While chimeric antigen T (CAR) T cell therapy has shown remarkable success in leukemia, lymphoma, and multiple myeloma, its effectiveness in solid tumors including glioblastoma (GBM) remains limited. It is crucial to understand mechanisms that reduce the efficacy of CAR T cell therapies and develop strategies to prevent tumor resistance. In this study, we conjectured that alterations in tumor cell-intrinsic interferon (IFN) signaling pathways contribute to establishment of immunosuppressive tumor microenvironment in solid tumors, leading to resistance of solid tumor cells to CAR T cell-mediated killing. We established syngeneic IFN signaling-deficient tumor models for murine IL-13Ra2 targeted CAR T cell therapy and showed that these models modulate the tumor microenvironment (TME), leading to resistance to CAR T cell therapy. We identified variations in gene expression associated with IFN signaling components and cytokines between IFN signaling-deficient tumor cells and wild type (WT) tumor cells after CAR T cell treatment. Furthermore, single-cell RNA sequencing and mass cytometry analysis of the tumor immune cell infiltrates in IFN-signaling deficient tumors compared to WT controls identified the immune-mediated causal components for the resistance of Janus Kinase1 knockout (JAK1/KO) tumors to CAR T cell therapy. CAR T cell-treated IFN signaling-deficient tumors presented decreased T-cell transcripts, with decreased frequency of CD8-early active, CD8-naive like T cells. Conversely, there were more regulatory and follicular T cells, exhausted endogenous T cells , and exhausted CAR T cells in treated IFN signaling-deficient tumors compared to treated WT tumors. The analyses also showed the superior enrichment and crosstalk of genes that identified fibroblasts, neutrophils, and myeloid cells in IFN signaling-deficient tumors compared to those of WT tumors. Mass cytometry analysis on the immune cells infiltrates of JAK1/KO and WT tumors post CAR T cell treatment corroborated the results from gene expression analysis. The potential cause of immune suppressive crosstalk in IFN signaling-deficient tumor niches could be attributed to the varied enhancement of receptor-ligand interactions such as SPP1+ tumor-associated macrophages (TAMs) and CD44+ cancer-associated fibroblasts (CAFs), as well as SPP1+ TAMs and integrins present on other cell lineages. To overcome resistance to CAR T cell therapies, we employed two distinct actionable approaches: triggering the immune microenvironment and disrupting the extracellular matrix. Unconjugated interferon signaling gene-15 (ISG-15) enhanced CAR T cell efficacy in an INF-signaling deficient model, increasing the recruitment of endogenous T cells and reshaping the TME. Anti-SPP1 blocking antibody was used to prime the JAK1/KO tumors prior to the treatment with CAR T cell therapy potentially via enhancing the persistence and trafficking of CAR T cells in the TME.
\r\n\r\nWe next identified immune signatures of 32 GBM patients who had progressive disease after CAR T cell treatment compared to those who had relatively stable disease or showed improvement. We identified the presence of fibroblasts and SPP1+ APOE+ C1QA+ C1QC+ myeloid cells in GBM signatures that are associated with immune suppression and resistance to therapy. Patients with GBM who exhibited a relatively stable response to treatment and increased T cell recruitment had differential expression of interferon regulatory factors (IRFs) and ISGs compared to patients with less response to the treatment. Our findings uncover a correlation between tumor-intrinsic driver mutations, the composition of the TME, and the responsiveness of solid tumors to CAR T cell therapy, providing insights into potential approaches to address resistance in IFN non-responsive tumors.
", "doi": "10.7907/jf79-pv58", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14084", "collection": "thesis", "collection_id": "14084", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02192021-010538691", "primary_object_url": { "basename": "chour_william_2021_thesis.pdf", "content": "final", "filesize": 140220437, "license": "other", "mime_type": "application/pdf", "url": "/14084/1/chour_william_2021_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Molecular Technologies for Antigen-Based Immunity", "author": [ { "family_name": "Chour", "given_name": "William", "orcid": "0000-0003-1817-0123", "clpid": "Chour-William" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "The presence and proliferation antigen-specific T cells is a defining characteristic of an adaptive immune response against various disease types (autoimmune, cancer, and infectious). The use of Class I and Class II peptide-major histocompatibility complex (pMHC) reagents to identify such cells, however, is technically difficult and expensive, and it has been challenging to refine synthesis protocols for higher yield and more efficient assembly to accommodate large-scale applications. This achievement would enable high-throughput capture of corresponding T cell receptors (TCR), which may be further used in clinical applications such as adoptive cell transfer therapies. Overcoming this hurdle requires the development and integration of various molecular technologies and analytical methods.
\r\n\r\nToward this end, the bulk of my thesis work, covered in Chapter 2, introduces these developments in the context of pMHCs, where the three subunits of each reagent are covalent linked together and expressed as a single protein. These single-chain trimer (SCT) technologies primarily consist of traditional DNA cloning and protein production techniques which have been streamlined for applications requiring output on the scale of 102-103 of reagents. This chapter serves as the foundation for much of the methodology discussed throughout the rest of my thesis, and thus should serve as a reference point. The generated constructs are also functionally validated here, and potential future research directions are outlined.
\r\n\r\nIn Chapter 3, I explore the use of this technology in the context of COVID-19 to enumerate antigen specificity of the CD8+ T cell immune response. Class I SCTs were constructed to present peptides across several SARS-CoV-2 protein domains, using various HLA alleles to match haplotyped participant blood samples. These reagents were then used to capture SARS-CoV-2-specific T cells through flow and nanoparticle cytometry to demonstrate HLA-dependent, domain-dependent immune responses. Identified TCRs were cloned into T cells for confirmation of antigen specificity and functional cytotoxicity.
\r\n\r\nIn Chapters 4 and 5, I explore potential pMHC applications in cancer antigen contexts, covering both tumor-associated and tumor-specific antigens. Through various collaborations across the west coast (UCLA, Parker Institute, Fred Hutchinson Cancer Research Center), I make use of the SCT platform to showcase new assays to discover and rank key tumor targets (Chapter 4). Finally, Chapter 5 is a reproduction of our lab\u2019s published work concerning identification of antigen-specific CD8+ T cells from melanoma cancer patients.
\r\n\r\nIn summary, the adaptation of SCTs in a high-throughput format allows for the rapid enumeration of antigen-specific T-cell receptor sequences. As demonstrated in the contexts of COVID-19 and cancer, this SCT platform enables subsequent downstream applications, such as single-cell, antigen-specific immunophenotypic mapping/analysis and target discovery for personalized immunotherapies.
", "doi": "10.7907/z20t-nq62", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13614", "collection": "thesis", "collection_id": "13614", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01102020-003449091", "type": "thesis", "title": "Resistance is Futile: Physical Science, Systems Biology and Single-Cell Analysis to Understanding the Plastic and Heterogeneous Nature of Melanoma and Their Role in Non-Genetic Drug Resistance", "author": [ { "family_name": "Su", "given_name": "Yapeng", "orcid": "0000-0002-6305-8467", "clpid": "Su-Yapeng" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Melanoma is the most deadly form of skin cancer due to its great metastatic potential. Targeted therapy that inhibits the BRAF-V600E driver mutation has shown impressive initial responses in melanoma patients. However, drug resistance, as the universal phenomenon for any cancer therapy, always limits treatment efficacy and compromises outcomes. As the early-step of resistance development, non-genetic mechanisms enable cancer cells to transition into a drug-resistant state in as early as a few days after drug treatment without alteration of the genome. This early mechanism is, to a large extent, due to the heterogeneous and highly plastic nature of tumor cells. Therefore, it imperative to understand the plastic and heterogeneous nature of the melanoma cells in order to identify combination therapies that can overcome resistance.
\r\n\r\nIn this thesis, we investigate these two fundamental natures of non-genetic drug resistance using BRAF inhibition of BRAF-mutant melanomas as the model system. These melanoma cells undergo multi-step, reversible drug-induced cell-state transitions from the original sensitive phenotype to a drug-resistant one.
\r\n\r\nWe first conducted bulk analysis to characterize the detailed kinetics of the entire transition from drug-sensitive state towards drug-resistant state, revealing expression changes of thousands of genes and extensive chromatin remodeling. A 3-step computational biology approach greatly simplified the complexity and revealed that the whole cell-state transition was controlled by a gene module activated within just the first three days of drug treatment, with the RelA transcription factor driving chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes towards resistance. From there, a detailed mechanism connecting tumor epigenetic plasticity with non-genetic drug resistance was resolved through in-depth molecular biology experiments. The mechanism was validated in clinical patient samples.
\r\n\r\nWe further investigated heterogeneity by moving from bulk cellular studies to single-cell analysis. The single-cell view further revealed that two driving forces from both cell-state interconversions and phenotype-specific drug selection control the cell-state transition dynamics. The single-cell studies also pinpointed the signaling network hub, RelA, as the driver molecule of the initiation of the adaptive transition. These two competing driving forces were further quantitatively modeled via a thermodynamic-inspired surprisal analysis and a modified Fokker-Planck-type kinetic model.
\r\n\r\nFinally, using integrated single-cell proteomic and metabolic technology I developed to characterize the early-stage signaling and metabolic changes upon initial drug responses, we further identified two distinct paths connecting drug-sensitive and drug-tolerant states. Melanoma cells exclusively traverse one of the two paths depending on the level of MITF in the drug-na\u00efve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities and are independently druggable.
\r\n\r\nIn total, this thesis combines and synergizes various physical science and systems biology approaches together with several unique single-cell technologies and analysis to obtain a deep and comprehensive understanding of non-genetic drug resistance in cancer. The findings from this thesis provide several novel insights into the rational design of effective combination therapy for overcoming the development of resistance in response to cancer treatments.
", "doi": "10.7907/78ZP-Y270", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:11559", "collection": "thesis", "collection_id": "11559", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292019-112017023", "type": "thesis", "title": "Bioanalytical Tools to Develop Rapid Diagnostics and Study Physiology", "author": [ { "family_name": "Rolando", "given_name": "Justin Charles", "orcid": "0000-0001-8948-319X", "clpid": "Rolando-Justin-Charles" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "clpid": "Ismagilov-R-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This work details the development of bioanalytical tools for use in rapid diagnostics (Chapters 2-4) and in the study of physiology (Chapters 5-6). This research harness the power of real-time, singlemolecule microfluidics to study loop-mediated isothermal amplification in urinary tract infections (Chapter 2), chlamydia (Chapter 3), and gonorrhea (Chapter 4). In Chapter 5, non-reactive beads are designed and optimized to study the impact of polymers on murine gastrointestinal mucosa. Chapter 6 details the implementation of a mass spectrometry method to quantify bile acids and investigate their interaction with the microbiota in the murine gastro-intestinal tract.
", "doi": "10.7907/99NT-WP75", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11572", "collection": "thesis", "collection_id": "11572", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302019-162535966", "type": "thesis", "title": "Phenotypic Antimicrobial Susceptibility Testing Based on Nucleic Acid Analysis", "author": [ { "family_name": "Schoepp", "given_name": "Nathan Garrett", "orcid": "0000-0002-2406-3693", "clpid": "Schoepp-Nathan-Garrett" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "clpid": "Ismagilov-R-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Antimicrobial resistance (AMR) is one of the most widely recognized threats to global health, and one that continues to grow as new mechanisms of resistance evolve and resistant pathogens spread. Antibiotics are a cornerstone of modern medicine, but their misuse and overuse has constantly and consistently reduced their efficacy to the critically low levels we observe today. As a result, the rate of mortality as a direct result of AMR is approaching over a million deaths annually, with 20-year projections in the ten-millions. Rapid, phenotypic antimicrobial susceptibility testing (AST) that could be performed at the point of care (most notably in \u2264 30 min) would decrease the overuse of antimicrobials, allow physicians to make informed choices about which antimicrobials to prescribe, and improve patient outcomes. Today no such method exists. The ultimate goal of the below work is to allow physicians to choose, instead of guess, which antibiotics to use. We envision that development of these tests into distributable diagnostics will drastically improve patient outcomes, curb the spread of resistance, strengthen global antibiotic stewardship, and forestall the post-antibiotic era.
", "doi": "10.7907/5F6B-F452", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:10993", "collection": "thesis", "collection_id": "10993", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012018-005336099", "type": "thesis", "title": "Advancing the Protein-Catalyzed Capture Agent Technology to New Frontiers", "author": [ { "family_name": "McCarthy", "given_name": "Amy Michelle", "orcid": "0000-0003-3456-0383", "clpid": "McCarthy-Amy-Michelle" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Peters", "given_name": "Jonas C.", "orcid": "0000-0002-6610-4414", "clpid": "Peters-J-C" }, { "family_name": "Davis", "given_name": "Mark E.", "orcid": "0000-0001-8294-1477", "clpid": "Davis-M-E" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Protein-catalyzed capture (PCC) agents are a nascent synthetic aptamer technology that was first disclosed in 2009. In addition to reviewing the different classes of peptide-based aptamers in chapter 1, this thesis records efforts to advance the PCC technology in two ways. First, in chapter 2 the development of a barcoded-rapid assay platform (B-RAP) technology enables the parallel analysis of up to fifteen PCC agents at once as well as dramatically shortening the time required to characterize the binding affinity for a pool of ligands from weeks to a couple of days. Secondly, the capture agent technology was utilized to target difficult proteins. Kirsten rat sarcoma (KRas) protein is a GTPase that acts as a light switch for several important cellular signaling pathways. Oncogenic variants of KRas are responsible for driving roughly 20-25% of all cancers, but KRas is considered \u201cundruggable\u201d from a small molecule targeting point of view. We report the identification of PCC ligands that bind to conserved allosteric switches on KRas and inhibit the protein\u2019s GTPase enzymatic activity. The biomarker Plasmodium falciparum Histidine Rich Protein II (HRP2) presents an unusual challenge as it is a highly variable, unstructured and sticky protein. In chapter 3 we report on efforts to develop low nM binding capture agents against highly prevalent epitopes of HRP2, and the use of medicinal chemistry optimization to prepare structurally related variants of the lead capture agent for probing the structure-activity relationship and how it affects binding to HRP2.", "doi": "10.7907/HHP5-1Z83", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:11069", "collection": "thesis", "collection_id": "11069", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06112018-181603942", "type": "thesis", "title": "Interrogating the Structural Landscape of Malaria Biomarkers with Epitope Targeted Peptide Capture Agents", "author": [ { "family_name": "Liang", "given_name": "JingXin", "orcid": "0000-0001-6600-8409", "clpid": "Liang-JingXin" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Antibodies have conventionally been used as molecular recognition agents against epitopes, or antigenic regions, for protein capture and detection. The ability of monoclonal and polyclonal antibodies to selectively bind their targets with high affinities makes them excellent agents for specific protein recognition. However, as large proteins themselves (~150 kDa), antibodies are susceptible to changes in pH, temperature, and biochemical environment, particularly proteolytic cleavage. Additionally, epitope binding on antibodies is reliant on their rigid tertiary structure to position key functional groups that facilitation antigen recognition. Retaining the integrity of the protein structure creates rigid limitations against chemical modifications of antibodies to suit unique needs.
\r\n\r\nProtein-catalyzed capture agents (PCCs) developed within the Heath group at Caltech address the limitation of antibodies as affinity agents. Using epitope-targeted in situ click screening methodology, the Heath group has developed peptidomimetic molecules that offer an alternative solution to antibodies. These PCCs exhibit high affinity and selectivity for their protein targets. As peptide-based molecules, PCCs can be engineered to be biochemically stable and resistant to changes in their chemical environment. Their peptide-based structures are readily amenable to chemical modifications and allow for adaptation to a range of applications.
\r\n\r\nThis thesis describes the development of PCCs against unique protein biomarkers for the detection of the most lethal species of malaria infection, Plasmodium falciparum. Malaria is a global health epidemic and its eradication is reliant on rapid and accurate diagnostics for prompt treatment. We targeted the P. falciparum specific biomarkers lactate dehydrogenase (LDH) and Histidine-rich protein 2 (HRP2), both of which present unique challenges for protein capture. The LDH biomarker is homologous across malaria species, whereas HRP2 is highly polymorphic and lacks distinct secondary structure. The variation in sensitivity of HRP2 detection by antibody-based tests has been attributed to the genetic polymorphism of the biomarker.
\r\n\r\nIn Chapter 1, we describe the development of high affinity PCCs that bind selectively to the LDH biomarker. We targeted an epitope that was highly homologous across LDH species. This chapter also details the expansion of mono-valent PCC agents into bivalent ligands using the protein architecture to select secondary ligands for binding improvement. For the HRP2 biomarker, we developed a multiple epitope targeting strategy to address protein polymorphism. We targeted for epitopes in HRP2 and developed PCCs that bind in the range of monoclonal antibodies.
\r\n\r\nChapter 2 details the expansion of PCC agents developed against HRP2 into multivalent molecules for improved binding. The development of bivalent ligands from combinatorial screening of linker libraries is presented. The optimal linker lengths determined by the screens are described.
\r\n\r\nIn Chapter 3, a general strategy for targeting the protein landscape to inhibit formation of a protein and biomolecule complex with PCCs against HRP2 is demonstrated. Specifically, the inhibition of heme sequestration by HRP2 is shown. A bivalent ligand that targets two epitopes on HRP2 is shown to have enhanced inhibitory potency over any single or cocktail combination of PCCs.
\r\n\r\nAltogether, the studies herein demonstrate the utility of peptidomimetic molecules as agents for protein capture and detection as well as a generalizable strategy of functional inhibition through epitope-targeting.
", "doi": "10.7907/rxtr-6152", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10411", "collection": "thesis", "collection_id": "10411", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09042017-140704721", "primary_object_url": { "basename": "Jungwoo_Kim_Thesis_Final.pdf", "content": "final", "filesize": 4993313, "license": "other", "mime_type": "application/pdf", "url": "/10411/1/Jungwoo_Kim_Thesis_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Microfluidic Analysis in Patient Biopsies: toward Precision Medicine for Glioblastoma Multiforme", "author": [ { "family_name": "Kim", "given_name": "Jungwoo", "orcid": "0000-0002-5215-2044", "clpid": "Kim-Jungwoo" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "clpid": "Shapiro-M-G" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Although every individual has a unique biology, most medicine still relies on the one-size-fits-all approach, which often fails in the treatment of heterogeneous diseases like cancer. An emerging approach to disease treatment is precision medicine, in which a specific treatment is tailored for individual patients using their biological information, including their genome, phenome, and proteome. Two clinical actions are important for implementing precision medicine in cancer therapies: choosing the correct drugs via patient stratification and choosing a suitable drug dosage and duration via drug response monitoring.
\r\n\r\nAfter selecting the potential drug candidate, it is crucial to monitor tumor response to drug therapy because cancer is a dynamic disease that can develop drug resistance. Although non-invasive tumor imaging techniques such as magnetic resonance imaging, computed tomography, and positron emission tomography can assess physical size and metabolic activity of tumors, these techniques have poor time resolution and cannot capture the dynamic changes of bio-molecules implicated with drug resistance. Thus, to effectively monitor drug response, supplemental diagnostic or prognostic markers must be routinely measured from patient biopsies. Unfortunately, routine monitoring of multiple biomarkers from patient biopsies is impractical, as conventional analytical assays require large sample amounts (up to 100-1,000 mg of tissue or 10 mL of blood).
\r\n\r\nIn response to this challenge, this thesis describes the development of various microfluidic technologies that can perform multiplexed measurements (up to 20-plex) using minute amounts of sample (10,000-100,000 cells or 30\u00b5L of blood) in a miniaturized analytical platform (maximum 75 \u00d7 26 \u00d7 1 mm footprint). We applied these technologies for drug screening and drug response monitoring in glioblastoma multiforme, a highly lethal brain tumor, assaying two different types of patient biopsies: cancer cells and blood.
\r\n\r\nFirst, we developed an integrated microfluidics-chip/beta particle imaging system that can screen for effective therapies using small amounts of patient-derived cell lines. Since glioblastoma cells have abnormally high glycolytic activity, this was used as a read-out for drug response. Single cells were isolated in micro-traps, and their glycolytic activity was quantitated using a radioactive probe. This platform can assess potential drug targets directly from patient biopsies without administering drugs to the patient.
\r\n\r\nSecond, we developed an in vitro diagnostic test that can monitor tumor drug resistance by measuring up to 14 proteins in finger-prick volumes of blood. This test relies on microfluidics and microarray patterning of antibodies to carry out multiplexed sandwich-type immunofluorescence assays. Using this technology and conventional tumor imaging techniques, we linked proteomic signatures to tumor growth, establishing diagnostic and prognostic models in two clinical treatment cases of bevacizumab and buparlisib. Moreover, we adopted the multiplexed proteomic measurement platform to rapidly screen out small peptide binding agents that target an oncogenic protein in glioblastoma.
\r\n\r\nThe microfluidic tools developed here are sample-efficient and highly informative, and we propose that these techniques could enable routine evaluation of drug response in a precision medicine workflow.
\r\n", "doi": "10.7907/Z9639MX2", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10249", "collection": "thesis", "collection_id": "10249", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022017-070813473", "type": "thesis", "title": "Targeting Undruggable Oncoprotein Epitopes with Protein Catalyzed Capture Agents", "author": [ { "family_name": "Henning", "given_name": "Ryan Kenneth", "orcid": "0000-0002-3783-2455", "clpid": "Henning-Ryan-Kenneth" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Hoelz", "given_name": "Andre", "orcid": "0000-0003-0923-3284", "clpid": "Hoelz-A" }, { "family_name": "Deshaies", "given_name": "Raymond Joseph", "orcid": "0000-0002-3671-9354", "clpid": "Deshaies-R-J" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The protein catalyzed capture (PCC) agent platform provides a new strategy to develop peptide-based ligands for difficult protein targets. This approach utilizes the target-guided in situ click reaction to allow the protein of interest to assemble its own binder. Developing a PCC agent begins with an epitope targeting strategy to develop anchor candidates against a specific region of interest on the target protein. This approach has been used to target diverse epitopes including unstructured hydrophobic regions, allosteric enzyme sites, and single amino acid point mutations. The process can then be iterated to expand a monoligand into a multiligand binder with affinity and selectivity that rivals monoclonal antibodies.
\r\n\r\nOne disease-associated protein of particular importance is the serine/threonine kinase Akt. Akt is a key regulator of signal transduction pathways and is implicated in many disease such as cancer, diabetes, and neurodegeneration. Several ligands for Akt have been developed recently with the PCC agent screening approach. PCC agents now exist that can alter Akt enzymatic activity, detect its position in the cell, identify mutations within the protein, and even cause its destruction within the cell. The first part of this thesis summarizes the prior efforts to develop PCC agents against Akt and then describes new applications for these reagents while the latter part describes efforts to develop new PCC agents against another interesting target.
\r\n\r\nChapter 1 provides a summary of the technology and describes how it has be utilized thus far. Chapter 2 describes how a PCC agent was used as an imaging probe capable of detecting Akt membrane localization. Chapter 3 provides several examples of the modularity of PCC agents and demonstrates how they can be used to influence a target protein in cells. A pair of allosteric Akt modulators were functionalized with a cell penetrating peptide for cellular delivery and were subsequently used to activate or inhibit Akt enzymatic activity. PCC agents can also be used as a targeting moiety to deliver a specific signal to a protein. When functionalized with a degradation tag the Akt-binding capture agents caused the protein to be degraded. This provides another demonstration of the usefulness of Proteolysis Targeting Chimeric Molecules, or PROTACs, in destroying disease-associated proteins. Finally, Chapter 4 describes the development of PCC agents against the oncoprotein K-RasG12D and how these molecules can be used to target this protein in new ways.
", "doi": "10.7907/Z9CJ8BJG", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10001", "collection": "thesis", "collection_id": "10001", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01032017-003321706", "type": "thesis", "title": "First-Principles-Based Simulations for G Protein-Coupled Receptor Activation and for Large-Scale Nonadiabatic Electron Dynamics", "author": [ { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0001-8182-6522", "clpid": "Dong-Sijia-S" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis focuses on simulating large molecular systems within and beyond the Born-Oppenheimer framework from first principles. Two approaches have been developed for very different but important applications.
\r\n\r\nThe first one is a hybrid method based on classical force fields that predicts the high-energy ensemble of three-dimensional structures of a class of proteins critical in human physiology: the G protein-coupled receptors (GPCRs). GPCRs' functions rely on their activation marked by a series of conformational changes related to binding of certain ligands, but the short of experimental structures has hampered the study of their activation mechanism and drug discovery. Our method, combining homology modeling, hierarchical sampling, and nanosecond-scale molecular dynamics, is one of the very few computational methods that can predict their active-state conformations and is one of the most computationally inexpensive. It enables the conformational landscape and the first quantitative energy landscape of GPCR activation to be efficiently mapped out.
\r\n\r\nThis method, named ActiveGEnSeMBLE, allows the inactive- and active-state conformations of GPCRs without an experimental structure to be systematically predicted. We have validated the method with one of the most well-studied GPCRs, human β2 adrenergic receptor (hβ2AR), and applied the method on a GPCR without an experimental structure, human somatostatin receptor 5 (hSSTR5). Insights on GPCR activation as well as structure prediction methods are discussed.
\r\n\r\nThe second one is a semiclassical approach for large-scale nonadiabatic dynamics of condensed systems in extreme conditions, termed Gaussian Hartree Approximated Quantum Mechanics (GHA-QM). Many nonadiabatic processes related to important applications (e.g. renewable energy) happen in large systems, but existing excited state dynamics methods are too computationally demanding for their long timescale simulations. GHA-QM is based on the electron force field (eFF) framework where we model electrons as Gaussian wavepackets and nuclei as classical point charges, and obtain a simplified solution to the time-dependent Schr\u00f6dinger equation as the equation of motion. We employ a force field philosophy approximating the total energy as a sum of electronic kinetic energies, electrostatic energies and a Pauli correction, which corrects for the lack of explicit antisymmetry in the wavefunctions. New designs of the Pauli potential and preliminary results on hydrogen systems are discussed. With the new development, we hope to improve the accuracy and range of applications of eFF to simulate the nonadiabatic dynamics of hundreds of thousands of electrons on nanosecond timescale.
", "doi": "10.7907/Z98C9T8D", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10335", "collection": "thesis", "collection_id": "10335", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06122017-230026717", "type": "thesis", "title": "DarwinDock and GAG-Dock: Methods and Applications for Small Molecule Docking", "author": [ { "family_name": "Griffith", "given_name": "Adam Reid", "clpid": "Griffith-Adam-Reid" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Computational modeling is an effective tool in studying complex biological systems. Docking of small molecule ligands in particular is useful both in understanding the functioning of proteins as well as in the development of pharmaceuticals. Together with experiment, modeling can often provide a thorough picture of a given system. Computation can often provide details that are difficult or impossible to determine experimentally, while experiments provide guidance on what calculations are useful or interesting. Our goal is to extend computational modeling, specifically ligand docking, to systems not previously possible, such as the challenging glycosaminoglycan (GAG) systems. In order to do this it was first necessary to develop an automatic way of performing docking without extensive user input and experimental knowledge to narrow the list of candidate poses. DarwinDock represents our efforts in this respect. It is a method for small-molecule docking that separates pose generation and scoring into separate stages, which allows for complete binding site sampling followed by efficient, hierarchical sampling. Our convergence criteria for complete sampling allows for diverse systems to be studied without prior knowledge of how large a set of poses needs to be to span a given binding site, making the procedure more automatic. We also replace bulky, nonpolar residues with alanine, which we refer to as \"alanization\". This allows the ligand to interact more closely with polar sidechains, which help to orient the ligand. Additionally, alanization reduces the impact of incorrect sidechain placement on ligand placement, a concern that sometimes requires user intervention. With DarwinDock working for standard small molecules, it was then necessary to modify the procedure to work on challenging GAG ligands, which are large and have strong negative charges. A modification to DarwinDock \u2013 GAG-Dock \u2013 allows the method to be applied to GAGs and protein surface interactions. GAGs are large, linear polysaccharides with strong negative charge. They typically interact with the surfaces of proteins, rather than the cavities favored by most small-molecule drugs. GAG-Dock systematically samples the protein surface for unknown binding sites and modifies the pose generation to allow for large, surface-interacting ligands. GAG-Dock allowed us to study several systems important for neuronal development and answer interesting questions posed by experiment. Finally, we needed a way to validate our predictions for GAG binding sites. We used a systematic approach to identify sets of beneficial mutations to the GAG binding sites by building up from individual in silico mutations. Standard mutation experiments typically employ large mutations, such as arginine to alanine, which decrease or destroy binding. However, such information is not always definitive, as large mutations can have wide-ranging effects beyond direct protein-ligand interactions. Mutations that increase binding, however, are less ambiguous because they must form new interactions with the ligand in order to affect binding energies or affinity. Therefore, we have identified and proposed sets of mutations for our GAG predictions for PTPs, NgR1, NgR3, and EphB3. We encourage our experimentalist colleagues to try these mutations and validate our predictions.
", "doi": "10.7907/Z91Z42GS", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9714", "collection": "thesis", "collection_id": "9714", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05092016-155820873", "primary_object_url": { "basename": "DorothyPan_Thesis_Edits2.pdf", "content": "final", "filesize": 20115454, "license": "other", "mime_type": "application/pdf", "url": "/9714/1/DorothyPan_Thesis_Edits2.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Development of a Cationic Mucic Acid Polymer-Based Nanoparticle siRNA Delivery System", "author": [ { "family_name": "Pan", "given_name": "Dorothy Weichi", "orcid": "0000-0003-4066-7750", "clpid": "Pan-Dorothy-Weichi" } ], "thesis_advisor": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Cancer chemotherapy has advanced from highly toxic drugs to more targeted treatments in the last 70 years. Chapter 1 opens with an introduction to targeted therapy for cancer. The benefits of using a nanoparticle to deliver therapeutics are discussed. We move on to siRNA in particular, and why it would be advantageous as a therapy. Specific to siRNA delivery are some challenges, such as nuclease degradation, quick clearance from circulation, needing to enter cells, and getting to the cytosol. We propose the development of a nanoparticle delivery system to tackle these challenges so that siRNA can be effective.
\r\n\r\nChapter 2 of this thesis discusses the synthesis and analysis of a cationic mucic acid polymer (cMAP) which condenses siRNA to form a nanoparticle. Various methods to add polyethylene glycol (PEG) for stabilizing the nanoparticle in physiologic solutions, including using a boronic acid binding to diols on mucic acid, forming a copolymer of cMAP with PEG, and creating a triblock with mPEG on both ends of cMAP. The goal of these various pegylation strategies was to increase the circulation time of the siRNA nanoparticle in the bloodstream to allow more of the nanoparticle to reach tumor tissue by the enhanced permeation and retention effect. We found that the triblock mPEG-cMAP-PEGm polymer condensed siRNA to form very stable 30-40 nm particles that circulated for the longest time \u2013 almost 10% of the formulation remained in the bloodstream of mice 1 h after intravenous injection.
\r\n\r\nChapter 3 explores the use of an antibody as a targeting agent for nanoparticles. Some antibodies of the IgG1 subtype are able to recruit natural killer cells that effect antibody dependent cellular cytotoxicity (ADCC) to kill the targeted cell to which the antibody is bound. There is evidence that the ADCC effect remains in antibody-drug conjugates, so we wanted to know whether the ADCC effect is preserved when the antibody is bound to a nanoparticle, which is a much larger and complex entity. We utilized antibodies against epidermal growth factor receptor with similar binding and pharmacokinetics, cetuximab and panitumumab, which differ in that cetuximab is an IgG1 and panitumumab is an IgG2 (which does not cause ADCC). Although a natural killer cell culture model showed that gold nanoparticles with a full antibody targeting agent can elicit target cell lysis, we found that this effect was not preserved in vivo. Whether this is due to the antibody not being accessible to immune cells or whether the natural killer cells are inactivated in a tumor xenograft remains unknown. It is possible that using a full antibody still has value if there are immune functions which are altered in a complex in vivo environment that are intact in an in vitro system, so the value of using a full antibody as a targeting agent versus using an antibody fragment or a protein such as transferrin is still open to further exploration.
\r\n\r\nIn chapter 4, nanoparticle targeting and endosomal escape are further discussed with respect to the cMAP nanoparticle system. A diboronic acid entity, which gives an order of magnitude greater binding (than boronic acid) to cMAP due to the vicinal diols in mucic acid, was synthesized, attached to 5kD or 10kD PEG, and conjugated to either transferrin or cetuximab. A histidine was incorporated into the triblock polymer between cMAP and the PEG blocks to allow for siRNA endosomal escape. Nanoparticle size remained 30-40 nm with a slightly negative ca. -3 mV zeta potential with the triblock polymer containing histidine and when targeting agents were added. Greater mRNA knockdown was seen with the endosomal escape mechanism than without. The nanoparticle formulations were able to knock down the targeted mRNA in vitro. Mixed effects suggesting function were seen in vivo.
\r\n\r\nChapter 5 summarizes the project and provides an outlook on siRNA delivery as well as targeted combination therapies for the future of personalized medicine in cancer treatment.
\r\n", "doi": "10.7907/Z9VM497J ", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9750", "collection": "thesis", "collection_id": "9750", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-124438217", "primary_object_url": { "basename": "jgood_thesis.pdf", "content": "final", "filesize": 3074066, "license": "other", "mime_type": "application/pdf", "url": "/9750/1/jgood_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Design and Applications of a Decade-Spanning Terahertz Frequency Comb Spectrometer: Doppler-limited Rotational Spectroscopy of Methanol and Methanol-OD", "author": [ { "family_name": "Good", "given_name": "Jacob Thomas", "clpid": "Good-Jacob-Thomas" } ], "thesis_advisor": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "local_group": [ { "literal": "Astronomy Department" }, { "literal": "div_chem" } ], "abstract": "This thesis details the design and applications of a terahertz (THz) frequency comb spectrometer. The spectrometer employs two offset locked Ti:Sapphire femtosecond oscillators with repetition rates of approximately 80 MHz, offset locked at 100 Hz to continuously sample a time delay of 12.5 ns at a maximum time delay resolution of 15.6 fs. These oscillators emit continuous pulse trains, allowing the generation of a THz pulse train by the master, or pump, oscillator and the sampling of this THz pulse train by the slave, or probe, oscillator via the electro-optic effect. Collecting a train of 16 consecutive THz pulses and taking the Fourier transform of this pulse train produces a decade-spanning frequency comb, from 0.25 to 2.5 THz, with a comb tooth width of 5 MHz and a comb tooth spacing of ~80 MHz. This frequency comb is suitable for Doppler-limited rotational spectroscopy of small molecules. Here, the data from 68 individual scans at slightly different pump oscillator repetition rates were combined, producing an interleaved THz frequency comb spectrum, with a maximum interval between comb teeth of 1.4 MHz, enabling THz frequency comb spectroscopy.
\r\n\r\nThe accuracy of the THz frequency comb spectrometer was tested, achieving a root mean square error of 92 kHz measuring selected absorption center frequencies of water vapor at 10 mTorr, and a root mean square error of 150 kHz in measurements of a K-stack of acetonitrile. This accuracy is sufficient for fitting of measured transitions to a model Hamiltonian to generate a predicted spectrum for molecules of interest in the fields of astronomy and physical chemistry. As such, the rotational spectra of methanol and methanol-OD were acquired by the spectrometer. Absorptions from 1.3 THz to 2.0 THz were compared to JPL catalog data for methanol and the spectrometer achieved an RMS error of 402 kHz, improving to 303 kHz when excluding low signal-to-noise absorptions. This level of accuracy compares favorably with the ~100 kHz accuracy achieved by JPL frequency multiplier submillimeter spectrometers. Additionally, the relative intensity performance of the THz frequency comb spectrometer is linear across the entire decade-spanning bandwidth, making it the preferred instrument for recovering lineshapes and taking absolute intensity measurements in the THz region. The data acquired by the Terahertz Frequency Comb Spectrometer for methanol-OD is of comparable accuracy to the methanol data and may be used to refine the fit parameters for the predicted spectrum of methanol-OD.
", "doi": "10.7907/Z9MW2F37", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9185", "collection": "thesis", "collection_id": "9185", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10012015-132559997", "primary_object_url": { "basename": "2015 - Alexander M Sutherland Thesis - Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics.pdf", "content": "final", "filesize": 7315760, "license": "other", "mime_type": "application/pdf", "url": "/9185/1/2015 - Alexander M Sutherland Thesis - Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics", "author": [ { "family_name": "Sutherland", "given_name": "Alexander Muir", "clpid": "Sutherland-Alexander-Muir" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "clpid": "Mazmanian-S-K" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The first chapter of this thesis deals with automating data gathering for single cell microfluidic tests. The programs developed saved significant amounts of time with no loss in accuracy. The technology from this chapter was applied to experiments in both Chapters 4 and 5.
\r\n\r\nThe second chapter describes the use of statistical learning to prognose if an anti-angiogenic drug (Bevacizumab) would successfully treat a glioblastoma multiforme tumor. This was conducted by first measuring protein levels from 92 blood samples using the DNA-encoded antibody library platform. This allowed the measure of 35 different proteins per sample, with comparable sensitivity to ELISA. Two statistical learning models were developed in order to predict whether the treatment would succeed. The first, logistic regression, predicted with 85% accuracy and an AUC of 0.901 using a five protein panel. These five proteins were statistically significant predictors and gave insight into the mechanism behind anti-angiogenic success/failure. The second model, an ensemble model of logistic regression, kNN, and random forest, predicted with a slightly higher accuracy of 87%.
\r\n\r\nThe third chapter details the development of a photocleavable conjugate that multiplexed cell surface detection in microfluidic devices. The method successfully detected streptavidin on coated beads with 92% positive predictive rate. Furthermore, chambers with 0, 1, 2, and 3+ beads were statistically distinguishable. The method was then used to detect CD3 on Jurkat T cells, yielding a positive predictive rate of 49% and false positive rate of 0%.
\r\n\r\nThe fourth chapter talks about the use of measuring T cell polyfunctionality in order to predict whether a patient will succeed an adoptive T cells transfer therapy. In 15 patients, we measured 10 proteins from individual T cells (~300 cells per patient). The polyfunctional strength index was calculated, which was then correlated with the patient's progress free survival (PFS) time. 52 other parameters measured in the single cell test were correlated with the PFS. No statistical correlator has been determined, however, and more data is necessary to reach a conclusion.
\r\n\r\nFinally, the fifth chapter talks about the interactions between T cells and how that affects their protein secretion. It was observed that T cells in direct contact selectively enhance their protein secretion, in some cases by over 5 fold. This occurred for Granzyme B, Perforin, CCL4, TNFa, and IFNg. IL- 10 was shown to decrease slightly upon contact. This phenomenon held true for T cells from all patients tested (n=8). Using single cell data, the theoretical protein secretion frequency was calculated for two cells and then compared to the observed rate of secretion for both two cells not in contact, and two cells in contact. In over 90% of cases, the theoretical protein secretion rate matched that of two cells not in contact.
", "doi": "10.7907/Z9PK0D3K", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9689", "collection": "thesis", "collection_id": "9689", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04282016-162609209", "primary_object_url": { "basename": "Clark_Andrew J_Thesis_04292016_Final.pdf", "content": "final", "filesize": 7462710, "license": "other", "mime_type": "application/pdf", "url": "/9689/1/Clark_Andrew J_Thesis_04292016_Final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Delivery of Targeted Nanoparticles Across the Blood-Brain Barrier Using a Detachable Targeting Ligand", "author": [ { "family_name": "Clark", "given_name": "Andrew James", "orcid": "0000-0003-4240-7119", "clpid": "Clark-Andrew-James" } ], "thesis_advisor": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "clpid": "Shapiro-M-G" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chronic diseases of the central nervous system are poorly treated due to the inability of most therapeutics to cross the blood-brain barrier. The blood-brain barrier is an anatomical and physiological barrier that severely restricts solute influx, including most drugs, from the blood to the brain. One promising method to overcome this obstacle is to use endogenous solute influx systems at the blood-brain barrier to transport drugs. Therapeutics designed to enter the brain through transcytosis by binding the transferrin receptor, however, are restricted within endothelial cells. The focus of this work was to develop a method to increase uptake of transferrin-containing nanoparticles into the brain by overcoming these restrictive processes.
\r\n\r\nTo accomplish this goal, nanoparticles were prepared with surface transferrin molecules bound through various liable chemical bonds. These nanoparticles were designed to shed the targeting molecule during transcytosis to allow increased accumulation of nanoparticles within the brain.
\r\n\r\nTransferrin was added to the surface of nanoparticles through either redox or pH sensitive chemistry. First, nanoparticles with transferrin bound through disulfide bonds were prepared. These nanoparticles showed decreased avidity for the transferrin receptor after exposure to reducing agents and increased ability to enter the brain in vivo compared to those lacking the disulfide link.
\r\n \r\nNext, transferrin was attached through a chemical bond that cleaves at mildly acidic pH. Nanoparticles containing a cleavable link between transferrin and gold nanoparticle cores were found to both cross an in vitro model of the blood-brain barrier and accumulate within the brain in significantly higher numbers than similar nanoparticles lacking the cleavable bond. Also, this increased accumulation was not seen when using this same strategy with an antibody to transferrin receptor, indicating that behavior of nanoparticles at the blood-brain barrier varies depending on what type of targeting ligand is used.
\r\n\r\nFinally, polymeric nanoparticles loaded with dopamine and utilizing a superior acid-cleavable targeting chemistry were investigated as a potential treatment for Parkinson\u2019s disease. These nanoparticles were capable of increasing dopamine quantities in the brains of healthy mice, highlighting the therapeutic potential of this design. Overall, this work describes a novel method to increase targeted nanoparticle accumulation in the brain.
\r\n", "doi": "10.7907/Z9WH2MZ6", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9703", "collection": "thesis", "collection_id": "9703", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05052016-123724002", "primary_object_url": { "basename": "Chaubard_Jean-Luc_Thesis_2016.pdf", "content": "final", "filesize": 18091047, "license": "other", "mime_type": "application/pdf", "url": "/9703/1/Chaubard_Jean-Luc_Thesis_2016.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Development of Chemoenzymatic Labeling Approaches for the Detection of Fucosylated Biomarkers", "author": [ { "family_name": "Chaubard", "given_name": "Jean-Luc", "clpid": "Chaubard-Jean-Luc" } ], "thesis_advisor": [ { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Lester", "given_name": "Henry A.", "clpid": "Lester-H-A" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Protein fucosylation regulates a diverse set of physiological functions such as memory and learning, development, and disease pathogenesis. However, our current understanding of these processes is far behind that of other post-translational modifications, such as phosphorylation. This is, in part, due to the lack of tools available for the study of this important protein modification. To address this need, I have developed novel chemoenzymatic methods that enable the labeling and detection of unique forms of fucosylation, specifically fucose-\u03b1(1-2)-galactose (Fuc\u03b1(1-2)Gal) and core fucose. Additionally, novel glycosyltransferase assays were developed in-house to aid in the future development of both new and existing chemoenzymatic approaches.
\r\n\r\nI have demonstrated that the approach to detect Fuc\u03b1(1-2)Gal is highly selective for this disaccharide motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of this motif on live cells, discriminating malignant from normal cells. I have also shown that the chemoenzymatic detection of core fucose exhibits superior specificity towards this glycan on a variety of complex N-glycans and when compared to current fucose-specific lectins. Further, the approach is amenable to detection of core fucosylated glycans from multiple biological settings, can be exploited as an antibody-conjugation method, and can be integrated into a diagnostic platform for the profiling of protein specific core fucosylation levels. These approaches represent new potential strategies for biomarker identification and expand the technologies available for understanding the role of these important fucosylated glycans in physiology and disease.
\r\n", "doi": "10.7907/Z9K35RN1", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:8662", "collection": "thesis", "collection_id": "8662", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09192014-121956600", "type": "thesis", "title": "Development of Metalloenzyme Dioxygen Reduction Cathodes", "author": [ { "family_name": "Agbo", "given_name": "Peter Chukwudi Ifeanychukwu", "clpid": "Agbo-Peter-Chukwudi-Ifeanychukwu" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The prime thrust of this dissertation is to advance the development of fuel cell dioxygen reduction cathodes that employ some variant of multicopper oxidase enzymes as the catalyst. The low earth-abundance of platinum metal and its correspondingly high market cost has prompted a general search amongst chemists and materials scientists for reasonable alternatives to this metal for facilitating catalytic dioxygen reduction chemistry. The multicopper oxidases (MCOs), which constitute a class of enzyme that naturally catalyze the reaction O2 + 4H+ + 4e- \u2192 2H2O, provide a promising set of biochemical contenders for fuel cell cathode catalysts. In MCOs, a substrate reduces a copper atom at the type 1 site, where charge is then transferred to a trinuclear copper cluster consisting of a mononuclear type 2 or \u201cnormal copper\u201d site and a binuclear type 3 copper site. Following the reduction of all four copper atoms in the enzyme, dioxygen is then reduced to water in two two-electron steps, upon binding to the trinuclear copper cluster. We identified an MCO, a laccase from the hyperthermophilic bacterium Thermus thermophilus strain HB27, as a promising candidate for cathodic fuel cell catalysis. This protein demonstrates resilience at high temperatures, exhibiting no denaturing transition at temperatures high as 95\u00b0C, conditions relevant to typical polymer electrolyte fuel cell operation.
\r\n\r\nIn Chapter I of this thesis, we discuss initial efforts to physically characterize the enzyme when operating as a heterogeneous cathode catalyst. Following this, in Chapter II we then outline the development of a model capable of describing the observed electrochemical behavior of this enzyme when operating on porous carbon electrodes. Developing a rigorous mathematical framework with which to describe this system had the potential to improve our understanding of MCO electrokinetics, while also providing a level of predictive power that might guide any future efforts to fabricate MCO cathodes with optimized electrochemical performance. In Chapter III we detail efforts to reduce electrode overpotentials through site-directed mutagenesis of the inner and outer-sphere ligands of the Cu sites in laccase, using electrochemical methods and electronic spectroscopy to try and understand the resultant behavior of our mutant constructs. Finally, in Chapter IV, we examine future work concerning the fabrication of enhanced MCO cathodes, exploring the possibility of new cathode materials and advanced enzyme deposition techniques.
", "doi": "10.7907/Z9MK69TD", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8662", "collection": "thesis", "collection_id": "8662", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09192014-121956600", "type": "thesis", "title": "Development of Metalloenzyme Dioxygen Reduction Cathodes", "author": [ { "family_name": "Agbo", "given_name": "Peter Chukwudi Ifeanychukwu", "clpid": "Agbo-Peter-Chukwudi-Ifeanychukwu" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The prime thrust of this dissertation is to advance the development of fuel cell dioxygen reduction cathodes that employ some variant of multicopper oxidase enzymes as the catalyst. The low earth-abundance of platinum metal and its correspondingly high market cost has prompted a general search amongst chemists and materials scientists for reasonable alternatives to this metal for facilitating catalytic dioxygen reduction chemistry. The multicopper oxidases (MCOs), which constitute a class of enzyme that naturally catalyze the reaction O2 + 4H+ + 4e- \u2192 2H2O, provide a promising set of biochemical contenders for fuel cell cathode catalysts. In MCOs, a substrate reduces a copper atom at the type 1 site, where charge is then transferred to a trinuclear copper cluster consisting of a mononuclear type 2 or \u201cnormal copper\u201d site and a binuclear type 3 copper site. Following the reduction of all four copper atoms in the enzyme, dioxygen is then reduced to water in two two-electron steps, upon binding to the trinuclear copper cluster. We identified an MCO, a laccase from the hyperthermophilic bacterium Thermus thermophilus strain HB27, as a promising candidate for cathodic fuel cell catalysis. This protein demonstrates resilience at high temperatures, exhibiting no denaturing transition at temperatures high as 95\u00b0C, conditions relevant to typical polymer electrolyte fuel cell operation.
\r\n\r\nIn Chapter I of this thesis, we discuss initial efforts to physically characterize the enzyme when operating as a heterogeneous cathode catalyst. Following this, in Chapter II we then outline the development of a model capable of describing the observed electrochemical behavior of this enzyme when operating on porous carbon electrodes. Developing a rigorous mathematical framework with which to describe this system had the potential to improve our understanding of MCO electrokinetics, while also providing a level of predictive power that might guide any future efforts to fabricate MCO cathodes with optimized electrochemical performance. In Chapter III we detail efforts to reduce electrode overpotentials through site-directed mutagenesis of the inner and outer-sphere ligands of the Cu sites in laccase, using electrochemical methods and electronic spectroscopy to try and understand the resultant behavior of our mutant constructs. Finally, in Chapter IV, we examine future work concerning the fabrication of enhanced MCO cathodes, exploring the possibility of new cathode materials and advanced enzyme deposition techniques.
", "doi": "10.7907/Z9MK69TD", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8812", "collection": "thesis", "collection_id": "8812", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04052015-200117829", "primary_object_url": { "basename": "JSK_Thesis_Full.pdf", "content": "final", "filesize": 37266574, "license": "other", "mime_type": "application/pdf", "url": "/8812/31/JSK_Thesis_Full.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Targeting DNA Repeat Sequences with Py-Im Polyamides", "author": [ { "family_name": "Kang", "given_name": "JeenJoo Sophia", "clpid": "Kang-JeenJoo-Sophia" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Hairpin pyrrole-imdazole polyamides are cell-permeable, sequence-programmable oligomers that bind in the minor groove of DNA. This thesis describes studies of Py-Im polyamides targeted to biologically important DNA repeat sequences for the purpose of modulating disease states. Design of a hairpin polyamide that binds the CG dyad, a site of DNA methylation that can become dysregulated in cancer, is described. We report the synthesis of a DNA methylation antagonist, its sequence specificity and affinity informed by Bind-n-Seq and iteratively designed, which improves inhibitory activity in a cell-free assay by 1000-fold to low nanomolar IC50. Additionally, a hairpin polyamide targeted to the telomeric sequence is found to trigger a slow necrotic-type cell death with the release of inflammatory molecules in a model of B cell lymphoma. The effects of the polyamide are unique in this class of oligomers; its effects are characterized and a functional assay of phagocytosis by macrophages is described. Additionally, hairpin polyamides targeted to pathologically expanded CTG\u2022CAG triplet repeat DNA sequences, the molecular cause of myotonic dystrophy type 1, are synthesized and assessed for toxicity. Lastly, ChIP-seq of Hypoxia-Inducible Factor is performed under hypoxia-induced conditions. The study results show that ChIP-seq can be employed to understand the genome-wide perturbation of Hypoxia-Inducible Factor occupancy by a Py-Im polyamide.", "doi": "10.7907/Z93R0QSQ", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8395", "collection": "thesis", "collection_id": "8395", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262014-170142267", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 13166034, "license": "other", "mime_type": "application/pdf", "url": "/8395/61/Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A Cocktail of Thermally Stable, Chemically Synthesized Capture Agents for the Efficient Detection of Anti-gp41 Antibodies from Human Sera and Techniques", "author": [ { "family_name": "Pfeilsticker", "given_name": "Jessica A.", "clpid": "Pfeilsticker-Jessica-A" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Clemons", "given_name": "William M.", "clpid": "Clemons-W-M" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60\u00b0C. ", "doi": "10.7907/0FT2-EF04", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7967", "collection": "thesis", "collection_id": "7967", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09302013-141151012", "primary_object_url": { "basename": "ThesisSubmittedToETD.pdf", "content": "final", "filesize": 5489618, "license": "other", "mime_type": "application/pdf", "url": "/7967/1/ThesisSubmittedToETD.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Vibrational Pooling and Constrained Equilibration on Surfaces", "author": [ { "family_name": "Boney", "given_name": "Evans T. D.", "clpid": "Boney-Evans-T-D" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this thesis, we provide a statistical theory for the vibrational pooling and fluorescence time dependence observed in infrared laser excitation of CO on an NaCl surface. The pooling is seen in experiment and in computer simulations. In the theory, we assume a rapid equilibration of the quanta in the substrate and minimize the free energy subject to the constraint at any time t of a fixed number of vibrational quanta N(t). At low incident intensity, the distribution is limited to one- quantum exchanges with the solid and so the Debye frequency of the solid plays a key role in limiting the range of this one-quantum domain. The resulting inverted vibrational equilibrium population depends only on fundamental parameters of the oscillator (\u03c9e and \u03c9e\u03c7e) and the surface (\u03c9D and T). Possible applications and relation to the Treanor gas phase treatment are discussed. Unlike the solid phase system, the gas phase system has no Debye-constraining maximum. We discuss the possible distributions for arbitrary N-conserving diatom-surface pairs, and include application to H:Si(111) as an example.
\r\n\r\nComputations are presented to describe and analyze the high levels of infrared laser-induced vibrational excitation of a monolayer of absorbed 13CO on a NaCl(100) surface. The calculations confirm that, for situations where the Debye frequency limited n domain restriction approximately holds, the vibrational state population deviates from a Boltzmann population linearly in n. Nonetheless, the full kinetic calculation is necessary to capture the result in detail.
\r\n\r\nWe discuss the one-to-one relationship between N and \u03b3 and the examine the state space of the new distribution function for varied \u03b3. We derive the Free Energy, F = N\u03b3kT \u2212 kTln(∑Pn), and effective chemical potential, \u03bcn \u2248 \u03b3kT, for the vibrational pool. We also find the anti correlation of neighbor vibrations leads to an emergent correlation that appears to extend further than nearest neighbor.
\r\n\r\n", "doi": "10.7907/JM2J-XX84", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8197", "collection": "thesis", "collection_id": "8197", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04222014-120506633", "primary_object_url": { "basename": "Holland_thesis_final.pdf", "content": "final", "filesize": 7943636, "license": "other", "mime_type": "application/pdf", "url": "/8197/1/Holland_thesis_final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Design, Construction, and Applications of a High-Resolution Terahertz Time-Domain Spectrometer", "author": [ { "family_name": "Holland", "given_name": "Daniel Brian", "clpid": "Holland-Daniel-Brian" } ], "thesis_advisor": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "local_group": [ { "literal": "Astronomy Department" }, { "literal": "div_chem" } ], "abstract": "This thesis reports on the design, construction, and initial applications of a high-resolution terahertz time-domain ASOPS spectrometer. The instrument employs asynchronous optical sampling (ASOPS) between two Ti:sapphire ultrafast lasers operating at a repetition rate of approximately 80 MHz, and we thus demonstrate a THz frequency resolution approaching the limit of that repetition rate. This is an order of magnitude improvement in resolution over typical THz time-domain spectrometers. The improved resolution is important for our primary effort of collecting THz spectra for far-infrared astronomy. We report on various spectroscopic applications including the THz rotational spectrum of water, where we achieve a mean frequency error, relative to established line centers, of 27.0 MHz. We also demonstrate application of the THz system to the long-duration observation of a coherent magnon mode in a anti-ferromagnetic yttrium iron oxide (YFeO3) crystal. Furthermore, we apply the all-optical virtual delay line of ASOPS to a transient thermoreflectance experiment for quickly measuring the thermal conductivity of semiconductors.", "doi": "10.7907/Z91J97QR", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8417", "collection": "thesis", "collection_id": "8417", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282014-232356909", "primary_object_url": { "basename": "Thesis_SL.pdf", "content": "final", "filesize": 80408295, "license": "other", "mime_type": "application/pdf", "url": "/8417/1/Thesis_SL.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Chelation-Enforced Metal-Arene Interactions: Insights into Substrate Binding and Catalvsis by Late Transition Metal Complexes", "author": [ { "family_name": "Lin", "given_name": "Sibo", "clpid": "Lin-Sibo" } ], "thesis_advisor": [ { "family_name": "Agapie", "given_name": "Theodor", "clpid": "Agapie-T" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Labinger", "given_name": "Jay A.", "clpid": "Labinger-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Understanding and catalyzing chemical reactions requiring multiple electron transfers is an endeavor relevant to many outstanding challenges in the field of chemistry. To study multi-electron reactions, a terphenyl diphosphine framework was designed to support one or more metals in multiple redox states via stabilizing interactions with the central arene of the terphenyl backbone. A variety of unusual compounds and reactions and their relevance toward prominent research efforts in chemistry are the subject of this dissertation.
\r\n\r\nChapter 2 introduces the para-terphenyl diphosphine framework and its coordination chemistry with group 10 transition metal centers. Both mononuclear and dinuclear compounds are characterized. In many cases, the metal center(s) are stabilized by the terphenyl central arene. These metal\u2013arene interactions are characterized both statically, in the solid state, and fluxionally, in solution. As a proof-of-principle, a dinickel framework is shown to span multiple redox states, showing that multielectron chemistry can be supported by the coordinatively flexible terphenyl diphosphine.
\r\n\r\nChapter 3 presents reactivity of the terphenyl diphosphine when bound to a metal center. Because of the dearomatizing effect of the metal center, the central arene of the ligand is susceptible to reactions that do not normally affect arenes. In particular, Ni-to-arene H-transfer and arene dihydrogenation reactions are presented. Additionally, evidence for reversibility of the Ni-to-arene H-transfer is discussed.
\r\n\r\nChapter 4 expands beyond the chelated metal-arene interactions of the previous chapters. A dipalladium(I) terphenyl diphosphine framework is used to bind a variety of exogenous organic ligands including arenes, dienes, heteroarenes, thioethers, and anionic ligands. The compounds are structurally characterized, and many ligands exhibit unprecedented bindng modes across two metal centers. The relative binding affinities are evaluated spectroscopically, and equilibrium binding constants for the examined ligands are determined to span over 13 orders of magnitude. As an application of this framework, mild hydrogenation conditions of bound thiophene are presented.
\r\n\r\nChapter 5 studies nickel-mediated C\u2013O bond cleavage of aryl alkyl ethers, a transformation with emerging applications in fields such as lignin biofuels and organic methodology. Other group members have shown the mechanism of C\u2013O bond cleavage of an aryl methyl ether incorporated into a meta-terphenyl diphosphine framework to proceed through \u03b2-H elimination of an alkoxide. First, the electronic selectivity of the model system is examined computationally and compared with catalytic systems. The lessons learned from the model system are then applied to isotopic labeling studies for catalytic aryl alkyl ether cleavage under dihydrogen. Results from selective deuteration experiments and mass spectrometry draw a clear analogy between the mechanisms of the model and catalytic systems that does not require dihydrogen for C\u2013O bond cleavage, although dihydrogen is proposed to play a role in catalyst activation and catalytic turnover.
\r\n\r\nAppendix A presents initial efforts toward heterodinuclear complexes as models for CO dehydrogenase and Fischer Tropsch chemistry. A catechol-incorporating terphenyl diphosphine is reported, and metal complexes thereof are discussed.
\r\n\r\nAppendix B highlights some structurally characterized terphenyl diphosphine complexes that either do not thematically belong in the research chapters or proved to be difficult to reproduce. These compounds show unusual coordination modes of the terphenyl diphosphine from which other researchers may glean insights.
", "doi": "10.7907/Z94T6G9T", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7960", "collection": "thesis", "collection_id": "7960", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09192013-114842407", "primary_object_url": { "basename": "Pheeney_Thesis Complied 09-19-2013.pdf", "content": "final", "filesize": 4478398, "license": "other", "mime_type": "application/pdf", "url": "/7960/1/Pheeney_Thesis Complied 09-19-2013.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Multiplexed DNA-Mediated Electrochemistry", "author": [ { "family_name": "Pheeney", "given_name": "Catrina Gale", "clpid": "Pheeney-Catrina-Gale" } ], "thesis_advisor": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of \u03c0-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the \u03c0-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA \u03c0-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.
\r\n\r\nFirst, Methylene Blue (MB\u2032) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB\u2032 was reduced through DNA-mediated charge transport. The redox signal intensity for MB\u2032-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB\u2032 on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB\u2032 at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.
\r\n\r\nNext, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening \u03c0-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA.\r\nFurther gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.
\r\n\r\nFinally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.
\r\n", "doi": "10.7907/PCF7-9669", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8248", "collection": "thesis", "collection_id": "8248", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05202014-111613067", "primary_object_url": { "basename": "Varghese-Joseph-2014Thesis.pdf", "content": "final", "filesize": 3382719, "license": "other", "mime_type": "application/pdf", "url": "/8248/31/Varghese-Joseph-2014Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Scanning Probe Studies of Thin Films", "author": [ { "family_name": "Varghese", "given_name": "Joseph O.", "clpid": "Varghese-Joseph-O" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The first part of this thesis deals with the phenomenon of thermoelectricity. It involves the improvement of the thermoelectric properties of silicon using innovative nanostructures. My contribution was to help fabricate these thermoelectric devices, and is the focus of this part of the thesis.
\r\n\r\nThe second part and primary focus of this thesis is the analysis of thin films using scanning probe techniques. These surface techniques include atomic force microscopy, electric force microscopy, Kelvin probe force microscopy, and scanning tunneling microscopy. The thin films studied are graphene and molybdenum disulfide, two remarkable materials that display unique two-dimensional qualities. These materials are shown to be useful in studying the properties of adsorbates trapped between them and the substrate on which they rest. Moreover, these adsorbed species are seen to affect the structural and electronic properties of the thin films themselves. Scanning probe analyses are particularly useful in elucidating the properties of these materials, as surface effects play a significant role in determining their characteristics.
\r\n\r\nThe final part of this thesis is concerned with the study of Akt in live cells using protein capture agents previously developed by my colleagues. The activation and degradation of Akt is investigated using various biological assays, including Western blots, in vitro kinase assays, and cell viability assays. Finally, the usefulness of synthetic capture agents in perturbing protein pathways and as delivery agents is assessed and analyzed.
\r\n", "doi": "10.7907/Z95B00DK", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8112", "collection": "thesis", "collection_id": "8112", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062014-172332538", "primary_object_url": { "basename": "Wei_Wei_2014_thesis.pdf", "content": "final", "filesize": 10594762, "license": "other", "mime_type": "application/pdf", "url": "/8112/1/Wei_Wei_2014_thesis.pdf", "version": "v10.0.0" }, "type": "thesis", "title": "Microfluidics-Based Single-Cell Functional Proteomics Microchip for Portraying Protein Signal Transduction Networks within the Framework of Physicochemical Principles, with Applications in Fundamental and Translational Cancer Research", "author": [ { "family_name": "Wei", "given_name": "Wei", "orcid": "0000-0002-1018-7708", "clpid": "Wei-Wei" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William L.", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly over the past 5 years and are providing unique opportunities. This thesis describes an emerging microfluidics-based toolkit for single cell functional proteomics, focusing on the development of the single cell barcode chips (SCBCs) with applications in fundamental and translational cancer research.
\r\n\r\nThe microchip designed to simultaneously quantify a panel of secreted, cytoplasmic and membrane proteins from single cells will be discussed at the beginning, which is the prototype for subsequent proteomic microchips with more sophisticated design in preclinical cancer research or clinical applications. The SCBCs are a highly versatile and information rich tool for single-cell functional proteomics. They are based upon isolating individual cells, or defined number of cells, within microchambers, each of which is equipped with a large antibody microarray (the barcode), with between a few hundred to ten thousand microchambers included within a single microchip. Functional proteomics assays at single-cell resolution yield unique pieces of information that significantly shape the way of thinking on cancer research. An in-depth discussion about analysis and interpretation of the unique information such as functional protein fluctuations and protein-protein correlative interactions will follow.
\r\n\r\nThe SCBC is a powerful tool to resolve the functional heterogeneity of cancer cells. It has the capacity to extract a comprehensive picture of the signal transduction network from single tumor cells and thus provides insight into the effect of targeted therapies on protein signaling networks. We will demonstrate this point through applying the SCBCs to investigate three isogenic cell lines of glioblastoma multiforme (GBM).
\r\n\r\nThe cancer cell population is highly heterogeneous with high-amplitude fluctuation at the single cell level, which in turn grants the robustness of the entire population. The concept that a stable population existing in the presence of random fluctuations is reminiscent of many physical systems that are successfully understood using statistical physics. Thus, tools derived from that field can probably be applied to using fluctuations to determine the nature of signaling networks. In the second part of the thesis, we will focus on such a case to use thermodynamics-motivated principles to understand cancer cell hypoxia, where single cell proteomics assays coupled with a quantitative version of Le Chatelier's principle derived from statistical mechanics yield detailed and surprising predictions, which were found to be correct in both cell line and primary tumor model.
\r\n\r\nThe third part of the thesis demonstrates the application of this technology in the preclinical cancer research to study the GBM cancer cell resistance to molecular targeted therapy. Physical approaches to anticipate therapy resistance and to identify effective therapy combinations will be discussed in detail. Our approach is based upon elucidating the signaling coordination within the phosphoprotein signaling pathways that are hyperactivated in human GBMs, and interrogating how that coordination responds to the perturbation of targeted inhibitor. Strongly coupled protein-protein interactions constitute most signaling cascades. A physical analogy of such a system is the strongly coupled atom-atom interactions in a crystal lattice. Similar to decomposing the atomic interactions into a series of independent normal vibrational modes, a simplified picture of signaling network coordination can also be achieved by diagonalizing protein-protein correlation or covariance matrices to decompose the pairwise correlative interactions into a set of distinct linear combinations of signaling proteins (i.e. independent signaling modes). By doing so, two independent signaling modes \u2013 one associated with mTOR signaling and a second associated with ERK/Src signaling have been resolved, which in turn allow us to anticipate resistance, and to design combination therapies that are effective, as well as identify those therapies and therapy combinations that will be ineffective. We validated our predictions in mouse tumor models and all predictions were borne out.
\r\n\r\nIn the last part, some preliminary results about the clinical translation of single-cell proteomics chips will be presented. The successful demonstration of our work on human-derived xenografts provides the rationale to extend our current work into the clinic. It will enable us to interrogate GBM tumor samples in a way that could potentially yield a straightforward, rapid interpretation so that we can give therapeutic guidance to the attending physicians within a clinical relevant time scale. The technical challenges of the clinical translation will be presented and our solutions to address the challenges will be discussed as well. A clinical case study will then follow, where some preliminary data collected from a pediatric GBM patient bearing an EGFR amplified tumor will be presented to demonstrate the general protocol and the workflow of the proposed clinical studies.
\r\n", "doi": "10.7907/Z9WS8R7G", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8207", "collection": "thesis", "collection_id": "8207", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04302014-134133118", "primary_object_url": { "basename": "Thesis_EYT.pdf", "content": "final", "filesize": 25776463, "license": "other", "mime_type": "application/pdf", "url": "/8207/1/Thesis_EYT.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Transition Metal Clusters Supported by Multinucleating Ligand Frameworks as Models of Biological Active Sites", "author": [ { "family_name": "Tsui", "given_name": "Emily Yuan", "orcid": "0000-0001-6419-3954", "clpid": "Tsui-Emily-Yuan" } ], "thesis_advisor": [ { "family_name": "Agapie", "given_name": "Theodor", "clpid": "Agapie-T" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Agapie", "given_name": "Theodor", "clpid": "Agapie-T" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation describes efforts to model biological active sites with small molecule clusters. The approach used took advantage of a multinucleating ligand to control the structure and nuclearity of the product complexes, allowing the study of many different homo- and heterometallic clusters. Chapter 2 describes the synthesis of the multinucleating hexapyridyl trialkoxy ligand used throughout this thesis and the synthesis of trinuclear first row transition metal complexes supported by this framework, with an emphasis on tricopper systems as models of biological multicopper oxidases. The magnetic susceptibility of these complexes were studied, and a linear relation was found between the Cu-O(alkoxide)-Cu angles and the antiferromagnetic coupling between copper centers. The triiron(II) and trizinc(II) complexes of the ligand were also isolated and structurally characterized.
\r\n\r\nChapter 3 describes the synthesis of a series of heterometallic tetranuclear manganese dioxido complexes with various incorporated apical redox-inactive metal cations (M = Na+, Ca2+, Sr2+, Zn2+, Y3+). Chapter 4 presents the synthesis of heterometallic trimanganese(IV) tetraoxido complexes structurally related to the CaMn3 subsite of the oxygen-evolving complex (OEC) of Photosystem II. The reduction potentials of these complexes were studied, and it was found that each isostructural series displays a linear correlation between the reduction potentials and the Lewis acidities of the incorporated redox-inactive metals. The slopes of the plotted lines for both the dioxido and tetraoxido clusters are the same, suggesting a more general relationship between the electrochemical potentials of heterometallic manganese oxido clusters and their \"spectator\" cations. Additionally, these studies suggest that Ca2+ plays a role in modulating the redox potential of the OEC for water oxidation.
\r\n\r\nChapter 5 presents studies of the effects of the redox-inactive metals on the reactivities of the heterometallic manganese complexes discussed in Chapters 3 and 4. Oxygen atom transfer from the clusters to phosphines is studied; although the reactivity is kinetically controlled in the tetraoxido clusters, the dioxido clusters with more Lewis acidic metal ions (Y3+ vs. Ca2+) appear to be more reactive. Investigations of hydrogen atom transfer and electron transfer rates are also discussed.
\r\n\r\nAppendix A describes the synthesis, and metallation reactions of a new dinucleating bis(N-heterocyclic carbene)ligand framework. Dicopper(I) and dicobalt(II) complexes of this ligand were prepared and structurally characterized. A dinickel(I) dichloride complex was synthesized, reduced, and found to activate carbon dioxide. Appendix B describes preliminary efforts to desymmetrize the manganese oxido clusters via functionalization of the basal multinucleating ligand used in the preceding sections of this dissertation. Finally, Appendix C presents some partially characterized side products and unexpected structures that were isolated throughout the course of these studies.
\r\n", "doi": "10.7907/CWJ4-QQ41", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8212", "collection": "thesis", "collection_id": "8212", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05042014-135648744", "primary_object_url": { "basename": "Daeffler May 2 2014.pdf", "content": "final", "filesize": 21926468, "license": "other", "mime_type": "application/pdf", "url": "/8212/1/Daeffler May 2 2014.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Functional Evaluation of Noncovalent Interactions in Neuroreceptors and Progress Toward the Expansion of Unnatural Amino Acid Methodology", "author": [ { "family_name": "Daeffler", "given_name": "Kristina Nicole-McCleary", "clpid": "Daeffler-Kristina-Nicole-McCleary" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.
\r\n\r\nIn chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-\u03c0 interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-\u03c0 interaction with dopamine.
\r\n\r\nChapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.
\r\n\r\nChapter 4 identifies a cation-\u03c0 interaction between glutamate and a tyrosine residue on loop C in the GluCl\u03b2 receptor. Using the recently published crystal structure of the homologous GluCl\u03b1 receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.
\r\n\r\nChapter 5 examines inherent properties of the GluCl\u03b1 receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.
", "doi": "10.7907/ST7S-DB65", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8398", "collection": "thesis", "collection_id": "8398", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272014-114201666", "primary_object_url": { "basename": "Deyle_Kaycie_2014_Thesis_Complete.pdf", "content": "final", "filesize": 3692951, "license": "other", "mime_type": "application/pdf", "url": "/8398/1/Deyle_Kaycie_2014_Thesis_Complete.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Development of Protein-Catalyzed Capture (PCC) Agents with Application to the Specific Targeting of the E17K Point Mutation of AKt1", "author": [ { "family_name": "Deyle", "given_name": "Kaycie Marie", "clpid": "Deyle-Kaycie-Marie" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.
\r\n\r\nThese technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.
", "doi": "10.7907/F8HW-TX51", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7527", "collection": "thesis", "collection_id": "7527", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03192013-100649773", "type": "thesis", "title": "Single Cell Proteomics Microchip to Profile Immune Function, with Applications in Stem Cell Biology, Translational Disease Mechanism Study and Clinical Therapeutics Monitoring", "author": [ { "family_name": "Ma", "given_name": "Chao", "clpid": "Ma-Chao" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Pine", "given_name": "Jerome", "clpid": "Pine-J" }, { "family_name": "Braun", "given_name": "Jonathan", "clpid": "Braun-J" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.
\r\n\r\nTo study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor \u2013 killer immunoglobulin-like receptor (KIR) \u2013 has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.
\r\n\r\nIn all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-\u03b1, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-\u03b1, IL-6 and GM-CSF. TLR stimulation activated the NF-\u03baB signaling in HSCs.\r\nSingle cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.
\r\n", "doi": "10.7907/2M7E-0P25", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7865", "collection": "thesis", "collection_id": "7865", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-111912342", "primary_object_url": { "basename": "Kiwook_Hwang_2013_thesis_final.pdf", "content": "final", "filesize": 24703251, "license": "other", "mime_type": "application/pdf", "url": "/7865/49/Kiwook_Hwang_2013_thesis_final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Biotechnologies for Cancer Diagnostics: Cell Sorting, Protein Analysis and Imaging of Cellular Metabolism", "author": [ { "family_name": "Hwang", "given_name": "Kiwook", "clpid": "Hwang-Kiwook" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Cai", "given_name": "Long", "clpid": "Cai-Long" }, { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called \u201cNucleic Acid Cell Sorting (NACS)\u201d, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.
\r\n \r\nSecondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called \u201cRadiopharmaceutical Imaging Chip\u201d (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.
\r\n \r\nThe last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.
\r\n", "doi": "10.7907/Z6DN-0483", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7858", "collection": "thesis", "collection_id": "7858", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-235430660", "primary_object_url": { "basename": "thesis_anag.pdf", "content": "final", "filesize": 18690309, "license": "other", "mime_type": "application/pdf", "url": "/7858/91/thesis_anag.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Developing Peptide Based Capture Agents for Diagnostics and Therapeutics ", "author": [ { "family_name": "Nag", "given_name": "Arundhati", "clpid": "Nag-Arundhati" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Cai", "given_name": "Long", "clpid": "Cai-Long" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.", "doi": "10.7907/Y064-VD39", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7817", "collection": "thesis", "collection_id": "7817", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012013-192515668", "primary_object_url": { "basename": "Aria_thesis_2013.pdf", "content": "final", "filesize": 25006301, "license": "other", "mime_type": "application/pdf", "url": "/7817/1/Aria_thesis_2013.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Control of Wettability of Carbon Nanotube Array by Reversible Dry Oxidation for Superhydrophobic Coating and Supercapacitor Applications", "author": [ { "family_name": "Aria", "given_name": "Adrianus Indrat", "clpid": "Aria-Adrianus-Indrat" } ], "thesis_advisor": [ { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" } ], "thesis_committee": [ { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "orcid": "0000-0002-2912-0001", "clpid": "Ravichandran-G" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" } ], "local_group": [ { "literal": "GALCIT" }, { "literal": "div_eng" } ], "abstract": "In this thesis, dry chemical modification methods involving UV/ozone, oxygen plasma, and vacuum annealing treatments are explored to precisely control the wettability of CNT arrays. By varying the exposure time of these treatments the surface concentration of oxygenated groups adsorbed on the CNT arrays can be controlled. CNT arrays with very low amount of oxygenated groups exhibit a superhydrophobic behavior. In addition to their extremely high static contact angle, they cannot be dispersed in DI water and their impedance in aqueous electrolytes is extremely high. These arrays have an extreme water repellency capability such that a water droplet will bounce off of their surface upon impact and a thin film of air is formed on their surface as they are immersed in a deep pool of water. In contrast, CNT arrays with very high surface concentration of oxygenated functional groups exhibit an extreme hydrophilic behavior. In addition to their extremely low static contact angle, they can be dispersed easily in DI water and their impedance in aqueous electrolytes is tremendously low. Since the bulk structure of the CNT arrays are preserved during the UV/ozone, oxygen plasma, and vacuum annealing treatments, all CNT arrays can be repeatedly switched between superhydrophilic and superhydrophobic, as long as their O/C ratio is kept below 18%.
\r\n\r\nThe effect of oxidation using UV/ozone and oxygen plasma treatments is highly reversible as long as the O/C ratio of the CNT arrays is kept below 18%. At O/C ratios higher than 18%, the effect of oxidation is no longer reversible. This irreversible oxidation is caused by irreversible changes to the CNT atomic structure during the oxidation process. During the oxidation process, CNT arrays undergo three different processes. For CNT arrays with O/C ratios lower than 40%, the oxidation process results in the functionalization of CNT outer walls by oxygenated groups. Although this functionalization process introduces defects, vacancies and micropores opening, the graphitic structure of the CNT is still largely intact. For CNT arrays with O/C ratios between 40% and 45%, the oxidation process results in the etching of CNT outer walls. This etching process introduces large scale defects and holes that can be obviously seen under TEM at high magnification. Most of these holes are found to be several layers deep and, in some cases, a large portion of the CNT side walls are cut open. For CNT arrays with O/C ratios higher than 45%, the oxidation process results in the exfoliation of the CNT walls and amorphization of the remaining CNT structure. This amorphization process can be implied from the disappearance of C-C sp2 peak in the XPS spectra associated with the pi-bond network.
\r\n\r\nThe impact behavior of water droplet impinging on superhydrophobic CNT arrays in a low viscosity regime is investigated for the first time. Here, the experimental data are presented in the form of several important impact behavior characteristics including critical Weber number, volume ratio, restitution coefficient, and maximum spreading diameter. As observed experimentally, three different impact regimes are identified while another impact regime is proposed. These regimes are partitioned by three critical Weber numbers, two of which are experimentally observed. The volume ratio between the primary and the secondary droplets is found to decrease with the increase of Weber number in all impact regimes other than the first one. In the first impact regime, this is found to be independent of Weber number since the droplet remains intact during and subsequent to the impingement. Experimental data show that the coefficient of restitution decreases with the increase of Weber number in all impact regimes. The rate of decrease of the coefficient of restitution in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Experimental data also show that the maximum spreading factor increases with the increase of Weber number in all impact regimes. The rate of increase of the maximum spreading factor in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Phenomenological approximations and interpretations of the experimental data, as well as brief comparisons to the previously proposed scaling laws, are shown here.
\r\n\r\nDry oxidation methods are used for the first time to characterize the influence of oxidation on the capacitive behavior of CNT array EDLCs. The capacitive behavior of CNT array EDLCs can be tailored by varying their oxygen content, represented by their O/C ratio. The specific capacitance of these CNT arrays increases with the increase of their oxygen content in both KOH and Et4NBF4/PC electrolytes. As a result, their gravimetric energy density increases with the increase of their oxygen content. However, their gravimetric power density decreases with the increase of their oxygen content. The optimally oxidized CNT arrays are able to withstand more than 35,000 charge/discharge cycles in Et4NBF4/PC at a current density of 5 A/g while only losing 10% of their original capacitance.
", "doi": "10.7907/B6MF-FX89", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:6865", "collection": "thesis", "collection_id": "6865", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03252012-235254880", "primary_object_url": { "basename": "Full.pdf", "content": "final", "filesize": 40574665, "license": "other", "mime_type": "application/pdf", "url": "/6865/21/Full.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Nanostructured Silicon Thermoelectrics", "author": [ { "family_name": "Yu", "given_name": "Jen-Kan", "clpid": "Yu-Jen-Kan" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The thesis discusses the thermoelectric properties of silicon nanostructures with a particular focus on their heat transport phenomenon. The aim of this thesis work is to design ultra-low thermal conductivity materials based on fundamental phonon physics. Silicon nanowires and silicon nanomeshes are the model nanostructure systems investigated in this thesis.
\r\n \r\nDegenerately boron-doped silicon nanowires (20 nm x 20 nm cross section) exhibit thermal conductivity, depending on the temperature of interest, roughly two orders of magnitude smaller than bulk silicon with similar impurity concentration. The reduction in thermal conductivity is presumably from increased boundary scattering of the thermal phonons. For smaller nanowire systems (e.g., 10 nm x 20 nm cross section), thermal conductivity lower than the amorphous limit is also observed. Dimensional crossover of the thermal phonons in these ultra-small nanowire systems is proposed to explain the thermal conductivity reduction. Thermoelectric figure-of-merit ZT~1, a two order of magnitude improvement is achieved in 20 nm x 20 nm silicon nanowires at 200K.
\r\n\r\nSilicon nanomeshes are designed to further reduce the thermal conductivity of silicon. The 2-D hole-array is patterned on the silicon nanomesh film as Bragg reflectors to slow down the phonon group velocity. From the direct thermal conductivity measurement via suspended microstructure platform, the coherent scattering mechanism effectively reduces the thermal conductivity of silicon by a factor of two from the nanowire value. In essence, the phononic metamaterial approach essentially creates a new class of silicon-based material with distinct phonon properties, in other words, the theoretical lower limit of thermal conductivity of silicon based on bulk dispersions no longer applies to the phononic nanomeshes. In addition, silicon nanomeshes exhibit bulk-like electrical conductivity rendering them potential high efficiency thermoelectrics.
\r\n\r\nIn Chapter 1, an introduction to the lattice thermal conductivity is given to point out the key parameters affecting the phonon transport, e.g., scattering mechanisms, phonon dispersions and phonon density-of-states. The thermoelectrics fundamentals are given in Chapter 2, as are the experimental results on silicon nanowires. The fabrication and measurement methodologies are also explained in this chapter. In Chapter 3, the phonon transport mechanism of the silicon nanomesh, a new class of phononic metamaterial, is investigated. A coherent phonon scattering mechanism is used to explain the unexpected phonon behaviors. A complete fabrication process flow is also developed in this chapter in order to fully release the nanostructure from the substrate for precise and accurate thermal conductivity measurement. In the last part of the thesis (Chapter 4), the phononic nanomesh approach is extended to a nanomesh superlattice structure. The architectural design is to incorporate interfacial thermal resistance or the Kapitza resistance to further reduce the thermal conductivity of silicon. In addition, device architecture consisting of self-assembled quantum dots is proposed to enhance the thermoelectric efficiency by energy-filtering mechanism.
\r\n", "doi": "10.7907/HPEF-BM21", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7052", "collection": "thesis", "collection_id": "7052", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182012-134600511", "primary_object_url": { "basename": "Thesis_Final.pdf", "content": "final", "filesize": 10246787, "license": "other", "mime_type": "application/pdf", "url": "/7052/1/Thesis_Final.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Targeting Tumors and the Kidney with siRNA Nanoparticles and Evaluation of Extracellular MicroRNA-based Methodologies to Track Their Activity", "author": [ { "family_name": "Zuckerman", "given_name": "Jonathan Eric", "clpid": "Zuckerman-Jonathan-Eric" } ], "thesis_advisor": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Ribas", "given_name": "Antoni", "clpid": "Ribas-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The goal of my thesis work is to discover new ways to enable the use of nanoparticle therapeutics to treat human disease. The work presented here touches on several areas in medicine and is united by a common theme: engineering ways to make, use, and evaluate therapeutics that maximize the benefit to the patient and minimize the harm. I have explored three interrelated strategies to achieve my objectives: (1) the use of targeted-nanoparticle-based therapeutics to deliver therapeutic entities to specific sites in the body, (2) the use of a highly specific type of therapeutic, siRNA, and (3) the evaluation of strategies for using extracellular microRNAs to non invasively monitor therapeutic activity and disease response to that activity.
\r\n\r\nIn Chapter 2, I present the first evidence of targeted-nanoparticle delivery of siRNA to solid tumors following systemic administration to patients. My coworkers and I demonstrate both dose-dependent accumulation of the siRNA nanoparticles and evidence of gene knockdown via the canonical RNAi mechanism.
\r\n\r\nChapters 3 \u2013 5 describe the therapeutic potential of targeted nanoparticles (one version used in the clinic and described in Chapter 2) for: (i) targeting ribonucleotide reductase subunit M2 in human melanoma cell lines (Chapter 3), (ii) Herceptin-targeted nanoparticles containing siRNA against Her2 in Her2(+) breast cancer (Chapter 4), and (iii) siRNA targeting the \u201cundruggable\u201d protein N-Ras for N-Ras mutant melanomas (Chapter 5).
\r\n\r\nChapters 6 \u2013 8 focus on the interaction of nanoparticles with the kidney. Chapter 6 explores a previously unknown phenomenon of size-dependent glomerular accumulation of nanoparticles. In Chapter 7, a new mechanism of clearance for polycation-polymer-based nucleic acid delivery systems is demonstrated, based on interactions between polymer components in the nanoparticle and the anionic surface of the renal filtration barrier, explaining the rapid clearance of these siRNA nanoparticle systems. Chapter 8 illustrates targeted-nanoparticle delivery of siRNA to the kidney.
\r\n\r\nIn Chapter 9, I test the hypothesis that analysis of tumor-secreted microRNAs within patient blood samples can be used as real-time markers of drug pharmacodynamics. Specifically, I focus on efforts to characterize microRNA expression patterns following pharmacologic inhibition of the oncogene BRAF in melanoma cells and their secreted exosomes.
", "doi": "10.7907/P4FF-NQ42", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6955", "collection": "thesis", "collection_id": "6955", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04222012-210013999", "primary_object_url": { "basename": "tham_douglas_2012_thesis.pdf", "content": "final", "filesize": 1694996, "license": "other", "mime_type": "application/pdf", "url": "/6955/1/tham_douglas_2012_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Silicon Nanostructure Photovoltaics", "author": [ { "family_name": "Tham", "given_name": "Douglas Weng Wah", "clpid": "Tham-Douglas-Weng-Wah" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Photovoltaic devices consisting of highly periodic, ultradense, silicon nanowire arrays and nanohole arrays have been fabricated with nominal nanowire widths of 20 nm, nanohole sizes of 12 nm, and lattice pitches of 32 nm, deep in the subwavelength regime for visible light. We have developed a set of surface passivation protocols that provide the extremely low surface recombination velocities typical of thick, high-quality, furnace-grown thermal silicon dioxide, but within an ultrathin layer on the order of 5 \u2013 10 nm thick. With this high quality oxide passivation, these devices exhibit good photovoltaic performance that rivals or exceeds all comparable devices reported in the literature. Using a collection of characterization techniques, including optical microscopy, scanning electron microscopy, cross-sectional transmission electron microscopy, and spectroscopic ellipsometry, we characterize the structure and morphology of these nanostructure arrays. The high perfection of the arrays enables absorptance calculations to be performed using rigorous coupled-wave analysis, which solves Maxwell\u2019s equations for periodic structures. The calculations show that these deep subwavelength nanostructures behave as homogeneous optical materials with effective refractive indices determined by the structural parameters. We solve approximate models to estimate their refractive indices. When the spectral responses of these devices were measured, their external quantum efficiencies track the calculated absorptances, except for a small multiplicative offset at shorter wavelengths due to a greater than unity internal quantum efficiency, which we estimate by dividing the absorptance into the external quantum efficiency. ", "doi": "10.7907/2B6T-Q315", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7066", "collection": "thesis", "collection_id": "7066", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05222012-224148199", "type": "thesis", "title": "Mechanistic Insights into Alkane C-H Activation and Functionalization by Metal Oxide Surfaces and Organometallic Complexes", "author": [ { "family_name": "Cheng", "given_name": "Mu-Jeng", "clpid": "Cheng-Mu-Jeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Alkanes are the major components of natural gas and petroleum; however, there are only few practical processes that can functionalize them into more valuable products such as alkene or alcohols. The reason for this difficulty is because alkanes possess strong and inert C-H bonds. The development of such a process that can convert alkanes to other more valuable functionalized hydrocarbons in a catalytic fashion would produce enormous economic benefits. The key to achieve this goal is to develop a proper catalyst. The catalysts can be organometallic complexes or metal oxide surfaces that catalyze alkane C-H activation and functionalization in homogeneous or heterogeneous conditions.
\r\n\r\nIn this thesis, we apply quantum mechanics to study the known alkane functionalization reactions to provide more insight into those catalytic processes, and we further utilize our computational results to design new reaction pathways for alkane functionalization. Each chapter presented herein constitutes an independent publication focusing on different aspects of the problem.
\r\n\r\nChapter 1: Single-Site Vanadyl Activation, Functionalization, and Reoxidation Reaction Mechanism for Propane Oxidative Dehydrogenation on the Cubic V4O10 Cluster: Vanadium oxide is a powerful heterogeneous catalyst that can convert oxidative dehydrogenation (ODH) of propane. Despite numerous studies, either computational or experimental, on this topic, no complete catalytic cycle is provided. In this paper, we examined the detailed mechanism for propane reacting with a V4O10 cluster to model the catalytic oxidative dehydrogenation (ODH) of propane on the V2O5(001) surface. We reported the mechanism of the complete catalytic cycle, including the regeneration of the reduced catalyst using gaseous O2, in which only a single vanadyl site is involved. This mechanism is applicable to propane ODH on the supported vanadium oxide catalysts where only monovanadate (O=V-(O)4-) species is present.
\r\n \r\nChapter 2: The Magnetic and Electronic Structure of Vanadyl Pyrophosphate from Density Functional Theory: We have studied the magnetic structure of the high-symmetry vanadyl pyrophosphate, focusing on the spin exchange couplings, applying density functional theory with exact exchange and the full three-dimensional periodicity to this system for the first time. Based on the local density of states and the response of spin couplings to varying the cell parameter a, we found that two major types of spin exchange couplings originate from different mechanisms: one from a super-exchange interaction and the other from a direct exchange interaction. Based on the variations in V\u2013O bond length as a function of strain along a, we found that the V\u2013O bonds of V\u2013(OPO)2\u2013V are covalent and rigid, whereas the bonds of V\u2013(O)2\u2013V are fragile and dative.
\r\n\r\nChapter 3: The Para-Substituent Effect and pH-Dependence of the Organometallic Baeyer-Villiger Oxidation of Rhenium-Carbon Bonds: Organometallic Baeyer-Villiger represents another means of oxidizing M-R to M-OR. In this work, we conducted a series of calculations with the goal of providing more insights into the reaction. We find that during this organometallic BV oxidation, the migrating phenyl plays the role of a nucleophile and the leaving group OH is nucleophile. Moreover, we also find that for R = Ph the reaction rate is much faster than that for R = Me, which is later confirmed by experiments.
\r\n\r\nChapter 4: Carbon-Oxygen Bond-Forming Mechanisms in Rhenium Oxo-Alkyl Complexes: Intramolecular 1,2-migration of hydrocarbyl across metal-oxo bonds is one of the few means of oxy-functionalizing M-R to M-OR bonds. This strategy works for R = Ph, but fails for R = Me and Et. In this work, we study these systems with the goal of understanding the reason. We find that when R = Me and Et the \u03b1-hydrogen is very acidic and easy to abstract even with weak base, such as the counter ion of the complex, leading to unwanted by-products. We find that these side reactions can be avoided by two means: (1) use counter ions with weaker basicity to increase proton abstraction barriers, and (2) use R = iPr, which has a higher migratory aptitude, to accelerate the 1,2-migration rate.
\r\n \r\nChapter 5: A Homolytic Oxy-Functionalization Mechanism: Intermolecular Hydrocarbyl Migration from M-R to Vanadyl Oxo: Oxy-functionalization M\u03b4+-R\u03b4- to M-OR bonds is one of the key challenges in the development of hydrocarbon hydroxylation catalysts. This can be achieved by limited means: (1) organometallic Baeyer-Villiger oxidation, and (2) intramolecular 1,2-migration of hydrocarbyl across metal-oxo bonds. In this work, we have examined C-O bond formation in the reaction of OVCl3 with Ph2Hg to generate phenol using quantum mechanics. Surprisingly, we find this reaction is through an unprecedented bimolecular, one-electron oxidation of the V-Ph bond by a second V=O moiety, not through the experimentally proposed intramolecular phenyl 1,2-migration across V=O bonds. Our calculations on the oxidation of Rh-CH3 and Ir-CH3 complexes by OVCl3 further suggest that the possibility of integrating this new oxidation mechanism into alkane oxidation catalytic cycles. We also give guidelines to choose the systems in which this oxidation mechanism may play an important role.
", "doi": "10.7907/K4XH-V434", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6750", "collection": "thesis", "collection_id": "6750", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12142011-124639130", "primary_object_url": { "basename": "Ruo-Gu_Thesis.pdf", "content": "final", "filesize": 3245935, "license": "other", "mime_type": "application/pdf", "url": "/6750/1/Ruo-Gu_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "High-Performance Silicon Nanowire Electronics", "author": [ { "family_name": "Huang", "given_name": "Ruo-Gu", "clpid": "Huang-Ruo-Gu" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Yariv", "given_name": "Amnon", "clpid": "Yariv-A" }, { "family_name": "Scherer", "given_name": "Axel", "clpid": "Scherer-A" }, { "family_name": "Schwab", "given_name": "Keith C.", "clpid": "Schwab-K-C" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis explores 10-nm wide Si nanowire (SiNW) field-effect transistors (FETs) for logic applications via the fabrication and testing of SiNW-based ring oscillators. Both SiNW surface treatments and dielectric annealing are reported for producing SiNW FETs that exhibit high performance in terms of large on/off-state current ratio (~108), low drain-induced barrier lowering (~30 mV), high carrier mobilities (~269 cm2/V\u2022s), and low subthreshold swing (~80 mV/dec). The performance of inverter and ring-oscillator circuits fabricated from these nanowire FETs is explored as well. The inverter demonstrates the highest voltage gain (~148) reported for a SiNW-based NOT gate, and the ring oscillator exhibits near rail-to-rail oscillation centered at 13.4 MHz. The static and dynamic characteristics of these NW devices indicate that these SiNW-based FET circuits are excellent candidates for various high-performance nanoelectronic applications.
\r\n\r\nA set of novel charge-trap non-volatile memory devices based on high-performance SiNW FETs are well investigated. These memory devices integrate Fe2O3 quantum dots (FeO QDs) as charge storage elements. A template-assisted assembly technique is used to align FeO QDs into a close-packed, ordered matrix within the trenches that separate highly aligned SiNWs, and thus store injected charges. A Fowler-Nordheim tunneling mechanism describes both the program and erase operations. The memory prototype demonstrates promising characteristics in terms of large threshold voltage shift (~1.3 V) and long data retention time (~3 \u00d7 106 s), and also allows for key components to be systematically varied. For example, varying the size of the QDs indicates that larger diameter QDs exhibit a larger memory window, suggesting the QD charging energy plays an important role in the carrier transport. The device temperature characteristics reveal an optimal window for device performance between 275K and 350K.
\r\n\r\nThe flexibility of integrating the charge-trap memory devices with the SiNW logic devices offers a low-cost embedded non-volatile memory solution. A building block for a SiNW-based field-programmable gate array (FPGA) is proposed in the future work.
\r\n", "doi": "10.7907/CG0M-QB27", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:5981", "collection": "thesis", "collection_id": "5981", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07292010-112948436", "primary_object_url": { "basename": "Paul_Clark_PhD_Thesis__8-10-2010.pdf", "content": "final", "filesize": 18243708, "license": "other", "mime_type": "application/pdf", "url": "/5981/1/Paul_Clark_PhD_Thesis__8-10-2010.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Synthesis of Interlocked Molecules by Olefin Metathesis", "author": [ { "family_name": "Clark", "given_name": "Paul Gregory", "clpid": "Clark-Paul-Gregory" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A large body of work in the Grubbs group has focused on the development of functional-group tolerant ruthenium alkylidene catalysts that perform a number of olefin metathesis reactions. These catalysts have seen application in a wide range of fields, including classic total synthesis as well as polymer and materials chemistry. One particular family of compounds, interlocked molecules, has benefitted greatly from these advances in catalyst stability and activity. This thesis describes several elusive and challenging interlocked architectures whose syntheses have been realized through the utilization of different types of ruthenium-catalyzed olefin metathesis reactions.\r\nRing-closing olefin metathesis has enabled the synthesis of a [c2]daisy-chain dimer with the ammonium binding site near the cap of the dimer. A deprotonated DCD possessing such a structural attribute will more forcefully seek to restore coordinating interactions upon reprotonation, enhancing its utility as a synthetic molecular actuator. Dimer functionalization facilitated incorporation into linear polymers, with a 48% size increase of an unbound, extended analogue of the polymer demonstrating slippage of the dimer units. Ongoing work is directed at further materials studies, in particular, exploring the synthesis of macroscopic networks containing the DCD units and analyzing the correlation between molecular-scale extension-contraction manipulations and resulting macro-scale changes.
\r\n\r\nA \"clipping\" approach to a polycatenated cyclic polymer, a structure that resembles a molecular \"charm bracelet\", has been described. The use of ring-opening metathesis polymerization of a carbamate monomer in the presence of a chain transfer agent allowed for the synthesis of a linear polymer that was subsequently functionalized and cyclized to the corresponding cyclic analogue. This cyclic polymer was characterized through a variety of techniques, and subjected to further functionalization reactions, affording a cyclic polyammonium scaffold. Diolefin polyether fragments were coordinated and \"clipped\" around the ammonium sites within the polymer backbone using ring-closing olefin metathesis, giving the molecular \"charm bracelet\". Confirmation of the interlocked nature of the product was achieved via 1H NMR spectroscopy and two-dimensional diffusion ordered NMR spectroscopy.
\r\n\r\nA simple strategy for a one-pot, multi-component synthesis of polyrotaxanes using acyclic diene metathesis polymerization was developed. The polyrotaxanes were characterized by traditional 1H NMR spectroscopy as well as size exclusion chromatography, and the interlocked topology was confirmed using two-dimension diffusion-ordered NMR spectroscopy. The dynamic, self-correcting nature of the ADMET polymerization was also explored through the equilibration of a capped polyammonium polymer in the presence of dibenzo-24-crown-8 ether and olefin metathesis catalysts. The efficiency and ease with which these mechanically interlocked macromolecules can be assembled should facilitate rapid modulation to achieve versatile polyrotaxane architectures.
\r\n\r\nFlexible, switchable [c2]daisy-chain dimers (DCDs) were synthesized, where the macromer ammonium binding site was adjacent to the crown-type recognition structure and separated from the cap by an alkyl chain. A DCD of this topology is expected to have an extended structure in the bound conformation (when the ammonium was coordinated to the crown). Several different macromer candidates were designed to allow access to DCDs with flexible alkyl chains between the ammonium binding site and the cap, and a number of synthetic routes were explored in an effort to access these challenging materials. While the first generation DCD structure proved to be unstable due to a labile ester linkage, work is continuing toward the development of several cap structures in an effort to replace the ester linkage with an ether linkage, which, in the second generation model systems, has proven much more stable to the acidic and basic conditions necessary to induce switching of the dimeric architecture.
\r\n\r\nOne of the efforts in our lab is directed at the synthesis of 18F-labeled nanoparticles to be used as tumor imaging agents in positron emission tomography. We have been working to optimize fluorine incorporation while minimizing NP crosslinking. Because of evidence of NP side-reactions with the potassium carbonate base, we have begun to use potassium benzoate solid-state beads. To analyze the fluorinated NPs, various sorbents were explored. It was found that silica sorbents rapidly reacted and bound to the NPs, while the NPs remained unreactive and mobile on alumina. Further analysis of the NPs has been accomplished using 2D-DOSY NMR spectroscopy. Future work with the NPs will involve a systematic evaluation of the role of water on the extent of fluorination, as well as functionalization of the NPs with Cy5.5 dye for use in studies on eyes to be done in collaboration with researchers at the Mayo Clinic.
\r\n", "doi": "10.7907/8C88-RT79", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6432", "collection": "thesis", "collection_id": "6432", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252011-091250250", "primary_object_url": { "basename": "Thesis_Peigen.pdf", "content": "final", "filesize": 11678980, "license": "other", "mime_type": "application/pdf", "url": "/6432/8/Thesis_Peigen.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Surface Chemistry at the Nanometer Scale", "author": [ { "family_name": "Cao", "given_name": "Peigen", "clpid": "Cao-Peigen" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "Kavli Nanoscience Institute" }, { "literal": "div_chem" } ], "abstract": "This thesis describes research towards understanding surface chemical and physical processes, as well as their effects on the underlying substrate properties, at the nanometer and atomic scales. We demonstrate a method to tune the density of etch pits on Si(111) during the chlorination process so as to change the surface reactivity. Subsequent grafting of an azide group to replace chlorine demonstrates an example of non-oxidative passivation of silicon surfaces with new functionalities. Depending upon the solvent used in the azidation process, it is shown to yield different azidation kinetic rates, different final azide coverages, and different surface-area distributions. Scanning tunneling spectroscopy studies show that both chlorination and azidation processes significantly modify the surface electronic structures, with the former leading to a non-zero density of states at the Fermi level.\r\n
\r\nOur studies on a new class of corrugation, i.e., wrinkles, in exfoliated graphene on SiO2 show that a \"three-for-six\" triangular pattern of atoms is exclusively and consistently observed on wrinkles, suggesting the local curvature of the wrinkle is a perturbation that breaks the six-fold symmetry of the graphene lattice. Lower electrical conductance is also found on the top of wrinkles compared to other regions of graphene. The wrinkles are characterized by the presence of midgap states, which is in agreement with recent theoretical predictions. A general method is also reported for reliably fabricating ultrahigh-density graphene nanoribbon (GNR) arrays. We have clearly observed how the properties of GNRs evolve as a function of number of graphene layers. The band gap (and so the on-off ratio) decreases as the number of layers increases. These results suggest that, in addition to single layer graphene, properties of GNRs of different thicknesses can also be harnessed for engineering GNRs as different building blocks towards FET applications.\r\n
\r\nA novel imaging technique, graphene-templated scanning probe microscopy, has been developed and applied for the study on the condensation process of water and small organic molecules on mica. We found that these molecular adlayers grow epitaxially on the mica substrate in a layer-by-layer fashion. In particular, submonolayers of water form atomically flat, faceted islands of height 0.37 plus or minus 0.02 nm, in agreement with the height of a monolayer of ice. The second adlayers also appear ice-like, and thicker layers appear liquid-like. This general mechanism, however, is not universal. Exclusively three-dimensional droplets of water are observed on chemically modified (hydrophobic) mica surfaces, suggesting a 3D growth mechanism.\r\n
\r\nThis thesis also includes my work on the design of a quartz-tuning-fork-based force sensor and related electronics for applications on low-temperature atomic force microscopy. Results show that the force-sensor-global-feedback circuit detector system induced lowest noise floor. The high detection sensitivity of this system demonstrates its ability to be used in frequency-modulated AFM at cryogenic temperatures. Surface topographic imaging of H-terminated Si(111) has been achieved at low temperatures.\r\n
", "doi": "10.7907/7EFV-V231", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6276", "collection": "thesis", "collection_id": "6276", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04012011-163924567", "primary_object_url": { "basename": "Thesis_Young_Shik_Shin_FINAL.pdf", "content": "final", "filesize": 6593562, "license": "other", "mime_type": "", "url": "/6276/10/Thesis_Young_Shik_Shin_FINAL.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Micro- and Nanotechnology-Based Platforms to Study Biology at Small Scale: From DNAs to Single Cells", "author": [ { "family_name": "Shin", "given_name": "Young Shik", "clpid": "Shin-Young-Shik" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis describes technology platforms for various biological applications at nano- and microscale. The first platform is the silicon nanowire (SiNW) field-effect-transistor (FET)-based biosensor. SiNW FETs have unique features such as label-free, real-time, and electrical measurement, which will be demonstrated with DNA and protein sensing. We further demonstrate that using different surface chemistry can modulate the sensitivity and dynamic range of the sensor. Debye screening, one of the major bottlenecks of the technology, is shown to be circumvented by using electrostatically immobilized capture DNA for DNA sensing and a small synthetic capture agent, peptide, for protein sensing. A model for the detection of analyte by SiNW sensors is also developed and utilized to extract DNA binding kinetic parameters, which shows the potential of the platform as a more sensitive version of surface plasmon resonance (SPR).
\r\n\r\nThe second part of this thesis focuses on a more practical and easily expandable technology, the microfluidics-based platform, to perform a single-cell-based protein analysis. We develop a flow patterning technology to generate highly parallel DNA barcodes that can be further utilized as a handle to immobilize protein capture agents, such as antibodies. As a first step, a protocol to make high-quality DNA micro-barcodes with an excellent uniformity is introduced. The uniform DNA barcode patterns enable us to perform protein detection from single cells in a microfluidic device that spans the whole glass microscope slide. A data set from about thousand experiments can be collected from a single test with the developed microfluidic device, owing to the good quality of DNA barcodes and DNA Encoded Antibody Libraries (DEAL) technology. This platform further demonstrates that multi-parameter protein detection at the single-cell level presents cellular heterogeneity which leads to new findings in biology. A quantitative version of the Le Chatelier\u2019s principle, as derived using information theory, is applied to analyze a large amount of data from this platform. This principle provides a quantitative prediction of the role of perturbations and allows a characterization of a protein\u2013protein interaction network.
\r\n\r\nLastly, another application of microfluidics is demonstrated for studying interfacial chemistry on lung surfactant systems under oxidative stress, along with mass spectrometry (MS) and molecular dynamic (MD) simulation results. The findings from the MS and MD simulations provide mechanistic details for the reaction of ozone with unsaturated phospholipids, leading to possible damage of the pulmonary system by ROS or direct ozone exposure. These investigations focus on molecular transformations that occur as a result of oxidative stress. Such molecular transformations can have a strong influence on the physical properties of the pulmonary surfactant (PS) system (i.e., the surface tension and elasticity of the interface), and therefore understanding how chemical transformations influence such physical properties can provide key insights into how the PS system responds to environmental challenges. Thus, we also propose utilizing microbubbles as a model system for investigating the physical transformations of the PS system when exposed to environmental challenges. The chemical composition change, along with physical property change, is analyzed by altered bubble size and oscillatory behavior which can provide an improved understanding of the physics of a PS system when it is subjected to oxidative stress.
", "doi": "10.7907/T590-G472", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6359", "collection": "thesis", "collection_id": "6359", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04272011-115528661", "primary_object_url": { "basename": "Ophir_Vermesh_-_PhD_Thesis_(Final).pdf", "content": "final", "filesize": 24522869, "license": "other", "mime_type": "application/pdf", "url": "/6359/1/Ophir_Vermesh_-_PhD_Thesis_(Final).pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Highly Informative Analytical Platforms for Rapid, Non-Invasive Diagnosis and Stratification of Patients with Cancer", "author": [ { "family_name": "Vermesh", "given_name": "Ophir", "clpid": "Vermesh-Ophir" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "As the tissue that contains the largest representation of the human proteome, blood is the most important fluid for clinical diagnostics. However, although changes of plasma protein profiles reflect physiological or pathological conditions associated with many human diseases, only a handful of plasma proteins are routinely used in clinical tests. Reasons for this include the intrinsic complexity of the plasma proteome, the heterogeneity of human diseases and the rapid degradation of proteins in sampled blood. The first part of this thesis reports an integrated microfluidic system, the integrated blood barcode chip (IBBC) that can sensitively sample a large panel of protein biomarkers over broad concentration ranges and within 10 minutes of sample collection. It enables on-chip blood separation and rapid measurement of a panel of plasma proteins from quantities of whole blood as small as those obtained by a finger prick. The device holds potential for inexpensive, noninvasive and informative clinical diagnoses, particularly in point-of-care settings.
\r\n\r\nProteomic approaches, on which the IBBC platform is based, have shown great promise in recent years for correctly classifying and diagnosing cancer patients. However, no large antibody-based microarray studies have yet been conducted to evaluate and validate plasma molecular signatures for detection of glioblastoma and monitoring of its response to therapy. In the second part of this thesis, plasma samples from 46 glioblastoma patients (72 total samples) are compared with those of 47 healthy controls with respect to the plasma levels of 35 different proteins known to be generally associated with tumor growth, survival, invasion, migration, and immune regulation. Average-linkage hierarchical clustering of the patient data stratified the two groups effectively, permitting accurate assignment of test samples into either GBM or healthy control groups with a sensitivity and specificity as high as 90% and 94%, respectively (when test samples within unbiased clusters were removed). The accuracy of these assignments improved (sensitivity and specificity as high as 94% and 96%, respectively) when the cluster analysis was repeated on increasingly trimmed sets of proteins that exhibited the most statistically significant (p < 0.05) differential expression. The diagnostic accuracy was also higher for test samples that fell into more homogeneous clusters. Intriguingly, test samples that fell within perfectly homogeneous clusters (all members belonging to the same group) could be diagnosed with 100% accuracy. Using the same 35-protein panel, we then analyzed plasma samples from GBM patients who were treated with the chemotherapeutic drug Avastin (Bevacizumab) in an effort to stratify patients based on treatment-responsiveness. Specifically, we compared 52 samples from (25) patients who exhibited tumor recurrence with 51 samples from (21) patients who did not exhibit recurrence. Again, several proteins were highly differentially expressed and cluster analysis provided effective stratification of patients between these two groups (sensitivity and specificity of 90% and 96%, respectively).
\r\n", "doi": "10.7907/40BR-TW68", "publication_date": "2011-06-10", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6247", "collection": "thesis", "collection_id": "6247", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02162011-180032183", "primary_object_url": { "basename": "Chang_Ho_Sohn_PhD_Thesis_16May11_final.pdf", "content": "final", "filesize": 7745538, "license": "other", "mime_type": "application/pdf", "url": "/6247/7/Chang_Ho_Sohn_PhD_Thesis_16May11_final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "New Reagents and Methods for Mass Spectrometry-based Proteomics Investigations", "author": [ { "family_name": "Sohn", "given_name": "Chang Ho", "clpid": "Sohn-Chang-Ho" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "New chemical reagents and methods have been employed for mass spectrometry (MS)-based proteomics investigations. Many chemical reagents are synthesized to be covalently attached to biomolecules, especially peptides and proteins. The properties of the resulting peptide conjugates are characterized by various tandem mass spectrometric techniques (e.g., collision-induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), infrared multiphoton dissociation (IRMPD), and free radical initiated peptide sequencing (FRIPS)). In Chapter 2, the effect of high electron affinity tags in ECD and ETD is investigated using their peptide conjugates. The initial intramolecular electron transfer from the high-lying Rydberg states to the covalently attached high electron affinity tag occurs in competition with the Coulomb stabilized \u03c0* orbitals of the amide bonds in the model peptides. This leads to the inhibition of the normal sequence of ECD and ETD processes, yielding no backbone fragmentations. In Chapter 3, selective disulfide bond cleavages are observed by the FRIPS method. A newly prepared TEMPO-based FRIPS reagent is labeled to model peptides containing disulfide bonds and subject to CID to monitor free radical induced cleavages. Highly selective C\u2013S and S\u2013S bond cleavages are observed and their reaction mechanisms are proposed. In Chapter 4, novel Caltech isobaric tags (CITs) for protein quantification are developed and validated using various model samples. A newly discovered low-energy gas-phase fragmentation pathway, a nucleophilic substitution of the N3 in the 1,2,3-triazole ring generated by copper-catalyzed azide-alkyne cycloaddition (CuAAC) inspired us to create CITs. This selective cleavage is applied to the formation of the reporter ions to quantify protein expression level in cells. Chapter 5 describes clickable cross-linkers (CXLs) developed for elucidation of three-dimensional protein structures and protein-protein interactions (PPIs). In CXLs, cross-linking reactions are separated from the conjugation of affinity tags, avoiding steric hindrance. Cross-linked peptides are enriched from the complex mixture of yeast lysate and cross-linked ubiquitin digests using avidin affinity chromatography, showing high sensitivity of the CXL-based analysis. The low-energy pathway used for CIT reagents is also adopted to produce the reporter ion, filtering MS/MS scans of cross-linked peptides from those of unmodified peptides.", "doi": "10.7907/HRF2-FJ21", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6218", "collection": "thesis", "collection_id": "6218", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12182010-040540249", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 6903650, "license": "other", "mime_type": "application/pdf", "url": "/6218/1/Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Technologies for Protein Analysis and Tissue Engineering, with Applications in Cancer", "author": [ { "family_name": "Vermesh", "given_name": "Udi Benjamin", "clpid": "Vermesh-Udi-Benjamin" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Gharib", "given_name": "Morteza", "orcid": "0000-0003-0754-4193", "clpid": "Gharib-M" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The first part of this thesis describes electrolyte transport through an array of 20 nm wide, 20 \u03bcm long SiO2 nanofluidic transistors. At sufficiently low ionic strength, the Debye screening length exceeds the channel width, and ion transport is limited by the negatively charged channel surfaces. At source-drain biases > 5 V, the current exhibits a sharp, nonlinear increase, with a 20 \u2212 50-fold conductance enhancement. This behavior is attributed to a breakdown of the zero-slip condition. Implications for peptide sequencing as well as energy conversion devices are discussed.
\r\n\r\nThe next part describes a technology for the detection of the highly aggressive brain cancer glioblastoma multiforme (GBM). In this study, we used an antibody-based microarray to compare plasma samples from glioblastoma patients and healthy controls with respect to the plasma levels of 35 different proteins known to be generally associated with tumor growth, survival, invasion, migration, and immune regulation. Average-linkage hierarchical clustering of the patient data stratified the two groups effectively, permitting accurate assignment of test samples into either GBM or healthy control groups with a sensitivity and specificity as high as 90 % and 94 %, respectively. Using the same 35-protein panel, we then analyzed plasma samples from GBM patients who were treated with the chemotherapeutic drug Avastin (Bevacizumab) and were able to effectively stratify patients based on treatment-responsiveness.
\r\n\r\nFinally, single-cell resolution patterning of tissue engineered structures is demonstrated. The proper functioning of engineered constructs for tissue and organ transplantation requires positioning different cell types in anatomically precise arrangements that mimic their configurations in native tissues. Toward this end, we have developed a technique that involves two microfluidic-patterning steps run perpendicularly to each other using \u201canchor\u201d and \u201cbridge\u201d DNA oligomers to create dense arrays of DNA grids which can then be converted into cell arrays. As a proof-of-concept, both a neuron-astrocyte construct and a pancreatic islet construct containing 2 distinct islet cell types were patterned separately as a dense array of cell grids. Once fixed in a hydrogel matrix, layers of patterned cells were then stacked to form 3-D tissue engineered constructs.
\r\n", "doi": "10.7907/21G2-0A20", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6506", "collection": "thesis", "collection_id": "6506", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072011-185553467", "primary_object_url": { "basename": "Ahmad_FinalThesis.pdf", "content": "final", "filesize": 9905679, "license": "other", "mime_type": "application/pdf", "url": "/6506/1/Ahmad_FinalThesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Microfluidics Platforms for Quantitative, Multiplexed Protein Detection", "author": [ { "family_name": "Ahmad", "given_name": "Habibullah", "clpid": "Ahmad-Habibullah" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Scherer", "given_name": "Axel", "clpid": "Scherer-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the development of microfluidic platforms that enable cheap, facile, rapid, and multi-parameter protein sensing. The first section of this work describes two strategies for high density DNA microarray patterning: microcontact printing and flow patterning. A protocol is provided for micron-scale alignment of multiple PDMS stamps to a single substrate, and a simple strategy to allow very low aspect-ratio stamping is enumerated.
\r\n\r\nThe second section describes the formation of high density antibody microarrays using flow patterned DNA microarrays in conjunction with DEAL chemistry, and applies these microarrays to biological measurements. The platform\u2019s performance is first characterized using a human chorionic gonadotropin assay, and is subsequently used to stratify 22 cancer patients from frozen serum samples by quantifying the levels of twelve serum proteins. A microfluidic plasma separation device is then detailed to allow for similar measurements from fresh finger pricks of blood.
\r\n\r\nThe third section of this work outlines improvements to the flow patterning platform through two alternate schemes: covalent attachment and DMSO patterning. Both protocols are shown to dramatically increase the consistency of microarray elements across a single chip when compared to the initial method. Theoretical simulations are used to describe the mechanism by which DMSO enhances patterning consistency.
\r\n\r\nThe fourth section describes the design and fabrication of a robotics system that is capable of autonomously interfacing and manipulating PDMS substrates, and its application to producing barcode microarrays. The resulting substrates show unprecedented consistency from chip to chip, and we demonstrate through massively parallel single-cell measurements that data derived from different substrates is statistically indistinguishable.
\r\n\r\nFinally, we introduce an integrated software and hardware package designed to facilitate and automate microfluidic control at the laboratory level. We further provide the technical details of a related system which optimizes and comprehensively automates microfluidic blood assays such that even non-technical users who have never worked with microfluidics can regularly obtain the same standard of data that is produced in the lab.
\r\n", "doi": "10.7907/04A6-YT31", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:5583", "collection": "thesis", "collection_id": "5583", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03092010-121643566", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 5771024, "license": "other", "mime_type": "application/pdf", "url": "/5583/11/Thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Rapid Construction of Protein Capture Agents with Chemically Designed Stability and Antibody-Like Recognition Properties", "author": [ { "family_name": "Agnew", "given_name": "Heather Dawn", "clpid": "Agnew-Heather-Dawn" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes technologies for the rapid and scalable production of high-affinity, high-specificity protein capture agents which possess the affinities and specificities of antibodies, but also exhibit improved chemical, biochemical, and physical stability. I will discuss how the chemical flexibility of comprehensive, one-bead-one-compound (OBOC) libraries of oligopeptides may be combined with iterative in situ click chemistry to select multi-ligand capture agents. Large OBOC libraries form the basis of individual peptide ligands, and also permit chemically designed stability through the incorporation of artificial (azide or acetylene) and non-natural amino acid building blocks. The in situ click chemistry method then utilizes the target protein as the catalyst, or template, for assembling its own biligand via formation of a 1,2,3-triazole linkage between two individual ligands (azide and acetylene). This process can be repeated to produce triligands, tetraligands, and other higher-order multi-ligands with an accompanying increase in affinity and specificity through cooperative interactions. Once found, multi-ligand capture agents can be produced in gram amounts via conventional synthetic methods such as the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). This is a general and robust strategy for the inexpensive, high-throughput construction of protein capture agents that can be exploited to detect protein biomarkers in multi-parameter clinical diagnostic assays.
\r\n\r\nWhile high-affinity protein capture agents represent a significant technology advance, they are just one component of what is necessary for highly multiplexed measurements of protein biomarkers. It is also important to develop or optimize the actual assay platforms that can enable sensitive multi-parameter protein measurements using these capture agents. Silicon nanowire (SiNW) nanoelectronic sensors can provide quantitative, label-free multi-parameter measurements of protein biomarkers in real time. However, SiNW sensors can be challenging to deploy because unprotected Si forms a native oxide layer that can significantly reduce the detection sensitivity of the nanowire sensors via dielectric shielding. Another technical challenge is the development of chemistries which allow for the selective encoding of nanowire surfaces with the capture agents. To overcome these challenges, the final part of this thesis presents a general method to functionalize organic and biological molecules on highly passivated Si(111) surfaces with minimal surface oxidation.
", "doi": "10.7907/1HJG-AQ59", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:3416", "collection": "thesis", "collection_id": "3416", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09092009-091741", "primary_object_url": { "basename": "Full_Thesis_final_version.pdf", "content": "final", "filesize": 8068557, "license": "other", "mime_type": "application/pdf", "url": "/3416/1/Full_Thesis_final_version.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Applications and Extensions of Living Ring-Opening Metathesis Polymerization", "author": [ { "family_name": "Matson", "given_name": "John B.", "orcid": "0000-0001-7984-5396", "clpid": "Matson-John-B" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Living ring-opening metathesis polymerization (ROMP) is a polymerization method that has recently become popular in the synthesis of complex polymers due to advances in olefin metathesis catalyst design. The unrivaled degree of functional group tolerance of the method, coupled with a high level of control and synthetic ease, make living ROMP a valuable tool in the assembly of complex nanostructures and functional polymers. Work in this thesis details methods for applying living ROMP in the assembly of complex nanostructures and extending the uses of living ROMP to end-functionalized polymers and to polymers synthesized in a catalyst economical manner.
\r\n\r\nChapter 2 describes the synthesis and radiofluorination of fluorine-18 functionalized nanoparticles assembled from polynorbornene block copolymers synthesized via living ROMP. The block copolymers include a hydrophobic photo-crosslinkable block made from a novel cinnamate-containing norbornene, as well as a hydrophilic block made from a PEGylated norbornene. Chapter 3 illustrates another application of ROMP-based nanoparticles in which polynorbornene block copolymers are assembled into Janus (hemispherical) nanoparticles.
\r\n\r\nA method for end-capping ROMP polymers using a symmetrical alpha\u2013bromoester-containing cis-olefin terminating agent is described in Chapter 4. Subsequent atom transfer radical polymerization (ATRP) from the functionalized chain end confirms complete end-functionalization and was used to synthesize mechanistically incompatible block copolymers. Chapter 5 extends this polymer end-functionalization approach to additional functional groups, including alcohols, bromides, thioacetates, fluorescent compounds, biotin, and others.
\r\n\r\nA thorough study of pulsed-addition ROMP (PA-ROMP) performed using a Symyx robotic system is presented in Chapter 6. Extending the end-capping methodology described in Chapters 4 and 5 to the synthesis of additional polymer chains led to a homo- and block copolymerization strategy that can produce more than one polymer chain per molecule of metal initiatior. The PA-ROMP strategy reduces catalyst consumption as much as sevenfold in the synthesis of polynorbornenes.
\r\n\r\nAppendix 1 describes the synthesis and ROMP of several norbornene monomers, including a copper-64 chelating norbornene, that were not addressed in the previous chapters but that may be useful for future studies on functional ROMP polymers and nanostructures. Appendix 2 contains additional mathematical details on PA-ROMP.
\r\n", "doi": "10.7907/4QZ8-CS23", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:6528", "collection": "thesis", "collection_id": "6528", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06242011-125949350", "type": "thesis", "title": "Unfolded States of Heme Proteins", "author": [ { "family_name": "Pribisko Yen", "given_name": "Melanie Anne", "clpid": "Pribisko-Yen-Melanie-Anne" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Clemons", "given_name": "William M.", "clpid": "Clemons-W-M" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Cytochromes adopt discrete structures when the heme cofactor is present. Since the heme provides crucial contacts in the native protein, this hydrophobic prosthetic group plays an important role in the folding mechanism and introduces interesting features into the folding landscape. Since the iron-porphyrin is sensitive to protein structure and environment, it also acts an optical probe and will be used in photophysical and photochemical studies of three alpha-helical proteins in the electron transport family of cytochromes: both horse heart and Saccharomyces cerevisiae iso-1 cytochrome c (cyt c), Rhodopseudomonas palustris cytochrome c' (cyt c'), and the engineered cytochrome cb\u2085\u2086\u2082(cyt cb\u2085\u2086\u2082) from E. coli cytochrome b\u2085\u2086\u2082.
\r\n\r\nThe work in this thesis expands upon previous research in the Gray Group that has shown heterogenous unfolded populations in these three alpha-helical proteins. Triplet state decay kinetics of Zn-substituted cytochrome c (Zn-cyt c) reveal the level of solvent exposure of the heme through an isotope effect and bimolecular quenching of lifetimes. Differences of the GuHCl, urea, and thermally-induced unfolded states between Zn- and Fe-cyt c, cyt c' and cb\u2085\u2086\u2082 were uncovered, revealing a distinct hydrophobic effect. The inability of elevated temperature to disrupt hydrophobic pockets was studied further for DNS(C102)-cyt c through FET kinetics that reveal a significant compact population at high temperature. Finally, initial experiments on macromolecular crowding of cyt c revealed only a slight effect on the equilibrium unfolded states.
", "doi": "10.7907/WWS3-C929", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5332", "collection": "thesis", "collection_id": "5332", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10262009-204842274", "primary_object_url": { "basename": "tpascal_thesis.pdf", "content": "final", "filesize": 11748720, "license": "other", "mime_type": "application/pdf", "url": "/5332/1/tpascal_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures", "author": [ { "family_name": "Pascal", "given_name": "Tod Augustin", "orcid": "0000-0003-2096-1143", "clpid": "Pascal-Tod-Augustin" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Although computer simulations have been applied to the calculation of solvation free energies for a wide range of molecules, reliable calculations including explicit consideration of entropy and quantum effects (zero-point energy corrections) are less common, owing to the enormous computational effort required by standard perturbation methods. Accurate calculations of entropies are essential if computer simulations are to become more useful tools for obtaining molecular insights into solvation and ligand binding phenomena.
\r\n\r\nWe report on the extension of a method of calculating exact entropies and quantum effects from standard MD simulations. This novel method is applied to the investigation of three model cases: 1) the folding of a DNA three-way junction 2) the efficacy of binding in a protein-protein interaction, critical in the pathogenesis of bacterial meningitis in neonates and 3) the free energy of water molecules at two extreme surfaces, as model systems for an investigation of the hydrophobic effect. We develop a scheme to partition the free energy into the per-atom components, and show that the water molecules in the first hydration shell have unique character. Understanding their nature is critical to discovering the underlying physics in these systems.
", "doi": "10.7907/P0JH-QM60", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5844", "collection": "thesis", "collection_id": "5844", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-132424180", "primary_object_url": { "basename": "thesis_jmueller_final.pdf", "content": "final", "filesize": 3921784, "license": "other", "mime_type": "application/pdf", "url": "/5844/1/thesis_jmueller_final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Structures, Energetics and Reactions of Hydrocarbons on Nickel", "author": [ { "family_name": "Mueller", "given_name": "Jonathan Edward", "orcid": "0000-0001-8811-8799", "clpid": "Mueller-Jonathan-Edward" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To better understand and improve reactive processes on nickel surfaces such as the catalytic steam reforming of hydrocarbons, the decomposition of hydrocarbons at fuel cell anodes, and the growth of carbon nanotubes, we have performed atomistic studies of hydrocarbon adsorption and decomposition on low index nickel surfaces and nickel catalyst nanoparticles. Quantum mechanics (QM) calculations utilizing the PBE flavor of density functional theory (DFT) were performed on all CHx and C2Hy species to determine their structures and energies on Ni(111). In good agreement with experiments, we find that CH is the most stable form of CHx on Ni(111). It is a stable intermediate in both methane dehydrogenation and CO methanation, while CH(2,ad) is only stable during methanation. We also find that nickel surface atoms play an important catalytic role in C-H bond formation and cleavage. For the C2Hy species we find a low surface coverage decomposition pathway proceeding through CHCHad, the most stable intermediate, and a high surface coverage pathway which proceeds through CCH3,ad, the next most stable intermediate. Our enthalpies along these pathways are consistent with experimental observations.
\r\n\r\nTo extend our study to larger systems and longer time scales, we have developed the ReaxFF reactive force field to describe hydrocarbon decomposition and reformation on nickel catalyst surfaces. The ReaxFF parameters were fit to geometries and energy surfaces from DFT calculations involving a large number of reaction pathways and equations of state for nickel, nickel carbides, and various hydrocarbon species chemisorbed on Ni(111), Ni(110) and Ni(100). The resulting ReaxFF description was validated against additional DFT data to demonstrate its accuracy, and used to perform reaction dynamics (RD) simulations on methyl decomposition for comparison with experiment. Finally ReaxFF RD simulations were applied to the chemisorption and decomposition of six different hydrocarbons (methane, acetylene, ethylene, benzene, cyclohexane and propylene) on a 468 atom nickel nanoparticle. These simulations realistically model hydrocarbon feedstock decomposition and provide reaction pathways relevant to this part of the carbon nanotube growth process. They show that C-C \u03c0 bonds provide a low barrier pathway for chemisorption, and that the low energy of subsurface C is an important driving force in breaking C-C bonds.
", "doi": "10.7907/RVXX-Z341", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5818", "collection": "thesis", "collection_id": "5818", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05192010-182707354", "primary_object_url": { "basename": "YanXia_complete_thesis.pdf", "content": "final", "filesize": 4398856, "license": "other", "mime_type": "application/pdf", "url": "/5818/9/YanXia_complete_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Syntheses of Polymers with Diverse Architectures via Metathesis Polymerization and Investigation of Their Structure-Property Relationships", "author": [ { "family_name": "Xia", "given_name": "Yan", "clpid": "Xia-Yan" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Metathesis polymerization using highly active, functional-group-tolerant catalysts is a powerful and versatile method for polymer synthesis. This thesis focuses on the preparation of a variety of advanced polymer architectures using well-defined ruthenium-based metathesis catalysts and the study of materials properties dictated by those unique macromolecular structures.
\r\n\r\nChapter 1 introduces olefin metathesis, metathesis polymerization, and recent developments in living/controlled polymerization and polymer functionalization. The goal is to provide a summary of the current toolbox of polymer chemists. The second part of Chapter 1 describes using these tools to synthesize different macromolecular architectures.
\r\n\r\nChapters 2 and 3 describe ring-expansion metathesis polymerization (REMP) using cyclic catalysts. Chapter 2 focuses on catalyst development, while Chapter 3 focuses on the REMP mechanism and cyclic polymer characterization.
\r\n\r\nChapters 4 and 5 focus on brush polymers. Chapter 4 describes the syntheses of linear and cyclic brush polymers using ring-opening metathesis polymerization (ROMP) and REMP of macromonomers (MMs), respectively. Chapter 5 describes the efficient synthesis of brush copolymers and the study of their melt state self-assembly into highly ordered nanostructures.
\r\n\r\nChapter 6 describes the synthesis and electro-optic response of well-defined liquid crystalline (LC) gels that were made from controlled end-linking of telechelic LC polymers. These gels possessed very fast, reversible electro-optic switching; the degree of response was closely related to network structure.
", "doi": "10.7907/WTBS-F528", "publication_date": "2010-06-11", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5239", "collection": "thesis", "collection_id": "5239", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07222008-023323", "primary_object_url": { "basename": "Thesis_YukiMatsuda.pdf", "content": "final", "filesize": 2985544, "license": "other", "mime_type": "application/pdf", "url": "/5239/1/Thesis_YukiMatsuda.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ab Initio Quantum Mechanical Studies in Electronic and Structural Properties of Carbon Nanotubes and Silicon Nanowires", "author": [ { "family_name": "Matsuda", "given_name": "Yuki", "clpid": "Matsuda-Yuki" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Bockrath", "given_name": "Marc William", "clpid": "Bockrath-M-W" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation focuses on ab-initio quantum mechanical calculations of nanoelectronics in three research topics: contact resistance properties of carbon nanotubes and graphenes (Chapters 1 through 3), electrical properties of carbon nanotubes (Chapter 4) and silicon nanowires (Chapter 5). Through all the chapters, the aim of the research is to provide useful guidelines for experimentalists.
\r\n\r\nChapter 1 presents the contact resistance of metal electrode\u2212carbon nanotube and metal electrode\u2212graphene interfaces for various deposited metals, based on first-principles quantum mechanical density functional and matrix Green\u2019s function methods. Chapters 2 and 3 describe inventive ways to enhance contact resistance properties as well as mechanical stabilities using \u201cmolecular anchors\u201d (Chapter 2) or using \"end-contacted\" (or end-on) electrodes (Chapter 3). Chapters 1 through 3 also provide useful guidelines for nanotube assembly process which is one of the main obstacles in nanoelectronics. Chapter 4 shows accurate and detailed band structure properties of single-walled carbon nanotubes using B3LYP hybrid functional, which are critical parameters in determining the electronic properties such as small band gaps (~0.1 eV) and effective masses. Chapter 5 details both structural and electronic properties of silicon nanowires. These results lead to the findings controlling the diameter and surface coverage by adsorbates (e.g., hydrogen) of silicon nanowires can be effectively used to optimize their properties for various applications.
\r\n\r\nAll the theoretical results are compared with other theoretical studies and experimental data. Notably, electronic studies using B3LYP show excellent agreement with experimental studies quantitatively, which previous quantum mechanical calculations had failed.
\r\n\r\nThese studies show how quantum mechanical predictions of complex phenomena can be effectively investigated computationally in nanomaterials and nanodevices. Given the difficulty, expense, and time required for experiments, theory may now be useful for high-throughout screening to identify the best conditions and materials before performing experiments.
\r\n", "doi": "10.7907/7FXD-ZQ68", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:5261", "collection": "thesis", "collection_id": "5261", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12102008-101354", "primary_object_url": { "basename": "Acknowledgements.pdf", "content": "final", "filesize": 95334, "license": "other", "mime_type": "application/pdf", "url": "/5261/1/Acknowledgements.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Electrical Detection of DNA Binding Proteins", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "clpid": "Gorodetsky-Alon-A" } ], "thesis_advisor": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The base pair stack of double helical DNA has proven to be an effective medium for charge transport. The \u03c0-stacked DNA base pairs can mediate charge transport (CT) chemistry over distances as long as 20 nm, and the reaction is exquisitely sensitive to DNA sequence-dependent conformation and dynamics. This sensitivity to perturbations in DNA structure and base pair stacking makes DNA-mediated charge transport chemistry an ideal methodology for the electrical detection of base mismatches, lesions, and protein binding. Efforts toward expanding the scope of electrochemistry at DNA-modified surfaces for biosensing applications are presented here.", "doi": "10.7907/VPKN-CV38", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:1930", "collection": "thesis", "collection_id": "1930", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05212009-221851", "primary_object_url": { "basename": "FinalThesis.pdf", "content": "final", "filesize": 20402703, "license": "other", "mime_type": "application/pdf", "url": "/1930/1/FinalThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems", "author": [ { "family_name": "Kim", "given_name": "Hyungjun", "orcid": "0000-0001-8261-9381", "clpid": "Kim-Hyungjun" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Multiscale and multiphysics simulation strategy is important to investigate complex problems in nature because it provides a systematic method to understand underpinning physics of the systems depending on the size. In this thesis, we discuss how such multiscale and multiphysics simulation framework can explain and rationalize the experimental observations in several nano- and biosystems. Furthermore, we exhibit the computational simulation methods that play major roles to rationally design novel materials with desired properties in next generation nano electronic devices, alternative energy materials, life science, and so on.
\r\n\r\nChapter 1 reviews the significance of multiscale and multiphysics simulation strategy. In this chapter, we briefly discuss the multiscale and multiphysics natures in nano- and bio-systems, and detailed examples are contained in the next chapters. Chapter 2 introduces an electric field induced conformational change mechanism, which is responsible for the unique current-voltage (I-V) behavior of nano device, negative differential resistance (NDR). In Chapter 3, the on/off kinetics of the Stoddart-Heath rotaxane-based programmable molecular electronic switch is discussed in terms of the free energy quantities. Chapter 4 explores sodium diffusion through the aluminum-doped zeolite BEA system, and the effect of water uptake amount is thoroughly discussed. This has importance for the application of zeolite to proton exchange membranes for fuel cells (PEMFC). In Chapters 5 and 6, the ion mobilities of tertiary and quaternary ammonium cations (precursors for lipids), and phosphatidylcholine (PC) lipid cations are investigated, respectively. In order to compute the ion mobilities of the precursors and entire lipids, we develop a modified trajectory (TJ) method dealing with the complicated integrals of interaction terms. QM and MD simulations are performed to determine the structures and charge distributions. In Chapter 7, we study how the model lung system of lipid monolayer with surfactant protein B (SP-B) responds to ozone introduction. In parallel with the field induced droplet ionization (FIDI) mass spectrometry study, MD simulations identify the distinct ozone reaction mechanism at the interface, and the role of SP-B at the pulmonary surfactant (PS) system on the oxidative stresses.
\r\n\r\nFrom these studies, we suggest various multiscale and multiphysics modeling approaches depending on the characteristics of systems and objectives. These efforts allow us to overcome the limited time- and length-scales of the monoscale simulations. In addition, we expect that an establishment of such multiscale modeling procedures will invoke interdisciplinary studies by tightly combining the developments occurring independently across fields.
\r\n", "doi": "10.7907/0PFF-R531", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2791", "collection": "thesis", "collection_id": "2791", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06302008-165534", "primary_object_url": { "basename": "BAS_complete_thesis.pdf", "content": "final", "filesize": 3881276, "license": "other", "mime_type": "application/pdf", "url": "/2791/1/BAS_complete_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Silicon Nanowires and Silicon/Molecular Interfaces for Nanoscale Electronics", "author": [ { "family_name": "Sheriff", "given_name": "Bonnie Ann", "clpid": "Sheriff-Bonnie-Ann" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the utilization of silicon nanowires and molecular films towards the realization of nanoscale electronics. The key enabling technology is the method in which the silicon nanowires are produced\u2014the superlattice nanowire pattern transfer (SNAP) method. The SNAP method allows for the simultaneous formation and alignment of metal or semiconducting nanowires using a template-mediated approach.
\r\n\r\nHigh-performance n- and p-type silicon nanowire field-effect transistors (FETs) were demonstrated. These FETs exhibited consistent performance and strong performance metrics such as high on/off ratios, high on-currents, high mobilities and low subthreshold swings. Due to the nanowire\u2019s large surface-area-to-volume ratio, surface states were shown to dominate performance, especially for the n-type FETs. Reducing the number of surface states improved performance significantly.
\r\n\r\nN- and p-type silicon nanowire FETs were integrated into complementary symmetry (CS) logic circuits. This required the development of a pattern doping technique that allowed for spatial control of doped regions. The inverter circuit was fabricated and tested. A gain of ~ 5 was consistently measured from 7 working inverter circuits. This demonstration provided the foundation for the eventual fabrication and characterization of the other Boolean logic functions.
\r\n\r\nA methodology was developed that optimizes the design of high-performance logic circuits constructed from Si NW p- and n-type FETs. Circuit performance can be predicted from individual fabricated NW FETs before prototype circuits are manufactured, resulting in a faster and more efficient design process. These results suggest design options for fabricating high performance NW circuits, which can then be implemented experimentally. The effectiveness of this methodology is shown by optimizing the gain of Si NW complementary symmetry inverter from an initially measured value of 8 to a gain of 45.
\r\n\r\nLastly, methods to covalently attach electronically interesting molecules via microcontact printing onto gold and silicon substrates were developed. In these studies, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction was used to form the covalent attachment. It was observed that the reaction would proceed readily by replacing the Cu catalyst in the stamp ink by a Cu coating on the stamp directly. This reaction proceeded quickly on both azide-terminated monolayers on Au and Si(111) substrates.
", "doi": "10.7907/Q13E-NB40", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2429", "collection": "thesis", "collection_id": "2429", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06032009-230415", "primary_object_url": { "basename": "CompleteThesis.pdf", "content": "final", "filesize": 7642916, "license": "other", "mime_type": "application/pdf", "url": "/2429/5/CompleteThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Developing High-Affinity Protein Capture Agents and Nanotechnology-Based Platforms for in vitro Diagnostics", "author": [ { "family_name": "Rohde", "given_name": "Rosemary Dyane", "clpid": "Rohde-Rosemary-Dyane" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this thesis, I describe projects that were aimed at improving ways to capture proteins for clinical diagnostics. Nanoelectronic sensors, such as silicon nanowires (SiNWs), can provide label-free quantitative measurements of protein biomarkers in real time. One technical challenge for SiNWs is to develop chemistry that can be applied for selectively encoding the nanowire surfaces with capture agents, thus making them sensors that have selectivity for specific proteins. Furthermore, because of the nature of how the sensor works, it is desirable to achieve this spatially selective chemical functionalization without having the silicon undergo oxidation. This method is described here and provides a general platform that can incorporate organic and biological molecules on Si (111) with minimal oxidation of the silicon surface.
\r\n\r\nThe development of these devices is, in part, driven by early diagnosis, treatment, monitoring, and personalized medicine\u2014 all of which are increasingly requiring quantitative, rapid, and multiparameter measurements. To begin achieving this goal, a large number of protein biomarkers need to be captured and quantitatively measured to create a diagnostic panel. One of the greatest challenges towards making protein-biomarker-based in vitro diagnostics inexpensive involves developing capture agents to detect the proteins. A major thrust of this thesis is to develop multi-valent, high-affinity and high-selectivity protein capture agents using in situ click chemistry. In situ click chemistry is a tool that utilizes the protein itself to catalyze the formation of a biligand from individual azide and alkyne ligands that are co-localized. Large one-bead one-compound (OBOC) libraries of peptides are used to form the body of these ligands, also providing high chemical diversity with minimal synthetic effort. This process can be repeated to identify a triligand, tetraligand, and so forth. Moreover, the resulting multiligand protein capture agents can be produced in gram-scale quantities with designed control over chemical and biochemical stability and water solubility. This is a general and robust method for inexpensive, high-throughput capture agent discovery that can be utilized to capture the relevant biomarker proteins for blood protein diagnostics.
\r\n", "doi": "10.7907/G70V-TC49", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2413", "collection": "thesis", "collection_id": "2413", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06022009-172223", "primary_object_url": { "basename": "06FullThesis.pdf", "content": "final", "filesize": 5764113, "license": "other", "mime_type": "application/pdf", "url": "/2413/6/06FullThesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "DNA Encoded Biotechnologies for Informative Cancer Diagnostics", "author": [ { "family_name": "Kwong", "given_name": "Gabriel Abner", "orcid": "0000-0002-6255-6755", "clpid": "Kwong-Gabriel-Abner" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Guo", "given_name": "Chin-Lin", "clpid": "Guo-Chin-Lin" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "clpid": "Bjorkman-P-J" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "clpid": "Mazmanian-S-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis describes the development of DNA-encoded, multi-parametric, sensing platforms for informative cancer diagnostics. In the first part of this thesis, I will present a technology called \u201cDNA-encoded antibody library (DEAL).\u201d In this approach, computationally derived, orthogonal ssDNA sequences are conjugated to antibodies specific for protein targets and cell surface markers. The resulting collection of conjugates is applied to a biological sample of interest, binds to their cognate antigens, and is detected after the complexes are hybridized to a glass substrate printed with spatially distinct complementary DNA sequences. By using DNA assembly, the DEAL platform enables the simultaneous detection of the major classes of biological molecules, namely nucleic acids, proteins and cells.
\r\n\r\nThe second part of this thesis focuses on the development of a cell sorting platform that can detect antigen-specific T cells called \u201cNucleic Acid Cell Sorting (NACS).\u201d In NACS, ssDNA encoding is used to assemble peptide major histocompatability complexes (p/MHC) on glass substrates by hybridization to cDNA microarrays. These assembled peptide/MHC microarrays are then used to sort mixed populations of antigen-specific T cells. This spatially encoded scheme addresses the widespread desire for methods that allow the multiplexed detection of antigen-specific T cells. The sensitivity and selectivity of NACS is similar to flow cytometry, demonstrated in key experiments with T cells derived from multiple sources, including endogenous and TCR-engineered T cells collected from cancer patients. Finally, this platform is used to monitor the persistence of cancer-specific T cells in peripheral blood collected from a patient undergoing T cellular immunotherapy.
\r\n\r\nLastly, a scheme for the detection of cell surface markers is presented. In this approach, DEAL and NACS conjugates prepared with UV labile ssDNA oligonucleotides are allowed to bind to target cell samples in solution. The ssDNA tags are released in solution by UV-induced photocleavage. The presence and expression of the cognate antigen is determined by collecting the pool of reporter ssDNA tags followed by exponential amplification by PCR. A DEAL conjugate specific for the oncogene EGFR was used to determine the expression level of EGFR in a low-passage brain tumor primary cell line. The feasibility of using ssDNA-p/MHC complexes for detecting unique TCRs was also demonstrated. Finally an experimental flow is described for integration with second generational high-throughput sequencing platforms for global and quantitative surface-ome profiling.
\r\n", "doi": "10.7907/AXMP-AM12", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2369", "collection": "thesis", "collection_id": "2369", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012009-021047", "primary_object_url": { "basename": "Full_Thesis.pdf", "content": "final", "filesize": 18582537, "license": "other", "mime_type": "", "url": "/2369/3/Full_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Nonlinear Electrical Properties of One-Dimensional Nanostructures", "author": [ { "family_name": "Xu", "given_name": "Ke", "orcid": "0000-0002-2788-194X", "clpid": "Xu-Ke" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A general method is first reported for reliably fabricating highly-ordered conventional superconductor nanowire arrays, with good control over nanowire cross section (down to 10 nm by 11 nm) and length (up to 200 microns). Nanowire size effects are systematically studied through electrical measurements and explained with theories. A comprehensive investigation of influence of nanowire length on superconductivity is reported for the first time.
\r\n\r\nWe further demonstrate the preparation and electrical properties of high-temperature superconductor nanowires. We find that high-temperature superconductivity can be retained in nanowires ~10 nm in width and >100 microns in length. All nanowires exhibit a superconducting transition above liquid nitrogen temperature, and a transition temperature width that depends strongly upon the nanowire dimensions.
\r\n\r\nThe experience gained from the above projects has allowed for the fabrication of superconductor films patterned with ultrahigh-density (pitch ~30 nm) two-dimensional arrays of nano-holes. Significantly enhanced critical currents are observed in such systems.
\r\n\r\nWe then describe a method for the assembly of nanoparticles into granular solids that can be tuned continuously from two dimensions to one dimension, and establish how electron transport evolves between these limits. We find that the energy barriers to transport increase in the one-dimensional limit, in both the variable-range-hopping and sequential-tunneling regimes. Furthermore, in the sequential-tunneling regime, we find an unexpected relationship that is peculiar to one-dimensional systems, between the temperature and the voltage at which the conductance becomes appreciable. These results are explained by extrapolating existing theories to one dimension.
\r\n\r\nWe also describe an approach to combine the geometric confinement of a Si nanowire and the electric field confinement from an array of ultrahigh-density top gates to form a concatenated array of coupled quantum dots. Reproducible confinement and coupling effects are observed.
\r\n\r\nWe have achieved single-atomic resolution in our scanning tunneling microscopy studies of graphene sheets on SiO2 substrates, from which we discovered significant changes in electronic states for bended regions in graphene sheets. We have also carried out the first systematic study on local conductance variations in graphene. Our results suggest large local variations in both the morphology and the electrical properties of graphene.
\r\n", "doi": "10.7907/BPK0-3V37", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2222", "collection": "thesis", "collection_id": "2222", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282009-131419", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 4341788, "license": "other", "mime_type": "application/pdf", "url": "/2222/1/main.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A Monte Carlo-Based Torsion Construction Algorithm for Ligand Design", "author": [ { "family_name": "Kekenes-Huskey", "given_name": "Peter Michael", "orcid": "0000-0001-7286-3022", "clpid": "Kekenes-Huskey-Peter-Michael" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A wealth of computational strategies [1,2,3,4,] is available for predicting the binding site and affinities of a putative ligand inside a target receptor. Although numerous techniques focus on the orientation of ligands or fragments thereof, few methods have delved into improving the accuracy of generating reliable ligand conformations within predicted binding modes. In an effort to comprehensively sample the torsion space available to a flexible ligand and focus on low-energy conformations, a recursive, Metropolis Monte Carlo (MC)-based rotamer design protocol has been developed. This approach recursively samples adjacent rotatable bonds from a defined anchor and directs the search along low-energy pathways, such that high-affinity conformations of the ligand can be identified. Furthermore, this program applies spatial constraints within the search that restrict the solutions to structurally dissimilar conformations, thus encouraging a diverse solution set. The performance of moleculeGL has been evaluated for a set of 55 co-crystals, for which the number of rotatable bonds ranged from 2 to 32. Approximately 80 percent of the structures are predicted within 2.0 A2 root mean square deviations (RMSD) with respect to the crystal structure, starting from an arbitrary ligand conformation. This level of accuracy suggests the program's applicability to the design of pharmacaphore substituents, for which the position of a chemically active pharmacaphore is well-known.", "doi": "10.7907/A1MQ-3116", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:1517", "collection": "thesis", "collection_id": "1517", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04262009-232200", "primary_object_url": { "basename": "thesis_all.pdf", "content": "final", "filesize": 3994474, "license": "other", "mime_type": "application/pdf", "url": "/1517/8/thesis_all.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Nonlinear Polymeric Architectures via Olefin Metathesis", "author": [ { "family_name": "Gorodetskaya", "given_name": "Irina A.", "clpid": "Gorodetskaya-Irina-A" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The research presented in this thesis focuses on application of olefin metathesis to the construction of hyperbranched and cyclic macromolecules. The olefin metathesis reaction is briefly reviewed in Chapter 1, along with its applications in polymer synthesis. A very mild, simple, and modular, olefin metathesis-based hyperbranched polymerization route is presented in Chapter 2. This method utilizes the cross metathesis selectivity of the functional group tolerant N-heterocyclic carbene ruthenium catalyst towards different types of alkenes, and it can be applied to the polymerization of many easily prepared ABn monomers. Moreover, the same method can be used to post-synthetically functionalize such polymers for realization of their substrate carrying potential. Chapter 3 describes one such functionalization example\u2014a pyrene analyte is attached to a metathesis derived hyperbranched polymer. This modification of the polymer provides insight into its solution structure relative to a linear analog. In addition, molecular weight control of the metathesis hyperbranched polymerization is discussed in detail in Chapter 4. The careful choice of the catalysts loading and the use of a multifunctional core are found to be important parameters in preparation of polymers which span a range of molecular weights.
\r\n\r\nEven well-established materials, such as polyethylene, can benefit from olefin metathesis and the unusual polymeric architectures it can efficiently create. For example, a cyclic polymer which lacks end groups, as opposed to having many end groups like a hyperbranched polymer, is expected to possess unique physical properties. The preparation of cyclic and linear polyethylenes and the study of their relative rheological properties are described in Chapter 5. The polymerization methodology outlined in this chapter takes advantage of ring-expansion metathesis polymerization\u2014a facile method for the synthesis of cyclic macromolecules. Some efforts directed at molecular weight control of this cyclic polymerization are also discussed.
\r\n", "doi": "10.7907/WRYR-4674", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2268", "collection": "thesis", "collection_id": "2268", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-094239", "primary_object_url": { "basename": "1-FullThesis.pdf", "content": "final", "filesize": 3698531, "license": "other", "mime_type": "application/pdf", "url": "/2268/1/1-FullThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Adrenergic Receptors: Model Systems for Investigation of GPCR Structure and Function", "author": [ { "family_name": "Wiencko", "given_name": "Heather L.", "clpid": "Wiencko-Heather-L" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Membrane proteins mediate intercellular communication, resulting in changes in the membrane and within the cell itself. One superfamily of integral membrane proteins, G-protein coupled receptors (GPCRs), are responsible for a vast diversity of processes. Their conformational flexibility and membrane environment pose challenges for direct structural characterization, and to date only five of the more than 1,000 known GPCRs have been characterized by high-resolution crystallography.
\r\n\r\nThe nine adrenergic GPCRs mediate the stress response throughout the body, and are implicated in diseases including hypertension and asthma. While they are among the best studied families of GPCRs, much remains to be learned about selectivity and activation. The first section of this work describes the ab initio structure prediction of the turkey beta-1 receptor and validation using a series of stabilizing mutations. This work preceded the currently available turkey beta-1 structure but shows good agreement, especially in the binding site. It validates the latest methods developed for GPCR structure prediction, emphasizes the role of a neutral charge scheme in energy determination, and explores a structure validation strategy based on stabilizing mutations rather than ligand docking. The next section uses the experimental beta-1 crystal structure as a starting point for nanosecond timescale molecular dynamics, exploring the roles of ligand binding in helix movement that contribute to the transition to an active state. These simulations reveal the early steps in receptor activation, beginning with tilting motions of transmembrane helices 5 and 6 and movement of transmembrane helix 1 closer into the protein core. The last section presents homology models of the human adrenergic receptors for which there are not yet crystal structures. The receptors most closely related to the target structures show the best results, while the less related ones will require further refinement. The best structures provide insight into the binding site of subtype selective antagonists, and can serve as the foundation for future studies. Over the course of these explorations, new subtleties in adrenergic structure have been illuminated, and may drive further exploration into selective binding and the activation mechanism of these and other receptors.
", "doi": "10.7907/S3RC-RZ59", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:3987", "collection": "thesis", "collection_id": "3987", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10082008-161705", "primary_object_url": { "basename": "ThesisFinale.pdf", "content": "final", "filesize": 2326393, "license": "other", "mime_type": "application/pdf", "url": "/3987/1/ThesisFinale.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Functionalized Polymers from Ring-Opening Metathesis Polymerization Through Monomer Design", "author": [ { "family_name": "Walker", "given_name": "Ron", "clpid": "Walker-Ron" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The focus of the research presented in this thesis deals with the synthesis and development of functionalized polymers using ring-opening metathesis polymerization (ROMP). The approach taken in developing the polymers presented within, feature the careful design and synthesis of a number of functionalized and unique monomers. A basic history and overview of olefin metathesis and polymer science is given in Chapter 1.
\r\n\r\nChapters 2 and 3 describe the development of controlled polymer architectures for use as barrier materials. This work was done in collaboration with Kuraray, Inc, which is a major manufacturer of commercial barrier materials. Also the structure-property relationships of these materials were studied to better understand how polymer architecture affects polymer properties.
\r\n\r\nChapter 4 discusses the controlled living ROMP of highly strained trans-cyclooctene. The knowledge and understanding of solvent effects during ROMP was also explored as a means to attenuate the rate of propagation during ROMP. Block copolymers containing polynorbornene and PCO were also synthesized and hydrogenated to form block copolymers containing blocks of linear, narrowly dispersed polyethylene.
\r\n\r\nChapter 5 describes the development of photodegradable polymer. By incorporating photodegradable links into a polymer chain, using ROMP, the polymer chain may be degraded upon irradiation with light.
", "doi": "10.7907/GC6K-CG98", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:320", "collection": "thesis", "collection_id": "320", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01242008-012650", "primary_object_url": { "basename": "Helia_Naeimi_PhD_Thesis.pdf", "content": "final", "filesize": 1357385, "license": "other", "mime_type": "application/pdf", "url": "/320/1/Helia_Naeimi_PhD_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Reliable Integration of Terascale Systems with Nanoscale Devices", "author": [ { "family_name": "Naeimi", "given_name": "Helia", "clpid": "Naeimi-Helia" } ], "thesis_advisor": [ { "family_name": "DeHon", "given_name": "Andre", "orcid": "0000-0001-9177-7699", "clpid": "DeHon-A" } ], "thesis_committee": [ { "family_name": "DeHon", "given_name": "Andre", "orcid": "0000-0001-9177-7699", "clpid": "DeHon-A" }, { "family_name": "Martin", "given_name": "Alain J.", "clpid": "Martin-A-J" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Nanotechnology design has attracted considerable attention in recent years and seems to be the technology for the future generation of the electronic devices, either as scaled and more restricted conventional lithographic technology, or as emerging sublithographic technologies, such as nanowires, carbon nanotubes, NDR (Negative Differential Resistance) devices, or other nanotechnology devices. Each of these technologies provides one or more design benefits including feature-size scaling, high on\u2013off ratios, and faster devices. However, all of these techniques share their most challenging design issue: reliability. Providing reliability is becoming constantly more challenging due to increases in both the device failure rate and system complexity. This work develops techniques that make achieving reliability in such systems feasible with practical area overhead and considerable improvement in area overhead and system reliability compared to related techniques.
\r\n\r\nConventional reliability techniques focus on low defect and fault rates, i.e., single event upset (SEU). These techniques cannot simply be scaled to larger systems with more unreliable devices. If these techniques are directly applied to the high defect and fault rate of the nanotechnology regime, they suffer impractically high overhead, or they may not achieve the desired reliability. Our approach in this thesis exploits the following design patterns to achieve a considerable area reduction compared to related works and achieve high reliability:
\r\n(1) Fine-grained reliability: In this technique, the system is partitioned into fine\u2013grained blocks, and the reliability is provided for each block. This technique is used to contain the area overhead and bound the impact on the throughput.
\r\n(2) Using alternative resources: This technique improves the design quality by sparing other resources when system is tight on one resource. In our work we replace some of the spacial redundancies with temporal redundancy to limit the area overhead. We further improve the system throughput to limit the throughput cost as well.
\r\n(3) Defect pattern matching: With this techniques, the defective resources are located and the design is reconfigured considering the defect pattern of the chip. Then the design configuration is mapped to the chip. This technique isolates the defective resources and make use of most of defect free resources.
\r\n(4) Global reliability: This technique is used to unify the reliability techniques used in different parts of the system. When using one unified technique to protect the system, the area overhead provided to protect one resource can be reused to protect other resources as well.
In the present work, we report considerable improvement in the area overhead using the above techniques. We show that using Fine-Grained Reliability, Alternative Resources, and Defect Pattern Matching, high permanent defect rates (e.g., 10%) which is the result of imperfect manufacturing can be tolerated with moderate area overhead (about 30% on average for typical designs). Again Using Alternative Resources and Fine-Grained Reliability improve the area overhead of the transient fault-tolerant designs by close to an order of magnitude compared to recent reliable works. Finally we report a fully reliable memory system that employs a Global Reliability scheme to tolerate permanent defects and transient faults, both in the memory and in the supporting logic and still achieves 100 Gbit/cm2 density for fault rate of 10\u221218 errors per bit per cycle and 10% junction defect rate.
", "doi": "10.7907/P842-7B49", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:320", "collection": "thesis", "collection_id": "320", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01242008-012650", "primary_object_url": { "basename": "Helia_Naeimi_PhD_Thesis.pdf", "content": "final", "filesize": 1357385, "license": "other", "mime_type": "application/pdf", "url": "/320/1/Helia_Naeimi_PhD_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Reliable Integration of Terascale Systems with Nanoscale Devices", "author": [ { "family_name": "Naeimi", "given_name": "Helia", "clpid": "Naeimi-Helia" } ], "thesis_advisor": [ { "family_name": "DeHon", "given_name": "Andre", "orcid": "0000-0001-9177-7699", "clpid": "DeHon-A" } ], "thesis_committee": [ { "family_name": "DeHon", "given_name": "Andre", "orcid": "0000-0001-9177-7699", "clpid": "DeHon-A" }, { "family_name": "Martin", "given_name": "Alain J.", "clpid": "Martin-A-J" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Ho", "given_name": "Tracey C.", "clpid": "Ho-Tracey" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Nanotechnology design has attracted considerable attention in recent years and seems to be the technology for the future generation of the electronic devices, either as scaled and more restricted conventional lithographic technology, or as emerging sublithographic technologies, such as nanowires, carbon nanotubes, NDR (Negative Differential Resistance) devices, or other nanotechnology devices. Each of these technologies provides one or more design benefits including feature-size scaling, high on\u2013off ratios, and faster devices. However, all of these techniques share their most challenging design issue: reliability. Providing reliability is becoming constantly more challenging due to increases in both the device failure rate and system complexity. This work develops techniques that make achieving reliability in such systems feasible with practical area overhead and considerable improvement in area overhead and system reliability compared to related techniques.
\r\n\r\nConventional reliability techniques focus on low defect and fault rates, i.e., single event upset (SEU). These techniques cannot simply be scaled to larger systems with more unreliable devices. If these techniques are directly applied to the high defect and fault rate of the nanotechnology regime, they suffer impractically high overhead, or they may not achieve the desired reliability. Our approach in this thesis exploits the following design patterns to achieve a considerable area reduction compared to related works and achieve high reliability:
\r\n(1) Fine-grained reliability: In this technique, the system is partitioned into fine\u2013grained blocks, and the reliability is provided for each block. This technique is used to contain the area overhead and bound the impact on the throughput.
\r\n(2) Using alternative resources: This technique improves the design quality by sparing other resources when system is tight on one resource. In our work we replace some of the spacial redundancies with temporal redundancy to limit the area overhead. We further improve the system throughput to limit the throughput cost as well.
\r\n(3) Defect pattern matching: With this techniques, the defective resources are located and the design is reconfigured considering the defect pattern of the chip. Then the design configuration is mapped to the chip. This technique isolates the defective resources and make use of most of defect free resources.
\r\n(4) Global reliability: This technique is used to unify the reliability techniques used in different parts of the system. When using one unified technique to protect the system, the area overhead provided to protect one resource can be reused to protect other resources as well.
In the present work, we report considerable improvement in the area overhead using the above techniques. We show that using Fine-Grained Reliability, Alternative Resources, and Defect Pattern Matching, high permanent defect rates (e.g., 10%) which is the result of imperfect manufacturing can be tolerated with moderate area overhead (about 30% on average for typical designs). Again Using Alternative Resources and Fine-Grained Reliability improve the area overhead of the transient fault-tolerant designs by close to an order of magnitude compared to recent reliable works. Finally we report a fully reliable memory system that employs a Global Reliability scheme to tolerate permanent defects and transient faults, both in the memory and in the supporting logic and still achieves 100 Gbit/cm2 density for fault rate of 10\u221218 errors per bit per cycle and 10% junction defect rate.
", "doi": "10.7907/P842-7B49", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2996", "collection": "thesis", "collection_id": "2996", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08012007-102846", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 7138051, "license": "other", "mime_type": "application/pdf", "url": "/2996/1/thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Single-Cell Gene-Expression Analysis by Quantitative RT-PCR", "author": [ { "family_name": "Warren", "given_name": "Luigi Andrea", "clpid": "Warren-Luigi-Andrea" } ], "thesis_advisor": [ { "family_name": "Quake", "given_name": "Stephen R.", "clpid": "Quake-S-R" } ], "thesis_committee": [ { "family_name": "Fraser", "given_name": "Scott E.", "clpid": "Fraser-S-E" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "clpid": "Rothenberg-E-V" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Sternberg", "given_name": "Paul W.", "clpid": "Sternberg-P-W" }, { "family_name": "Quake", "given_name": "Stephen R.", "clpid": "Quake-S-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The problem of development has long been one of the key issues in biology. With stem-cell therapies on the horizon, the \u201creverse engineering\u201d of developmental programs promises to become a task of great practical significance. We now understand the general schemes by which transcriptional networks regulate cellular differentiation and morphogenesis. These genetic circuits function as complex state machines which, over the course of development, undergo sequenced transitions that bring cells to specific end states. A variety of different gene-expression assays can be used to follow these transitions. The sensitivity of the assays now in common use limits the resolution with which we can follow the activity of genetic-regulatory networks. This thesis describes two projects aimed at refining an established gene-profiling method, quantitative RT-PCR, so that it can be used to profile transcriptional-network states cross-sectionally within developing cell populations at single-cell resolution. Two advanced qRT-PCR protocols were developed to support these projects, one based on microfluidic \u201cdigital PCR,\u201d the other based on multiplexed \u201cpreamplification PCR.\u201d These protocols were used to measure transcription-factor expression in hematopoietic progenitor cells, and to evaluate the effects of aging on the stability of gene regulation. In their current form, the digital PCR and preamplification techniques will permit the analysis of perhaps a few hundred to a few thousand cells in a single-cell survey. By combining microfluidic-chip assays with the preamplification method, it will soon be possible to scale up to the analysis of many thousands of cells, while profiling many different transcription factors in each individual cell. This should facilitate the modeling of the transcriptional networks which control cellular differentiation as we press forward into the era of \u201ctissue engineering.\"", "doi": "10.7907/PJ42-XB85", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:217", "collection": "thesis", "collection_id": "217", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01172008-141725", "primary_object_url": { "basename": "Boukai_Thesis.pdf", "content": "final", "filesize": 1836812, "license": "other", "mime_type": "application/pdf", "url": "/217/1/Boukai_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Thermoelectric Properties of Bismuth and Silicon Nanowires", "author": [ { "family_name": "Boukai", "given_name": "Akram Issam", "clpid": "Boukai-Akram-Issam" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Thermoelectric materials convert temperature differences into electricity and vice versa. Such materials utilize the Seebeck effect for power generation and the Peltier effect for refrigeration. In the Seebeck effect, a temperature gradient across a material causes the diffusion of charged carriers across that gradient, thus creating a voltage difference between the hot and cold ends of the material. Conversely, the Peltier effect explains the fact that when current flows through a material a temperature gradient arises because the charged carriers exchange thermal energy at the contacts. Thermoelectrics perform these functions without moving parts and they do not pollute. This makes them highly reliable and more importantly attractive as renewable energy sources, especially at a time when global warming is a growing concern. However, thermoelectrics find only limited use because of their poor efficiency.
\r\n \t\r\nThe efficiency of a thermoelectric material is determined by the dimensionless figure of merit,ZT = S\u00b2\u03c3T/\u03ba , where S is the thermoelectric power, defined as the thermoelectric voltage, V, produced per degree temperature difference \u0394T , \u03c3 is the electrical conductivity, \u03ba is the thermal conductivity, and T is the temperature. To maximize ZT, S must be large so that a small temperature difference can create a large voltage, \u03c3 must be large in order to minimize joule heating losses, and \u03ba must be small to reduce heat leakage and maintain a temperature difference. Maximizing ZT is challenging because optimizing one physical parameter often adversely affects another. The best commercially available thermoelectric devices are alloys of Bi2Te3 and have a ZT of 1 which corresponds to a carnot efficiency of ~10%. My research has focused on achieving efficient thermoelectric performance from the single component systems of bismuth and silicon nanowires.
\r\n\r\nBismuth nanowires are predicted to undergo a semi-metal to semiconductor transition below a size of 50 nm which should increase the thermopower and thus ZT. Limited experimental evidence by other groups has been acquired to support this claim. Through electric field gating measurements and by tuning the nanowire size, we have shown that no such transition occurs. Instead, surface states dominate the electric transport at a size smaller than 50 nm and bismuth remains a semimetal.
\r\n\r\nBulk silicon is a poor thermoelectric due to its large thermal conductivity. However, silicon nanowires may have a dramatically reduced thermal conductivity. By varying the nanowire size and impurity doping levels, ZT values representing an approximately 100-fold improvement over bulk silicon are achieved over a broad temperature range, including a ZT ~ 1 at 200K. Independent measurements of S, \u03c3, and \u03ba, combined with theory, indicate that the improved efficiency originates from phonon effects. The thermal conductivity is reduced and the thermopower is enhanced. These results are expected to apply to other classes of semiconductor nanomaterials.
\r\n", "doi": "10.7907/QEE9-4H11", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:5236", "collection": "thesis", "collection_id": "5236", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06252007-174232", "primary_object_url": { "basename": "Erin_N_Guidry_Thesis.pdf", "content": "final", "filesize": 8594369, "license": "other", "mime_type": "application/pdf", "url": "/5236/1/Erin_N_Guidry_Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Interlocked Molecules Using Olefin Metathesis", "author": [ { "family_name": "Guidry", "given_name": "Erin Nicole", "clpid": "Guidry-Erin-Nicole" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Olefin metathesis has been employed in the efficient syntheses of a [2]catenane with the templation being provided by the recognition between a secondary ammonium ion and a crown ether. In one approach, a crown ether precursor has been clipped around an NH2+ center situated in a macrocyclic ring, yielding the mechanically interlocked compound. In the other approach, the reversible nature of olefin metathesis allows for a magic ring synthesis to occur wherein two free macrocycles can be employed as the stationary materials, leading to the formation of the same [2]catenane.
\r\n\r\nA strategy for the formation of mechanically interlocked polymers is presented. Ring-closing olefin metathesis has been shown to provide a very high yielding route to [c2]daisy-chains suitably functionalized to allow their one-step conversion to bis-olefins which can be used as monomers in ADMET polymerizations to afford mechanically interlocked polymers. Metathesis, in two different guises is making a hitherto unreachable goal in synthesis a reality.
\r\n\r\nA method for the production of cyclic polyammonium ions is presented which utilizes a polymer cyclization of azide terminated linear polymer based on the \u201cclick\u201d reaction. An azide terminated polymer was prepared using ROMP in the presence of chain transfer agents (CTA). Formation of cyclic polycateanes was explored utilizing the mutual recognition between secondary ammonium ions and crown ether macrocyles. The product of the RCM of linear crown ether dienes around cyclic polyammonium ions was investigated using 2D-DOSY.
\r\n\r\nThe ring-opening metathesis polymerization of a [2]catenane was investigated, using both a cyclic metathesis catalyst and bulky metathesis catalysts for the formation of cyclic polycatenanes and polyrotaxanes respectively. While it was found that the [2]catenane monomer could function as a ROMP monomer, no interlocked polymers were observed as products from the polymerization. Linear impurities present in either or both the [2]catenane monomer and the metathesis catalysts are believed to be responsible for the formation of the non-interlocked polyether and free macrocycle. These results highlight the critical role of purity to the successful formation of cyclic or linear interlocked polymer using a ROMP process.
", "doi": "10.7907/XBXB-6931", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2259", "collection": "thesis", "collection_id": "2259", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-140215", "primary_object_url": { "basename": "clv_thesis.pdf", "content": "final", "filesize": 14756797, "license": "other", "mime_type": "application/pdf", "url": "/2259/1/clv_thesis.pdf", "version": "v1.0.0" }, "type": "thesis", "title": "Development and Evaluation of Protein Design Methods for Functional Targets", "author": [ { "family_name": "Vizcarra", "given_name": "Christina Luisa", "clpid": "Vizcarra-Christina-Luisa" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Computational protein design seeks to identify amino acid sequences that will fold into a specified three-dimensional structure. Extending this technique from identification of sequences that retain a native structure to the design of sequences that will carry out a function has been a significant challenge. Modeling the energetics of catalysis and binding requires considerations that may not be necessary for the design of folded, stable proteins. I have investigated models for protein electrostatics with the goal of improving current methods for the design of functional molecules. The work in this thesis is focused on the Poisson-Boltzmann model, a dielectric continuum model that describes the effect of solvent polarization on the electrostatic potential in a protein. I found that this model is amenable to design calculations, as judged by its ability to be decomposed into terms that are used in sequence selection.
\r\n\r\nAside from energy estimation, there are a number of assumptions that are made in protein design in order to make the problem computationally tractable. Because of these assumptions, and also because of incomplete models of protein function, it is expected that many proteins sequences will need to be experimentally characterized to find one that meets a difficult design goal. To this end, I examined methods for using computational tools to produce libraries of protein sequences. These studies showed that (1) structure-based, computational library design methods can be used to generate libraries with a high number of folded proteins and (2) computational design is a promising tool for generating highly mutated proteins with a diverse range of functions.
", "doi": "10.7907/G16E-JZ97", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2341", "collection": "thesis", "collection_id": "2341", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312007-142846", "primary_object_url": { "basename": "JE_Green_Thesis.pdf", "content": "final", "filesize": 13833237, "license": "other", "mime_type": "application/pdf", "url": "/2341/7/JE_Green_Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ultra-Dense Nano- and Molecular-Electronic Circuits", "author": [ { "family_name": "Green", "given_name": "Jonathan Earl", "clpid": "Green-Jonathan-Earl" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes research towards the realization of large-scale, ultra-dense nanowire-based circuits. The primary means for the construction of such circuits is the superlattice nanowire pattern transfer (SNAP) technique. This technique was optimized for the fabrication of large nanowire arrays containing over 1000 nanowires at narrow pitch and aligned over millimeter length scales. Silicon nanowire arrays were fabricated with wire widths down to ten nanometers, and with precisely-controlled electronic properties and bulk-like resistivity values through the use of diffusion doping and the selection of high-quality silicon-on-insulator substrates.
\r\n\r\nA binary tree demultiplexer circuit allows the unique addressing of N nanowires from within an ultra-dense array using of order 2xlog2(N) control wires. An implementation of this circuit was experimentally demonstrated to bridge from the submicrometer dimensions of lithographic patterning to the nanometer-scale dimensions of SNAP patterning. This circuit utilized field-effect gating by relatively large control wires to address individual nanowires from within a 150-nanowire array patterned at a wire width and pitch of 13 and 34 nanometers, respectively.
\r\n\r\nSilicon- and metal-nanowire arrays were integrated with [2]rotaxane molecular materials for the fabrication of an ultra-dense, 160,000-bit crosspoint molecular electronic memory circuit. This circuit is patterned at a record density of 1x10^11 bits per square centimeter (device-pitch of 33 nanometers), and contains bistable, electrochemically addressable [2]rotaxane switching molecules as the data storage elements within the individual crosspoint junctions. Defective junctions could be readily identified through electronic testing and isolated through software coding. The working bits could then be configured to form a functional memory circuit. The molecular-mechanical nature of the switching mechanism was confirmed through volatility measurements.
\r\n\r\nAn optimized two-step chlorination/methylation protocol was used to methyl passivate thin (~20-nanometer) silicon(111)-on-insulator microelectronic device surfaces, that were then demonstrated to be stable in air for arbitrarily long periods, and to resist oxidation due to common microelectronic fabrication procedures and wet-chemical treatments. Additionally, temperature-dependent mobility data showed that methylated silicon-on-insulator surfaces can be prepared with bulk-like mobility characteristics through careful optimization of the methylation reaction protocol.
\r\n", "doi": "10.7907/HCQH-2S48", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2030", "collection": "thesis", "collection_id": "2030", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-194737", "primary_object_url": { "basename": "Choi_Jang_Wook_2007.pdf", "content": "final", "filesize": 3856438, "license": "other", "mime_type": "application/pdf", "url": "/2030/10/Choi_Jang_Wook_2007.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Bistable [2]Rotaxane Based Molecular Electronics: Fundamentals and Applications", "author": [ { "family_name": "Choi", "given_name": "Jang Wook", "orcid": "0000-0001-8783-0901", "clpid": "Choi-Jang-Wook" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Bistable [2]rotaxanes are a unique class of supramolecules that have two constitutional isomers. Upon sandwiched between two electrodes, these two isomeric states show different conducting states, thus behaving as molecular switches. In this thesis, I describe how the bistable [2]rotaxanes have been investigated to ensure that the switching characteristics in solid-state devices are those of the bistable [2]rotaxanes and not those of extraneous elements. In addition, integration of these molecules onto ultradense nanowire arrays to constitute a memory circuit is presented.
\r\n\r\nThe bistable [2]rotaxanes have been examined in various environments to study kinetics and ground-state thermodynamics between both isomeric states. In the kinetic study, as molecules are embedded in more viscous environments (solution\u2192polymer gel\u2192solid-state device), a key step in switching cycle slows down significantly, thus reflecting the environments where the molecules are surrounded. In thermodynamic study, one of the major units in the molecular structure was modified and then equilibrium population ratio between both isomeric states was monitored at various temperatures. In both solution and solid-state devices, the population ratio of the modified [2]rotaxane was more sensitive to temperature. This result is very critical in that the properties of devices can be tailored by manipulating the structure of molecular components.
\r\n\r\nThe bistable [2]rotaxanes were integrated into crossbar nanowire arrays to constitute a memory circuit. Ultra-dense nanowire arrays used as electrodes are generated by superlattice nanowire pattern transfer (SNAP) method. Due to extremely narrow pitch (~33 nm) of the SNAP nanowire arrays, the device sets a remarkable record in memory density (~1011 Bits/cm2). Although the circuits were found to have large numbers of defects, those defects were identified through electronic testing and the working bits were configured to form a fully functional random access memory for storing and retrieving information.
\r\n\r\nFinally, nanofluidic devices have been developed by utilizing the SNAP method. Due to small channel dimensions (< Debye screening length), passage of ions was modulated by electrostatic interactions between the ions and the nanochannel walls. Devices are being developed to quantify isoelectric points of peptides so that ultimately, the device could function as a protein identifier at a single molecule level.
", "doi": "10.7907/X6Q6-HD24", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2024", "collection": "thesis", "collection_id": "2024", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-151027", "primary_object_url": { "basename": "FullThesis.pdf", "content": "final", "filesize": 9456838, "license": "other", "mime_type": "application/pdf", "url": "/2024/7/FullThesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Silicon Nanowires as Biological Sensors and Highly Efficient Thermoelectric Materials", "author": [ { "family_name": "Bunimovich", "given_name": "Yuri Leonid", "orcid": "0000-0002-7920-8781", "clpid": "Bunimovich-Yuri-Leonid" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Roukes", "given_name": "Michael Lee", "clpid": "Roukes-M-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Silicon nanowires are of significant interest because of their novel properties which afford new functions. Here, we study silicon nanowires fabricated via a well established top down approach called superlattice nanowire pattern transfer (SNAP). In the first part of the thesis, nanowires are utilized for biological sensing of DNA and proteins in an electrolyte solution. Important electronic and surface properties are considered as means to optimize the device sensitivity. The removal of silicon-oxide interface is shown to improve the limit of detection by two orders of magnitude. The sensitivity can be further improved by the reduction of the doping level to 1017 cm-3. In this way, sub-femtomolar concentration of oligonucleotides in physiological conditions can be detected. While the Debye screening is circumvented by the electrostatic adsorption of primary DNA on the amine-terminated monolayer, the detection of proteins is limited by the size of the antibodies. In low ionic strength solution, ~10\u00b5M, human IL2 cytokine is detectable at 1 to 10pM concentrations. Furthermore, a model is developed which allows the determination of kinetic parameters and absolute analyte concentrations from the real-time resistance of the nanowires. This model is consistent with Langmuir model, and could, in principle, be used to determine the amount of low abundance biological molecules at concentrations below those detectable with other label-free methods, such as surface plasmon resonance technique. In addition, a novel electrochemical technique is developed which allows the spatially-selective functionalization of silicon nanowires and the construction of a small library of proteins. In the second part, the discovery of highly efficient thermoelectric materials based on silicon nanowires is discussed. A relatively simple, scalable, and single component system of silicon nanowires with figure of merit of ~1 at room temperature is developed. ZT can be tuned at various temperatures to exceed unity by varying nanowire size and/or impurity doping level. Such enhancement in ZT compared to the bulk value is achieved by significantly perturbing the phonon-mediated heat transport in a nanowire. Decreased thermal conductivities and longer lifetimes of long-wavelength phonons in a nanowire are major reasons for an increased thermoelectric efficiency of these structures.", "doi": "10.7907/EY6H-XK94", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2755", "collection": "thesis", "collection_id": "2755", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06282006-103230", "primary_object_url": { "basename": "jmfinalthesis.pdf", "content": "final", "filesize": 9371133, "license": "other", "mime_type": "application/pdf", "url": "/2755/1/jmfinalthesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Single Mammalian Cell Gene Expression Analysis Using Microfluidics", "author": [ { "family_name": "Marcus", "given_name": "Joshua Scott", "clpid": "Marcus-Joshua-Scott" } ], "thesis_advisor": [ { "family_name": "Quake", "given_name": "Stephen R.", "orcid": "0000-0002-1613-0809", "clpid": "Quake-S-R" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Campbell", "given_name": "Judith L.", "orcid": "0000-0001-8291-5551", "clpid": "Campbell-J-L" }, { "family_name": "Quake", "given_name": "Stephen R.", "orcid": "0000-0002-1613-0809", "clpid": "Quake-S-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Single cell gene expression studies hold great promise for deciphering the ubiquitous heterogeneity present in biological organisms. Although much progress has been made in the field, tools to study gene expression (specific and global) in single cells are generally lacking. This thesis describes the development of novel microfluidic technologies and processes capable of processing single cells to first strand cDNA in a parallel fashion, thereby filling a void in the single cell biology field. The author then utilizes the technology to probe for transcriptional noise in ubiquitous genes present in single mammalian cells. The noise measured far exceeds any measurement reported to this date, and was shown to be attenuated during the G2 stage of the cell cycle. The work presented here is first hand proof that technological innovation is a key component in undertaking novel science.", "doi": "10.7907/M3GA-PT31", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2333", "collection": "thesis", "collection_id": "2333", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312006-163455", "primary_object_url": { "basename": "Julie_Biteen_PhD_Thesis_2006.PDF", "content": "final", "filesize": 42282605, "license": "other", "mime_type": "application/pdf", "url": "/2333/1/Julie_Biteen_PhD_Thesis_2006.PDF", "version": "v2.0.0" }, "type": "thesis", "title": "Plasmon-Enhanced Silicon Nanocrystal Luminescence for Optoelectronic Applications", "author": [ { "family_name": "Biteen", "given_name": "Julie Suzanne", "orcid": "0000-0003-2038-6484", "clpid": "Biteen-Julie-Suzanne" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "On the path toward the realization of silicon-based optical emitters for integrated microelectronics, this thesis studies the optoelectronic properties of silicon nanocrystals as a function of their surface passivation and their interactions with plasmonic materials. The first part of the thesis utilizes controlled oxidation exposures and photoluminescence spectroscopy to verify previous theoretical and computational predictions of oxygen-related surface states that effectively narrow the energy band gap of small silicon nanocrystals. The focus of the second half of the thesis is on experimental and computational studies of enhanced luminescence from silicon nanocrystals in the near field of noble metal nanostructures.
\r\n\r\nSurface plasmon enhancement is a technique that has only recently been applied to semiconductor nanocrystal luminescence. This thesis thoroughly investigates the emission of silicon nanocrystals coupled to gold and silver nanostructures to achieve a new level of understanding of the enhancement effect. By pairing silicon nanocrystals to metal nanostructures, up to ten-fold increases in the luminescence intensity are realized, concomitant with enhancements of the radiative decay rate, the absorbance cross section, and the quantum efficiency. Moreover, coupling at the plasmon resonance frequency is used to tune the nanocrystal emission spectrum. A computational exploration of these experimental observations indicates that the enhancement effects can be ascribed to emission in the concentrated local field that results from the excitation of metal particle plasmon modes. Finally, the process of coupling silicon nanocrystal emitters to plasmonic metals is applied to a silicon-nanocrystal light-emitting diode, and enhanced electroluminescence is realized.
", "doi": "10.7907/B77G-WS08", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2655", "collection": "thesis", "collection_id": "2655", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06202006-113417", "primary_object_url": { "basename": "Ceres_PhD_Thesis.pdf", "content": "final", "filesize": 12510610, "license": "other", "mime_type": "application/pdf", "url": "/2655/1/Ceres_PhD_Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Electron Transfer at DNA-Modified Electrodes", "author": [ { "family_name": "Ceres", "given_name": "Donato Marino", "clpid": "Ceres-Donato-Marino" } ], "thesis_advisor": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The DNA pi stack provides an efficient pathway for transport of electron and electron holes. Ground-state electron transport is furthermore extremely sensitive to subtle DNA structural perturbations, such as a single base mismatch, that alter pi-stacking. As a result, DNA-modified electrodes have allowed the development of highly sensitive diagnostic devices for the detection of base mismatches, lesions, and mutations. We have been able to apply DNA-mediated charge transduction, using a methylene blue/ferricyanide electrocatalytic cycle, in a DNA chip format for the detection of a single base mismatches at a microelectrode. Electrocatalysis is detected at DNA-modified electrodes down to 40 um electrode in diameter, where 108 DNA molecules are responsible for the electron transduction. This exquisite sensitivity both for mismatch detection irrespective of sequence context and to a small number of molecules is an important requisite for the development of a device able to detect multiple genetic variations in the absence of DNA amplification.
\r\n\r\nWe have also investigated in detail the electrochemical properties of DNA films. DNA is a highly charged molecule and, when self-assembled on a gold surface in a dense array, its properties are similar to those of polyelectrolyte films. We have found that the structure of the DNA film is sensitive to ion concentration and identity. Variations of the electrostatic potential across the film can sensitively affect both thermodynamics and kinetics of redox reporters incorporated in the film. Methylene blue reduction in the DNA film occurs via a two electron, one proton process. The Pourbaix diagram is linear in the case of a monovalent anionic buffer, while it is curved in phosphate buffer. Electron transfer kinetics are also affected by the relative concentration of divalent anions: at low pH the film is compressed in the linker portion and the rate of electron transfer is faster. Based on this understanding of the electrostatic balance inside the DNA film, a new analytical tool for monitoring hybridization events on gold surfaces has been developed using electrochemical impedance spectroscopy of ferricyanide.
\r\n\r\nIn order to explore the electron transport properties of DNA films mechanistically scanning tunneling microscopy (STM) has also been employed. These experiments provide a first opportunity to examine DNA conductivity under physiological conditions. These STM experiments on DNA films show that DNA, when perpendicularly oriented with respect to the surface, is coupled to the STM tip and the local density of states contribute to the measured tunneling current. At positive biases, when the surface is positive, the DNA is tilted towards the surface and as a result decoupled from the tip; the DNA appears \"transparent\" and the underlying surface instead is imaged. Also important is the integrity of the base stack. When the percentage of DNA duplexes containing a single base mismatch in the film is increased, the conductivity of the film decreases. The STM tip, being held at a constant current, approaches the DNA film until, at a critical mismatch content, the tip must penetrate the film and image resolution is lost. The current versus voltage characteristic of the DNA film has furthermore been determined through a new scanning tunneling spectroscopic technique that provides highly stable and reproducible measurements. We find that DNA duplex films under physiological conditions exhibit negative differential resistance, which is a feature that is typical of resonant electron tunneling via energetically localized molecular orbitals. This observation provides an experimental evidence for the existence of localized states within the DNA HOMO-LUMO gap that can be responsible for the ground state electron transport observed in electrochemical experiments.
", "doi": "10.7907/vdyv-zf71", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:3107", "collection": "thesis", "collection_id": "3107", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08132004-132724", "primary_object_url": { "basename": "IMR_thesis_final_copy.pdf", "content": "final", "filesize": 2271401, "license": "other", "mime_type": "application/pdf", "url": "/3107/1/IMR_thesis_final_copy.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Functionalized Polymers and Surfaces via Ring-Opening Metathesis Polymerization", "author": [ { "family_name": "Rutenberg", "given_name": "Isaac Michael", "orcid": "0000-0003-0969-4523", "clpid": "Rutenberg-Isaac-Michael" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The research presented in this thesis focuses on the preparation of functionalized polymers using olefin metathesis polymerization methods. A portion of this research is also devoted to the development of applications for metathesis-derived polymers.
\r\n\r\nThree distinct types of olefin metathesis polymerizations can be recognized within this work. Ring-opening metathesis polymerization (ROMP) is the most prevalent type, followed by acyclic diene metathesis (ADMET) polymerization and a hybrid of the ROMP and ADMET mechanisms known as ring-opening-insertion metathesis polymerization (ROIMP).
\r\n\r\nMany of the concepts that appear throughout this thesis are introduced in Chapter 1. Olefin metathesis occupies a central role in each of the subsequent chapters; detailed descriptions of the mechanism and important olefin metathesis catalysts are provided. The chapter also includes background information regarding polymers, polymer properties and the application of ROMP in the construction of electronic devices.
\r\n\r\nAlthough the utility of ADMET does not yet seem to match that of ROMP, valuable information can be obtained from ADMET polymerizations. In an effort to elucidate catalytic activity, Chapter 2 details a comparison of the ADMET polymerizations of terminal and non-terminal dienes.
\r\n\r\nExperimental investigations involving ROIMP, a novel method for the production of A,B-alternating copolymers, is presented in Appendix A. The mechanism of ROIMP is conceptually very different from the mechanisms of either step growth or chain growth polymerizations. Efforts toward understanding the mechanism of ROIMP using a mathematical model are discussed in Chapter 3.
\r\n\r\nPolymeric chain transfer agents (PCTAs) suitable for ROMP reactions are polymers that contain a single, metathesis-active olefin. These polymers are the focus of Chapter 4 and can be used in the preparation of novel block copolymers. As an example, Appendix B presents the preparation of block copolymers consisting of polyacetylene and various commodity polymers.
\r\n\r\nFinally, the development of applications for surface-initiated ROMP (SI-ROMP) is discussed in Chapter 5 and Appendix C. Polymer films prepared using SI-ROMP are shown to be viable dielectric layers in thin-film transistors, and research is presented involving microcontact printing and dip pen nanolithography as methods for forming patterned SI-ROMP polymer films.
\r\n", "doi": "10.7907/5Z6Y-G191", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2079", "collection": "thesis", "collection_id": "2079", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262004-111123", "type": "thesis", "title": "Design and Characterization of Layered Tunnel Barriers for Nonvolatile Memory Applications", "author": [ { "family_name": "Casperson", "given_name": "Julie Diane", "clpid": "Casperson-Julie-Diane" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The main limitations of floating gate memory devices (Flash memory) are the long program (microsecond) and erase times (~ 1 \u00b5s) inherent to the charging of floating gates using Fowler-Nordheim tunneling. An alternative to the integration of homogeneous dielectric tunnel barriers present in standard Flash memory is to use layered tunnel barriers made of high-k heterostructures. This allows for an effective lowering in barrier height under applied bias, resulting in shorter write/erase times while maintaining long retention times.
\r\n\r\nTo assess these types of dielectric structures, tunneling probability simulations were performed using an effective mass-model, allowing us to predict current-voltage (I-V) characteristics and optimize the layered tunnel barrier structure. Based on our results, we correlated dielectric constants and band offsets with respect to silicon in order to help identify possible materials from which to construct these layered barriers. This survey allowed for the determination of promising high-k materials heterostructures: Si\u2083N\u2084 / Al\u2082O\u2083 / Si\u2083N\u2084 / Si\u2083N\u2084 and HfO\u2082 / Al\u2082O\u2083 / HfO\u2082.
\r\n\r\nWe performed a series of physical and electrical characterization experiments on single-layer as well as two- and three-layer structures of Si\u2083N\u2084, Al\u2082O\u2083, and HfO\u2082. Transmission electron microscopy and I-V measurements were used to correlate the physical effects of high-temperature annealing on the electrical properties of the films, allowing us to determine the ideal processing conditions. Construction of Fowler-Nordheim plots from experimental I-V data gave qualitative evidence of barrier lowering in the multi-layer structures.
\r\n\r\nWe developed a bias-dependent photoemission technique for quantitative determination of the band-offsets between silicon and our dielectric barriers, which is found to be highly dependent on the applied bias. For SiO\u2082 (and other single-layer materials), image potential barrier lowering simulations predict the barrier profile as a function of voltage, allowing us to report the band-offsets for these materials in a more complete way than was previously possible. Also, by characterizing multi-layer structures of HfO\u2082 and Al\u2082O\u2083, we have been able to quantitatively measure the effective barrier height of these structures over a wide range of biases and prove barrier lowering. Analysis by an electrostatic model allowed us to accurately simulate the barrier lowering results over all voltage ranges.
", "doi": "10.7907/D90P-6821", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" } ]