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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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" } ]