name": "Or", "given_name": "Yizhar", "orcid": "0000-0002-9091-9357", "clpid": "Or-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We study the dynamic stability of low Reynolds number swimming near a plane wall from a control-theoretic viewpoint. We consider a special class of swimmers having a constant shape, focus on steady motion parallel to the wall, and derive conditions under which it is passively stable without sensing or feedback. We study the geometric structure of the swimming equation and highlight the relation between stability and reversing symmetry of the dynamical system. Finally, our numerical simulations reveal the existence of stable periodic motion. The results have implications for design of miniature robotic swimmers, as well as for explaining the attraction of micro-organisms to surfaces.", "doi": "10.1103/PhysRevE.79.045302", "issn": "1539-3755", "publisher": "American Physical Society", "publication": "Physical Review E", "publication_date": "2009-04", "series_number": "4", "volume": "79", "issue": "4", "pages": "045302" }, { "id": "authors:0qa9f-gx913", "collection": "authors", "collection_id": "0qa9f-gx913", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090416-092107354", "type": "article", "title": "To Drop or Not to Drop: Design Principles for Kalman Filtering Over Wireless Fading Channels", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "It is the general assumption that in estimation and control over wireless links, the receiver should drop any erroneous packets. While this approach is appropriate for non real-time data-network applications, it can result in instability and loss of performance in networked control systems. In this technical note we consider estimation of a multiple-input multiple-output dynamical system over a mobile fading communication channel using a Kalman filter. We show that the communication protocols suitable for other already-existing applications like data networks may not be entirely applicable for estimation and control of a rapidly changing dynamical system. We then develop new design paradigms in terms of handling noisy packets for such delay-sensitive applications. We reformulate the estimation problem to include the impact of stochastic communication noise in the erroneous packets. We prove that, in the absence of a permanent cross-layer information path, packet drop should be designed to balance information loss and communication noise in order to optimize the performance.", "doi": "10.1109/TAC.2008.2008331", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2009-02", "series_number": "2", "volume": "54", "issue": "2", "pages": "376-381" }, { "id": "authors:pr3md-m1f83", "collection": "authors", "collection_id": "pr3md-m1f83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-145008185", "type": "book_section", "title": "Optimal sensor hop selection: Sensor energy minimization and network lifetime maximization with guaranteed system performance", "book_title": "47th IEEE Conference on Decision and Control", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Johansson", "given_name": "Karl Henrik", "clpid": "Johansson-K-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider state estimation carried over a sensor network. A fusion center forms a local multi-hop tree of sensors and gateways and fuses the data into a state estimate. It is shown that the optimal estimator over a sensor tree is given by a Kalman filter of certain structure. The number of hops that the sensors use to communicate data with the fusion center is optimized such that either the overall transmission energy is minimized or the network lifetime is maximized. In both cases the fusion center provides a specified level of estimation accuracy. Some heuristic algorithms are proposed which lead to suboptimal solutions in the energy minimization problem, while an algorithm that leads to the global optimal solution is proposed in the lifetime maximization problem. In both cases, the algorithms are shown to have low computational complexity. Examples are provided to demonstrate the theory and algorithms.", "doi": "10.1109/CDC.2008.4738663", "isbn": "978-1-4244-3123-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-12", "pages": "2344-2349" }, { "id": "authors:ksrb5-sks83", "collection": "authors", "collection_id": "ksrb5-sks83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-143454266", "type": "book_section", "title": "Design and performance of in vitro transcription rate regulatory circuits", "book_title": "47th IEEE Conference on Decision and Control", "author": [ { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper proposes a synthetic in vitro circuit that aims at regulating the rate of RNA transcription through positive feedback interactions. This design is dual to a previously synthesized transcriptional rate regulator based on self-repression. Two DNA templates are designed to interact through their transcripts, creating cross activating feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis-Menten kinetics involving all the present chemical species. This circuit is then compared to its regulatory counterpart based on negative feedback. A global sensitivity analysis reveals the fundamental features of the two designs by evaluating their equilibrium response to changes in the most crucial parameters of the system.", "doi": "10.1109/CDC.2008.4739253", "isbn": "978-1-4244-3123-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-12", "pages": "161-166" }, { "id": "authors:xe98t-9dg72", "collection": "authors", "collection_id": "xe98t-9dg72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DUNng08", "type": "article", "title": "Regulatory activity revealed by dynamic correlations in gene expression noise", "author": [ { "family_name": "Dunlop", "given_name": "Mary J.", "clpid": "Dunlop-M-J" }, { "family_name": "Cox", "given_name": "Robert Sidney, III", "clpid": "Cox-R-S-III" }, { "family_name": "Levine", "given_name": "Joseph H.", "clpid": "Levine-J-H" }, { "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" } ], "abstract": "Gene regulatory interactions are context dependent, active in some cellular states but not in others. Stochastic fluctuations, or 'noise', in gene expression propagate through active, but not inactive, regulatory links^(1,2). Thus, correlations in gene expression noise could provide a noninvasive means to probe the activity states of regulatory links. However, global, 'extrinsic', noise sources generate correlations even without direct regulatory links. Here we show that single-cell time-lapse microscopy, by revealing time lags due to regulation, can discriminate between active regulatory connections and extrinsic noise. We demonstrate this principle mathematically, using stochastic modeling, and experimentally, using simple synthetic gene circuits. We then use this approach to analyze dynamic noise correlations in the galactose metabolism genes of Escherichia coli. We find that the CRP-GalS-GalE feed-forward loop is inactive in standard conditions but can become active in a GalR mutant. These results show how noise can help analyze the context dependence of regulatory interactions in endogenous gene circuits.", "doi": "10.1038/ng.281", "pmcid": "PMC2829635", "issn": "1061-4036", "publisher": "Nature Publishing Group", "publication": "Nature Genetics", "publication_date": "2008-12", "series_number": "12", "volume": "40", "issue": "12", "pages": "1493-1498" }, { "id": "authors:rddvz-9wc82", "collection": "authors", "collection_id": "rddvz-9wc82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100726-104209965", "type": "book_section", "title": "Kalman Filtering Over A Packet Dropping Network: A Probabilistic Approach", "book_title": "10th Annual Conference on Control, Automation, Robotics, and Vision, 2008", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of state estimation of a discrete time process over a packet dropping network. Previous pioneering work on Kalman filtering with intermittent observations is concerned with the asymptotic behavior of E[P_k], i.e., the expected value of the error covariance, for a given packet arrival rate. We consider a different performance metric, Pr[P_k \u2264 M], i.e., the probability that P_k is bounded by a given M, and we derive lower and upper bounds on Pr[P_k \u2264 M]. We are also able to recover the results in the literature when using Pr[P_k \u2264 M] as a metric for scalar systems. Examples are provided to illustrate the theory developed in the paper.", "doi": "10.1109/ICARCV.2008.4795489", "isbn": "978-1-4244-2286-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-12", "pages": "41-46" }, { "id": "authors:rrnt4-76r98", "collection": "authors", "collection_id": "rrnt4-76r98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:EPSa08", "type": "article", "title": "Probabilistic performance of state estimation across a lossy network", "author": [ { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Tiwari", "given_name": "Abhishek", "clpid": "Tiwari-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider a discrete time state estimation problem over a packet-based network. In each discrete time step, a measurement packet is sent across a lossy network to an estimator unit consisting of a modified Kalman filter. Using the designed estimator algorithm, the importance of placing a measurement buffer at the sensor that allows transmission of the current and several previous measurements is shown. Previous pioneering work on Kalman filtering with intermittent observation losses is concerned with the asymptotic behavior of the expected value of the error covariance, i.e. E [P-k] < \u221e as k \u2192 \u221e. We consider a different performance metric, namely a probabilistic statement of the error covariance Pr[P-k \u2264 M] \u2265 1 - \u03b5, meaning that with high probability the error covariance is bounded above at any instant in time. Provided the estimator error covariance has an upper bound whenever a measurement packet arrives, we show that for any finite M this statement will hold so long as the probability of receiving a measurement packet is nonzero. We also give an explicit relationship between M and E and provide examples to illustrate the theory.", "doi": "10.1016/j.automatica.2008.05.026", "issn": "0005-1098", "publisher": "Elsevier", "publication": "Automatica", "publication_date": "2008-12", "series_number": "12", "volume": "44", "issue": "12", "pages": "3046-3053" }, { "id": "authors:s5v92-9f839", "collection": "authors", "collection_id": "s5v92-9f839", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:INAjgcd08", "type": "article", "title": "Framework for low-observable trajectory generation in presence of multiple radars", "author": [ { "family_name": "Inanc", "given_name": "Tamer", "clpid": "Inanc -T" }, { "family_name": "Muezzinoglu", "given_name": "Mehmet K.", "clpid": "Muezzinoglu-M-K" }, { "family_name": "Misovec", "given_name": "Kathleen", "clpid": "Misovec-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper explores the problem of finding a real-time optimal trajectory for unmanned aerial vehicles to minimize their probability of detection by opponent multiple radar detection systems. The problem is handled using the nonlinear trajectory generation method developed by Milam et al. (Milam, M., Mushambi, K., and Murray, R., \"New Computational Approach to Real-Time Trajectory Generation for Constrained Mechanical Systems,\" Proceedings of the 39th IEEE Conference on Decision and Control, Vol. 1, Institute of Electrical and Electronics Engineers, New York, Dec. 2000, pp. 845-851.) The paper presents a formulation of the trajectory generation task as an optimal control problem, where temporal constraints allow periods of high observability interspersed with periods of low observability. This feature can be used strategically to aid in avoiding detection by an opponent radar. The guidance is provided in the form of sampled tabular data. It is then shown that the success of nonlinear trajectory generation on the proposed low-observable trajectory generation problem depends upon an accurate parameterization of the guidance data. In particular, such an approximator is desired to have a compact architecture, a minimum number of design parameters, and a smooth continuously differentiable input-output mapping. Artificial neural networks as universal approximators are known to possess these features, and thus are considered here as appropriate candidates for this task. Comparison of artificial neural networks against B-spline approximators is provided, as well. Numerical simulations on multiple radar scenarios illustrate unmanned air vehicle trajectories optimized for both detectability and time.", "doi": "10.2514/1.35287", "issn": "0731-5090", "publisher": "AIAA", "publication": "Journal of Guidance, Control, and Dynamics", "publication_date": "2008-11", "series_number": "6", "volume": "31", "issue": "6", "pages": "1740-1749" }, { "id": "authors:p6779-0mp04", "collection": "authors", "collection_id": "p6779-0mp04", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2008.003", "type": "monograph", "title": "Periodically Controlled Hybrid Systems: Verifying A Controller for An Autonomous Vehicle", "author": [ { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Mitra", "given_name": "Sayan", "clpid": "Mitra-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Lamperski", "given_name": "Andrew", "clpid": "Lamperski-A" } ], "abstract": "This paper introduces Periodically Controlled Hybrid Automata (PCHA) for describing a class of hybrid control systems. In a PCHA, control actions occur roughly periodically while internal and input actions, may occur in the interim changing the discrete-state or the setpoint. Based on periodicity and subtangential conditions, a new sufficient condition for verifying invariance of PCHAs is presented. This technique is used in verifying safety of the planner-controller subsystem of an autonomous ground vehicle, and in deriving geometric properties of planner generated paths that can be followed safely by the controller under environmental uncertainties.", "publisher": "California Institute of Technology", "publication_date": "2008-10-17" }, { "id": "authors:jbwc2-haj66", "collection": "authors", "collection_id": "jbwc2-haj66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-142007113", "type": "book_section", "title": "Dynamics of escaping flight initiations of Drosophila melanogaster", "book_title": "2008 2nd IEEE RAS & EMBS International Conference on Biomedical Robotics and Biomechatronics", "author": [ { "family_name": "Zabala", "given_name": "Francisco A.", "clpid": "Zabala-F-A" }, { "family_name": "Card", "given_name": "Gwyneth M.", "orcid": "0000-0002-7679-3639", "clpid": "Card-G-M" }, { "family_name": "Fontaine", "given_name": "Ebraheem I.", "clpid": "Fontaine-E-I" }, { "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" } ], "abstract": "We present a reconstruction of the dynamics of flight initiation from kinematic data extracted from high-speed video recordings of the fruit fly Drosophila melanogaster. The dichotomy observed in this insectpsilas flight initiation sequences, generated by the presence or absence of visual stimuli, clearly generates two contrasting sets of dynamics once the flies become airborne. By calculating reaction forces and moments using the unconstrained motion formulation for a rigid body, we assess the flypsilas responses amidst these two dynamic patterns as a step towards refining our understanding of insect flight control.", "doi": "10.1109/BIOROB.2008.4762921", "isbn": "978-1-4244-2882-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-10", "pages": "1-6" }, { "id": "authors:yxy9x-pem71", "collection": "authors", "collection_id": "yxy9x-pem71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200127-094633815", "type": "book_section", "title": "Robust Model Predictive Control with a Safety Mode: Applied to Small-Body Proximity Operations", "book_title": "AIAA Guidance, Navigation and Control Conference and Exhibit", "author": [ { "family_name": "Carson", "given_name": "John M., III", "clpid": "Carson-J-M-III" }, { "family_name": "A\u00e7\u0131kme\u015fe", "given_name": "Beh\u00e7et", "clpid": "A\u00e7\u0131kme\u015fe-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "MacMynowski", "given_name": "Douglas G.", "orcid": "0000-0003-1987-9417", "clpid": "MacMartin-D-G" } ], "abstract": "Safe and robust G&C (Guidance and Control) algorithms for onboard implementation are developed by augmenting a model predictive control technique with a safety mode. The application example herein is spacecraft small-body proximity operations where model and constraint uncertainty warrant G&C algorithms with a degree of autonomous, onboard decision capability. The algorithm enforces state and control constraints and merges two operational modes: (I) standard mode guides the spacecraft to the proximity of a target state in a robust and resolvable model-predictive manner, (II) safety mode, if activated, maintains the spacecraft near a safety reference for all time. The algorithm utilizes separate feedforward and feedback components. In standard mode, the feedforward guidance solutions come from a way-point generation algorithm that uses a discrete linear-time-varying dynamics model. This approach provides a convex formulation of the problem (solvable onboard as a second-order cone program) that includes control and state constraints; the safety-mode availability adds a constraint in this standard-mode formulation as well. The feedback guarantees standard-mode resolvability to update the guidance profile in a robust, model-predictive manner. In safety mode, an offline-designed feedforward policy with the added feedback maintains the spacecraft in a hovering state in the proximity of its position at safety-mode activation time; this provides robustness to unexpected state-constraint changes such as unexpected ground proximity during landing operations. A simulation demonstrating both the standard and safety modes is provided for a spacecraft\nautonomous-descent scenario toward a small asteroid with an uncertain gravity model and errors in the surface altitude constraint.", "doi": "10.2514/6.2008-7243", "isbn": "978-1-60086-999-0", "publisher": "American Institute of Aeronautics and Astronautics", "place_of_publication": "Reston, VA", "publication_date": "2008-08", "pages": "Art. No. 2008-7243" }, { "id": "authors:mt3tg-02637", "collection": "authors", "collection_id": "mt3tg-02637", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-145913467", "type": "book_section", "title": "Convergence properties of dynamic agents consensus networks with broken links", "book_title": "2008 American Control Conference", "author": [ { "family_name": "Di Cairano", "given_name": "S.", "clpid": "Di-Cairano-S" }, { "family_name": "Pasini", "given_name": "A.", "clpid": "Pasini-A" }, { "family_name": "Bemporad", "given_name": "A.", "clpid": "Bemporad-A" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Convergence properties of distributed consensus protocols on networks of dynamical agents have been analyzed by combinations of algebraic graph theory and control theory tools under certain assumptions, such as strong connectivity. Strong connectivity can be regarded as the requirement that the information of each agent propagates to all the others, possibly with intermediate steps and manipulations. However, because of network failures or malicious attacks, it is possible that this assumption no longer holds, so that some agents are only receiving or only transmitting information from other subsets of agents. In this case, strong connectivity is replaced by weak connectivity. We analyze the convergence properties of distributed consensus on directed graphs with weakly connected components. We show conditions for which the agreement is reached, and, for the cases in which such conditions do not hold, we provide bounds on the residual disagreement.", "doi": "10.1109/ACC.2008.4586682", "isbn": "978-1-4244-2078-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-06", "pages": "1362-1367" }, { "id": "authors:tavz4-qfw65", "collection": "authors", "collection_id": "tavz4-qfw65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100512-105503658", "type": "book_section", "title": "Design, modeling and synthesis of an in vitro transcription rate regulatory circuit", "book_title": "American Control Conference, 2008", "author": [ { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Forsberg", "given_name": "Per-Ola", "clpid": "Forsberg-O-O" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes the design, modeling and realization of a synthetic in vitro circuit that aims at regulating the rate of mRNA transcription. Two DNA templates are designed to interact through their transcripts, creating negative feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis-Menten kinetics involving all the present chemical species. The DNA strands were accordingly designed, following thermodynamics principles and minimizing unwanted interactions. Preliminary experimental results show that the circuit is performing the expected task, by matching at steady state the transcription rates of the two DNA templates.", "doi": "10.1109/ACC.2008.4586915", "isbn": "978-1-4244-2078-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-06", "pages": "2786-2791" }, { "id": "authors:0ttgm-fzx60", "collection": "authors", "collection_id": "0ttgm-fzx60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100623-113414565", "type": "book_section", "title": "Safety Verification of Fault Tolerant Goal-based Control Programs with Estimation Uncertainty", "book_title": "American Control Conference, 2008", "author": [ { "family_name": "Braman", "given_name": "Julia M. B.", "clpid": "Braman-J-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Fault tolerance and safety verification of control systems that have state variable estimation uncertainty are essential for the success of autonomous robotic systems. A software control architecture called mission data system, developed at the Jet Propulsion Laboratory, uses goal networks as the control program for autonomous systems. Certain types of goal networks can be converted into linear hybrid systems and verified for safety using existing symbolic model checking software. A process for calculating the probability of failure of certain classes of verifiable goal networks due to state estimation uncertainty is presented. A verifiable example task is presented and the failure probability of the control program based on estimation uncertainty is found.", "doi": "10.1109/ACC.2008.4586461", "isbn": "978-1-4244-2078-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-06", "pages": "27-32" }, { "id": "authors:mqxny-1w830", "collection": "authors", "collection_id": "mqxny-1w830", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-145441234", "type": "book_section", "title": "Nonlinear lateral control strategy for nonholonomic vehicles", "book_title": "2008 American Control Conference", "author": [ { "family_name": "Linderoth", "given_name": "Magnus", "clpid": "Linderoth-M" }, { "family_name": "Soltesz", "given_name": "Kristian", "clpid": "Soltesz-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper proposes an intuitive nonlinear lateral control strategy for trajectory tracking in autonomous nonholonomic vehicles. The controller has been implemented and verified in Alice, Team Caltech's contribution to the 2007 DARPA Urban Challenge competition for autonomous motorcars. A kinematic model is derived. The control law is described and analyzed. Results from simulations and field tests are given and evaluated. Finally, the key features of the proposed controller are reviewed, followed by a discussion of some limitations of the proposed strategy.", "doi": "10.1109/ACC.2008.4586988", "isbn": "978-1-4244-2078-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2008-06", "pages": "3219-3224" }, { "id": "authors:7w8h6-7pb67", "collection": "authors", "collection_id": "7w8h6-7pb67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180815-095447771", "type": "article", "title": "Communication and sensing trade\u2010offs in cooperative mobile networks", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider the impact of communication noise on distributed sensing and estimation in mobile networks. We characterize when a node should rely on getting information from others and when it should rely on self exploration. In doing so, we explore the trade\u2010offs between sensing and communication by finding the optimum network configuration under communication constraints. We also show how to achieve the optimum configuration in a distributed manner. While our main results are presented in one dimension (1D), we provide insight into the two dimension (2D) setup and extend a number of key results to 2D.", "doi": "10.1002/asjc.16", "issn": "1561-8625", "publisher": "Wiley", "publication": "Asian Journal of Control", "publication_date": "2008-03", "series_number": "2", "volume": "10", "issue": "2", "pages": "156-170" }, { "id": "authors:yzs24-xsx88", "collection": "authors", "collection_id": "yzs24-xsx88", "cite_using_url": "https://resolver.caltech.edu/CaltechBOOK:2008.003", "type": "book", "title": "Feedback Systems: An Introduction for Scientists and Engineers", "author": [ { "family_name": "\u00c5str\u00f6m", "given_name": "Karl Johan", "clpid": "\u00c5str\u00f6m-K-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This book provides an introduction to the basic principles and tools for the design and analysis of feedback systems. It is intended to serve a diverse audience of scientists and engineers who are interested in understanding and utilizing feedback in physical, biological, information and social systems.We have attempted to keep the mathematical prerequisites to a minimum while being careful not to sacrifice rigor in the process. We have also attempted to make use of examples from a variety of disciplines, illustrating the generality of many of the tools while at the same time showing how they can be applied in specific application domains. \n\nA major goal of this book is to present a concise and insightful view of the current knowledge in feedback and control systems. The field of control started by teaching everything that was known at the time and, as new knowledge was acquired, additional courses were developed to cover new techniques. A consequence of this evolution is that introductory courses have remained the same for many years, and it is often necessary to take many individual courses in order to obtain a good perspective on the field. In developing this book, we have attempted to condense the current knowledge by emphasizing fundamental concepts. We believe that it is important to understand why feedback is useful, to know the language and basic mathematics of control and to grasp the key paradigms that have been developed over the past half century. It is also important to be able to solve simple feedback problems using back-of-the-envelope techniques, to recognize fundamental limitations and difficult control problems and to have a feel for available design methods. \n\nThis book was originally developed for use in an experimental course at Caltech involving students from a wide set of backgrounds. The course was offered to undergraduates at the junior and senior levels in traditional engineering disciplines, as well as first- and second-year graduate students in engineering and science. This latter group included graduate students in biology, computer science and physics. Over the course of several years, the text has been classroom tested at Caltech and at Lund University, and the feedback from many students and colleagues has been incorporated to help improve the readability and accessibility of the material. \n\nBecause of its intended audience, this book is organized in a slightly unusual fashion compared to many other books on feedback and control. In particular, we introduce a number of concepts in the text that are normally reserved for second-year courses on control and hence often not available to students who are not control systems majors. This has been done at the expense of certain traditional topics, which we felt that the astute student could learn independently and are often explored through the exercises. Examples of topics that we have included are nonlinear dynamics, Lyapunov stability analysis, the matrix exponential, reachability and observability, and fundamental limits of performance and robustness. Topics that we have deemphasized include root locus techniques, lead/lag compensation and detailed rules for generating Bode and Nyquist plots by hand. \n\nSeveral features of the book are designed to facilitate its dual function as a basic engineering text and as an introduction for researchers in natural, information and social sciences. The bulk of the material is intended to be used regardless of the audience and covers the core principles and tools in the analysis and design of feedback systems. Advanced sections, marked by the \"dangerous bend\" symbol shown here, contain material that requires a slightly more technical background, of the sort that would be expected of senior undergraduates in engineering. A few sections are marked by two dangerous bend symbols and are intended for readers with more specialized backgrounds, identified at the beginning of the section. To limit the length of the text, several standard results and extensions are given in the exercises, with appropriate hints toward their solutions. \n\nTo further augment the printed material contained here, a companion web site has been developed and is available from the publisher's web page: http://press.princeton.edu/titles/8701.html \nThe web site contains a database of frequently asked questions, supplemental examples and exercises, and lecture material for courses based on this text. The material is organized by chapter and includes a summary of the major points in the text as well as links to external resources. The web site also contains the source code for many examples in the book, as well as utilities to implement the techniques described in the text. Most of the code was originally written using MATLAB M-files but was also tested with LabView MathScript to ensure compatibility with both packages. Many files can also be run using other scripting languages such as Octave, SciLab, SysQuake and Xmath. \n\nThe first half of the book focuses almost exclusively on state space control systems. We begin in Chapter 2 with a description of modeling of physical, biological and information systems using ordinary differential equations and difference equations. Chapter 3 presents a number of examples in some detail, primarily as a reference for problems that will be used throughout the text. Following this, Chapter 4 looks at the dynamic behavior of models, including definitions of stability and more complicated nonlinear behavior. We provide advanced sections in this\nchapter on Lyapunov stability analysis because we find that it is useful in a broad array of applications and is frequently a topic that is not introduced until later in\none's studies. \n\nThe remaining three chapters of the first half of the book focus on linear systems, beginning with a description of input/output behavior in Chapter 5. In Chapter 6, we formally introduce feedback systems by demonstrating how state space control laws can be designed. This is followed in Chapter 7 by material on output feedback and estimators. Chapters 6 and 7 introduce the key concepts of reachability and observability, which give tremendous insight into the choice of actuators and sensors, whether for engineered or natural systems. \n\nThe second half of the book presents material that is often considered to be from the field of \"classical control.\" This includes the transfer function, introduced in Chapter 8, which is a fundamental tool for understanding feedback systems. Using transfer functions, one can begin to analyze the stability of feedback systems using frequency domain analysis, including the ability to reason about the closed loop behavior of a system from its open loop characteristics. This is the subject of Chapter 9, which revolves around the Nyquist stability criterion. \n\nIn Chapters 10 and 11, we again look at the design problem, focusing first on proportional-integral-derivative (PID) controllers and then on the more general process of loop shaping. PID control is by far the most common design technique in control systems and a useful tool for any student. The chapter on frequency domain design introduces many of the ideas of modern control theory, including the sensitivity function. In Chapter 12, we combine the results from the second half of the book to analyze some of the fundamental trade-offs between robustness and performance. This is also a key chapter illustrating the power of the techniques that have been developed and serving as an introduction for more advanced studies. \n\nThe book is designed for use in a 10- to 15-week course in feedback systems that provides many of the key concepts needed in a variety of disciplines. For a 10-week course, Chapters 1\u20132, 4\u20136 and 8\u201311 can each be covered in a week's time, with the omission of some topics from the final chapters. A more leisurely course, spread out over 14\u201315 weeks, could cover the entire book, with 2 weeks on modeling (Chapters 2 and 3) \u2014 particularly for students without much background in ordinary differential equations \u2014 and 2 weeks on robust performance (Chapter 12). \n\nThe mathematical prerequisites for the book are modest and in keeping with our goal of providing an introduction that serves a broad audience. We assume familiarity with the basic tools of linear algebra, including matrices, vectors and eigenvalues. These are typically covered in a sophomore-level course on the subject, and the textbooks by Apostol [10], Arnold [13] and Strang [187] can serve as good references. Similarly, we assume basic knowledge of differential equations, including the concepts of homogeneous and particular solutions for linear ordinary differential equations in one variable. Apostol [10] and Boyce and DiPrima [42] cover this material well. Finally, we also make use of complex numbers and functions and, in some of the advanced sections, more detailed concepts in complex variables that are typically covered in a junior-level engineering or physics course in mathematical methods. Apostol [9] or Stewart [186] can be used for the basic material, with Ahlfors [6], Marsden and Hoffman [146] or Saff and Snider [172] being good references for the more advanced material. We have chosen not to include appendices summarizing these various topics since there are a number of good books available. \n\nOne additional choice that we felt was important was the decision not to rely on a knowledge of Laplace transforms in the book. While their use is by far the most common approach to teaching feedback systems in engineering, many students in the natural and information sciences may lack the necessary mathematical background. Since Laplace transforms are not required in any essential way, we have included them only in an advanced section intended to tie things together for students with that background. Of course, we make tremendous use of transfer functions, which we introduce through the notion of response to exponential inputs, an approach we feel is more accessible to a broad array of scientists and engineers. For classes in which students have already had Laplace transforms, it should be quite natural to build on this background in the appropriate sections of the text. \n\nAcknowledgments: The authors would like to thank the many people who helped during the preparation of this book. The idea for writing this book came in part from a report on future directions in control [155] to which Stephen Boyd, Roger Brockett, John Doyle and Gunter Stein were major contributors. Kristi Morgansen and Hideo Mabuchi helped teach early versions of the course at Caltech on which much of the text is based, and Steve Waydo served as the head TA for the course taught at Caltech in 2003\u20132004 and provided numerous comments and corrections. Charlotta Johnsson and Anton Cervin taught from early versions of the manuscript in Lund in 2003\u20132007 and gave very useful feedback. Other colleagues and students who provided feedback and advice include Leif Andersson, John Carson, K. Mani Chandy, Michel Charpentier, Domitilla Del Vecchio, Kate Galloway, Per Hagander, Toivo Henningsson Perby, Joseph Hellerstein, George Hines, Tore H\u00e4gglund, Cole Lepine, Anders Rantzer, Anders Robertsson, Dawn Tilbury and Francisco Zabala. The reviewers for Princeton University Press and Tom Robbins at NI Press also provided valuable comments that significantly improved the organization, layout and focus of the book. Our editor, Vickie Kearn, was a great source of encouragement and help throughout the publishing process. Finally, we would like to thank Caltech, Lund University and the University of California at Santa Barbara for providing many resources, stimulating colleagues and students, and pleasant working environments that greatly aided in the writing of this book.", "isbn": "978-0-691-13576-2", "publisher": "Princeton University Press", "place_of_publication": "Princeton, NJ", "publication_date": "2008-01-30" }, { "id": "authors:f23by-q5h03", "collection": "authors", "collection_id": "f23by-q5h03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100715-135111003", "type": "book_section", "title": "Situational reasoning for road driving in an urban environment", "book_title": "Intelligent vehicle control systems : proceedings of the 2nd International Workshop on Intelligent Vehicle Control Systems, IVCS 2008", "author": [ { "family_name": "Du Toit", "given_name": "Noel E.", "clpid": "Du-Toit-N-E" }, { "family_name": "Wongpiromsarn", "given_name": "Tichakorn", "clpid": "Wongpiromsarn-T" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Robot navigation in urban environments requires situational reasoning.\nGiven the complexity of the environment and the behavior specified by traffic\nrules, it is necessary to recognize the current situation to impose the correct\ntraffic rules. In an attempt to manage the complexity of the situational reasoning\nsubsystem, this paper describes a finite state machine model to govern the situational\nreasoning process. The logic state machine and its interaction with the\nplanning system are discussed. The approach was implemented on Alice, Team\nCaltech's entry into the 2007 DARPA Urban Challenge. Results from the qualifying\nrounds are discussed. The approach is validated and the shortcomings of\nthe implementation are identified.", "isbn": "978-989-8111-34-0", "publisher": "INSTICC Press", "publication_date": "2008", "pages": "30-39" }, { "id": "authors:zbwv0-90r27", "collection": "authors", "collection_id": "zbwv0-90r27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100826-114646843", "type": "book_section", "title": "Estimation Schemes for Networked Control Systems Using UDP-Like Communication", "book_title": "46th IEEE Conference on Decision and Control", "author": [ { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this work we consider a class of networked control systems (NCS) when the control signal is sent to the plant via a UDP-like communication protocol, the controller sends a communication packet to the plant across a lossy network but the controller does not receive any acknowledgement signal indicating the status of reception/delivery of the control packet. Standard observer based estimators assume the estimator has knowledge of what control signal is applied to the plant, but under the UDP-like communication scheme the estimator does not know what control is applied. Continuing previous work, we present a simple estimation algorithm consisting of a state estimator and mode observer. For single input systems we can add an extra control signal that guarantees recovery of the fate of the control packet. Using a modified state feedback with the added input we can guarantee the estimation error is bounded as is the expected value of the state. This extra input is removed and sufficient conditions on the system properties are given to assure the estimation remain bounded. Comparisons are made between the algorithm presented and the method of unknown input observer. Simulations are provided to demonstrate the algorithm.", "doi": "10.1109/CDC.2007.4434841", "isbn": "978-1-4244-1497-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-12", "pages": "3945-3951" }, { "id": "authors:78v71-3ye02", "collection": "authors", "collection_id": "78v71-3ye02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100923-141354531", "type": "book_section", "title": "Random consensus protocol in large-scale networks", "book_title": "46th IEEE Conference on Decision and Control", "author": [ { "family_name": "Jin", "given_name": "Zhipu", "clpid": "Jin-Zhipu" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "One of the main performance issues for consensus\nprotocols is the convergence speed. In this paper, we focus on the\nconvergence behavior of discrete-time consensus protocols over\nlarge-scale sensor networks with uniformly random deployment,\nwhich are modelled as Poisson random graphs. Instead of\nusing the random rewiring procedure, we introduce a deterministic\nprinciple to locate certain \"chosen nodes\" in the network\nand add \"virtual\" shortcuts among them so that the number\nof iterations to achieve average consensus drops dramatically.\nSimulation results are presented to verify the efficiency of this\napproach. Moreover, a random consensus protocol is proposed,\nin which virtual shortcuts are implemented by random routes.", "doi": "10.1109/CDC.2007.4434765", "isbn": "978-1-4244-1497-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-12", "pages": "4227-4232" }, { "id": "authors:77s02-vk389", "collection": "authors", "collection_id": "77s02-vk389", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101105-135641397", "type": "book_section", "title": "Change Sensor Topology When Needed: How to Efficiently Use System Resources in Control and Estimation Over Wireless Networks", "book_title": "46th IEEE Conference on Decision and Control", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Johansson", "given_name": "Karl Henrik", "clpid": "Johansson-K-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "New control paradigms are needed for large networks\nof wireless sensors and actuators in order to efficiently\nutilize system resources. In this paper we consider when\nfeedback control loops are formed locally to detect, monitor, and counteract disturbances that hit a plant at random instances in time and space. A sensor node that detects a disturbance dynamically forms a local multi-hop tree of sensors and fuse the data into a state estimate. It is shown that the optimal estimator over a sensor tree is given by a Kalman filter of certain structure. The tree is optimized such that the overall transmission energy is minimized but guarantees a specified level of estimation accuracy. A sensor network reconfiguration algorithm is presented that leads to a suboptimal solution and has low computational complexity. A linear control law based\non the state estimate is applied and it is argued that it leads to a closed-loop control system that minimizes a quadratic cost function. The sensor network reconfiguration and the feedback control law are illustrated on an example.", "doi": "10.1109/CDC.2007.4434979", "isbn": "978-1-4244-1497-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-12", "pages": "5478-5485" }, { "id": "authors:z8pcw-2xs29", "collection": "authors", "collection_id": "z8pcw-2xs29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100820-081349938", "type": "book_section", "title": "Safety verification of a fault tolerant reconfigurable autonomous goal-based robotic control system", "book_title": "2007 IEEE/RSJ International Conference on Intelligent Robots and Systems", "author": [ { "family_name": "Braman", "given_name": "Julia M. B.", "clpid": "Braman-J-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Wagner", "given_name": "David A.", "clpid": "Wagner-D-A" } ], "abstract": "Fault tolerance and safety verification of control\nsystems are essential for the success of autonomous robotic\nsystems. A control architecture called Mission Data System\n(MDS), developed at the Jet Propulsion Laboratory, takes\na goal-based control approach. In this paper, a method for\nconverting goal network control programs into linear hybrid\nsystems is developed. The linear hybrid system can then be\nverified for safety in the presence of failures using existing\nsymbolic model checkers. An example task is simulated in\nMDS and successfully verified using HyTech, a symbolic model\nchecking software for linear hybrid systems.", "doi": "10.1109/IROS.2007.4399230", "isbn": "978-1-4244-0911-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-11", "pages": "859-864" }, { "id": "authors:wm81w-wgx51", "collection": "authors", "collection_id": "wm81w-wgx51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101105-135833649", "type": "book_section", "title": "Effective Sensor Scheduling Schemes in a Sensor Network by\n Employing Feedback in the Communication Loop", "book_title": "2007 IEEE International Conference on Control Applications", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Sinopoli", "given_name": "Bruno", "clpid": "Sinopoli-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider a state estimation problem over a bandwidth limited network. A sensor network consisting of N sensors is used to observe the states of M plants, but only p \u2264 N sensors can transmit their measurements to a centralized estimator at each time. Therefore a suitable scheme that schedules the proper sensors to access the network at each time so that the total estimation error is minimized is required. We propose four different sensor scheduling schemes. The static and stochastic schemes assume no feedback from the estimator to the scheduler, while the two dynamic schemes, Maximum Error First (MEF) and Maximum Deduction First (MDF) assume such feedback is available. We compare the four schemes via some examples and show MEF and MDF schemes perform better than the static and stochastic schemes, which demonstrates that feedback can play an important role in this remote state estimation problem. We also show that MDF performs better than MEF as MDF considers the total estimation error while MEF considers the individual estimation error.", "doi": "10.1109/CCA.2007.4389365", "isbn": "978-1-4244-0440-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-10", "pages": "1006-1011" }, { "id": "authors:35g6h-68711", "collection": "authors", "collection_id": "35g6h-68711", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101015-111038468", "type": "book_section", "title": "Kalman Filtering with Uncertain Process and Measurement Noise\n Covariances with Application to State Estimation in Sensor Networks", "book_title": "2007 IEEE International Conference on Control Applications", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Johansson", "given_name": "Karl Henrik", "clpid": "Johansson-K-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Distributed state estimation under uncertain process\nand measurement noise covariances is considered. An\nalgorithm based on sensor fusion using Kalman filtering is\ninvestigated. It is shown that if the covariances are decomposed into a known nominal covariance plus an uncertainty term, then the uncertainty of the actual estimation error covariance for the Kalman filter grows linearly with the size of the uncertainty term. This result is extended to the sensor fusion scheme to give an upper bound on the actual error covariance for the fused state estimate. Examples are provided to illustrate how the theory can be applied in practice.", "doi": "10.1109/CCA.2007.4389369", "isbn": "978-1-4244-0440-7", "publisher": "IEEE", "publication_date": "2007-10", "pages": "1031-1036" }, { "id": "authors:qsj9z-k9q65", "collection": "authors", "collection_id": "qsj9z-k9q65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101019-100253770", "type": "article", "title": "Recent Research in Cooperative Control of Multivehicle Systems", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents a survey of recent research in cooperative control of multivehicle systems, using a common mathematical framework to allow different methods to be described in a unified way. The survey has three primary parts: an overview of current applications of cooperative control, a summary of some of the key technical approaches that have been explored, and a description of some possible future directions for research. Specific technical areas that are discussed include formation control, cooperative tasking, spatiotemporal planning, and consensus.", "doi": "10.1115/1.2766721", "issn": "0022-0434", "publisher": "American Society of Mechanical Engineers", "publication": "Journal of Dynamic Systems, Measurement, and Control", "publication_date": "2007-09", "series_number": "5", "volume": "129", "issue": "5", "pages": "571-583" }, { "id": "authors:yk813-ckb60", "collection": "authors", "collection_id": "yk813-ckb60", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2007.001", "type": "monograph", "title": "Conversion and verification procedure for goal-based control programs", "author": [ { "family_name": "Braman", "given_name": "J. M. B.", "clpid": "Braman-J-M-B" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Fault tolerance and safety verification of control systems are essential for the success of autonomous robotic systems. A control architecture called Mission Data System, developed at the Jet Propulsion Laboratory, takes a goal-based control approach. In this paper, a method for converting goal network control programs into linear hybrid systems is developed. The linear hybrid system can then be verified for safety in the presence of failures using existing symbolic model checkers. An example task is developed and successfully verified using HyTech, a symbolic model checking software for linear hybrid systems.", "publisher": "California Institute of Technology", "publication_date": "2007-08-17" }, { "id": "authors:a7h63-n0272", "collection": "authors", "collection_id": "a7h63-n0272", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DANacc07", "type": "book_section", "title": "Estimation over Communication Networks: Performance Bounds and Achievability Results", "book_title": "American Control Conference (ACC 2007), New York, NY, 11-13 July 2007", "author": [ { "family_name": "Dana", "given_name": "A. F.", "clpid": "Dana-A-F" }, { "family_name": "Gupta", "given_name": "V.", "clpid": "Gupta-V" }, { "family_name": "Hespanha", "given_name": "J. P.", "clpid": "Hespanha-J-P" }, { "family_name": "Hassibi", "given_name": "B.", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper considers the problem of estimation over communication networks. Suppose a sensor is taking measurements of a dynamic process. However the process needs to be estimated at a remote location connected to the sensor through a network of communication links that drop packets stochastically. We provide a framework for computing the optimal performance in the sense of expected error covariance. Using this framework we characterize the dependency of the performance on the topology of the network and the packet dropping process. For independent and memoryless packet dropping processes we find the steady-state error for some classes of networks and obtain lower and upper bounds for the performance of a general network. Finally we find a necessary and sufficient condition for the stability of the estimate error covariance for general networks with spatially correlated and Markov type dropping process. This interesting condition has a max-cut interpretation.", "doi": "10.1109/ACC.2007.4282933", "isbn": "1-4244-0989-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-07-30", "pages": "3450-3455" }, { "id": "authors:pj8aj-92n12", "collection": "authors", "collection_id": "pj8aj-92n12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100506-100128102", "type": "book_section", "title": "Biologically Inspired Feedback Design for Drosophila Flight", "book_title": "American Control Conference, 2007. ACC '07", "author": [ { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Waydo", "given_name": "Stephen", "clpid": "Waydo-S" }, { "family_name": "Fuller", "given_name": "Sawyer B.", "clpid": "Fuller-S-B" }, { "family_name": "Dickson", "given_name": "Will", "clpid": "Dickson-W" }, { "family_name": "Straw", "given_name": "Andrew D.", "orcid": "0000-0001-8381-0858", "clpid": "Straw-A-D" }, { "family_name": "Dickinson", "given_name": "Michael H.", "orcid": "0000-0002-8587-9936", "clpid": "Dickinson-M-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We use a biologically motivated model of the Drosophila's flight mechanics and sensor processing to design a feedback control scheme to regulate forward flight. The model used for insect flight is the grand unified fly (GUF) [3] simulation consisting of rigid body kinematics, aerodynamic forces and moments, sensory systems, and a 3D environment model. We seek to design a control algorithm that will convert the sensory signals into proper wing beat commands to regulate forward flight. Modulating the wing beat frequency and mean stroke angle produces changes in the flight envelope. The sensory signals consist of estimates of rotational velocity from the haltere organs and translational velocity estimates from visual elementary motion detectors (EMD's) and matched retinal velocity filters. The controller is designed based on a longitudinal model of the flight dynamics. Feedforward commands are generated based on a desired forward velocity. The dynamics are linearized around this operating point and a feedback controller designed to correct deviations from the operating point. The control algorithm is implemented in the GUF simulator and achieves the desired tracking of the forward reference velocities and exhibits biologically realistic responses.", "doi": "10.1109/ACC.2007.4282971", "isbn": "1-4244-0988-8", "publisher": "IEEE", "place_of_publication": "New York, NY", "publication_date": "2007-07", "pages": "3395-3401" }, { "id": "authors:n7m3j-ya748", "collection": "authors", "collection_id": "n7m3j-ya748", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101015-111128782", "type": "book_section", "title": "Frequency-Weighted Model Reduction with Applications to Structured Models", "book_title": "American Control Conference 2007", "author": [ { "family_name": "Sandberg", "given_name": "Henrik", "clpid": "Sandberg-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, a frequency-weighted extension of a\nrecently proposed model reduction method for linear systems\nis presented. The method uses convex optimization and can be\nused both with sample data and exact models. We also obtain\nbounds on the frequency-weighted error. The method is combined\nwith a rank-minimization heuristic to approximate multiinput\u2013\nmulti-output systems.We also present two applications\u2014\nenvironment compensation and simplification of interconnected\nmodels \u2014 where we argue the proposed methods are useful.", "doi": "10.1109/ACC.2007.4282746", "isbn": "978-1-4244-0988-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-07", "pages": "941-946" }, { "id": "authors:b9qam-5mp43", "collection": "authors", "collection_id": "b9qam-5mp43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100827-104901767", "type": "book_section", "title": "A Multi-Model Approach to Identification of Biosynthetic Pathways", "book_title": "American Control Conference, 2007. ACC '07", "author": [ { "family_name": "Dunlop", "given_name": "Mary J.", "clpid": "Dunlop-M-J" }, { "family_name": "Franco", "given_name": "Elisa", "orcid": "0000-0003-1103-2668", "clpid": "Franco-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present an identification framework for biochemical systems that allows multiple candidate models to be compared. This framework is designed to select a model that fits the data while maintaining model simplicity. The model identification task is divided into a parameter estimation stage and a model comparison stage. Model selection is based on calculating Akaike's information criterion, which is a systematic method for determining the model that best represents a set of experimental data. Two case studies are presented: a simulated transcriptional control circuit and a system of oscillators that has been built and characterized in vitro. In both examples the multi-model framework is able to discriminate between model candidates to select the one that best describes the data.", "doi": "10.1109/ACC.2007.4282720", "isbn": "1-4244-0988-8", "publisher": "IEEE", "place_of_publication": "New York, NY", "publication_date": "2007-07", "pages": "1600-1605" }, { "id": "authors:xf23x-sq947", "collection": "authors", "collection_id": "xf23x-sq947", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150331-142947811", "type": "book_section", "title": "Control Over a Network: Using Actuation Buffers to Reduce Transmission Frequency", "book_title": "2007 European Control Conference (ECC)", "author": [ { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-Ling" }, { "family_name": "Di Cairano", "given_name": "Stefano", "clpid": "Di-Cairano-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider a discrete time linear feedback control system with additive noise where the control signals are sent across a network from the controller to the actuators. Due to network considerations it is desired to reduce the transmission frequency of the control signals. We show that by including a finite sequence of predicted control signals in each communication packet the frequency of transmission can be reduced by transmitting only when the previously sent sequence has run out, although as a consequence the closed loop error will increase. We introduce a communication protocol, which we call Input Difference Transmission Scheme (IDTS), that transmits control packets when the difference between newly computed control values and the predicted control sequence previously transmitted is larger than a certain threshold. This threshold is a design parameter and we show how the closed loop behavior varies with this threshold. Simulation results are provided to augment the theory.", "doi": "10.23919/ECC.2007.7068661", "isbn": "978-3-9524173-8-6", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-07", "pages": "597-602" }, { "id": "authors:d1jhb-br618", "collection": "authors", "collection_id": "d1jhb-br618", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170427-143640907", "type": "book_section", "title": "Estimation for Nonlinear Dynamical Systems over Packet-Dropping Networks", "book_title": "2007 American Control Conference", "author": [ { "family_name": "Jin", "given_name": "Zhipu", "clpid": "Jin-Zhipu" }, { "family_name": "Ko", "given_name": "Chih-Kai", "clpid": "Ko-Chih-Kai" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Two approaches, extended Kalman filter (EKF) and moving horizon estimation (MHE), are discussed for state estimation for nonlinear dynamical systems over packet-dropping networks. For EKF, we provide sufficient conditions that guarantee a bounded EKF error covariance. For MHE, a natural scheme on organizing the finite horizon window is proposed to handle intermittent observations. A nonlinear programming software package, SNOPT, is employed in MHE and the formulation for constraints is discussed in detail. Examples and simulation results are presented.", "doi": "10.1109/ACC.2007.4283063", "isbn": "1-4244-0988-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-07", "pages": "5037-5042" }, { "id": "authors:zfrny-1v790", "collection": "authors", "collection_id": "zfrny-1v790", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170426-174355371", "type": "book_section", "title": "To Drop or Not to Drop: Receiver Design Principles for Estimation over Wireless Links", "book_title": "2007 American Control Conference", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider estimation of a multiple-input multiple-output dynamical system over a wireless fading communication channel using a Kalman filter. We are interested in finding the optimum receiver design in terms of handing noisy samples. We reformulate the estimation problem to include the impact of stochastic communication noise in the noisy packets. We will show how the eigenvalues of the state transition matrix A affect the optimum receiver design. We prove that, in the absence of a cross-layer information path, packet drop should be designed to balance information loss and communication noise in order to optimize the performance. In the presence of a cross-layer path, we show that keeping all the packets will minimize the average estimation error covariance. We also derive the stability condition in the presence of noisy packets and prove that it is independent of the shape of the communication noise variance or availability of a cross-layer information path.", "doi": "10.1109/ACC.2007.4282593", "isbn": "1-4244-0988-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-07", "pages": "2762-2768" }, { "id": "authors:0x9gc-13w17", "collection": "authors", "collection_id": "0x9gc-13w17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAYieeetcst07", "type": "article", "title": "UAV as a Reliable Wingman: A Flight Demonstration", "author": [ { "family_name": "Waydo", "given_name": "S.", "clpid": "Waydo-S" }, { "family_name": "Hauser", "given_name": "J.", "clpid": "Hauser-J" }, { "family_name": "Bailey", "given_name": "R.", "clpid": "Bailey-R" }, { "family_name": "Klavins", "given_name": "E.", "clpid": "Klavins-E" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this brief, we present the results from a flight experiment demonstrating two significant advances in software enabled control: optimization-based control using real-time trajectory generation and logical programming environments for formal analysis of control software. Our demonstration platform consisted of a human-piloted F-15 jet flying together with an autonomous T-33 jet. We describe the behavior of the system in two scenarios. In the first, nominal state communications were present and the autonomous aircraft maintained formation as the human pilot flew maneuvers. In the second, we imposed the loss of high-rate communications and demonstrated an autonomous safe \"lost wingman\" procedure to increase separation and reacquire contact. The flight demonstration included both a nominal formation flight component and an execution of the lost wingman scenario.", "doi": "10.1109/TCST.2007.899172", "issn": "1063-6536", "publisher": "IEEE Transactions on Control Systems Technology", "publication": "IEEE Transactions on Control Systems Technology", "publication_date": "2007-07", "series_number": "4", "volume": "15", "issue": "4", "pages": "680-688" }, { "id": "authors:zdsv6-qc182", "collection": "authors", "collection_id": "zdsv6-qc182", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170420-134616638", "type": "book_section", "title": "Analysis of a Digital Clock for Molecular Computing", "book_title": "2007 American Control Conference", "author": [ { "family_name": "Ugander", "given_name": "Johan", "clpid": "Ugander-J" }, { "family_name": "Dunlop", "given_name": "Mary J.", "clpid": "Dunlop-M-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The control of synthetic genetic regulatory networks is an emerging engineering challenge. In this study, we propose a new synthetic genetic network that behaves as a digital clock, producing square waveform oscillations. We analyze two models of the network: a deterministic model based on Michaelis-Menten kinetics, as well as a stochastic model based on the Gillespie algorithm. Both models predict regions of oscillatory behavior; the deterministic model provides insight into the conditions required to produce the oscillating clock-like behavior, while the stochastic model is truer to natural dynamics. Intracellular stochasticity is seen to contribute phase noise to the oscillator, and we propose improvements for the network and discuss the conceptual foundations of these improvements.", "doi": "10.1109/ACC.2007.4282583", "isbn": "1-4244-0988-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2007-07", "pages": "1595-1599" }, { "id": "authors:90y8e-k4732", "collection": "authors", "collection_id": "90y8e-k4732", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MEHieeeacmtn07", "type": "article", "title": "Asynchronous Distributed Averaging on Communication Networks", "author": [ { "family_name": "Mehyar", "given_name": "Mortada", "clpid": "Mehyar-M" }, { "family_name": "Spanos", "given_name": "Demetri", "clpid": "Spanos-D-P" }, { "family_name": "Pongsajapan", "given_name": "John", "clpid": "Pongsajapan-J" }, { "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" } ], "abstract": "Distributed algorithms for averaging have attracted interest in the control and sensing literature. However, previous works have not addressed some practical concerns that will arise in actual implementations on packet-switched communication networks such as the Internet. In this paper, we present several implementable algorithms that are robust to asynchronism and dynamic topology changes. The algorithms are completely distributed and do not require any global coordination. In addition, they can be proven to converge under very general asynchronous timing assumptions. Our results are verified by both simulation and experiments on Planetlab, a real-world TCP/IP network. We also present some extensions that are likely to be useful in applications.", "doi": "10.1109/TNET.2007.893226", "issn": "1063-6692", "publisher": "IEEE/ACM Transactions on Networking", "publication": "IEEE/ACM Transactions on Networking", "publication_date": "2007-06", "series_number": "3", "volume": "15", "issue": "3", "pages": "512-520" }, { "id": "authors:dyha8-v6k82", "collection": "authors", "collection_id": "dyha8-v6k82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150205-075834386", "type": "article", "title": "Optimal LQG control across packet-dropping links", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We examine two special cases of the problem of optimal linear quadratic Gaussian control of a system whose state is being measured by sensors that communicate with the controller over packet-dropping links. We pose the problem as an information transmission problem. Using a separation principle, we decompose the problem into a standard LQR state-feedback controller design, along with an optimal encoder\u2013decoder design for propagating and using the information across the unreliable links. Our design is optimal among all causal algorithms for any arbitrary packet-drop pattern. Further, the solution is appealing from a practical point of view because it can be implemented as a small modification of an existing LQG control design.", "doi": "10.1016/j.sysconle.2006.11.003", "issn": "0167-6911", "publisher": "Elsevier", "publication": "Systems & Control Letters", "publication_date": "2007-06", "series_number": "6", "volume": "56", "issue": "6", "pages": "439-446" }, { "id": "authors:yte6k-tjg27", "collection": "authors", "collection_id": "yte6k-tjg27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200429-082712784", "type": "book_section", "title": "Verification Procedure for Generalized Goal-based Control Programs", "book_title": "AIAA Infotech@Aerospace 2007 Conference and Exhibit", "author": [ { "family_name": "Braman", "given_name": "Julia M. B.", "clpid": "Braman-J-M-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Ingham", "given_name": "Michel D.", "clpid": "Ingham-M-D" } ], "abstract": "Safety verification of fault-tolerant control systems is essential for the success of autonomous robotic systems. A control architecture called Mission Data System, developed at the Jet Propulsion Laboratory, takes a goal-based control approach. In this paper, the development of a method for converting a goal network control program into a hybrid system is given and a process for converting logic associated with the goal network into transition conditions for the hybrid automata is developed. The resulting hybrid system can then be verified for safety in the presence or failures using existing symbolic model checkers. An example task and goal network is designed, converted to hybrid automata, and verified using symbolic model checking software for hybrid systems.", "doi": "10.2514/6.2007-3010", "isbn": "978-1-62410-017-8", "publisher": "American Institute of Aeronautics and Astronautics", "place_of_publication": "Reston, VA", "publication_date": "2007-05-07", "pages": "Art. No. 2007-3010" }, { "id": "authors:2tygx-7h647", "collection": "authors", "collection_id": "2tygx-7h647", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170516-160431062", "type": "book_section", "title": "On the robustness of distributed algorithms", "book_title": "Proceedings of the 45th IEEE Conference on Decision and Control", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Langbort", "given_name": "Cedric", "clpid": "Langbort-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In recent years, numerous distributed algorithms have been proposed which, when executed by a team of dynamic agents, result in the completion of a joint task. However, for any such algorithm to be practical, one should be able to guarantee that the task is still satisfactorily executed even when agents fail to communicate with others or to perform their designated actions correctly. In this paper, we present a concept of robustness which is well-suited for general distributed algorithms for teams of dynamic agents. Our definition extends a similar notion introduced in the distributed computation literature for consensus problems. We illustrate the definition by considering a variety of algorithms.", "doi": "10.1109/CDC.2006.377451", "isbn": "1-4244-0171-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006-12", "pages": "3473-3478" }, { "id": "authors:sserq-1s660", "collection": "authors", "collection_id": "sserq-1s660", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170516-165501295", "type": "book_section", "title": "Distributed Sensing and Estimation Under Communication Constraints", "book_title": "Proceedings of the 45th IEEE Conference on Decision and Control", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider the impact of imperfect communication links on distributed sensing and estimation in mobile networks. First we find optimum sensing regions and sensor positions under communication constraints. We show that the optimum sensor configuration consists of overlapping sensing regions. We then show how the nodes can achieve the optimum configuration in a distributed manner.", "doi": "10.1109/CDC.2006.376939", "isbn": "1-4244-0171-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006-12", "pages": "1013-1018" }, { "id": "authors:a1wc3-sxr36", "collection": "authors", "collection_id": "a1wc3-sxr36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170516-161356985", "type": "book_section", "title": "On Sensor Coverage by Mobile Sensors", "book_title": "Proceedings of the 45th IEEE Conference on Decision and Control", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Jeffcoat", "given_name": "David E.", "clpid": "Jeffcoat-D-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We study the problem of using a small number of mobile sensors to monitor various threats in a geographical area. Using some recent results on stochastic sensor scheduling, we propose a stochastic sensor movement strategy. We present simple conditions under which it is not possible to maintain a bounded estimate error covariance for all the threats. We also study a simple sub-optimal algorithm to generate stochastic trajectories. Simulations are presented to illustrate the results.", "doi": "10.1109/CDC.2006.377220", "isbn": "1-4244-0171-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006-12", "pages": "5912-5917" }, { "id": "authors:vwspg-f5d57", "collection": "authors", "collection_id": "vwspg-f5d57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GUPacc06", "type": "book_section", "title": "On the effect of quantization on performance at high rates", "book_title": "American Control Conference (ACC 2006), Minneapolis, MN, 14-16 June 2006", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Dana", "given_name": "Amir F.", "clpid": "Dana-A-F" }, { "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" } ], "abstract": "We study the effect of quantization on the performance of a scalar dynamical system in the high rate regime. We evaluate the LQ cost for two commonly used quantizers: uniform and logarithmic and provide a lower bound on performance of any centroid-based quantizer based on entropy arguments. We also consider the case when the channel drops data packets stochastically.", "doi": "10.1109/ACC.2006.1656407", "isbn": "1-4244-0210-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006-07-24", "pages": "1364-1369" }, { "id": "authors:pkjv2-c9k76", "collection": "authors", "collection_id": "pkjv2-c9k76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110209-135047997", "type": "book_section", "title": "Model-based estimation of off-highway road geometry using single-axis LADAR and inertial sensing", "book_title": "Proceedings 2006 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Cremean", "given_name": "Lars B.", "clpid": "Cremean-L-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper applies some previously studied extended\nKalman filter techniques for planar road geometry estimation\nto the domain of autonomous navigation of off-highway\nvehicles. In this work, a clothoid model of the road geometry is\nconstructed and estimated recursively based on road features\nextracted from single-axis LADAR range measurements. We\npresent a method for feature extraction of the road centerline\nin the image plane, and describe its application to recursive\nestimation of the road geometry. We analyze the performance of\nour method against simulated motion of varied road geometries\nand against closed-loop detection, tracking and following of\ndesert roads. Our method accomodates full 6 DOF motion of\nthe vehicle as it navigates, constructs consistent estimates of the\nroad geometry with respect to a fixed global reference frame,\nand requires an estimate of the sensor pose for each range\nmeasurement.", "doi": "10.1109/ROBOT.2006.1641945", "isbn": "0-7803-9505-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006-06-26", "pages": "1661-1666" }, { "id": "authors:w303c-z5n22", "collection": "authors", "collection_id": "w303c-z5n22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110203-083444872", "type": "book_section", "title": "A decentralized motion coordination strategy for dynamic target tracking", "book_title": "Proceedings 2006 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents a decentralized motion planning\nalgorithm for the distributed sensing of a noisy dynamical\nprocess by multiple cooperating mobile sensor agents. This\nproblem is motivated by localization and tracking tasks of\ndynamic targets. Our gradient-descent method is based on a\ncost function that measures the overall quality of sensing. We\nalso investigate the role of imperfect communication between\nsensor agents in this framework, and examine the trade-offs in\nperformance between sensing and communication. Simulations\nillustrate the basic characteristics of the algorithms.", "doi": "10.1109/ROBOT.2006.1642064", "isbn": "0-7803-9505-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006-05", "pages": "2416-2422" }, { "id": "authors:5j7kx-bdm52", "collection": "authors", "collection_id": "5j7kx-bdm52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110426-130530739", "type": "article", "title": "On a stochastic sensor selection algorithm with applications in sensor scheduling and sensor coverage", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this note we consider the following problem. Suppose a set of sensors is jointly trying to estimate a process. One sensor takes a measurement at every time step and the measurements are then exchanged among all the sensors. What is the sensor schedule that results in the minimum error covariance? We describe a stochastic sensor selection strategy that is easy to implement and is computationally tractable. The problem described above comes up in many domains out of which we discuss two. In the sensor selection problem, there are multiple sensors that cannot operate simultaneously (e.g., sonars in the same frequency band). Thus measurements need to be scheduled. In the sensor coverage problem, a geographical area needs to be covered by mobile sensors each with limited range. Thus from every position, the sensors obtain a different view-point of the area and the sensors need to optimize their trajectories. The algorithm is applied to these problems and illustrated through simple examples.", "doi": "10.1016/j.automatica.2005.09.016", "issn": "0005-1098", "publisher": "Elsevier", "publication": "Automatica", "publication_date": "2006-02", "series_number": "2", "volume": "42", "issue": "2", "pages": "251-260" }, { "id": "authors:cs1cy-78146", "collection": "authors", "collection_id": "cs1cy-78146", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:ROWjfm06", "type": "article", "title": "Linear models for control of cavity flow oscillations", "author": [ { "family_name": "Rowley", "given_name": "Clarence W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Williams", "given_name": "David R.", "clpid": "Williams-D-R" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "MacMynowski", "given_name": "Douglas G.", "orcid": "0000-0003-1987-9417", "clpid": "MacMartin-D-G" } ], "abstract": "Models for understanding and controlling oscillations in the flow past a rectangular cavity are developed. These models may be used to guide control designs, to understand performance limits of feedback, and to interpret experimental results. Traditionally, cavity oscillations are assumed to be self-sustained: no external disturbances are necessary to maintain the oscillations, and amplitudes are limited by nonlinearities. We present experimental data which suggests that in some regimes, the oscillations may not be self-sustained, but lightly damped: oscillations are sustained by external forcing, such as boundary-layer turbulence. In these regimes, linear models suffice to describe the behaviour, and the final amplitude of oscillations depends on the characteristics of the external disturbances. These linear models are particularly appropriate for describing cavities in which feedback has been used for noise suppression, as the oscillations are small and nonlinearities are less likely to be important. It is shown that increasing the gain too much in such feedback control experiments can lead to a peak-splitting phenomenon, which is explained by the linear models. Fundamental performance limits indicate that peak splitting is likely to occur for narrow-bandwidth actuators and controllers.", "doi": "10.1017/S0022112005007299", "issn": "0022-1120", "publisher": "Cambridge University Press", "publication": "Journal of Fluid Mechanics", "publication_date": "2006-01-25", "volume": "547", "pages": "317-330" }, { "id": "authors:ghj29-acz31", "collection": "authors", "collection_id": "ghj29-acz31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110707-134914811", "type": "book_section", "title": "Distributed Control over Failing Channels", "book_title": "Networked Embedded Sensing and Control", "author": [ { "family_name": "Langbort", "given_name": "C\u00e9dric", "clpid": "Langbort-C" }, { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Antsaklis", "given_name": "P. J.", "clpid": "Antsaklis-P-J" }, { "family_name": "Tabuada", "given_name": "P.", "clpid": "Tabuada-P" } ], "abstract": "We give sufficient convex conditions for the existence of a distributed controller, with the same interconnection structure as the plant, when the latter is composed of heterogeneous subsystems that communicate with their neighbors over packet-dropping channels. Our linear matrix inequalities generalize previous results for the case of ideal communication links and, although conservative, are typically far more tractable for large-scale systems than recently obtained sufficient and necessary conditions.", "doi": "10.1007/11533382_22", "isbn": "3-540-32794-0", "publisher": "Springer", "place_of_publication": "New York", "publication_date": "2006", "pages": "325-342" }, { "id": "authors:gf9ym-tbh42", "collection": "authors", "collection_id": "gf9ym-tbh42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110720-075738157", "type": "book_section", "title": "Optimum Allocation of Computing Resources in\n Networked Sensing and Control", "book_title": "Proceedings of the 2006 American Control Conference", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider task scheduling when\nsensing and controlling over a network with packet dropping\nlinks. We find optimum ways of allocating limited computing\nresources for estimation and control of a number of linear\ndynamical systems with different characteristics over communication\nlinks with different qualities. We find theoretical\nexpressions relating the optimum sampling rates of the dynamical\nsystems to the characteristics of the communication links\nand dynamics of the plants. We derive optimum ways of task\nscheduling for two performance metrics: decay rate and the\nasymptotic value. The work lays the theoretical foundations\nfor considering the impact of both limited computing and\ncommunication resources on estimation and control.", "doi": "10.1109/ACC.2006.1657261", "isbn": "1-4244-0209-3", "publisher": "IEEE", "place_of_publication": "New York", "publication_date": "2006", "pages": "3507-3512" }, { "id": "authors:82yvb-x8n64", "collection": "authors", "collection_id": "82yvb-x8n64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110629-092232291", "type": "book_section", "title": "Dynamic Sensor Coverage with Uncertainty Feedback : Analysis Using Iterated Maps", "book_title": "Proceedings of the 2006 American Control Conference", "author": [ { "family_name": "Tiwari", "given_name": "Abhishek", "clpid": "Tiwari-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents an analysis of the dynamic\nsensor coverage problem with uncertainty feedback. We consider a simple case of two spatially separate uncertain systems 1 and 2. In an earlier paper we introduced the dynamic sensor coverage problem and gave two stochastic sensor motion algorithms to solve the problem. We take a deterministic approach in this paper, the sensor decides to measure system 1 or 2 based on the relative uncertainty of its estimates of the states of the two systems. Error covariance is used as a metric\nfor uncertainty of estimates. Based on the sensor measurements\nthe error covariance evolves according to the Lyapunov or the\nRiccati map. The uncertainty space is partitioned and each\npartition has a different sensor motion decision associated with\nit. For a certain class of partitions we prove the existence\nand local stability of a unique periodic steady state orbit. We\nprove global stability for a scalar special case. We also show\nby way of an example that by changing certain parameters in\nthese partitions stable orbits of higher periods can be obtained.\nImplications of this work and comparisons with existing work\nin the sensor scheduling and sensor coverage literature are\nalso presented. In the end we present a discussion on future\nextensions of this work. Simulation examples are provided to\nillustrate the main concepts.", "doi": "10.1109/ACC.2006.1657671", "isbn": "1-4244-0209-3", "publisher": "IEEE", "place_of_publication": "New York, NY", "publication_date": "2006", "pages": "5929-5934" }, { "id": "authors:q5ffq-d8975", "collection": "authors", "collection_id": "q5ffq-d8975", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110720-090204055", "type": "book_section", "title": "Networked control systems with norm bounded uncertainties: a stability analysis", "book_title": "Proceedings of the 2006 American Control Conference", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider a robust networked\ncontrol problem. We consider linear unstable and uncertain\ndiscrete time plants with networks between the sensors and\ncontroller as well as the controller and plant. We investigate\ntwo defining characteristics of networked control systems and\nthe impact uncertainty has on these. Namely, the minimum data\nrates required for the two networks and the tolerable data drop\nout in the form of packet losses. We are able to derive sufficient\nconditions in terms of the minimum data rate and minimum\npacket arrival rate to ensure stability of the closed loop system.", "doi": "10.1109/ACC.2006.1656645", "isbn": "1-4244-0209-3", "publisher": "IEEE", "place_of_publication": "New York", "publication_date": "2006", "pages": "2783-2788" }, { "id": "authors:r3yjh-1jq87", "collection": "authors", "collection_id": "r3yjh-1jq87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-093845327", "type": "book_section", "title": "Towards a Packet-based Control Theory - Part II: Rate Issues", "book_title": "2006 American Control Conference", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Following our first paper of stabilizing a Linear\nTime Invariant (LTI) system in a packet-based network, which\nappeared in ACC 05, this paper further studies various rate\nissues associated with networked control systems. Specifically, networks with finite bandwidth and packet drops and systems with finite control inputs are studied in detail. Similar to what we did in the previous paper, we assume that the state information is transmitted to the controller over a packet-based network. We also assume that there is a perfect link from the controller to the plant. However, we change the notion of the system being asymptotically stable to almost sure stable which is in a probabilistic framework. This is because packet drops by the network introduce unavoidable randomness. With\nthe notion of almost sure stability, various rate results under different settings are given. Examples and simulations are provided to demonstrate the results.", "doi": "10.1109/ACC.2006.1657257", "isbn": "1-4244-0209-3", "publisher": "IEEE", "place_of_publication": "New York, NY", "publication_date": "2006", "pages": "3482-3487" }, { "id": "authors:ty67t-0pv17", "collection": "authors", "collection_id": "ty67t-0pv17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110203-112414637", "type": "book_section", "title": "An Estimation Algorithm for a Class of Networked Control Systems Using UDP-Like Communication Schemes", "book_title": "Proceedings of the 45th IEEE Conference on Decision and Control", "author": [ { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this work we consider a class of networked control systems (NCS) when the control signal is sent to the plant via a UDP-like communication protocol. In this case the controller sends a communication packet to the plant across a lossy network, but the controller does not receive any acknowledgement signal indicating the status of the control packet. Standard observer based estimators assume the estimator has knowledge of what control signal is applied to the plant. Under the UDP-like protocol the controller/estimator does not have explicit knowledge whether the control signals have been applied to the plant or not. We present a simple estimation and control algorithm that consists of a state and mode observer as well as a constraint on the control signal sent to the plant. For the class of systems considered, discrete time LTI plants where at least one of the states that is directly affected by the input is also part of the measurement vector, the estimator is able to recover the fate of the control packet from the measurement at the next timestep and exhibit better performance than other naive schemes. For single-input-single-output (SISO) systems we are able to show convergence properties of the estimation error and closed loop stability. Simulations are provided to demonstrate the algorithm and show its effectiveness.", "doi": "10.1109/CDC.2006.377481", "isbn": "978-1-4244-0170-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006", "pages": "5597-5603" }, { "id": "authors:vbcph-3a988", "collection": "authors", "collection_id": "vbcph-3a988", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110225-084451186", "type": "book_section", "title": "Multi-Hop Relay Protocols for Fast Consensus Seeking", "book_title": "Proceedings of the 45th IEEE Conference on Decision and Control", "author": [ { "family_name": "Jin", "given_name": "Zhipu", "clpid": "Jin-Z" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Consensus protocols are distributed algorithms in\nnetworked multi-agent systems. Based on the local information,\nagents automatically converge to a common consensus state\nand the convergence speed is determined by the algebraic\nconnectivity of the communication network. In order to achieve\na fast consensus seeking, we propose the multi-hop relay\nprotocols, where each agent can expand its knowledge by\nemploying multi-hop paths in the network.We demonstrate that\nmulti-hop relay protocols can enlarge the algebraic connectivity\nwithout physically changing the network topology. Moreover,\ncommunication delays are discussed and a tradeoff is identified\nbetween the convergence speed and the time delay sensitivity.", "doi": "10.1109/CDC.2006.377298", "isbn": "1-4244-0171-2", "publisher": "IEEE", "place_of_publication": "Piscataway, N.J.", "publication_date": "2006", "pages": "1001-1006" }, { "id": "authors:vjdfm-ztk86", "collection": "authors", "collection_id": "vjdfm-ztk86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110615-112206500", "type": "book_section", "title": "The Effect of Sensor Health on State Estimation", "book_title": "Proceedings of the 45th IEEE Conference on Decision and Control", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider the problem of state\nestimation using the standard Kalman filter recursions which\ntakes account of the available sensor health information. Given\na stochastic description of the sensor health, we are able\nto show that the expected error covariance converges to a\nunique value for all initial values, while the available previous\nwork only showed the upper bound of the expected error\ncovariance converges. Our approach provides both theoretical\nvalue to the analysis as well as the potential to get tighter\nupper bound. Our results provide a criterion of evaluating\nthe sensor measurement. In the multisensor fusion problem,\ndepending on the system error tolerance levels, it can then be\ndetermined whether to fuse a particular sensor measurement\nor not. Examples and simulations are provided to assist the\ntheory.", "doi": "10.1109/CDC.2006.377482", "isbn": "978-1-4244-0170-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2006", "pages": "3315-3320" }, { "id": "authors:3kcrp-ge931", "collection": "authors", "collection_id": "3kcrp-ge931", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110822-085321885", "type": "book_section", "title": "Receiver Design Principles for Estimation over Fading Channels", "book_title": "2005 44th IEEE Conference on Decision and Control & European Control Conference", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we consider estimation of dynamical\nsystems over wireless communication channels. We show\nthat the communication protocols suitable for non real-time\napplications like data networks may not be entirely applicable for estimation and control of a rapidly changing dynamical system. We then develop new design paradigms for these applications to show how noisy packets should be handled in the receiver. We prove that, in the presence of a crosslayer feedback, keeping all the packets will both maximize the stability range and minimize the estimation error variance. In the absence of such a feedback, we show that keeping all the packets still maximizes the stability range, independent of the shape of the communication noise profile. In order to optimize the performance, in the absence of a cross-layer feedback, we prove that packet drop should be designed to balance information loss and communication noise.", "doi": "10.1109/CDC.2005.1582199", "isbn": "0-7803-9567-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-12", "pages": "464-469" }, { "id": "authors:nz65n-12k40", "collection": "authors", "collection_id": "nz65n-12k40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110818-111717130", "type": "book_section", "title": "State estimation utilizing multiple description coding over lossy networks", "book_title": "2005 44th IEEE Conference on Decision and Control & European Control Conference", "author": [ { "family_name": "Jin", "given_name": "Zhipu", "clpid": "Jin-Zhipu" }, { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "For state estimation in networked control systems,\nthe impact of packet dropping over network links is an important problem. In this paper, we introduce multiple description (MD) source coding scheme to improve the statistical stability and performance of the estimation error covariance of Kalman filter with packet loss. We consider about two cases: when the packet loss over network links occurs in an i.i.d. fashion or in a bursty fashion. Compared with the traditional single description source coding, MD coding scheme can greatly improve the\nperformance of Kalman filter over a large set of packet loss\nscenarios in both cases.", "doi": "10.1109/CDC.2005.1582267", "isbn": "0-7803-9567-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-12", "pages": "872-878" }, { "id": "authors:r1c0j-4yr78", "collection": "authors", "collection_id": "r1c0j-4yr78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-155010781", "type": "book_section", "title": "A Control-Oriented Analysis of Bio-inspired Visuomotor Convergence", "book_title": "44th IEEE Conference on Decision and Control", "author": [ { "family_name": "Humbert", "given_name": "J. Sean", "clpid": "Humbert-J-S" }, { "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" } ], "abstract": "Insects exhibit incredibly robust closed loop fight dynamics in the face of uncertainties. A fundamental principle contributing to this unparalleled behavior is rapid processing and convergence of visual sensory information to fight motor commands via spatial wide-field integration, accomplished by retinal motion pattern sensitive interneurons (LPTCs) in the lobula plate portion of the visual ganglia. With in a control- theoretic frame work, models for spatially continuous retinal image flow and wide-field integration processing are developed, establishing the connection between image flow kernels (retinal motion pattern sensitivities) and the feedback terms they represent. It is shown that these out puts are sufficient to stabilize speed regulation and terrain following tasks. 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 fight control applications.", "doi": "10.1109/CDC.2005.1582162", "isbn": "0-7803-9567-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-12", "pages": "245-250" }, { "id": "authors:5hdpq-54347", "collection": "authors", "collection_id": "5hdpq-54347", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110817-110410615", "type": "book_section", "title": "On Sensor Fusion in the Presence of Packet-dropping Communication Channels", "book_title": "2005 44th IEEE Conference on Decision and Control & European Control Conference", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we look at the problem of multisensor data fusion when data is being communicated over channels that drop packets randomly. We are motivated by the use of wireless links for communication among nodes in upcoming sensor networks. We wish to identify the information that should be communicated by each node to others given that some of the information it had transmitted earlier might have been lost. We solve the problem exactly for the case of two sensors and study the performance of the algorithm when more sensors are present. For the two-sensor case, the performance of our algorithm is optimal in the sense that if a packet is received from the other sensor, it is equivalent to receiving all previous measurements, irrespective of the packet drop pattern.", "doi": "10.1109/CDC.2005.1582712", "isbn": "0-7803-9567-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-12", "pages": "3547-3552" }, { "id": "authors:4yh97-6b303", "collection": "authors", "collection_id": "4yh97-6b303", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170517-164222886", "type": "book_section", "title": "Distributed Averaging on Asynchronous Communication Networks", "book_title": "Proceedings of the 44th IEEE Conference on Decision and Control", "author": [ { "family_name": "Mehyar", "given_name": "Mortada", "clpid": "Mehyar-M" }, { "family_name": "Spanos", "given_name": "Demetri", "clpid": "Spanos-D-P" }, { "family_name": "Pongsajapan", "given_name": "John", "clpid": "Pongsajapan-J" }, { "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" } ], "abstract": "Distributed algorithms for averaging have attracted interest in the control and sensing literature. However, previous works have not addressed some practical concerns that will arise in actual implementations on packet-switched communication networks such as the Internet. In this paper, we present several implementable algorithms that are robust to asynchronism and dynamic topology changes. The algorithms do not require global coordination and can be proven to converge under very general asynchronous timing assumptions. Our results are verified by both simulation and experiments on a real-world TCP/IP network.", "doi": "10.1109/CDC.2005.1583363", "isbn": "0-7803-9567-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-12", "pages": "7446-7451" }, { "id": "authors:wp4p6-drp43", "collection": "authors", "collection_id": "wp4p6-drp43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110825-140024412", "type": "book_section", "title": "Estimation with Information Loss: Asymptotic Analysis and Error Bounds", "book_title": "2005 44th IEEE Conference on Decision and Control & European Control Conference", "author": [ { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Tiwari", "given_name": "Abhishek", "clpid": "Tiwari-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider a discrete time state estimation problem over a packet-based network. In each discrete time step, the measurement is sent to a Kalman filter with some probability that it is received or dropped. Previous pioneering work on Kalman filtering with intermittent observation losses shows that there exists a certain threshold of the packet dropping rate below which the estimator is stable in the expected sense. That work assumes that packets are dropped independently between all time steps. However we give a completely different point of view. On the one hand, it is not required that the packets are dropped independently but just that the information gain \u03c0_g, defined to be the limit of the ratio of the number of received packets n during N time steps as N goes to infinity, exists. On the other hand, we show that for any given \u03c0g, as long as \u03c0_g> 0, the estimator is stable almost surely, i.e. for any given \u03b5 > 0, the error covariance matrix P_k is bounded by a finite matrix M, with probability 1 -\u03b5. We also give explicit formula for the relationship between M and \u03b5. We consider the case where the observation matrix is invertible.", "doi": "10.1109/CDC.2005.1582324", "isbn": "0-7803-9567-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-12", "pages": "1215-1221" }, { "id": "authors:s13fp-hdz90", "collection": "authors", "collection_id": "s13fp-hdz90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130703-133331635", "type": "book_section", "title": "Estimation of linear stochastic systems over a queueing network", "book_title": "2005 Systems Communications, Proceedings", "author": [ { "family_name": "Epstein", "given_name": "Michael", "clpid": "Epstein-M" }, { "family_name": "Tiwari", "given_name": "Abhishek", "clpid": "Tiwari-A" }, { "family_name": "Shi", "given_name": "Ling", "clpid": "Shi-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider the standard state estimation problem over a congested packet-based network. The network is modeled as a queue with a single server processing the packets. This provides a framework to consider the effect of packet drops, packet delays and bursty losses on state estimation. We use a modified Kalman Filter with buffer to cope with delayed packets. We analyze the stability of the estimates with varying buffer length and queue size. We use high order Markov chains for our analysis. Simulation examples are presented to illustrate the theory.", "doi": "10.1109/ICW.2005.46", "isbn": "0-7695-2422-2", "publisher": "IEEE Computer Society", "place_of_publication": "Los Alamitos, CA", "publication_date": "2005-08", "pages": "389-394" }, { "id": "authors:bg776-6h587", "collection": "authors", "collection_id": "bg776-6h587", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170725-151737146", "type": "article", "title": "Sensorimotor convergence in visual navigation and flight control systems", "author": [ { "family_name": "Humbert", "given_name": "J. Sean", "clpid": "Humbert-J-S" }, { "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" } ], "abstract": "Insects exhibit unparalleled and incredibly robust flight dynamics in the face of uncertainties. A fundamental principle contributing to this amazing behavior is rapid processing and convergence of visual sensory information to flight motor commands via spatial wide-field integration, accomplished by motion pattern sensitive interneurons in the lobula plate portion of the visual ganglia. Within a control-theoretic framework, a model for wide-field integration of retinal image flow is developed, establishing the connection between image flow kernels (retinal motion pattern sensitivities) and the feedback terms they represent. It is demonstrated that the proposed output feedback methodology is sufficient to give rise to experimentally observed navigational heuristics as the centering and forward speed regulation responses exhibited by honeybees.", "doi": "10.3182/20050703-6-CZ-1902.02003", "issn": "1474-6670", "publisher": "Elsevier", "publication": "IFAC Proceedings Volumes", "publication_date": "2005-07", "series_number": "1", "volume": "38", "issue": "1", "pages": "253-258" }, { "id": "authors:dd0ap-kct14", "collection": "authors", "collection_id": "dd0ap-kct14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170725-103031239", "type": "article", "title": "Cascade Discrete-Continuous State Estimators for a Class of Monotone Systems", "author": [ { "family_name": "Del Vecchio", "given_name": "D.", "clpid": "Del-Vecchio-D" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "A cascade discrete-continuous state estimator is proposed for a class of monotone systems with both continuous and discrete state. The proposed estimator exploits the partial order preserved by the system dynamics in order to satisfy two properties. First, its computation complexity scales with the number of variables to be estimated instead of scaling with the size of the discrete state space. Second, a separation principle holds: the continuous state estimation error is bounded by a monotonically decreasing function of the discrete state estimation error, the latter one converging to zero. A multi-robot example is proposed.", "doi": "10.3182/20050703-6-CZ-1902.00335", "issn": "1474-6670", "publisher": "Elsevier", "publication": "IFAC Proceedings Volumes", "publication_date": "2005-07", "series_number": "1", "volume": "38", "issue": "1", "pages": "307-312" }, { "id": "authors:etf17-73312", "collection": "authors", "collection_id": "etf17-73312", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150210-072226646", "type": "book_section", "title": "On LQG control across a stochastic packet-dropping link", "book_title": "Proceedings of the 2005 American Control Conference", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Spanos", "given_name": "Demetri", "clpid": "Spanos-D-P" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider the problem of\noptimal Linear Quadratic Gaussian control of a system\nin which communication between the sensor and the\ncontroller occurs across a packet-dropping link. We first\nprove a separation principle that allows us to solve this\nproblem using a standard LQR state-feedback design,\nalong with an optimal algorithm for propagating and\nusing the information across the unreliable link. Then\nwe present one such optimal algorithm, which consists\nof a Kalman filter at the sensor side of the link, and a\nswitched linear filter at the controller side. Our design\ndoes not assume any statistical model of the packet drop\nevents, and is thus optimal for any arbitrary packet\ndrop pattern. Further, the solution is appealing from a\npractical point of view because it can be implemented as\na small modification of an existing LQG control design.", "doi": "10.1109/ACC.2005.1469960", "isbn": "0-7803-9098-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-06", "pages": "360-365" }, { "id": "authors:ggncp-vex58", "collection": "authors", "collection_id": "ggncp-vex58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170408-172516757", "type": "article", "title": "Receding horizon control of vectored thrust flight experiment", "author": [ { "family_name": "Milam", "given_name": "M. B.", "clpid": "Milam-M-B" }, { "family_name": "Franz", "given_name": "R.", "clpid": "Franz-R" }, { "family_name": "Hauser", "given_name": "J. E.", "clpid": "Hauser-J-E" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Abstract:\nThe application of a constrained receding horizon control technique to stabilise an indoor vectored-thrust flight experiment, known as the Caltech ducted fan, is given. The receding horizon control problem is formulated as a constrained optimal control problem and solved in real time with an efficient, computational method that combines nonlinear control theory, B-spline basis functions, and nonlinear programming. Characteristic issues, including non-zero computational times, convergence properties, choice of horizon length and terminal cost are discussed. The study validates the applicability of real-time receding horizon control for constrained systems with fast dynamics.", "doi": "10.1049/ip-cta:20059031", "issn": "1350-2379", "publisher": "IEE", "publication": "IEE Proceedings - Control Theory and Applications", "publication_date": "2005-05", "series_number": "3", "volume": "152", "issue": "3", "pages": "340-348" }, { "id": "authors:58zas-knn35", "collection": "authors", "collection_id": "58zas-knn35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SPAipsn05", "type": "book_section", "title": "Approximate distributed Kalman filtering in sensor networks with quantifiable performance", "book_title": "Fourth International Symposium on Information Processing in Sensor Networks, 2005 (IPSN 2005)", "author": [ { "family_name": "Spanos", "given_name": "Demetri P.", "clpid": "Spanos-D-P" }, { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We analyze the performance of an approximate distributed Kalman filter proposed in recent work on distributed coordination. This approach to distributed estimation is novel in that it admits a systematic analysis of its performance as various network quantities such as connection density, topology, and bandwidth are varied. Our main contribution is a frequency-domain characterization of the distributed estimator's steady-state performance; this is quantified in terms of a special matrix associated with the connection topology called the graph Laplacian, and also the rate of message exchange between immediate neighbors in the communication network.", "doi": "10.1109/IPSN.2005.1440912", "isbn": "0-7803-9201-9", "publisher": "IEEE", "place_of_publication": "Los Alamitos, CA", "publication_date": "2005-04-15", "pages": "133-139" }, { "id": "authors:zx30k-y0y67", "collection": "authors", "collection_id": "zx30k-y0y67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110811-104030081", "type": "book_section", "title": "An Experimental Platform for Motion Estimation and\n Maneuver Characterization in High Speed Off-Road Driving", "book_title": "Proceedings of the 2005 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Huang", "given_name": "Haomiao", "clpid": "Huang-H" }, { "family_name": "Chamberlain", "given_name": "Lyle", "clpid": "Chamberlain-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes a low-cost experimental platform for investigating control and dynamics of a vehicle performing high speed sliding turns in an off-road environment. The hardware design and field performance of the vehicle are discussed. State and control input data were recorded during a series of human-controlled off-road driving maneuvers. Analysis performed on the data demonstrates the ability to detect slippage and measure sideslip angle. Preliminary classification of human control inputs using pattern recognition techniques shows the ability to match steering inputs with vehicle trajectories that can be used to develop motion primitives for vehicle control. These tools and techniques will be used for the development of high speed autonomous off-road driving.", "doi": "10.1109/ROBOT.2005.1570585", "isbn": "0-7803-8914-X", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-04", "pages": "3090-3095" }, { "id": "authors:6tvvj-z0f93", "collection": "authors", "collection_id": "6tvvj-z0f93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-072421791", "type": "book_section", "title": "Scheduling for Distributed Sensor Networks with Single Sensor Measurement per Time Step", "book_title": "2004 IEEE International Conference on Robotics and Automation, Proceedings. ICRA '04", "author": [ { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Burdick", "given_name": "Joel", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We examine the problem of distributed estimation when only one sensor can take a measurement per time step. We solve for the optimal recursive estimation algorithm when the sensor switching schedule is given. We then consider the effect of noise in communication channels. We also investigate the problem of determining an optimal sensor switching strategy. We see that this problem involves searching a tree in general and propose two strategies for pruning the tree to minimize the computation. The first is a sliding window strategy motivated by the Viterbi algorithm, and the second one uses thresholding. The performance of the algorithms is illustrated using numerical examples.", "doi": "10.1109/ROBOT.2004.1307149", "isbn": "0-7803-8232-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-04", "pages": "187-192" }, { "id": "authors:2y774-3te25", "collection": "authors", "collection_id": "2y774-3te25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161201-132855346", "type": "book_section", "title": "Communication and sensing trade-offs in decentralized mobile sensor networks: a cross-layer design approach", "book_title": "IPSN 2005. Fourth International Symposium on Information Processing in Sensor Networks, 2005", "author": [ { "family_name": "Mostofi", "given_name": "Yasamin", "clpid": "Mostofi-Y" }, { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" } ], "abstract": "In this paper we characterize the impact of imperfect communication on the performance of a decentralized mobile sensor network. We first examine and demonstrate the trade-offs between communication and sensing objectives, by determining the optimal sensor configurations when introducing imperfect communication. We further illustrate the performance degradation caused by non-ideal communication links in a decentralized mobile sensor network. To address this, we propose a decentralized motion-planning algorithm that considers communication effects. The algorithm is a cross-layer design based on the proper interface of physical and application layers. Simulation results will show the performance improvement attained by utilizing this algorithm.", "doi": "10.1109/IPSN.2005.1440910", "isbn": "0-7803-9201-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2005-04", "pages": "118-125" }, { "id": "authors:3jq7g-yg461", "collection": "authors", "collection_id": "3jq7g-yg461", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170725-125802135", "type": "book_section", "title": "Existence of Cascade Discrete-Continuous State Estimators for Systems on a Partial Order", "book_title": "Hybrid Systems: Computation and Control", "author": [ { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Morari", "given_name": "Manfred", "clpid": "Morari-M" }, { "family_name": "Thiele", "given_name": "Lothar", "clpid": "Thiele-L" } ], "abstract": "In this paper, a cascade discrete-continuous state estimator on a partial order is proposed and its existence investigated. The continuous state estimation error is bounded by a monotonically nonincreasing function of the discrete state estimation error, with both the estimation errors converging to zero. This work shows that the lattice approach to estimation is general as the proposed estimator can be constructed for any observable and discrete state observable system. The main advantage of using the lattice approach for estimation becomes clear when the system has monotone properties that can be exploited in the estimator design. In such a case, the computational complexity of the estimator can be drastically reduced and tractability can be achieved. Some examples are proposed to illustrate these ideas.", "doi": "10.1007/978-3-540-31954-2_15", "isbn": "978-3-540-25108-8", "publisher": "Springer", "place_of_publication": "Berlin", "publication_date": "2005-03", "pages": "226-241" }, { "id": "authors:njzp3-m9k38", "collection": "authors", "collection_id": "njzp3-m9k38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190627-094444006", "type": "book_section", "title": "On a decentralized active sensing strategy using mobile sensor platforms in a network", "book_title": "43rd IEEE Conference on Decision and Control", "author": [ { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider the problem of active sensing using mobile nodes as a sensor network to estimate the state of a dynamic target. We propose a gradient-search-based decentralized algorithm that demonstrates the benefits of distributed sensing. We then examine the task of tracking multiple targets, and address it via a simple extension to our algorithm. Simulation results show that our simple decentralized approach performs quite well and leads to interesting cooperative behavior.", "doi": "10.1109/CDC.2004.1430327", "isbn": "0-7803-8682-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2004-12", "pages": "1914-1919" }, { "id": "authors:27qye-ckm71", "collection": "authors", "collection_id": "27qye-ckm71", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2004.008", "type": "monograph", "title": "On a stochastic sensor selection algorithm with applications in sensor scheduling and sensor coverage", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this note we consider the following problem. Suppose a set of sensors is jointly trying to estimate a process. One sensor takes a measurement at every time step and the measurements are then exchanged among all the sensors. What is the sensor schedule that results in the minimum error covariance? We describe a stochastic sensor selection strategy that is easy to implement and is computationally tractable. The problem described above comes up in many domains out of which we discuss two. In the sensor selection problem, there are multliple sensors that cannot operate simultaneously (e.g., sonars in the same frequency band). Thus measurements need to be scheduled. In the sensor coverage problem, a geographical area needs to be covered by mobile sensors each with limited range. Thus from every position, the sensors obtain a different view-point of the area and the sensors need to optimize their positions. The algorithm is applied to these problems and illustrated through simple examples.", "publisher": "California Institute of Technology", "publication_date": "2004-10-10" }, { "id": "authors:rf9tb-den49", "collection": "authors", "collection_id": "rf9tb-den49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MURieeecsm04", "type": "article", "title": "A new approach to teaching feedback", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Waydo", "given_name": "Stephen", "clpid": "Waydo-S" }, { "family_name": "Cremean", "given_name": "Lars B.", "clpid": "Cremean-L-B" }, { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" } ], "abstract": "The Control and Dynamical Systems (CDS) Department at the California Institute of Technology (Caltech) has revised its entry-level curriculum in dynamics, feedback, and control with the goals of updating the subject matter to include modern tools and making control tools accessible to a nontraditional audience. One of the approaches made was to divide the introductory control theory class into two tracks, with a conceptual track geared toward students who need only a conceptual overview of control tools and an analytical track providing a more detailed mathematical treatment of feedback. The conceptual track, CDS 101, which is mainly discussed in the paper, is intended for advanced students in science and engineering who can benefit from an overview of control techniques but who might not have the need for the mathematical depth underlying the material. Special attention is paid to ensuring that the course is accessible to students from biological, physical, and information sciences, using examples from these domains to illustrate concepts. The goal of the course is to enable students to use the principles and tools of feedback in their research activities.", "doi": "10.1109/MCS.2004.1337856", "issn": "0272-1708", "publisher": "IEEE", "publication": "IEEE Control Systems Magazine", "publication_date": "2004-10", "series_number": "5", "volume": "24", "issue": "5", "pages": "38-42" }, { "id": "authors:t2gnt-vd720", "collection": "authors", "collection_id": "t2gnt-vd720", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:OLFieeetac04", "type": "article", "title": "Consensus problems in networks of agents with switching topology and time-delays", "author": [ { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we discuss consensus problems for networks of dynamic agents with fixed and switching topologies. We analyze three cases: 1) directed networks with fixed topology; 2) directed networks with switching topology; and 3) undirected networks with communication time-delays and fixed topology. We introduce two consensus protocols for networks with and without time-delays and provide a convergence analysis in all three cases. We establish a direct connection between the algebraic connectivity (or Fiedler eigenvalue) of the network and the performance (or negotiation speed) of a linear consensus protocol. This required the generalization of the notion of algebraic connectivity of undirected graphs to digraphs. It turns out that balanced digraphs play a key role in addressing average-consensus problems. We introduce disagreement functions for convergence analysis of consensus protocols. A disagreement function is a Lyapunov function for the disagreement network dynamics. We proposed a simple disagreement function that is a common Lyapunov function for the disagreement dynamics of a directed network with switching topology. A distinctive feature of this work is to address consensus problems for networks with directed information flow. We provide analytical tools that rely on algebraic graph theory, matrix theory, and control theory. Simulations are provided that demonstrate the effectiveness of our theoretical results.", "doi": "10.1109/TAC.2004.834113", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2004-09", "series_number": "9", "volume": "49", "issue": "9", "pages": "1520-1533" }, { "id": "authors:kh9pq-wj662", "collection": "authors", "collection_id": "kh9pq-wj662", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:FAXieeetac04", "type": "article", "title": "Information flow and cooperative control of vehicle formations", "author": [ { "family_name": "Fax", "given_name": "J. Alexander", "clpid": "Fax-J-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of cooperation among a collection of vehicles performing a shared task using intervehicle communication to coordinate their actions. Tools from algebraic graph theory prove useful in modeling the communication network and relating its topology to formation stability. We prove a Nyquist criterion that uses the eigenvalues of the graph Laplacian matrix to determine the effect of the communication topology 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 decomposes formation stability into two components: Stability of this is achieved information flow for the given graph and stability of an individual vehicle for the given controller. The information flow can thus be rendered highly robust to changes in the graph, enabling tight formation control despite limitations in intervehicle communication capability.", "doi": "10.1109/TAC.2004.834433", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "2004-09", "series_number": "9", "volume": "49", "issue": "9", "pages": "1465-1476" }, { "id": "authors:4978t-yv173", "collection": "authors", "collection_id": "4978t-yv173", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2004.006", "type": "monograph", "title": "A Sub-optimal Algorithm to Synthesize Control Laws for a Network of Dynamic Agents", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We study the synthesis problem of an LQR controller when the matrix describing the control law is constrained to lie in a particular vector space. Our motivation is the use of such control laws to stabilize networks of autonomous agents in a decentralized fashion; with the information flow being dictated by the constraints of a pre-specified topology. In this paper, we consider the finite-horizon version of the problem and provide both a computationally intensive optimal solution and a sub-optimal solution that is computationally more tractable. Then we apply the technique to the decentralized vehicle formation control problem and show that the loss in performance due to the use of the sub-optimal solution is not huge; however the topology can have a large effect on performance.", "publisher": "California Institute of Technology", "publication_date": "2004-08" }, { "id": "authors:s9j8v-mpz83", "collection": "authors", "collection_id": "s9j8v-mpz83", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2004.007", "type": "monograph", "title": "Optimal LQG Control Across a Packet-Dropping Link", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Spanos", "given_name": "Demetri", "clpid": "Spanos-D" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We examine optimal Linear Quadratic Gaussian control for a system in which communication between the sensor (output of the plant) and the controller occurs across a packet-dropping link. We extend the familiar LQG separation principle to this problem that allows us to solve this problem using a standard LQR state-feedback design, along with an optimal algorithm for propagating and using the information across the unreliable link. We present one such optimal algorithm, which consists of a Kalman Filter at the sensor side of the link, and a switched linear filter at the controller side. Our design does not assume any statistical model of the packet drop events, and is thus optimal for an arbitrary packet drop pattern. Further, the solution is appealing from a practical point of view because it can be implemented as a small modification of an existing LQG control design.", "publisher": "California Institute of Technology", "publication_date": "2004-08" }, { "id": "authors:ce0j2-w8k30", "collection": "authors", "collection_id": "ce0j2-w8k30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GALprb04", "type": "article", "title": "Effective transition rates for epitaxial growth using fast modulation", "author": [ { "family_name": "Gallivan", "given_name": "Martha A.", "clpid": "Gallivan-M-A" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Thin-film deposition is an industrially important process that is highly dependent on the processing conditions. Most films are grown under constant conditions, but a few studies show that modified properties may be obtained with periodic inputs. However, assessing the effects of modulation experimentally becomes impractical with increasing material complexity. Here we consider periodic conditions in which the period is short relative to the time scales of growth. We analyze a stochastic model of thin-film growth, computing effective transition rates associated with rapid periodic process parameters. Combinations of effective rates may exist that are not attainable under steady conditions, potentially enabling new film properties. An algorithm is presented to construct the periodic input for a desired set of effective transition rates. These ideas are demonstrated in three simple examples using kinetic Monte Carlo simulations of epitaxial growth.", "doi": "10.1103/PhysRevB.70.045409", "issn": "1098-0121", "publisher": "Physical Review B", "publication": "Physical Review B", "publication_date": "2004-07-15", "series_number": "4", "volume": "70", "issue": "4", "pages": "Art. No. 045409" }, { "id": "authors:nv60m-4fn90", "collection": "authors", "collection_id": "nv60m-4fn90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190322-120335030", "type": "book_section", "title": "Vision as a compensatory mechanism for disturbance rejection in upwind flight", "book_title": "Proceedings of the 2004 American Control Conference", "author": [ { "family_name": "Reiser", "given_name": "Michael B.", "clpid": "Reiser-M-B" }, { "family_name": "Humbert", "given_name": "J. Sean", "clpid": "Humbert-J-S" }, { "family_name": "Dunlop", "given_name": "Mary J.", "clpid": "Dunlop-M-J" }, { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "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" } ], "abstract": "Recent experimental results demonstrate that flies possess a robust tendency to orient towards the frontally-centered focus of the visual motion field that typically occurs during upwind flight. We present a closed loop flight model, with a control algorithm based on feedback of the location of the visual focus of contraction, which is affected by changes in wind direction. The feasibility of visually guided upwind orientation is demonstrated with a model derived from current understanding of the biomechanics and sensorimotor computation of insects. The matched filter approach used to model the visual system computations compares extremely well with open-loop experimental data.", "doi": "10.23919/acc.2004.1383623", "isbn": "0780383354", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2004-07", "pages": "311-316" }, { "id": "authors:s5ytf-w0r28", "collection": "authors", "collection_id": "s5ytf-w0r28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-070629438", "type": "book_section", "title": "On the synthesis of control laws for a network of autonomous agents", "book_title": "Proceedings of the 2004 American Control Conference", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We study the synthesis problem of a LQR controller when the matrix describing the control law is additionally constrained to lie in a particular vector space. Our motivation is the use of such control laws to stabilize networks of autonomous agents in a decentralized fashion; with the information flow being dictated by the constraints of a pre-specified topology. We formulate the problem as an optimization problem and provide numerical procedures to solve it. Then, we apply the technique to the decentralized vehicle formation control problem and show that the topology can have a significant effect on the optimal cost.", "isbn": "0-7803-8335-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2004-07", "pages": "4927-4932" }, { "id": "authors:vswwf-tx625", "collection": "authors", "collection_id": "vswwf-tx625", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-071543730", "type": "book_section", "title": "Sensor scheduling algorithms requiring limited computation", "book_title": "IEEE International Conference on Acoustics, Speech, and Signal Processing, 2004. Proceedings. (ICASSP '04)", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Chung", "given_name": "Timothy", "clpid": "Chung-Timothy-H" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we consider the scenario where many sensors co-operate to estimate a process. Only one sensor can take a measurement at any time step. We wish to come up with optimal sensor scheduling algorithms. The problem is motivated by the use of sonar range-finders used by the vehicles on the Caltech Multi-Vehicle Wireless Testbed. We see that this problem involves searching a tree in general and propose and analyze two strategies for pruning the tree to keep the computation limited. The first is a sliding window strategy motivated by the Viterbi algorithm, and the second one uses thresholding. We also study a technique that employs choosing the sensors randomly from a probability distribution which can then be optimized. The performance of the algorithms are illustrated with the help of numerical examples.", "doi": "10.1109/ICASSP.2004.1326672", "isbn": "0-7803-8484-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2004-05", "pages": "825-828" }, { "id": "authors:2fex1-0xr95", "collection": "authors", "collection_id": "2fex1-0xr95", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190214-075224908", "type": "article", "title": "Model reduction for compressible flows using POD and Galerkin projection", "author": [ { "family_name": "Rowley", "given_name": "Clarence W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a framework for applying the method of proper orthogonal decomposition (POD) and Galerkin projection to compressible fluids. For incompressible flows, only the kinematic variables are important, and the techniques are well known. In a compressible flow, both the kinematic and thermodynamic variables are dynamically important, and must be included in the configuration space. We introduce an energy-based inner product which may be used to obtain POD modes for this configuration space. We then obtain an approximate version of the Navier\u2013Stokes equations, valid for cold flows at moderate Mach number, and project these equations onto a POD basis. The resulting equations of motion are quadratic, and are much simpler than projections of the full compressible Navier\u2013Stokes equations.", "doi": "10.1016/j.physd.2003.03.001", "issn": "0167-2789", "publisher": "Elsevier", "publication": "Physica D", "publication_date": "2004-02-15", "series_number": "1-2", "volume": "189", "issue": "1-2", "pages": "115-129" }, { "id": "authors:dggje-96y63", "collection": "authors", "collection_id": "dggje-96y63", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2004.003", "type": "monograph", "title": "Distributed Receding Horizon Control with Application to Multi-Vehicle Formation Stabilization", "author": [ { "family_name": "Dunbar", "given_name": "William B.", "clpid": "Dunbar-W-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the control of interacting subsystems whose dynamics and constraints are uncoupled, but whose state vectors are coupled non-separably in a single centralized cost function of a finite horizon optimal control problem. For a given centralized cost structure, we generate distributed optimal control problems for each subsystem and establish that the distributed receding horizon implementation is asymptotically stabilizing. The communication requirements between subsystems with coupling in the cost function are that each subsystem obtain the previous optimal control trajectory of those subsystems at each receding horizon update. The key requirements for stability are that each distributed optimal control not deviate too far from the previous optimal control, and that the receding horizon updates happen sufficiently fast. The theory is applied in simulation for stabilization of a formation of vehicles.", "publisher": "California Institute of Technology", "publication_date": "2004-01-01" }, { "id": "authors:1y01d-zzv48", "collection": "authors", "collection_id": "1y01d-zzv48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190826-124740570", "type": "book_section", "title": "Discrete State Estimators for a Class of Hybrid Systems on a Lattice", "book_title": "Hybrid Systems: Computation and Control", "author": [ { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "contributor": [ { "family_name": "Alur", "given_name": "Rajeev", "clpid": "Alur-R" }, { "family_name": "Pappas", "given_name": "George J.", "clpid": "Pappas-G-J" } ], "abstract": "In this paper we consider the problem of estimating discrete variables in a class of hybrid systems where we assume that the continuous variables are available for measurement. Using lattice and order theory we develop a frame-work for constructing a discrete state estimator on an enlarged space of variables with lattice structure, which updates only two variables at each step. We apply our ideas to a multi-robot system example, the RoboFlag Drill.", "doi": "10.1007/978-3-540-24743-2_21", "isbn": "9783540212591", "publisher": "Springer", "place_of_publication": "Berlin, Heidelberg", "publication_date": "2004", "pages": "311-325" }, { "id": "authors:1phkj-1vd63", "collection": "authors", "collection_id": "1phkj-1vd63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-071040084", "type": "monograph", "title": "Scheduling for Distributed Sensor Networks", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Chung", "given_name": "Timothy H.", "clpid": "Chung-Timothy-H" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We examine the problem of distributed estimation when only one sensor can take a measurement per time step. The measurements are then exchanged among the sensors. The problem is motivated by the use of sonar range-finders used by the vehicles on the Caltech Multi-Vehicle Wireless Testbed. We solve for the optimal recursive estimation algorithm when the sensor switching schedule is given. Then we investigate several approaches for determining an optimal sensor switching strategy. We see that this problem involves searching a tree in general and propose and analyze two strategies for pruning the tree to keep the computation limited. The first is a sliding window strategy motivated by the Viterbi algorithm, and the second one uses thresholding. We also study a technique that employs choosing the sensors randomly from a probability distribution which can then be optimized. The performance of the algorithms are illustrated with the help of numerical examples.", "publisher": "Caltech Library", "publication_date": "2004" }, { "id": "authors:kff11-yt740", "collection": "authors", "collection_id": "kff11-yt740", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140730-101719175", "type": "article", "title": "Decomposition of human motion into dynamics-based primitives with application to drawing tasks", "author": [ { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "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" } ], "abstract": "Using tools from dynamical systems and systems identification, we develop a framework for the study of primitives for human motion, which we refer to as movemes. The objective is understanding human motion by decomposing it into a sequence of elementary building blocks that belong to a known alphabet of dynamical systems. We develop a segmentation and classification algorithm in order to reduce a complex activity into the sequence of movemes that have generated it. We test our ideas on data sampled from five human subjects who were drawing figures using a computer mouse. Our experiments show that we are able to distinguish between movemes and recognize them even when they take place in activities containing an unspecified number of movemes.", "doi": "10.1016/S0005-1098(03)00250-4", "issn": "0005-1098", "publisher": "Elsevier", "publication": "Automatica", "publication_date": "2003-12", "series_number": "12", "volume": "39", "issue": "12", "pages": "2085-2098" }, { "id": "authors:gc44e-ch547", "collection": "authors", "collection_id": "gc44e-ch547", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150513-074656184", "type": "book_section", "title": "Classification of human actions into dynamics based primitives with application to drawing tasks", "book_title": "European Control Conference (ECC 2003)", "author": [ { "family_name": "Del Vecchio", "given_name": "D.", "clpid": "Del-Vecchio-D" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "P.", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" } ], "abstract": "We develop the study of primitives of human motion, which we refer to as movemes. The idea is to understand human motion by decomposing it into a sequence of elementary building blocks that belong to a known alphabet of dynamical systems. How can we construct an alphabet of movemes from human data? In this paper we address this issue by introducing the notion of well-posednes. Using examples from human drawing data, we show that the well-posedness notion can be applied in practice so to establish if sets of actions, viewed as signals in time, can define movemes.", "isbn": "978-3-9524173-7-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2003-09", "pages": "445-450" }, { "id": "authors:yz4wn-e7971", "collection": "authors", "collection_id": "yz4wn-e7971", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150513-085011394", "type": "book_section", "title": "Nonlinear and cooperative control of multiple hovercraft with input constraints", "book_title": "2003 European Control Conference", "author": [ { "family_name": "Dunbar", "given_name": "William B.", "clpid": "Dunbar-W-B" }, { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we introduce an approach for distributed nonlinear control of multiple hovercraft-type underactuated vehicles with bounded and unidirectional inputs. First, a bounded nonlinear controller is given for stabilization and tracking of a single vehicle, using a cascade backstepping method. Then, this controller is combined with a distributed gradient-based control for multi-vehicle formation stabilization using formation potential functions previously constructed. The vehicles are used in the Caltech Multi-Vehicle Wireless Testbed (MVWT). We provide simulation and experimental results for stabilization and tracking of a single vehicle, and a simulation of stabilization of a six-vehicle formation, demonstrating that in all cases the control bounds and the control objective are satisfied.", "isbn": "978-3-9524173-7-9", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2003-09", "pages": "1917-1922" }, { "id": "authors:c6kgq-jhx19", "collection": "authors", "collection_id": "c6kgq-jhx19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170522-153018041", "type": "book_section", "title": "Consensus protocols for networks of dynamic agents", "book_title": "Proceedings of the 2003 American Control Conference, 2003", "author": [ { "family_name": "Saber", "given_name": "Reza Olfati", "clpid": "Saber-R-O" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we introduce linear and nonlinear consensus protocols for networks of dynamic agents that allow the \nagents to agree in a distributed and cooperative fashion. \nWe consider the cases of networks with communication time-delays and channels that have filtering effects. \nWe find a tight upper bound on the maximum fixed time-delay \nthat can be tolerated in the network. It turns out that the \nconnectivity of the network is the key in reaching a \nconsensus. The case of agreement with bounded inputs is \nconsidered by analyzing the convergence of a class of nonlinear protocols. A Lyapunov function is introduced that \nquantifies the total disagreement among the nodes of a \nnetwork. Simulation results are provided for agreement in networks with communication time-delays and constrained inputs.", "doi": "10.1109/ACC.2003.1239709", "isbn": "0-7803-7896-2", "publisher": "IEEE", "place_of_publication": "Piscatway, NJ", "publication_date": "2003-06", "pages": "951-956" }, { "id": "authors:8sffr-adw28", "collection": "authors", "collection_id": "8sffr-adw28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111018-134102626", "type": "book_section", "title": "Segmentation of human motion into dynamics based primitives with application to drawing tasks", "book_title": "Proceedings of the 2003 American Control Conference", "author": [ { "family_name": "Del Vecchio", "given_name": "D.", "clpid": "Del-Vecchio-D" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Perona", "given_name": "Pietro", "orcid": "0000-0002-7583-5809", "clpid": "Perona-P" } ], "abstract": "Using tools from dynamical systems and systems identification we develop a framework for the study of decomposition of human motion. The objective is understanding human motion by decomposing it into a\nsequence of elementary building blocks, which we refer\nto as movemes, which belong to a known alphabet of\ndynamical systems: We develop classification and segmentation algorithms with error analysis and we test\nthem on human drawing data.", "doi": "10.1109/ACC.2003.1239860", "isbn": "0780378962", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2003-06", "pages": "1816-1823" }, { "id": "authors:vdwtz-5xz08", "collection": "authors", "collection_id": "vdwtz-5xz08", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2003.005", "type": "monograph", "title": "Agreement Problems in Networks with Directed Graphs and Switching Topology", "author": [ { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we provide tools for convergence and performance analysis of an agreement protocol for a network of integrator agents with directed information flow. Moreover, we analyze algorithmic robustness of this consensus protocol for the case of a network with mobile nodes and switching topology. We establish a connection between the Fiedler eigenvalue of the graph Laplacian and the performance of this agreement protocol. We demostrate that a class of directed graphs, called balanced graphs, have a crucial role in solving average-consensus problems. Based on the properties of balanced graphs, a group disagreement function (i.e. Lyapunov function) is proposed for convergence analysis of this agreement protocol for networks with directed graphs. This group disagreement function is later used for convergence analysis for the agreement problem in networks with switching topology. We provide simulation results that are consistent with our theoretical results and demonstrate the effectiveness of the proposed analytical tools.", "publisher": "California Institute of Technology", "publication_date": "2003-01-01" }, { "id": "authors:necme-9ea48", "collection": "authors", "collection_id": "necme-9ea48", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2003.008", "type": "monograph", "title": "Flat systems, equivalence and trajectory generation", "author": [ { "family_name": "Martin", "given_name": "Phillipe", "clpid": "Martin-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Rouchon", "given_name": "Pierre", "clpid": "Rouchon-P" } ], "abstract": "Flat systems, an important subclass of nonlinear control systems introduced\nvia differential-algebraic methods, are defined in a differential\ngeometric framework. We utilize the infinite dimensional geometry developed\nby Vinogradov and coworkers: a control system is a diffiety, or more\nprecisely, an ordinary diffiety, i.e. a smooth infinite-dimensional manifold\nequipped with a privileged vector field. After recalling the definition of\na Lie-Backlund mapping, we say that two systems are equivalent if they\nare related by a Lie-Backlund isomorphism. Flat systems are those systems\nwhich are equivalent to a controllable linear one. The interest of\nsuch an abstract setting relies mainly on the fact that the above system\nequivalence is interpreted in terms of endogenous dynamic feedback. The\npresentation is as elementary as possible and illustrated by the VTOL\naircraft.", "publisher": "California Institute of Technology", "publication_date": "2003-01-01" }, { "id": "authors:rgqvm-ad468", "collection": "authors", "collection_id": "rgqvm-ad468", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2003.012", "type": "monograph", "title": "Information Flow and Cooperative Control of Vehicle Formations", "author": [ { "family_name": "Fax", "given_name": "J. Alexander", "clpid": "Fax-J-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We consider the problem of cooperation among a collection of vehicles performing a shared\ntask using intervehicle communication to coordinate their actions. We apply tools from graph theory to relate the topology of the communication network to formation stability. We prove a Nyquist criterion that uses the eigenvalues of the graph Laplacian matrix to determine the effect\nof the graph on formation stability. We also propose a method for decentralized information\nexchange between vehicles. This approach realizes a dynamical system that supplies each vehicle\nwith a common reference to be used for cooperative motion. We prove a separation principle\nthat states that formation stability is achieved if the information flow is stable for the given\ngraph and if the local controller stabilizes the vehicle. The information flow can be rendered\nhighly robust to changes in the graph, thus enabling tight formation control despite limitations\nin intervehicle communication capability.", "publisher": "California Institute of Technology", "publication_date": "2003-01-01" }, { "id": "authors:wyqkk-pmv02", "collection": "authors", "collection_id": "wyqkk-pmv02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-075328058", "type": "book_section", "title": "On the control of jump linear Markov systems with Markov state estimation", "book_title": "Proceedings of the 2003 American Control Conference, 2003.", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "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" } ], "abstract": "We analyze a jump linear Markov system being stabilized using a linear controller. We consider the case when the Markov state is associated with the probability distribution of a measured variable. We assume that the Markov state is not known, but rather is being estimated based on the observations of the variable. We present conditions for the stability of such a system and also solve the optimal LQR control problem for the case when the state estimate update uses only the last observation value. In particular we consider a suboptimal version of the casual Viterbi estimation algorithm and show that a separation property does not hold between the optimal control and the Markov state estimate. Some simple examples are also presented.", "doi": "10.1109/ACC.2003.1243762", "isbn": "0-7803-7896-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2003", "pages": "2893-2898" }, { "id": "authors:tp3v1-zfe08", "collection": "authors", "collection_id": "tp3v1-zfe08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150211-070320141", "type": "book_section", "title": "Stability analysis of stochastically varying formations of dynamic agents", "book_title": "42nd IEEE Conference on Decision and Control, 2003. Proceedings.", "author": [ { "family_name": "Gupta", "given_name": "Vijay", "clpid": "Gupta-V" }, { "family_name": "Hassibi", "given_name": "Babak", "orcid": "0000-0002-1375-5838", "clpid": "Hassibi-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We analyze a network of dynamic agents where the topology of the network specifies the information flow between the agents. We present an analysis method for such a system for both consensus and formation stabilization problems. To consider the general features introduced by the information flow topology, we consider the case of agent dynamics being a single integrator. Then we show that the method of analysis can be extended to more general cases of complicated agent dynamics, non-ideal links for information flow, etc. We also consider the case when the topology of the network is changing over time. The focus of the paper is on obtaining conditions for the stability of the formation that can be checked in a decentralized way.", "doi": "10.1109/CDC.2003.1272613", "isbn": "0-7803-7924-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2003", "pages": "504-509" }, { "id": "authors:w3btx-2kq60", "collection": "authors", "collection_id": "w3btx-2kq60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190214-123721078", "type": "book_section", "title": "On the choice of norm for modeling compressible flow dynamics at reduced-order using the POD", "book_title": "Proceedings of the 41st IEEE Conference on Decision and Control", "author": [ { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Rowley", "given_name": "Clancy W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Freund", "given_name": "Jonathan B.", "clpid": "Freund-J-B" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We use POD (proper orthogonal decomposition)/Galerkin projection to investigate and derive reduced-order models of the dynamics of compressible flows. We examine DNS data for two flows, a turbulent M=0.9 jet and self-sustained oscillations in the flow over an open cavity, and show how different choices of norm lead to different definitions of the energetic structures, and, for the cavity, to different reduced-order models of the dynamics. For the jet, we show that the near-field dynamics are fairly well represented by relatively few modes, but that key processes of interest, such as acoustic radiation, are not well captured by norms that are defined based on volume integrals of pressure and velocity. For the cavity flow, we demonstrate that vector-valued POD modes lead to reduced-order models that are much more effective (accurate and stable) than scalar-valued modes defined independently for different flow variables.", "doi": "10.1109/CDC.2002.1184376", "isbn": "0-7803-7516-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2002-12", "pages": "3273-3278" }, { "id": "authors:fj01n-me678", "collection": "authors", "collection_id": "fj01n-me678", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:OLFcdc02b", "type": "book_section", "title": "Graph rigidity and distributed formation stabilization of multi-vehicle systems", "book_title": "Proceedings of the 41st IEEE Conference on Decision and Control, December 10-13, 2002, Las Vegas, Nevada, USA", "author": [ { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We provide a graph theoretical framework that allows us to formally define formations of multiple vehicles and the issues arising in uniqueness of graph realizations and its connection to stability of formations. The notion of graph rigidity is crucial in identifying the shape variables of a formation and an appropriate potential function associated with the formation. This allows formulation of meaningful optimization or nonlinear control problems for formation stabilization/tacking, in addition to formal representation of split, rejoin, and reconfiguration maneuvers for multi-vehicle formations. We introduce an algebra that consists of performing some basic operations on graphs which allow creation of larger rigid-by-construction graphs by combining smaller rigid subgraphs. This is particularly useful in performing and representing rejoin/split maneuvers of multiple formations in a distributed fashion.", "isbn": "0-7803-7516-5", "publisher": "IEEE", "place_of_publication": "Los Alamitos, CA", "publication_date": "2002-12", "pages": "2965-2971" }, { "id": "authors:9f2jt-mt183", "collection": "authors", "collection_id": "9f2jt-mt183", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:OLFcdc02a", "type": "book_section", "title": "Distributed structural stabilization and tracking for formations of dynamic multi-agents", "book_title": "Proceedings of the 41st IEEE Conference on Decision and Control, December 10-13, 2002, Las Vegas, Nevada, USA", "author": [ { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We provide a theoretical framework that consists of graph theoretical and Lyapunov-based approaches to stability analysis and distributed control of multi-agent formations. This framework relays on the notion of graph rigidity as a means of identifying the shape variables of a formation. Using this approach, we can formally define formations of multiple vehicles and three types of stabilization/tracking problems for dynamic multi-agent systems. We show how these three problems can be addressed mutually independent of each other for a formation of two agents. Then, we introduce a procedure called dynamic node augmentation that allows construction of a larger formation with more agents that can be rendered structurally stable in a distributed manner from some initial formation that is structurally stable. We provide two examples of formations that can be controlled using this approach, namely, the V-formation and the diamond formation.", "isbn": "0-7803-7516-5", "publisher": "IEEE", "place_of_publication": "Los Alamitos, CA", "publication_date": "2002-12", "pages": "209-215" }, { "id": "authors:qp5x4-psg54", "collection": "authors", "collection_id": "qp5x4-psg54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190709-092100972", "type": "conference_item", "title": "Model-based control of cavity oscillations. II - System identification and analysis", "author": [ { "family_name": "Rowley", "given_name": "Clarence W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Williams", "given_name": "David R.", "clpid": "Williams-D-R" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "MacMartin", "given_name": "Douglas G.", "orcid": "0000-0003-1987-9417", "clpid": "MacMartin-D-G" }, { "family_name": "Fabris", "given_name": "Drazin", "clpid": "Fabris-Drazin" } ], "abstract": "Experiments using active control to reduce oscillations in the flow past a rectangular cavity have uncovered surprising phenomena: in the controlled system, often new frequencies of oscillation appear, and often the main frequency of oscillation is split into two sideband frequencies. The goal of this paper is to explain these effects using physics-based models, and to use these ideas to guide control design.\n\nWe present a linear model for the cavity flow, based on the physical mechanisms of the familiar Rossiter model. Experimental data indicates that under many operating conditions, the oscillations are not self-sustained, but in fact are caused by amplification of external disturbances. We present some experimental results demonstrating the peak-splitting phenomena mentioned above, use the physics-based model to study the phenomena, and discuss fundamental performance limitations which limit the achievable performance of any control scheme.", "doi": "10.2514/6.2002-972", "publisher": "American Institute of Aeronautics and Astronautics", "publication_date": "2002-08-22" }, { "id": "authors:wjnxe-wpe88", "collection": "authors", "collection_id": "wjnxe-wpe88", "cite_using_url": "https://resolver.caltech.edu/CaltechBOOK:2002.001", "type": "book", "title": "Control in an Information Rich World: Report of the Panel on Future Directions in Control, Dynamics, and Systems", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The field of control provides the principles and methods used to design engineering systems that maintain desirable performance by automatically adapting to changes in the environment. Over the last forty years the field has seen huge advances, leveraging technology improvements in sensing and computation with breakthroughs in the underlying principles and mathematics. Control systems now play critical roles in many fields, including manufacturing, electronics, communications, transportation,\ncomputers and networks, and many military systems. \n\nAs we begin the 21st Century, the opportunities to apply control principles and methods are exploding. Computation, communication and sensing are becoming increasingly inexpensive and ubiquitous, with more and more devices including embedded processors, sensors, and networking hardware. This will make possible the development of machines with a degree of intelligence and reactivity that will influence nearly every aspect of life on this planet, including not just the products available, but the very environment in which we live. \n\nNew developments in this increasingly information rich world will require a significant expansion of the basic tool sets of control. The complexity of the control ideas involved in the operation of the Internet, semi-autonomous command and control systems, and enterprise-wide supply chain management, for example, are on the boundary of what can be done with available methods. Future applications in aerospace and transportation, information and networks, robotics and intelligent machines, biology and medicine, and materials and processing will create systems that are well beyond our current levels of complexity, and new research is required to enable such developments. \n\nThe purpose of this report is to spell out some of the prospects for control in the current and future technological environment, to describe the role the field will play in military, commercial, and scientific applications over the next decade, and to recommend actions required to enable new breakthroughs in engineering and technology through application of control research.", "isbn": "0898715288", "publisher": "Society for Industrial and Applied Mathematics", "place_of_publication": "Philadelphia, PA", "publication_date": "2002-08-15" }, { "id": "authors:0myqq-78716", "collection": "authors", "collection_id": "0myqq-78716", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160930-145845741", "type": "book_section", "title": "Primitives for Human Motion: A Dynamical Approach", "author": [ { "family_name": "Del Vecchio", "given_name": "Domitilla", "clpid": "Del-Vecchio-D" }, { "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" } ], "abstract": "Using tools from dynamical systems theory and systems identification theory we develop the study of primitives for human motion which we refer to as movemes. We\nintroduce basic definitions of dynamical independence\nof linear time-invariant dynamical systems (LTI) and\nsegmentability of signals and we develop classification and segmentation algorithms for two dimensional motions. We test our ideas on data sampled from four human subjects who were engaged in a simple real-life activity including two movemes. Our experiments show that we are able to distinguish between the two movemes and recognize\nthem even when they take place in an activity containing more than one moveme.", "doi": "10.3182/20020721-6-ES-1901.01313", "publisher": "IFAC", "publication_date": "2002-07" }, { "id": "authors:p4zqn-knd81", "collection": "authors", "collection_id": "p4zqn-knd81", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140703-135258516", "type": "publication_deliverable", "title": "California Extremely Large Telescope: Conceptual Design for a Thirty-Meter Telescope", "author": [ { "family_name": "Cohen", "given_name": "Judith G.", "orcid": "0000-0002-8039-4673", "clpid": "Cohen-J-G" }, { "family_name": "Dekany", "given_name": "Richard", "clpid": "Dekany-Richard" }, { "family_name": "Djorgovski", "given_name": "S. G.", "orcid": "0000-0002-0603-3087", "clpid": "Djorgovski-S-G" }, { "family_name": "Ellis", "given_name": "Richard S.", "orcid": "0000-0001-7782-7071", "clpid": "Ellis-R-S" }, { "family_name": "Kulkarni", "given_name": "S. R.", "orcid": "0000-0001-5390-8563", "clpid": "Kulkarni-S-R" }, { "family_name": "MacMartin", "given_name": "Douglas G.", "orcid": "0000-0003-1987-9417", "clpid": "MacMartin-D-G" }, { "family_name": "Matthews", "given_name": "K.", "clpid": "Matthews-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Padin", "given_name": "S.", "clpid": "Padin-S" }, { "family_name": "Sargent", "given_name": "Wallace L. W.", "clpid": "Sargent-W-L-W" }, { "family_name": "Steidel", "given_name": "Charles C.", "orcid": "0000-0002-4834-7260", "clpid": "Steidel-C-C" }, { "family_name": "Taylor", "given_name": "Keith", "clpid": "Taylor-K" }, { "family_name": "Tombrello", "given_name": "T. A.", "clpid": "Tombrello-T-A" }, { "literal": "California Institute of Technology" }, { "literal": "University of California" } ], "abstract": "Following great success in the creation of the Keck Observatory, scientists at the California Institute of\nTechnology and the University of California have begun to explore the scientific and technical prospects\nfor a much larger telescope. The Keck telescopes will remain the largest telescopes in the world for a\nnumber of years, with many decades of forefront research ahead after that. Though these telescopes\nhave produced dramatic discoveries, it is already clear that even larger telescopes must be built if we\nare to address some of the most profound questions about our universe. The time required to build a\nlarger telescope is approximately ten years, and the California community is presently well-positioned\nto begin its design and construction. The same scientists who conceived, led the design, and guided\nthe construction of the Keck Observatory have been intensely engaged in a study of the prospects for\nan extremely large telescope. Building on our experience with the Keck Observatory, we have concluded\nthat the large telescope is feasible and is within the bounds set by present-day technology. Our reference\ntelescope has a diameter of 30 meters, the largest size we believe can be built with acceptable risk. The\nproject is currently designated the California Extremely Large Telescope (CELT).", "publisher": "California Institute of Technology", "publication_date": "2002-06" }, { "id": "authors:r6jj4-0v905", "collection": "authors", "collection_id": "r6jj4-0v905", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190718-165126408", "type": "conference_item", "title": "Model-based control of cavity oscillations. I - Experiments", "author": [ { "family_name": "Williams", "given_name": "David R.", "clpid": "Williams-D-R" }, { "family_name": "Rowley", "given_name": "Clarence W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "MacMartin", "given_name": "Douglas G.", "orcid": "0000-0003-1987-9417", "clpid": "MacMartin-D-G" }, { "family_name": "Fabris", "given_name": "Drazin", "clpid": "Fabris-Drazin" }, { "family_name": "Albertson", "given_name": "Julie", "clpid": "Albertson-Julie" } ], "abstract": "An experimental investigation of acoustic mode noise suppression was conducted in a cavity using a digital controller with a linear control algorithm. The control algorithm was based on flow field physics similar to the Rossiter model for acoustic resonance. Details of the controller and results from its implementation are presented in the companion paper by Rowley, et al.\n\nHere the experiments and some details of the flow field development are described, which were done primarily at Mach number 0.34 corresponding to single mode resonance in the cavity. A novel method using feedback control to suppress the resonant mode and open-loop forcing to inject a non-resonant mode was developed for system identification. The results were used to obtain empirical transfer functions of the components of resonance, and measurements of the shear layer growth for use in the design of the control algorithm.", "doi": "10.2514/6.2002-971", "publisher": "American Institute of Aeronautics and Astronautics", "publication_date": "2002-01" }, { "id": "authors:0tsab-w9b27", "collection": "authors", "collection_id": "0tsab-w9b27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170814-124254157", "type": "article", "title": "Information flow and cooperative control of vehicle formations", "author": [ { "family_name": "Fax", "given_name": "J. Alexander", "clpid": "Fax-J-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Vehicles in formation often lack global information regarding the state of all the vehicles, a deficiency which can lead to instability and poor performance. In this paper, we demonstrate how exchange of minimal amounts of information between vehicles can be designed to realize a dynamical system which supplies each vehicle with a shared reference trajectory. When the information flow law is placed in the control loop, a separation principle is proven which guarantees stability of the formation and convergence of the information flow law regardless of the information flow topology.", "doi": "10.3182/20020721-6-ES-1901.00100", "issn": "1474-6670", "publisher": "Elsevier", "publication": "IFAC Proceedings Volumes", "publication_date": "2002", "series_number": "1", "volume": "35", "issue": "1", "pages": "115-120" }, { "id": "authors:bs4d5-7z144", "collection": "authors", "collection_id": "bs4d5-7z144", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170824-092713962", "type": "article", "title": "Distributed cooperative control of multiple vehicle formations using structural potential functions", "author": [ { "family_name": "Olfati-Saber", "given_name": "Reza", "clpid": "Olfati-Saber-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper, we propose a framework for formation stabilization of multiple autonomous vehicles in a distributed fashion. Each vehicle is assumed to have simple dynamics, i.e. a double-integrator, with a directed (or an undirected) information flow over the formation graph of the vehicles. Our goal is to find a distributed control law (with an efficient computational cost) for each vehicle that makes use of limited information regarding the state of other vehicles. Here, the key idea in formation stabilization is the use of natural potential functions obtained from structural constraints of a desired formation in a way that leads to a collision-free, distributed, and bounded state feedback law for each vehicle.", "doi": "10.3182/20020721-6-ES-1901.00244", "issn": "1474-6670", "publisher": "Elsevier", "publication": "IFAC Proceedings Volumes", "publication_date": "2002", "series_number": "1", "volume": "35", "issue": "1", "pages": "495-500" }, { "id": "authors:p5ck3-40155", "collection": "authors", "collection_id": "p5ck3-40155", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111109-145851328", "type": "book_section", "title": "Nonlinear control methods for planar carangiform robot fish locomotion", "book_title": "2001 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Morgansen", "given_name": "Kristi A.", "clpid": "Morgansen-K-A" }, { "family_name": "Duindam", "given_name": "Vincent", "clpid": "Duindam-V" }, { "family_name": "Mason", "given_name": "Richard J.", "clpid": "Mason-R-J" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Considers the design of motion control algorithms for robot fish. We present modeling, control design, and experimental trajectory tracking results for an experimental planar robotic fish system that is propelled using carangiform-like locomotion. Our model for the fish's propulsion is based on quasi-steady fluid flow. Using this model, we propose gaits for forward and turning trajectories and analyze system response under such control strategies. Our models and predictions are verified by experiment.", "doi": "10.1109/ROBOT.2001.932588", "isbn": "0-7803-6576-3", "publisher": "IEEE", "place_of_publication": "Pitscataway, NJ", "publication_date": "2001-05", "pages": "427-434" }, { "id": "authors:476q0-75d28", "collection": "authors", "collection_id": "476q0-75d28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190726-104731145", "type": "conference_item", "title": "Dynamical models for control of cavity oscillations", "author": [ { "family_name": "Rowley", "given_name": "Clarence W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We investigate nonlinear dynamical models for self-sustained oscillations in the flow past a rectangular cavity. The models are based on the method of Proper Orthogonal Decomposition (POD) and Galerkin projection, and we introduce an inner product and formulation of the equations of motion which enables one to use vector-valued POD modes for compressible flows. We obtain models between 3 and 20 states, which accurately describe both the short-time and long-time dynamics. This is a substantial improvement over previous models based on scalar-valued POD modes, which capture the dynamics for short time, but deviate for long time.", "doi": "10.2514/6.2001-2126", "publisher": "American Institute of Aeronautics and Astronautics", "publication_date": "2001-05" }, { "id": "authors:fnn3t-hae17", "collection": "authors", "collection_id": "fnn3t-hae17", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:2001.01-007", "type": "monograph", "title": "Graph Laplacians and Stabilization of Vehicle Formations", "author": [ { "family_name": "Fax", "given_name": "J. Alexander", "clpid": "Fax-J-A" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Control of vehicle formations has emerged as a topic of significant interest to the controls community. In this paper, we merge tools from graph theory and control theory to derive stability criteria for formation stabilization. The interconnection between vehicles (i.e., which vehicles are sensed by other vehicles) is modeled as a graph, and the eigenvalues of the Laplacian matrix of the graph are used in stating a Nyquist-like stability criterion for vehicle formations. The location of the Laplacian eigenvalues can be correlated to the graph structure, and therefore used to identify desirable and undesirable formation interconnection topologies.", "publisher": "California Institute of Technology", "publication_date": "2001-01-01" }, { "id": "authors:7tc7z-zr779", "collection": "authors", "collection_id": "7tc7z-zr779", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101008-094957238", "type": "book_section", "title": "J_2 Dynamics and Formation Flight", "book_title": "Proceedings of AIAA Guidance, Navigation, and Control Conference, 2001", "author": [ { "family_name": "Koon", "given_name": "Wang Sang", "clpid": "Koon-W-S" }, { "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": "Masdemont", "given_name": "Josep", "clpid": "Masdemont-J" } ], "abstract": "We study the dynamics of the relative motion of\nsatellites in the gravitational field of the Earth, including\nthe effects of the bulge of the Earth (the J_2\neffect). Using Routh reduction and dynamical systems\nideas, a method is found that locates orbits\nsuch that a cluster of satellites remains close with\nvery little dispersing, even with no controls.", "isbn": "9781563474835", "publisher": "American Institute of Aeronautics and Astronautics", "place_of_publication": "Reston, VA", "publication_date": "2001", "pages": "1-7" }, { "id": "authors:n9cw0-6z661", "collection": "authors", "collection_id": "n9cw0-6z661", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190726-104731320", "type": "conference_item", "title": "POD Based Models of Self-Sustained Oscillations in the Flow Past an Open Cavity", "author": [ { "family_name": "Rowley", "given_name": "Clarence W.", "orcid": "0000-0002-9099-5739", "clpid": "Rowley-C-W" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The goal of this work is to provide accurate dynamical models of oscillations in the flow past a rectangular cavity, for the purpose of bifurcation analysis and control. We have performed an extensive set of direct numerical simulations which provide the data used to derive and evaluate the models. Based on the method of Proper Orthogonal Decomposition (POD) and Galerkin projection, we obtain low-order models (from 6 to 60 states) which capture the dynamics very accurately over a few periods of oscillation, but deviate for long time.", "doi": "10.2514/6.2000-1969", "publisher": "American Institute of Aeronautics and Astronautics", "publication_date": "2000-06" }, { "id": "authors:5r9fz-1q467", "collection": "authors", "collection_id": "5r9fz-1q467", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1999.CIT-CDS-99-001", "type": "monograph", "title": "Geometric Approaches to Control in the Presence of Magnitude and Rate Saturations", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper gives a survey of some recent results on control of systems with magnitude and rate limits, motivated by problems in real-time trajectory generation and tracking for unmanned aerial vehicles. Two problems are considered: stabilization using ``nonlinear wrappers'' to rescale a given control law and real-time trajectory generation using differential flatness. For both problems, simplified versions of the general problem are studied using tools from differential geometry and nonlinear control to give insights into the limitations imposed by magnitude and rate limits and provide insights into constructive solutions to the trajectory generation and tracking problems.", "publisher": "California Institute of Technology", "publication_date": "1999-01-01" }, { "id": "authors:m3j71-n6y18", "collection": "authors", "collection_id": "m3j71-n6y18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LEWsiamr99", "type": "article", "title": "Configuration Controllability of Simple Mechanical Control Systems", "author": [ { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we present a definition of 'configuration controllability' for mechanical systems whose Lagrangian is kinetic energy with respect to a Riemannian metric minus potential energy. A computable test for this new version of controllability is derived. This condition involves an object that we call the symmetric product. Of particular interest is a definition of 'equilibrium controllability' for which we are able to derive computable sufficient conditions. Examples illustrate the theory.", "doi": "10.1137/S0036144599351065", "issn": "0036-1445", "publisher": "SIAM Review", "publication": "SIAM Review", "publication_date": "1999", "series_number": "3", "volume": "41", "issue": "3", "pages": "555-574" }, { "id": "authors:7h200-jt424", "collection": "authors", "collection_id": "7h200-jt424", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GLAcdc98", "type": "book_section", "title": "Model reduction, centering, and the Karhunen-Loeve expansion", "book_title": "IEEE Conference on Decision and Control, 37th (CDC 1998), Tampa, FL, 16-18 December 1998", "author": [ { "family_name": "Glava\u0161ki", "given_name": "Sonja", "clpid": "Glava\u0161ki-S" }, { "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" } ], "abstract": "We propose a new computationally efficient modeling method that captures a given translation symmetry in a system. To obtain a low order approximate system of ODEs, prior to performing a Karhunen Loeve expansion, we process the available data set using a \"centering\" procedure. This approach has been shown to be efficient in nonlinear scalar wave equations.", "doi": "10.1109/CDC.1998.758639", "isbn": "0-7803-4394-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1998-12", "pages": "2071-2076" }, { "id": "authors:d9y01-f4g15", "collection": "authors", "collection_id": "d9y01-f4g15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KELacc98", "type": "book_section", "title": "Modelling and experimental investigation of carangiform locomotion for control", "book_title": "Proceedings of the 1998 American Control Conference, 21-26 June 1998, Philadelphia PA", "author": [ { "family_name": "Kelly", "given_name": "Scott D.", "clpid": "Kelly-S-D" }, { "family_name": "Mason", "given_name": "Richard J.", "clpid": "Mason-R-J" }, { "family_name": "Anhalt", "given_name": "Carl T.", "clpid": "Anhalt-C-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel W.", "clpid": "Burdick-J-W" } ], "abstract": "We propose a model for planar carangiform swimming based on conservative equations for the interaction of a rigid body and an incompressible fluid. We account 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 to that predicted by unsteady hydrodynamics. Our analysis of thrust generation by an oscillating hydrofoil allows us to characterize and evaluate certain families of gaits. Our final swimming model takes the form of a control-affine nonlinear system.", "doi": "10.1109/ACC.1998.703619", "isbn": "0-7803-4530-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1998-06", "pages": "1271-1276" }, { "id": "authors:jgtcd-pbg29", "collection": "authors", "collection_id": "jgtcd-pbg29", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1998.CIT-CDS-98-009", "type": "monograph", "title": "Discrete Function Approximation: Numerical Tools for Nonlinear Control", "author": [ { "family_name": "Muruhan", "given_name": "Rathinam", "clpid": "Muruhan-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We describe a method for discrete representation of continuous functions and show how this may be used for typical computations in nonlinear control desi gn. The method involves representing functions by their values and finitely many derivatives at discrete set of points on the domain. We propose a grid structure based on a hierarchy of rectangular boxes that provides flexibility in placing grid points densely in some regions and sparsely in the other. The grids possess enough structure to facilitate easy interpolation schemes based on piecewise polynomials. We illustrate the method using a simple example where we compute the feedback linearizing output of a system.", "publisher": "California Institute of Technology", "publication_date": "1998-01-01" }, { "id": "authors:sk5yt-68524", "collection": "authors", "collection_id": "sk5yt-68524", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1998.CIT-CDS-98-001", "type": "monograph", "title": "Evaluation of Bleed Valve Rate Requirements in Nonlinear Control of Rotating Stall on Axial Flow Compressors", "author": [ { "family_name": "Yeung", "given_name": "S.", "clpid": "Yeung-S" }, { "family_name": "Wang", "given_name": "Y.", "clpid": "Wang-Y" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we evaluate the actuator rate requirements for control of rotating stall using a bleed valve and provide tools for predicting these requirements. Modification of both the stable and unstable parts of the compressor characteristic via addition of continuous air injection serves to reduce the requirement of a bleed valve used for the purpose of rotating stall stabilization. Analytical tools based on low order models (2-3 states) and simulation tools based on a reduced order model (37 states) are described. A bleed actuator rate limit study is presented to compare the actuator requirements predicted by theory, simulation, and experiment. The comparisons show that the predictions obtained from theory and simulations share the same trend as the experiments, with increasing accuracy as the complexity of the underlying model increases. Some insights on the design of a bleed-compressor pair are given.", "publisher": "California Institute of Technology", "publication_date": "1998-01-01" }, { "id": "authors:v9wzx-40j87", "collection": "authors", "collection_id": "v9wzx-40j87", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1997.014", "type": "monograph", "title": "Nonlinear Rescaling of Control Laws with Application to Stabilization in the Presence of Magnitude Saturation", "author": [ { "family_name": "Morin", "given_name": "Pascal", "clpid": "Morin-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Praly", "given_name": "L.", "clpid": "Praly-L" } ], "abstract": "Motivated by some recent results on the stabilization of homogeneous systems, we present a gain-scheduling approach for the stabilization of non-linear systems. Given\na one-parameter family of stabilizing feedbacks and associated Lyapunov functions, we show how the parameter can be rescaled as a function of the state to give a new\nstabilizing controller. In the case of homogeneous systems, we obtain generalizations of some existing results. We show that this approach can also be applied to nonhomogeneous\nsystems. In particular, the main application considered in this paper is to the problem of stabilization with magnitude limitations. For this problem, we develop a design method for single-input controllable systems with eigenvalues in the left closed plane.", "publisher": "California Institute of Technology", "publication_date": "1997-11" }, { "id": "authors:xz0xc-bjh80", "collection": "authors", "collection_id": "xz0xc-bjh80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MCLieeetac97", "type": "article", "title": "Exponential stabilization of driftless nonlinear control systems using homogeneous feedback", "author": [ { "family_name": "M'Closkey", "given_name": "Robert T.", "clpid": "M'Closkey-R-T" }, { "family_name": "Murray", "given_name": "Ruchard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper focuses on the problem of exponential stabilization of controllable, driftless systems using time-varying, homogeneous feedback. The analysis is performed with respect to a homogeneous norm in a nonstandard dilation that is compatible with the algebraic structure of the control Lie algebra. It can be shown that any continuous, time-varying controller that achieves exponential stability relative to the Euclidean norm is necessarily non-Lipschitz. Despite these restrictions, we provide a set of constructive, sufficient conditions for extending smooth, asymptotic stabilizers to homogeneous, exponential stabilizers. The modified feedbacks are everywhere continuous, smooth away from the origin, and can be extended to a large class of systems with torque inputs. The feedback laws are applied to an experimental mobile robot and show significant improvement in convergence rate over smooth stabilizers.", "doi": "10.1109/9.580865", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "1997-05", "series_number": "5", "volume": "42", "issue": "5", "pages": "614-628" }, { "id": "authors:9c31n-drs27", "collection": "authors", "collection_id": "9c31n-drs27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LEWsiamjco97", "type": "article", "title": "Configuration Controllability of Simple Mechanical Control Systems", "author": [ { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we present a definition of \"configuration controllability\" for mechanical systems whose Lagrangian is kinetic energy with respect to a Riemannian metric minus potential energy. A computable test for this new version of controllability is derived. This condition involves an object which we call the symmetric product. Of particular interest is a definition of \"equilibrium controllability\" for which we are able to derive computable sufficient conditions. Examples illustrate the theory.", "doi": "10.1137/S0363012995287155", "issn": "0363-0129", "publisher": "SIAM Journal on Control and Optimization", "publication": "SIAM Journal on Control and Optimization", "publication_date": "1997-05", "series_number": "3", "volume": "35", "issue": "3", "pages": "766-790" }, { "id": "authors:dp0rr-v2p13", "collection": "authors", "collection_id": "dp0rr-v2p13", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1997.CIT-CDS-97-012", "type": "monograph", "title": "System Identification for Limit Cycling Systems: A Case Study for Combustion Instabilities", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Jacobsen", "given_name": "C.A.", "clpid": "Jacobsen-C-A" }, { "family_name": "Casas", "given_name": "R.", "clpid": "Casas-R" }, { "family_name": "Khibnik", "given_name": "A.I.", "clpid": "Khibnik-A-I" }, { "family_name": "Johnson", "given_name": "C.R. Jr.", "clpid": "Johnson-C-R-J" }, { "family_name": "Bitmead", "given_name": "R.", "clpid": "Bitmead-R" }, { "family_name": "Peracchio", "given_name": "A.A.", "clpid": "Peracchio-A-A" } ], "abstract": "This paper presents a case study in system identification for limit \ncycling systems. The focus of the paper is on (a) the use of model \nstructure derived from physcal considerations and (b) the use of algorithms \nfor the identification of component subsystems of this model structure. \nThe physical process used in this case study is that of a reduced order \nmodel for combustion instabilities for lean premixed systems. The \nidentification techniques applied in this paper are the use of linear system \nidentification tools (prediction error methods), time delay estimation (based on \nKalman filter harmonic estimation methods) and qualitative validation of \nmodel properties using harmonic balance and describing function methods. \nThe novelty of the paper, apart from its practical application, is that \nclosed loop limit cycle data is used together with a priori process \nstructural knowledge to identify both linear dynamic forward and nonlinear \nfeedback paths. Future work will address the refinement of the process \npresented in this paper, the use of alternative algorithms and also the use \nof control approachs for the validated model structure obtained from \nthis paper.", "publisher": "California Institute of Technology", "publication_date": "1997-01-01" }, { "id": "authors:vz43m-e3g52", "collection": "authors", "collection_id": "vz43m-e3g52", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1997.CIT-CDS-96-017", "type": "monograph", "title": "Real Time Trajectory Generation for Differentially Flat Systems", "author": [ { "family_name": "van Nieuwstadt", "given_name": "Michiel J.", "clpid": "van-Nieuwstadt-M-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper considers the problem of real time trajectory generation \nand tracking for nonlinear control systems. We employ a two degree of \nfreedom approach that separates the nonlinear tracking problem into real \ntime trajectory generation followed by local (gain-scheduled) \nstabilization. The central problem which we consider is how to generate, possibly \nwith some delay, a feasible state space and input trajectory in real \ntime from an output trajectory that is given online. We propose two \nalgorithms that solve the real time trajectory generation problem for \ndifferentially flat systems with (possibly non-minimum phase) zero dynamics. One \nis based on receding horizon point to point steering, the other allows \nadditional minimization of a cost function. Both algorithms explicitly address \nthe tradeoff between stability and performance and we prove convergence \nof the algorithms for a reasonable class of output trajectories. To \nillustrate the application of these techniques to physical systems, we present \nexperimental results using a vectored thrust flight control experiment built at \nCaltech. A brief introduction to differentially flat systems and its \nrelationship with feedback linearization is also included.", "publisher": "California Institute of Technology", "publication_date": "1997-01-01" }, { "id": "authors:qh0me-t9d81", "collection": "authors", "collection_id": "qh0me-t9d81", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1997.CIT-CDS-97-003", "type": "monograph", "title": "Tracking for Fully Actuated Mechanical Systems: A Geometric Framework", "author": [ { "family_name": "Bullo", "given_name": "Francesco", "clpid": "Bullo-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We present a general framework for the control of Lagrangian \nsystems with as many inputs as degrees of freedom. Relying on the geometry \nof mechanical systems on manifolds, we propose a design algorithm for \nthe tracking problem. The notion of error function and transport map \nlead to a proper definition of configuration and velocity error. These \nare the crucial ingredients in designing a proportional derivative \nfeedback and feedforward controller. The proposed approach includes as \nspecial cases a variety of results on control of manipulators, pointing \ndevices and autonomous vehicles. Our design provides particular insight \ninto both aerospace and underwater applications where the configuration \nmanifold is a Lie group.", "publisher": "California Institute of Technology", "publication_date": "1997-01-01" }, { "id": "authors:r7d0r-2ws36", "collection": "authors", "collection_id": "r7d0r-2ws36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100713-091226984", "type": "article", "title": "Nonholonomic Mechanical Systems with Symmetry", "author": [ { "family_name": "Bloch", "given_name": "Anthony M.", "clpid": "Bloch-A-M" }, { "family_name": "Krishnaprasad", "given_name": "P. S.", "clpid": "Krishnaprasad-P-S" }, { "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" } ], "abstract": "This work develops the geometry and dynamics of mechanical systems with nonholonomic constraints and symmetry from the perspective of Lagrangian mechanics and with a view to control-theoretical applications. The basic methodology is that of geometric mechanics applied to the Lagrange-d'Alembert formulation, generalizing the use of connections and momentum maps associated with a given symmetry group to this case. We begin by formulating the mechanics of nonholonomic systems using an Ehresmann connection to model the constraints, and show how the curvature of this connection enters into Lagrange's equations. Unlike the situation with standard configuration-space constraints, the presence of symmetries in the nonholonomic case may or may not lead to conservation laws. However, the momentum map determined by the symmetry group still satisfies a useful differential equation that decouples from the group variables. This momentum equation, which plays an important role in control problems, involves parallel transport operators and is computed explicitly in coordinates. An alternative description using a ldquobody reference framerdquo relates part of the momentum equation to the components of the Euler-Poincar\u00e9 equations along those symmetry directions consistent with the constraints. One of the purposes of this paper is to derive this evolution equation for the momentum and to distinguish geometrically and mechanically the cases where it is conserved and those where it is not. An example of the former is a ball or vertical disk rolling on a flat plane and an example of the latter is the snakeboard, a modified version of the skateboard which uses momentum coupling for locomotion generation. We construct a synthesis of the mechanical connection and the Ehresmann connection defining the constraints, obtaining an important new object we call the nonholonomic connection. When the nonholonomic connection is a principal connection for the given symmetry group, we show how to perform Lagrangian reduction in the presence of nonholonomic constraints, generalizing previous results which only held in special cases. Several detailed examples are given to illustrate the theory.", "doi": "10.1007/BF02199365", "issn": "0003-9527", "publisher": "Springer", "publication": "Archive for Rational Mechanics and Analysis", "publication_date": "1996-12", "series_number": "1", "volume": "136", "issue": "1", "pages": "21-99" }, { "id": "authors:aez2d-10a90", "collection": "authors", "collection_id": "aez2d-10a90", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1996.018", "type": "monograph", "title": "Configuration Flatness of Lagrangian Systems Underactuated by One Control", "author": [ { "family_name": "Rathinam", "given_name": "Muruhan", "clpid": "Rathinam-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Lagrangian control systems that are differentially flat with flat outputs that only depend on configuration variables are said to be configuration flat. We provide a complete characterisation of configuration flatness for systems with n degrees of freedom and n - 1 controls whose range of control forces only depends on configuration and whose Lagrangian has the form of kinetic energy minus potential. The method presented allows us to determine if such a system is configuration flat and, if so provides a constructive method for finding all possible configuration flat outputs. Our characterisation relates configuration flatness to Riemannian geometry. We illustrate the method by two examples.", "publisher": "California Institute of Technology", "publication_date": "1996-09-27" }, { "id": "authors:mg3f9-08n32", "collection": "authors", "collection_id": "mg3f9-08n32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200310-145803556", "type": "article", "title": "Robust Nonlinear Control Theory with Applications to Aerospace Vehicles", "author": [ { "family_name": "Doyle", "given_name": "John", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper is a very brief outline of an invited poster session giving a first-year progress report on a research program with the above title being carried out in the Control and Dynamical Systems (CDS) department at Caltech. This 5-year grant funded by the AFOSR Partnership for Research Excellence Transition (PRET) Program has a special emphasis on transitioning new methods to industrial practice and thus involves a high level of industrial participation. The focus of our program is fundamental research in general methods of analysis and design of complex uncertain nonlinear systems, from creating new mathematical theory to working to make that theory help engineers solve a variety of real industrial problems. Caltech's Control and Dynamical Systems department was created with precisely this goal, which is shared by our industrial collaborators, led by Honeywell. Further details will be available at the poster session.", "doi": "10.1016/s1474-6670(17)58916-8", "issn": "1474-6670", "publisher": "Pergamon", "publication": "IFAC Proceedings Volumes", "publication_date": "1996-06", "series_number": "1", "volume": "29", "issue": "1", "pages": "7624-7629" }, { "id": "authors:nc5x7-9sp27", "collection": "authors", "collection_id": "nc5x7-9sp27", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1996.CIT-CDS-96-006", "type": "monograph", "title": "Configuration Flatness of Lagrangian Systems Underactuated by One Control", "author": [ { "family_name": "Rathinam", "given_name": "Muruhan", "clpid": "Rathinam-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Lagrangian control systems that are differentially flat with flat \noutputs that only depend on configuration variables are said to be \nconfiguration flat. We provide a complete characterisation of configuration \nflatness for systems with $n$ degrees of freedom and $n-1$ controls whose \nrange of control forces only depends on configuration and whose \nLagrangian has the form of kinetic energy minus potential. The method \npresented allows us to determine if such a system is configuration flat and, \nif so provides a constructive method for finding all possible \nconfiguration flat outputs. Our characterisation relates configuration flatness \nto Riemannian geometry. We illustrate the method by two examples.", "publisher": "California Institute of Technology", "publication_date": "1996-01-01" }, { "id": "authors:atdba-tj579", "collection": "authors", "collection_id": "atdba-tj579", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1996.CIT-CDS-96-015", "type": "monograph", "title": "An Experimental Comparison of Tradeoffs in Using Compliant Manipulators for Robotic Grasping Tasks", "author": [ { "family_name": "Sur", "given_name": "Sudipto", "clpid": "Sur-S" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Controllers developed for control of flexible-link robots in hybrid\nforce-position control tasks by a new singular perturbation analysis\nof flexible manipulators are implemented on an experimental two-robot\ngrasping setup. Performance criteria are defined for the grasping\ntask. We present preliminary experimental data to show the tradeoffs\nbetween controller complexity and performance enhancement as we deal\nwith greater flexibility. Various performance criteria are set up and\nexperimental results are discussed within that setting. We conclude\nthat large flexibility can be controlled and can lead to reasonable\nperformances.", "publisher": "California Institute of Technology", "publication_date": "1996-01-01" }, { "id": "authors:b81as-p1483", "collection": "authors", "collection_id": "b81as-p1483", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1996.CIT-CDS-96-007", "type": "monograph", "title": "Decomposition for Control Systems on Manifolds with an Affine Connection", "author": [ { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this letter we present a decomposition for control systems whose \ndrift vector field is the geodesic spray associated with an affine \nconnection. With the geometric insight gained with this decomposition, we are \nable to easily prove some special results for this class of control \nsystems. Examples illustrate the theory.", "publisher": "California Institute of Technology", "publication_date": "1996-01-01" }, { "id": "authors:3s283-kvz40", "collection": "authors", "collection_id": "3s283-kvz40", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1996.CIT-CDS-95-029", "type": "monograph", "title": "Active Control of an Axial Flow Compressor via Pulsed Air Injection", "author": [ { "family_name": "D'Andrea", "given_name": "Raffaello", "clpid": "D'Andrea-R" }, { "family_name": "Behnken", "given_name": "Robert L.", "clpid": "Behnken-R-L" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper presents the use of pulsed air injection \nto control the onset of rotating stall in a low-speed, axial flow \ncompressor. By measuring the unsteady pressures near the rotor face, a control \nalgorithm determines the magnitude and phase of the first mode of rotating \nstall and controls the injection of air in the front of the rotor face. \nExperimental results show that this technique slightly extends the stall point \nof the compressor and eliminates the hysteresis loop normally \nassociated with rotating stall. A parametric study is used to determine the \noptimal control parameters for suppression of stall. Analytic \nresults---using a low-dimensional model developed by Moore and Greitzer combined \nwith an unsteady shift in the compressor characteristic to model the \ninjectors---give further insights into the operation of the controller. Based on \nthis model, we show that the behavior of the experiment can be explained \nas a change in the bifurcation behavior of the system under nonlinear \nfeedback. A higher fidelity simulation model is then used to further verify \nsome of the specific performance characteristics that are observed in \nexperiments.", "publisher": "California Institute of Technology", "publication_date": "1996-01-01" }, { "id": "authors:3pgzc-w6562", "collection": "authors", "collection_id": "3pgzc-w6562", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142358983", "type": "book_section", "title": "Approximate trajectory generation for differentially flat systems with zero dynamics", "book_title": "Proceedings of 1995 34th IEEE Conference on Decision and Control", "author": [ { "family_name": "van Nieuwstadt", "given_name": "Michiel J.", "clpid": "van-Nieuwstadt-M-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes algorithms to generate trajectories for differentially flat systems with zero dynamics. Zero dynamics in flat systems occur when the flat outputs are not the tracking outputs. This means that the output trajectories can be fully parametrized by the flat outputs, but that there is some additional freedom left. This freedom can be exploited to minimize a cost criterion. We parametrize the differentially flat outputs by basis functions, and solve for the parameters so as to track a prescribed trajectory approximately while minimizing a cost function. We give examples of such systems, and present simulations and experimental data. We focus on implementation issues and point out the computational cost involved in the various problems.", "doi": "10.1109/cdc.1995.478902", "isbn": "0780326857", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-12", "pages": "4224-4230" }, { "id": "authors:b4yer-qag47", "collection": "authors", "collection_id": "b4yer-qag47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142359062", "type": "book_section", "title": "Robust performance analysis for a class of uncertain nonlinear systems", "book_title": "Proceedings of 1995 34th IEEE Conference on Decision and Control", "author": [ { "family_name": "Tierno", "given_name": "Jorge E.", "clpid": "Tierno-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Performance analysis of a large class of nonlinear systems is proven to be equivalent to performance analysis of a constrained uncertain linear system, for which computable analysis methods have already been developed.", "doi": "10.1109/cdc.1995.480382", "isbn": "0780326857", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-12", "pages": "1684-1689" }, { "id": "authors:qp6q8-rr689", "collection": "authors", "collection_id": "qp6q8-rr689", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142358825", "type": "book_section", "title": "Control of rotating stall in a low-speed axial flow compressor using pulsed air injection: modeling, simulations, and experimental validation", "book_title": "Proceedings of 1995 34th IEEE Conference on Decision and Control", "author": [ { "family_name": "Behnken", "given_name": "Robert L.", "clpid": "Behnken-R-L" }, { "family_name": "D'Andrea", "given_name": "Raffaello", "clpid": "D'Andrea-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Previous results in the use of pulsed air injection for active control of rotating stall have suggested that air injectors have the effect of shifting the steady state compressor characteristic. In this paper we analyze the effect of a compressor characteristic actuation scheme for the three state Moore Greitzer compression system model. It is shown that closed loop feedback based on the square magnitude of the first rotating stall mode can be used to decrease the hysteresis region associated with the transition from unstalled to stalled and back to unstalled operation. The compressor characteristic shifting idea is then applied to a higher fidelity distributed model in which the characteristic shifting has phase content in addition to the magnitude content captured by the three state model. The optimal phasing of the air injection relative to the sensed position of the stall cell is determined via simulation and the results found to agree with those obtained via an experimental parametric study on the Caltech low-speed axial flow compressor.", "doi": "10.1109/cdc.1995.478613", "isbn": "0780326857", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-12", "pages": "3056-3061" }, { "id": "authors:gpja1-7cy31", "collection": "authors", "collection_id": "gpja1-7cy31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142358906", "type": "book_section", "title": "Configuration controllability for a class of mechanical systems", "book_title": "Proceedings of 1995 34th IEEE Conference on Decision and Control", "author": [ { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "We define a notion of controllability for mechanical systems which determines the configurations which are accessible from a given configuration. We derive sufficient conditions for this notion of controllability in terms of the given inputs, their Lie brackets, and their covariant derivatives.", "doi": "10.1109/cdc.1995.478914", "isbn": "0780326857", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-12", "pages": "4288-4293" }, { "id": "authors:seskv-grc42", "collection": "authors", "collection_id": "seskv-grc42", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-94-006", "type": "monograph", "title": "Differential Flatness and Absolute Equivalence", "author": [ { "family_name": "van Nieuwstadt", "given_name": "Michiel", "clpid": "van-Nieuwstadt-M-J" }, { "family_name": "Rathinam", "given_name": "Muruhan", "clpid": "Rathinam-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we give a formulation of differential flatness---a concept originally introduced by Fleiss, Levine, Martin, and Rouchon---in terms of absolute equivalence between exterior differential systems. Systems which are differentially flat have several useful properties which can be exploited to generate effective control strategies for nonlinear systems. The original definition of flatness was given in the context of differentiable algebra, and required that all mappings be meromorphic functions. Our formulation of flatness does not require any algebraic structure and allows one to use tools from exterior differential systems to help characterize differentially flat systems. In particular, we shown that in the case of single input control systems (i.e., codimension 2 Pfaffian systems), a system is differentially flat if and only if it is feedback linearizable via static state feedback. However, in higher codimensions feedback linearizability and flatness are *not* equivalent: one must be careful with the role of time as well the use of prolongations which may not be realizable as dynamic feedbacks in a control setting. Applications of differential flatness to nonlinear control systems and open questions will be discussed. Revised 14 Aug 95", "publisher": "California Institute of Technology", "publication_date": "1995-08-14" }, { "id": "authors:nzpt9-8h376", "collection": "authors", "collection_id": "nzpt9-8h376", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142359300", "type": "book_section", "title": "An efficient algorithm for performance analysis of nonlinear control systems", "book_title": "Proceedings of 1995 American Control Conference - ACC'95", "author": [ { "family_name": "Tierno", "given_name": "Jorge E.", "clpid": "Tierno-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" } ], "abstract": "A numerical algorithm for computing necessary conditions for performance specifications is developed for nonlinear uncertain systems. The algorithm is similar in nature and behavior to the power algorithm for the \u00b5 lower bound, and does not rely on a descent method. The algorithm is applied to a practical example.", "doi": "10.1109/acc.1995.532342", "isbn": "0780324455", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-06", "pages": "2717-2721" }, { "id": "authors:nqp8v-mae83", "collection": "authors", "collection_id": "nqp8v-mae83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142359220", "type": "book_section", "title": "An experimental comparison of controllers for a vectored thrust, ducted fan engine", "book_title": "Proceedings of 1995 American Control Conference - ACC'95", "author": [ { "family_name": "Kantner", "given_name": "Michael", "clpid": "Kantner-M" }, { "family_name": "Bodenheimer", "given_name": "Bobby", "clpid": "Bodenheimer-B" }, { "family_name": "Bendotti", "given_name": "Pascale", "clpid": "Bendotti-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Experimental comparisons between four different control design methodologies are applied to a small vectored thrust engine. Each controller is applied to three trajectories of varying aggressiveness. The control strategies considered are LQR, \u210b\u221e, gain scheduling, and feedback linearization. The experiments show that gain scheduling is essential to achieving good performance. The strengths and weaknesses of each methodology are also examined.", "doi": "10.1109/acc.1995.531229", "isbn": "0780324455", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-06", "pages": "1956-1961" }, { "id": "authors:t154n-f4e63", "collection": "authors", "collection_id": "t154n-f4e63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:TILieeetac95", "type": "article", "title": "Trajectory generation for the N-trailer problem using Goursat normal form", "author": [ { "family_name": "Tilbury", "given_name": "Dawn", "clpid": "Tilbury-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "Develops the machinery of exterior differential forms, more particularly the Goursat normal form for a Pfaffian system, for solving nonholonomic motion planning problems, i.e., motion planning for systems with nonintegrable velocity constraints. The authors use this technique to solve the problem of steering a mobile robot with n trailers. The authors present an algorithm for finding a family of transformations which will convert the system of rolling constraints on the wheels of the robot with n trailers into the Goursat canonical form. Two of these transformations are studied in detail. The Goursat normal form for exterior differential systems is dual to the so-called chained-form for vector fields that has been studied previously. Consequently, the authors are able to give the state feedback law and change of coordinates to convert the N-trailer system into chained-form. Three methods for planning trajectories for chained-form systems using sinusoids, piecewise constants, and polynomials as inputs are presented. The motion planning strategy is therefore to first convert the N-trailer system into Goursat form, use this to find the chained-form coordinates, plan a path for the corresponding chained-form system, and then transform the resulting trajectory back into the original coordinates. Simulations and frames of movie animations of the N-trailer system for parallel parking and backing into a loading dock using this strategy are included.", "doi": "10.1109/9.384215", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "1995-05", "series_number": "5", "volume": "40", "issue": "5", "pages": "802-819" }, { "id": "authors:wsb7y-2d766", "collection": "authors", "collection_id": "wsb7y-2d766", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142359139", "type": "book_section", "title": "The mechanics of undulatory locomotion: the mixed kinematic and dynamic case", "book_title": "Proceedings of 1995 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Ostrowski", "given_name": "Jim", "clpid": "Ostrowski-J-P" }, { "family_name": "Burdick", "given_name": "Joel", "clpid": "Burdick-J-W" }, { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper studies the mechanics of undulatory locomotion. This type of locomotion is generated by a coupling of internal shape changes to external non-holonomic constraints. Employing methods from geometric mechanics, the authors use the dynamic symmetries and kinematic constraints to develop a specialized form of the dynamic equations which govern undulatory systems. These equations are written in terms of physically meaningful and intuitively appealing variables that show the role of internal shape changes in driving locomotion.", "doi": "10.1109/robot.1995.525549", "isbn": "0780319656", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1995-05", "pages": "1945-1951" }, { "id": "authors:rawy5-knx49", "collection": "authors", "collection_id": "rawy5-knx49", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-94-013", "type": "monograph", "title": "Nonholonomic Mechanical Systems with Symmetry", "author": [ { "family_name": "Bloch", "given_name": "A. M.", "clpid": "Bloch-A-M" }, { "family_name": "Krishnaprasad", "given_name": "P. S.", "clpid": "Krishnaprasad-P-S" }, { "family_name": "Marsden", "given_name": "J. E.", "clpid": "Marsden-J-E" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This work develops the geometry and dynamics of mechanical systems with nonholonomic constraints and symmetry from the perspective of Lagrangian mechanics and with a view to control theoretical applications. The basic methodology is that of geometric mechanics applied to the formulation of Lagrange d'Alembert, generalizing the use of connections and momentum maps associated with a given symmetry group to this case. We begin by formulating the mechanics of nonholonomic systems using an Ehresmann connection to model the constraints, and show how the curvature of this connection enters into Lagrange's equations. Unlike the situation with standard configuration space constraints, the presence of symmetries in the nonholonomic case may or may not lead to conservation laws. However, the momentum map determined by the symmetry group still satisfies a useful differential equation that decouples from the group variables. This momentum equation, which plays an important role in control problems, involves parallel transport operators and is computed explicitly in coordinates. An alternative description using a ``body reference frame'' relates part of the momentum equation to the components of the Euler-Poincar\\'{e} equations along those symmetry directions consistent with the constraints. One of the purposes of this paper is to derive this evolution equation for the momentum and to distinguish geometrically and mechanically the cases where it is conserved and those where it is not. An example of the former is a ball or vertical disk rolling on a flat plane and an example of the latter is the snakeboard, a modified version of the skateboard which uses momentum coupling for locomotion generation. We construct a synthesis of the mechanical connection and the Ehresmann connection defining the constraints, obtaining an important new object we call the nonholonomic connection. When the nonholonomic connection is a principal connection for the given symmetry group, we show how to perform Lagrangian reduction in the presence of nonholonomic constraints, generalizing previous results which only held in special cases. Several detailed examples are given to illustrate the theory. September 1994 Revised, March 1995 Revised, June 1995", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:czz6z-zm965", "collection": "authors", "collection_id": "czz6z-zm965", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-95-012", "type": "monograph", "title": "Exponential Stabilization of Driftless Nonlinear Control Systems using Homogeneous Feedback", "author": [ { "family_name": "M'Closkey", "given_name": "Robert T.", "clpid": "M'Closkey-R-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper focuses on the problem of exponential stabilization of\ncontrollable, driftless systems using time-varying, homogeneous\nfeedback. The analysis is performed with respect to a homogeneous\nnorm in a non-standard dilation that is compatible with the algebraic\nstructure of the control Lie algebra. Using this structure, we show\nthat any continuous, time-varying controller that achieves exponential\nstabilization relative to the Euclidean norm is necessarily\nnon-Lipschitz. Despite these restrictions, we provide a set of\nconstructive, sufficient conditions for extending smooth, asymptotic\nstabilizers to homogeneous, exponential stabilizers. The modified\nfeedbacks are everywhere continuous, smooth away from the origin, and\ncan be extended to a large class of systems with torque inputs. The\nfeedback laws are applied to an experimental mobile robot and show\nsignificant improvement in convergence rate over smooth stabilizers.", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:5fs0n-0vw05", "collection": "authors", "collection_id": "5fs0n-0vw05", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-95-032", "type": "monograph", "title": "Numerically Efficient Robustness Analysis of Trajectory Tracking for Nonlinear Systems", "author": [ { "family_name": "Tierno", "given_name": "Jorge E.", "clpid": "Tierno-J-E" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Doyle", "given_name": "John C.", "orcid": "0000-0002-1828-2486", "clpid": "Doyle-J-C" }, { "family_name": "Gregory", "given_name": "Irene M.", "clpid": "Gregory-I-M" } ], "abstract": "A numerical algorithm for computing necessary conditions for \nperformance specifications is developed for nonlinear uncertain systems \nfollowing a prescribed trajectory. This algorithm provides a computational \nefficient means of evaluating the performance of a nonlinear system in the \npresence of noise, real parametric uncertainty, and unmodeled dynamics. The \nalgorithm is similar in nature and behavior to the power algorithm for the mu \nlower bound, and does not rely on a descent method. The algorithm is \napplied to two flight control examples.", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:s9dkh-10a09", "collection": "authors", "collection_id": "s9dkh-10a09", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-95-025", "type": "monograph", "title": "A Homotopy Algorithm for Approximating Geometric Distributions by Integrable Systems", "author": [ { "family_name": "Sluis", "given_name": "Willem M.", "clpid": "Sluis-W-M" }, { "family_name": "Banaszuk", "given_name": "Andrzej", "clpid": "Banaszuk-A" }, { "family_name": "Hauser", "given_name": "John", "clpid": "Hauser-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In the geometric theory of nonlinear control systems, the notion of a\ndistribution and the dual notion of codistribution play a central\nrole. Many results in nonlinear control theory require certain\ndistributions to be integrable. Distributions (and codistributions)\nare not generically integrable and, moreover, the integrability\nproperty is not likely to persist under small perturbations of the\nsystem. Therefore, it is natural to consider the problem of\napproximating a given codistribution by an integrable codistribution,\nand to determine to what extent such an approximation may be used for\nobtaining approximate solutions to various problems in control\ntheory. In this note, we concentrate on the purely mathematical\nproblem of approximating a given codistribution by an integrable\ncodistribution. We present an algorithm for approximating an\nm-dimensional nonintegrable codistribution by an integrable one using\na homotopy approach. The method yields an approximating codistribution\nthat agrees with the original codistribution on an m-dimensional\nsubmanifold E_0 of R^n.", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:dan54-2aa27", "collection": "authors", "collection_id": "dan54-2aa27", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-95-015", "type": "monograph", "title": "Configuration Controllability of Simple Mechanical Control Systems", "author": [ { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we present a definition of \"configuration controllability\"\nfor mechanical systems whose Lagrangian is kinetic energy with\nrespect to a Riemannian metric minus potential energy. A computable\ntest for this new version of controllability is also derived. This \ncondition involves a new object which we call the {\\em symmetric\nproduct}. Of particular interest is a definition of \"equilibrium controllability\"\nfor which we are able to derive computable sufficient conditions.\nExamples illustrate the theory.", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:fjkqw-v1p46", "collection": "authors", "collection_id": "fjkqw-v1p46", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-95-005", "type": "monograph", "title": "Control on the Sphere and Reduced Attitude Stabilization", "author": [ { "family_name": "Bullo", "given_name": "Francesco", "clpid": "Bullo-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sarti", "given_name": "Augusto", "clpid": "Sarti-A" } ], "abstract": "This paper focuses on a new geometric approach to (fully actuated)\ncontrol systems on the sphere. Our control laws exploit the basic and\nintuitive notions of geodesic direction and of distance between\npoints, and generalize the classical proportional plus derivative\nfeedback (PD) without the need of arbitrary local coordinate charts.\nThe stability analysis relies on an appropriate Lyapunov function,\nwhere the notion of distance and its properties are exploited. This\nmethodology then applies to spin-axis stabilization of a spacecraft\nactuated by only two control torques: discarding the rotation about\nthe unactuated axis, a reduced system is considered, whose state is in\nfact defined on the sphere. For this reduced stabilization problem\nour approach allows us not only to deal optimally with the inevitable\nsingularity, but also to achieve simplicity, versatility and\n(coordinate independent) adaptive capabilities.", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:wgq2y-5kk21", "collection": "authors", "collection_id": "wgq2y-5kk21", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1995.CIT-CDS-95-010", "type": "monograph", "title": "Proportional Derivative (PD) Control on the Euclidean Group", "author": [ { "family_name": "Bullo", "given_name": "Francesco", "clpid": "Bullo-F" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we study the stabilization problem for control \nsystems defined on SE(3) (the special Euclidean group of rigid-body \nmotions) and its subgroups. Assuming one actuator is available for each \ndegree of freedom, we exploit geometric properties of Lie groups (and \ncorresponding Lie algebras) to generalize the classical proportional derivative \n(PD) control in a coordinate-free way. For the SO(3) case, the \ncompactness of the group gives rise to a natural metric structure and to a \nnatural choice of preferred control direction: an optimal (in the sense of \ngeodesic) solution is given to the attitude control problem. In the SE(3) \ncase, no natural metric is uniquely defined, so that more freedom is left \nin the control design. Different formulations of PD feedback can be \nadopted by extending the SO(3) approach to the whole of SE(3) or by \nbreaking the problem into a control problem on SO(3) x R^3. For the simple \nSE(2) case, simulations are reported to illustrate the behavior of the \ndifferent choices. We also discuss the trajectory tracking problem and show \nhow to reduce it to a stabilization problem, mimicking the usual \napproach in R^n. Finally, regarding the case of underactuated control \nsystems, we derive linear and homogeneous approximating vector fields for \nstandard systems on SO(3) and SE(3).", "publisher": "California Institute of Technology", "publication_date": "1995-01-01" }, { "id": "authors:mx7y8-13475", "collection": "authors", "collection_id": "mx7y8-13475", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-130817404", "type": "book_section", "title": "Exponential stabilization of driftless nonlinear control systems via time-varying, homogeneous feedback", "author": [ { "family_name": "M'Closkey", "given_name": "Robert T.", "orcid": "0000-0003-1443-8217", "clpid": "M'Closkey-R-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper brings together results from a number of different areas in control theory to provide an algorithm for the synthesis of locally exponentially stabilizing control laws for a large class of driftless nonlinear control systems. The stability is defined with respect to a nonstandard dilation and is termed \"\u03b4-exponential\" stability. The \u03b4-exponential stabilization relies on the use of feedbacks which render the closed loop vector field homogeneous with respect to a dilation. These feedbacks are generated from a modification of Pomet's algorithm (1992) for smooth feedbacks. Converse Lyapunov theorems for time-periodic homogeneous vector fields guarantee that local exponential stability is maintained in the presence of higher order (with respect to the dilation) perturbing terms.", "doi": "10.1109/CDC.1994.411139", "publisher": "IEEE", "publication_date": "1994-12" }, { "id": "authors:4708p-er762", "collection": "authors", "collection_id": "4708p-er762", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190319-091908577", "type": "book_section", "title": "Differential flatness and absolute equivalence", "book_title": "Proceedings of 1994 33rd IEEE Conference on Decision and Control", "author": [ { "family_name": "van Nieuwstadt", "given_name": "M.", "clpid": "van-Nieuwstadt-M-J" }, { "family_name": "Rathinam", "given_name": "M.", "clpid": "Rathinam-M" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we give a formulation of differential flatness-a concept originally introduced by Fliess, Levine, Martin, and Rouchon (1992)-in terms of absolute equivalence between exterior differential systems. Systems which are differentially flat have several useful properties which can be exploited to generate effective control strategies for nonlinear systems. The original definition of flatness was given in the context of differential algebra, and required that all mappings be meromorphic functions. Our formulation of flatness does not require any algebraic structure and allows one to use tools from exterior differential systems to help characterize differentially flat systems. In particular, we show that in the case of single input control systems (i.e., codimension 2 Pfaffian systems), a system is differentially flat if and only if it is feedback linearizable via static state feedback. However, in higher codimensions feedback linearizability and flatness are not equivalent: one must be careful with the role of time as well the use of prolongations which may not be realizable as dynamic feedbacks in a control setting. Applications of differential flatness to nonlinear control systems and open questions are also discussed.", "doi": "10.1109/CDC.1994.410908", "isbn": "0-7803-1968-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1994-12", "pages": "326-332" }, { "id": "authors:606zf-tfc37", "collection": "authors", "collection_id": "606zf-tfc37", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-150352226", "type": "article", "title": "A motion planner for nonholonomic mobile robots", "author": [ { "family_name": "Laumond", "given_name": "Jean-Paul", "clpid": "Laumond-J-P" }, { "family_name": "Jacobs", "given_name": "Paul E.", "clpid": "Jacobs-P-E" }, { "family_name": "Ta\u00efx", "given_name": "Michel", "clpid": "Ta\u00efx-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper considers the problem of motion planning for a car-like robot (i.e., a mobile robot with a nonholonomic constraint whose turning radius is lower-bounded). We present a fast and exact planner for our mobile robot model, based upon recursive subdivision of a collision-free path generated by a lower-level geometric planner that ignores the motion constraints. The resultant trajectory is optimized to give a path that is of near-minimal length in its homotopy class. Our claims of high speed are supported by experimental results for implementations that assume a robot moving amid polygonal obstacles. The completeness and the complexity of the algorithm are proven using an appropriate metric in the configuration space R^2 x S^1 of the robot. This metric is defined by using the length of the shortest paths in the absence of obstacles as the distance between two configurations. We prove that the new induced topology and the classical one are the same. Although we concentrate upon the car-like robot, the generalization of these techniques leads to new theoretical issues involving sub-Riemannian geometry and to practical results for nonholonomic motion planning.", "doi": "10.1109/70.326564", "issn": "1042-296X", "publisher": "IEEE", "publication": "IEEE Transactions on Robotics and Automation", "publication_date": "1994-10", "series_number": "5", "volume": "10", "issue": "5", "pages": "577-593" }, { "id": "authors:sfw9j-c6p61", "collection": "authors", "collection_id": "sfw9j-c6p61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-093858769", "type": "book_section", "title": "Experiments in exponential stabilization of a mobile robot towing a trailer", "book_title": "Proceedings of 1994 American Control Conference (ACC '94)", "author": [ { "family_name": "M'Closkey", "given_name": "Robert T.", "orcid": "0000-0003-1443-8217", "clpid": "M'Closkey-R-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Applies some previously developed control laws for stabilization of mechanical systems with non-holonomic constraints to an experimental system consisting of a mobile robot towing a trailer. The authors verify the applicability of various control laws which have appeared in the recent literature, and compare the performance of these controllers in an experimental setting. In particular, the authors show that time-periodic, non-smooth controllers can be used to achieve exponential stability of a desired equilibrium configuration, and that these controllers outperform smooth, time-varying control laws. The authors also point out several practical considerations which must be taken into account when implementing these controllers.", "doi": "10.1109/ACC.1994.751893", "isbn": "0-7803-1783-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1994-07", "pages": "988-993" }, { "id": "authors:naf8d-ha130", "collection": "authors", "collection_id": "naf8d-ha130", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-140628400", "type": "book_section", "title": "Design and construction of a small ducted fan engine for nonlinear control experiments", "book_title": "Proceedings of 1994 American Control Conference", "author": [ { "family_name": "Choi", "given_name": "Henry", "clpid": "Choi-Henry" }, { "family_name": "Sturdza", "given_name": "Peter", "clpid": "Sturdza-P" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper describes the design and construction of a small ducted fan engine which is being used for experimental research in robust nonlinear control of high-performance vectored thrust aircraft. The fan consists of a high-efficiency electric motor with a 6-inch diameter blade, capable of generating up to 9 Newtons of thrust. Flaps on the fan allow the thrust to be vectored from side to side and even reversed. The engine is mounted on a three degree of freedom stand which allows horizontal and vertical translation as well as unrestricted pitch angle. We give a detailed description of the design and construction of the fan and its analytical and empirical models. Initial PID controllers for altitude and pitch angle stabilization are included to verify the system model and indicate future avenues of research.", "doi": "10.1109/ACC.1994.735033", "isbn": "0-7803-1783-1", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1994-07", "pages": "2618-2622" }, { "id": "authors:9tscv-9m103", "collection": "authors", "collection_id": "9tscv-9m103", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-142601604", "type": "book_section", "title": "Nonholonomic mechanics and locomotion: the snakeboard example", "book_title": "Proceedings of the 1994 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Ostrowski", "given_name": "Jim", "clpid": "Ostrowski-J" }, { "family_name": "Lewis", "given_name": "Andrew", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Burdick", "given_name": "Joel", "clpid": "Burdick-J-W" } ], "abstract": "Analysis and simulations are performed for a simplified model of a commercially available variant of the skateboard, known as the Snakeboard. Although the model exhibits basic gait patterns seen in a large number of locomotion problems, the analysis tools currently available do not apply to this problem. The difficulty lies primarily in the way in which the nonholonomic constraints enter into the system. As a first step towards understanding systems represented by their model the authors present the equations of motion and perform some controllability analysis for the snakeboard. The authors also perform numerical simulations of possible gait patterns which are characteristic of snakeboard locomotion.", "doi": "10.1109/ROBOT.1994.351153", "isbn": "0-8186-5330-2", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1994-05", "pages": "2391-2397" }, { "id": "authors:ssytx-z6q73", "collection": "authors", "collection_id": "ssytx-z6q73", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1994.CIT-CDS-94-014", "type": "monograph", "title": "Geometric Phases and Robotic Locomotion", "author": [ { "family_name": "Kelly", "given_name": "Scott D.", "clpid": "Kelly-S-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Robotic locomotion is based in a variety of instances upon cyclic changes in the shape of a robot mechanism. Certain variations in shape exploit the constrained nature of a robot's interaction with its environment to generate net motion. This is true for legged robots, snakelike robots, and wheeled mobile robots undertaking maneuvers such as parallel parking. In this paper we explore the use of tools from differential geometry to model and analyze this class of locomotion mechanisms in a unified way. In particular, we describe locomotion in terms of the geometric phase associated with a connection on a principal bundle, and address issues such as controllability and choice of gait. We also provide an introduction to the basic mathematical concepts which we require and apply the theory to numerous example systems.", "publisher": "California Institute of Technology", "publication_date": "1994-01-01" }, { "id": "authors:2pdbe-k1104", "collection": "authors", "collection_id": "2pdbe-k1104", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1994.CIT-CDS-94-016", "type": "monograph", "title": "Variational Principles for Constrained Systems: Theory and Experiment", "author": [ { "family_name": "Lewis", "given_name": "Andrew D.", "clpid": "Lewis-A-D" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper we present two methods, the nonholonomic method and the\nvakonomic method, for deriving equations of motion for a\nmechanical system with constraints. The resulting equations are compared.\nResults are also presented from an experiment for a model system: a ball\nrolling without sliding on a rotating table. Both sets of equations of\nmotion for the model system are compared with the experimental results. The\neffects of various forms of friction are considered in the nonholonomic\nequations. With appropriate friction terms, the nonholonomic equations of\nmotion for the model system give reasonable agreement with the experimental\nobservations.", "publisher": "California Institute of Technology", "publication_date": "1994-01-01" }, { "id": "authors:ghgf3-cps38", "collection": "authors", "collection_id": "ghgf3-cps38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:WALieeetac94", "type": "article", "title": "Stabilization of trajectories for systems with nonholonomic constraints", "author": [ { "family_name": "Walsh", "given_name": "G.", "clpid": "Walsh-G" }, { "family_name": "Tilbury", "given_name": "D.", "clpid": "Tilbury-D" }, { "family_name": "Sastry", "given_name": "S.", "clpid": "Sastry-S-Shankar" }, { "family_name": "Murray", "given_name": "R.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Laumond", "given_name": "J. P.", "clpid": "Laumond-J-P" } ], "abstract": "A new technique for stabilizing nonholonomic systems to trajectories is presented. It is well known that such systems cannot be stabilized to a point using smooth static-state feedback. In this note, we suggest the use of control laws for stabilizing a system about a trajectory, instead of a point. Given a nonlinear system and a desired (nominal) feasible trajectory, the note gives an explicit control law which will locally exponentially stabilize the system to the desired trajectory. The theory is applied to several examples, including a car-like robot.", "doi": "10.1109/9.273373", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "1994-01", "series_number": "1", "volume": "39", "issue": "1", "pages": "216-222" }, { "id": "authors:8nycy-k3v09", "collection": "authors", "collection_id": "8nycy-k3v09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-140045299", "type": "book_section", "title": "Trajectory generation for the N-trailer problem using Goursat normal form", "book_title": "32nd IEEE Conference on Decision and Control", "author": [ { "family_name": "Tilbury", "given_name": "D.", "clpid": "Tilbury-D" }, { "family_name": "Murray", "given_name": "R. M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S.", "clpid": "Sastry-S-Shankar" } ], "abstract": "Shows how the machinery of exterior differential systems can be used to help solve nonholonomic motion planning problems. Since the Goursat normal form, for exterior differential systems is dual to chained form for vector fields, the authors solve the problem of steering a mobile robot with N trailers by converting the system into chained form, doing the path-planning in the chained form coordinates, and converting the path back into the original coordinates. Simulations of the N-trailer system parallel parking and backing into a loading dock are included.", "doi": "10.1109/CDC.1993.325330", "isbn": "0-7803-1298-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1993-12", "pages": "971-977" }, { "id": "authors:ngmby-qvv73", "collection": "authors", "collection_id": "ngmby-qvv73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-160152940", "type": "book_section", "title": "Nonholonomic systems and exponential convergence: some analysis tools", "book_title": "Proceedings of 32nd IEEE Conference on Decision and Control", "author": [ { "family_name": "M'Closkey", "given_name": "Robert T.", "orcid": "0000-0003-1443-8217", "clpid": "M'Closkey-R-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "In this paper the authors make a contribution to the analysis of nonholonomic systems with exponential rates of convergence. A key idea is the use of control laws which render the closed loop system homogeneous with respect to a dilation. The analysis is applied to nonholonomic systems in power form and consists of two steps. The first step is a reduction to an invariant set and then the application of an averaging result. The averaging theorem is a stability result for C^0 homogeneous order zero vector fields.", "doi": "10.1109/CDC.1993.325324", "isbn": "0-7803-1298-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1993-12", "pages": "943-948" }, { "id": "authors:4tarb-bky02", "collection": "authors", "collection_id": "4tarb-bky02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-100713740", "type": "book_section", "title": "Applications and extensions of Goursat normal form to control of nonlinear systems", "book_title": "Proceedings of 32nd IEEE Conference on Decision and Control", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "The Goursat normal form theorem gives conditions under which a Pfaffian exterior differential system is equivalent to a certain normal form. This paper details how the Goursat normal form and its extensions provide a unified framework for understanding feedback linearization, chained form, and differential flatness.", "doi": "10.1109/CDC.1993.325849", "isbn": "0-7803-1298-8", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1993-12", "pages": "3425-3430" }, { "id": "authors:m3bgc-epq27", "collection": "authors", "collection_id": "m3bgc-epq27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-123339977", "type": "book_section", "title": "Convergence Rates for Nonholonomic Systems in Power Form", "book_title": "1993 American Control Conference", "author": [ { "family_name": "M'Closkey", "given_name": "Robert T.", "clpid": "M'Closkey-R-T" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper investigates the convergence rates of several controllers for low dimenional nonholonomic systems in power form. The method of multiple scales is found to be effective in determining the asymptotic form of the solutions. The general form of the perturbation solutions indicates how parameters in the control laws may be chosen to achieve a desired convergence rate. A detailed analysis of controllers exhibiting exponential convergence is included.", "doi": "10.23919/ACC.1993.4793446", "isbn": "0-7803-0860-3", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1993-06", "pages": "2967-2972" }, { "id": "authors:4g4pk-07277", "collection": "authors", "collection_id": "4g4pk-07277", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MURieeetac93", "type": "article", "title": "Nonholonomic motion planning: steering using sinusoids", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "Methods for steering systems with nonholonomic constraints between arbitrary configurations are investigated. Suboptimal trajectories are derived for systems that are not in canonical form. Systems in which it takes more than one level of bracketing to achieve controllability are considered. The trajectories use sinusoids at integrally related frequencies to achieve motion at a given bracketing level. A class of systems that can be steered using sinusoids (claimed systems) is defined. Conditions under which a class of two-input systems can be converted into this form are given.", "doi": "10.1109/9.277235", "issn": "0018-9286", "publisher": "IEEE", "publication": "IEEE Transactions on Automatic Control", "publication_date": "1993-05", "series_number": "5", "volume": "38", "issue": "5", "pages": "700-716" }, { "id": "authors:k6nfw-w6073", "collection": "authors", "collection_id": "k6nfw-w6073", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190320-134725249", "type": "book_section", "title": "Nonholonomic control systems: from steering to stabilization with sinusoids", "book_title": "Proceedings of the 31st IEEE Conference on Decision and Control", "author": [ { "family_name": "Teel", "given_name": "Andrew R.", "clpid": "Teel-A-R" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Walsh", "given_name": "Greg", "clpid": "Walsh-G" } ], "abstract": "The authors present a control law for globally asymptotically stabilizing a class of controllable nonlinear systems without drift. The control law combines earlier work in steering nonholonomic systems using sinusoids at integrally related frequencies, with the ideas in recent results on globally stabilizing linear and nonlinear systems through the use of saturation functions. Simulation results for stabilizing a simple kinematic model of an automobile are included.", "doi": "10.1109/CDC.1992.371456", "isbn": "0-7803-0872-7", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1992-12", "pages": "1603-1609" }, { "id": "authors:5t4mg-yfy72", "collection": "authors", "collection_id": "5t4mg-yfy72", "cite_using_url": "https://resolver.caltech.edu/CaltechCDSTR:1992.002", "type": "monograph", "title": "Nilpotent Bases for a Class of Non-Integrable Distributions with Applications to Trajectory Generation for Nonholonomic Systems", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "This paper develops a constructive method for finding a nilpotent basis for a special class of smooth nonholonomic distributions. The main tool is the use of the Goursat normal form theorem which arises in the study of exterior differential systems. The results are applied to the problem of finding a set of nilpotent input vector fields for a nonholonomic control system, which can then used to construct explicit trajectories to drive the system between any two points. A kinematic model of a rolling penny is used to illustrate this approach. The methods presented here extend previous work using \"chained form\" and cast that work into a coordinate-free setting.", "publisher": "California Institute of Technology", "publication_date": "1992-10-14" }, { "id": "authors:9vh36-1dy86", "collection": "authors", "collection_id": "9vh36-1dy86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-145135101", "type": "book_section", "title": "Steering car-like systems with trailers using sinusoids", "book_title": "Proceedings 1992 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Tilbury", "given_name": "D.", "clpid": "Tilbury-D" }, { "family_name": "Laumond", "given_name": "J.-P.", "clpid": "Laumond-J-P" }, { "family_name": "Murray", "given_name": "R.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" }, { "family_name": "Walsh", "given_name": "G.", "clpid": "Walsh-G" } ], "abstract": "Methods for steering car-like robots with trailers are investigated. A connection is demonstrated between Murray and Sastry's (1990, 1991) work of steering with integrally related sinusoids and Sussmann and Liu's (1991) recent work on asymptotic behavior of systems with high-frequency sinusoids as inputs. The merits of coordinate transformations, relative to the convergence properties, are discussed. Simulation results for a car-like robot with two trailers are presented.", "doi": "10.1109/ROBOT.1992.219988", "isbn": "0-8186-2720-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1992-05", "pages": "1993-1998" }, { "id": "authors:57zdy-p9b76", "collection": "authors", "collection_id": "57zdy-p9b76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190319-101351233", "type": "book_section", "title": "Stabilization of trajectories for systems with nonholonomic constraints", "book_title": "Proceedings 1992 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Walsh", "given_name": "G.", "clpid": "Walsh-G" }, { "family_name": "Tilbury", "given_name": "D.", "clpid": "Tilbury-D" }, { "family_name": "Sastry", "given_name": "S.", "clpid": "Sastry-S-Shankar" }, { "family_name": "Murray", "given_name": "R.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Laumond", "given_name": "J. P.", "clpid": "Laumond-J-P" } ], "abstract": "A technique for stabilizing nonholonomic systems to trajectories is presented. It is well known that such systems cannot be stabilized to a point using smooth static-state feedback. The authors suggest the use of control laws for stabilizing a system about a trajectory, instead of a point. Given a nonlinear system and a desired nominal feasible trajectory, an explicit control law which will locally exponentially stabilize the system to the desired trajectory is given. The theory is applied to several examples, including a car-like robot.", "doi": "10.1109/ROBOT.1992.219987", "isbn": "0-8186-2720-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1992-05", "pages": "1999-2004" }, { "id": "authors:zq8eg-dqa10", "collection": "authors", "collection_id": "zq8eg-dqa10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-132947215", "type": "book_section", "title": "An experimental study of hierarchical control laws for grasping and manipulation using a two-fingered planar hand", "book_title": "1992 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Hollerbach", "given_name": "Karin", "clpid": "Hollerbach-K" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "Compares the performance of hierarchical and single-level controllers in a grasping context, and concludes that for rapid, planar grasping motions of heavy objects the performance of a hierarchical control structure is superior to that of the two single-level controllers tested. Although the theory discussed applies to grasping problems of arbitrary complexity, the focus is on planar, two-fingered grasping for the sake of clarity and to simplify implementation and experimental testing of the proposed control algorithms. The control algorithms have been implemented on a multifingered hand.", "doi": "10.1109/ROBOT.1992.220015", "isbn": "0-8186-2720-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1992-05", "pages": "2770-2775" }, { "id": "authors:mgg1a-7cf80", "collection": "authors", "collection_id": "mgg1a-7cf80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190319-105627176", "type": "book_section", "title": "Steering nonholonomic systems in chained form", "book_title": "Proceedings of the 30th IEEE Conference on Decision and Control", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "The authors introduce a nilpotent form, called a chained form, for nonholonomic control systems. For the case of a nonholonomic system with two inputs, they give constructive conditions for the existence of a feedback transformation which puts the system into chained form, and show how to steer the system between arbitrary states. Examples are presented for steering a car and a car with a trailer attached: other examples can be found in the areas of space robotics and multifingered robot hands. The present results also have applications in the area of nilpotentization of distributions of vector fields on R^n.", "doi": "10.1109/CDC.1991.261508", "isbn": "0-7803-0450-0", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1991-12", "pages": "1121-1126" }, { "id": "authors:78rcq-fkd03", "collection": "authors", "collection_id": "78rcq-fkd03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190319-081854942", "type": "book_section", "title": "Steering nonholonomic systems using sinusoids", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "Methods for steering systems with nonholonomic constraints between arbitrary configurations are investigated. R.W. Brockett (1981) derived the optimal controls for a set of canonical systems in which the tangent space to the configuration manifold is spanned by the input vector fields and their (first-order) Lie brackets. Using Brockett's result as motivation, the authors derive suboptimal trajectories for systems which are not in canonical form and consider systems in which it takes more than one level of bracketing to achieve controllability. These trajectories use sinusoids at integrally related frequencies to achieve motion at a given bracketing level. Examples and simulation results are presented.", "doi": "10.1109/CDC.1990.203994", "publisher": "IEEE", "publication_date": "1990-12" }, { "id": "authors:6afdr-0h669", "collection": "authors", "collection_id": "6afdr-0h669", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190319-104216033", "type": "book_section", "title": "Nonlinear controllers for non-integrable systems: the Acrobot example", "author": [ { "family_name": "Hauser", "given_name": "John", "clpid": "Hauser-J" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" } ], "abstract": "Recent developments in the theory of geometric nonlinear control provide powerful methods for controller design for a large class of nonlinear systems. Many systems, however, do not satisfy the restrictive conditions necessary for either full state linearization [6, 5] or input-output linearization with internal stability [2]. In this paper, we present an approach to controller design based on finding a linearizable nonlinear system that well approximates the true system over a desirable region.\nWe outline an engineering procedure for constructing\nthe approximating nonlinear system given the true system. We\ndemonstrate this approach by designing a nonlinear controller for a simple mechanical system patterned after a gymnast performing on a single parallel bar.", "doi": "10.23919/ACC.1990.4790817", "publisher": "IEEE", "publication_date": "1990-05" }, { "id": "authors:t5x4c-98828", "collection": "authors", "collection_id": "t5x4c-98828", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190318-135736981", "type": "book_section", "title": "Control primitives for robot systems", "book_title": "Proceedings 1990 IEEE International Conference on Robotics and Automation", "author": [ { "family_name": "Deno", "given_name": "D. Curtis", "clpid": "Deno-D-C" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Pister", "given_name": "Kristofer S. J.", "clpid": "Pister-K-S-J" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "A methodology is developed for describing of hierarchical control of robot systems in a manner which is faithful to the underlying mechanics, structured enough to be used as an interpreted language, and sufficiently flexible to encompass a wide variety of systems. A consistent set of primitive operations which form the core of a robot system description and control language is presented. This language, motivated by the hierarchical organization of neuromuscular systems, is capable of describing a large class of robot systems under a variety of single-level and distributed control schemes.", "doi": "10.1109/ROBOT.1990.126280", "isbn": "0-8186-9061-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1990-05", "pages": "1866-1871" }, { "id": "authors:7arjy-b3y74", "collection": "authors", "collection_id": "7arjy-b3y74", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190315-135551524", "type": "book_section", "title": "Control experiments in planar manipulation and grasping", "book_title": "1989 International Conference on Robotics and Automation", "author": [ { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Sastry", "given_name": "S. Shankar", "clpid": "Sastry-S-Shankar" } ], "abstract": "Many algorithms have been proposed in the literature for control of multifingered robot hands. The authors compare the performance of several of these algorithms, as well as some extensions of more conventional manipulator control laws, in the case of planar grasping. Based on experiments performed on Styx, the most effective control laws are found to be the simple joint control law and the generalized computed torque law. The computed torque control law is shown to be an attractive alternative for position control of multifingered hands.", "doi": "10.1109/ROBOT.1989.100054", "isbn": "0-8186-1938-4", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "1989-05", "pages": "624-629" } ]