VictorJuiz/thesis huggingface dataset:
Optically Detected Magnetic Resonance of Nitrogen Vacancy Centers in Unique Diamond Samples

Nitrogen-vacancy (NV) centers are defects in diamond with unique physical properties that make them potentially useful for a number of applications. Their emission is spin-state dependent, enabling the use of optically-detected magnetic resonance (ODMR) to study their spin states. The stability of their emission and the ability to functionalize diamond surfaces make them superior biomarkers for fluorescence imaging. Finally, their atypically long spin coherence times enable their use as a quantum bit in quantum information applications. This dissertation is concerned with the fact that the spin state of the NV center can be optically polarized, or initialized. If such polarization could be used to align the nuclear spins in a sample external to the diamond and thus enhance the raw magnetic resonance signal for any sample, magnetic resonance technology such as NMR Spectroscopy and MR Imaging could be improved dramatically./nIn an effort to understand if use of the NV center to improve magnetic resonance technology is possible and to determine the best strategy for future protocols, this dissertation forms a detailed analysis of the ODMR spectroscopy of NV centers in nanodiamond powder and 13C-enriched diamond. These are two modalities that could make this transfer of polarization to nuclei in an external sample possible. Nanodiamond powder, for example, increases the number of NV defects exposed to an external sample by orders of magnitude relative to a single crystal sample. On the other hand, 13C in diamond could be used to mediate the transfer of polarization from NV centers to external nuclei, due to the fact that the 13C concentration can be tuned to be from 4 to 6 orders of magnitude greater than the NV center, and they would be closer to the surface where interaction with external spins is greatest. Such points make both media, nanodiamond powder and 13C-enriched diamond, attractive candidates for testing these ideas. Any information on how the spectroscopy and dynamics of the defect changes in both forms of diamond is therefore critical to any strategy of enhancing nuclear spin signal with NV centers in diamond./nThis dissertation first describes inherent limitations in magnetic resonance techniques and how they could be improved with NV centers. NV center properties, properties of diamond, practical experimentation information, and detailed information on simulating spectra are all summarized. Results are presented on the current understanding of NV center behavior in these two forms of diamond. Finally, it is the goal of this dissertation to construct a system for testing polarization transfer from NV centers in diamond to an external sample. The progress made on developing this system, instructions for preparing the system for experiments, and current knowledge of troubleshooting the failure modes of the system are described in detail.

Advisor: Pines, Alexander
From the Molecular to the Bulk: A Size-Resolved Perspective on the Structural and Thermodynamic Properties of Hydrated Ions

In this dissertation, phenomena related to ion hydration are investigated in gas-phase clusters of ions and water molecules. Hydrated ions are generated using electrospray ionization and trapped using a Fourier transform ion cyclotron resonance mass spectrometer. A variety of ion activation techniques are used to probe the structures and reactivities of these ions, including infrared photodissociation (IRPD), ultraviolet photodissociation, blackbody infrared dissociation, and electron capture dissociation. IRPD spectra of alkali metal ions, ion pairs, and the protein denaturant guanidinium reveal how the delicate balance of noncovalent interactions between ions and water molecules establishes inner shell hydration motifs that can affect the hydrogen bond network of surrounding water molecules. In the case of guanidinium, molecular hydration structures determined by IRPD spectroscopy and ab initio calculations reveal that the ion is amphiphilic, and this is related to its bulk property as a protein denaturant in solution. The effects of ions on the hydrogen bond network of water are investigated by studying extensively hydrated ions in nanometer-sized droplets, or “nanodrops”. IRPD spectra of nanodrops containing a single La3+ ion and up to 550 water molecules indicate that the trivalent ion can frustrate the onset of crystallinity in these cold water clusters by altering the hydrogen bond network of water located remotely from the ion. Spectroscopy of nanodrop surfaces provides further evidence that multiply charged ions can affect the structural and electrostatic properties of nanodrops. These experimental data are supported by molecular dynamics simulations analyzed with custom-built software, and provide compelling evidence that ions can affect the structure of water well outside the first solvation shell – a point of contentious debate in the current literature. Using an extrapolation method, properties derived from cluster measurements such as surface “free” O–H stretching frequencies are related to their corresponding values at neutral interfaces, providing a link between cluster and bulk measurements. In addition to the aforementioned structural studies, thermodynamic information about the reductions of hydrated transition metal ions is obtained using the ion nanocalorimetry technique. A major improvement to this technique is introduced where ion-electron recombination energies are derived from laser calibration experiments. A value for the absolute reduction potential of the standard hydrogen electrode is deduced from the absolute reduction potential measured for the Cu2+/Cu+ redox pair, which should be more accurate than previously reported values. Ion nanocalorimetry is also used to measure, for the first time, the one-electron reduction potentials of several transition metal ions that are difficult to probe in solution due to the phenomenon of potential inversion.

Advisor: Williams, Evan R.
Semi-Targeted Exposome Strategies to Measure Biomarkers of Exposure and Disease Associated with Type II Diabetes in Asian Indians

The prevalence of type II diabetes (T2D) is escalating worldwide, yet incidence rates differ dramatically between ethnic groups. Some known risk factors of T2D include diet, exercise, and genetic inheritability, yet these factors alone cannot fully explain the differences observed between populations. Better approaches are needed to identify other non-genetic factors, such as toxic chemical exposures, that are related to T2D, particularly in highly-susceptible populations. The exposome is a relatively new concept used to investigate causes of disease due to endogenous and exogenous exposures. This dissertation aims to use semi-targeted exposomics to examine biomarkers of exposure and disease that are associated with T2D. Chapter 1, the introduction, discusses the broader objectives of exposomics, including ideal comparison populations for identifying underlying causes of chronic disease. In the case of T2D, Asian Indians are a population of great interest, with a 3-4-fold higher risk of T2D than European white counterparts. Chapter 2 examines blood concentrations of environmental pollutants in small volumes of plasma in Asian Indian immigrants and a low-risk comparison group, European whites. This study is the first to investigate associations between persistent organic pollutants and T2D in Asian Indians. Chapter 3 describes a method to measure sources of variability in a potential biomarker of T2D, microRNA (miRNA). This study demonstrates the importance of empirically measuring technical and biological sources of variability and using simulations to inform power calculations for new biomarkers of interest. Chapter 4 takes lessons learned from Chapter 3 and applies them to a case-control study on plasma miRNA in Asian Indians. In the concluding Chapter 5, the current state of research on T2D as it relates to blood biomarkers of environmental exposures and disease are described for Asian Indians and other highly susceptible groups.

Advisor: Smith, Martyn T
Zhang, Luoping
Operational Control and Survivability Enhancement of Asymmetric Wave-Energy Converters

The aim of this research is to study the operational and survivability modes of asymmetric wave-energy converters (AWEC). “The Berkeley Wedge” (TBW), a one-degree-of-freedom, asymmetrical, energy-capturing, floating breakwater, which is relatively free from viscosity effects, is used as a canonical problem of study./nFor the operational mode, the focus of the analysis is to optimize the power-to-load ratio of TBW. Linear hydrodynamic theory was used to calculate bounds on the expected time-averaged power (TAP), the corresponding surge restraining force, pitch restraining torque, and power take-off (PTO) control force. This thesis formulates the optimal control problem to incorporate metrics that provide a measure of the surge restraining force, pitch restraining torque, and PTO control force. The controller handles an objective function with competing terms, so as to maximize power capture while minimizing structural and actuator loads. In achieving these goals, a per-unit gain in TAP would not lead to a greater per-unit demand in structural strength, hence yielding a favorable benefit-to-cost ratio. Demonstrative results in the form of TAP, reactive TAP, and the amplitudes of the surge restraining force, pitch restraining torque, and PTO control force are shown for TBW example./nTo provide guidance for improving the survivability of the AWECs, analysis of the extreme forces they experience in deep-water breaking waves was conducted. The forces were obtained by computation using the Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH) method and also by model-scaled experiments (conducted at the RFS Model Testing Facility of the University of California at Berkeley). Breaking waves were first generated for both physical and computational modeling by developing appropriate time histories of the wavemaker, using potential-flow theory. Plunging breakers and wave forces at two target locations by computations were verified by experiments. The effects of different drafts of TBW on the force reduction were studied. To increase the survivability while maintaining the operational draft of the TBW, pressure-relief channel (PRC), a new scheme that allows water to flow through TBW was implemented. The PRC effectiveness in reducing the extreme wave forces was demonstrated computationally. With guidance from these computations, a design is proposed to illustrate an effective way to install and operate the PRCs so as to increase the survivability of TBW and similar devices in extreme sea states.

Advisor: Yeung, Ronald W
Gatekeepers and Trailblazers: Essays in Microeconomics

This thesis studies dynamic markets with endogenous entry, where access hurdles are either an explicit feature of the market or an implicit result of productive externalities./nThe first chapter concerns markets of influence, where formal gatekeepers are in charge of selecting and promoting the most promising ideas. I model this as a two-sided matching market between a continuum of experts and a finite number of gatekeepers under sequential directed search. Real-world examples include academic publishing, venture capitalism or political agenda setting. Uniqueness of the resulting equilibrium allows for clear-cut pre- dictions: First, sorting may fail in equilibrium. Second, gatekeepers may have an incentive to add artificial delay. Such red tape occurs in equilibrium – and only at the top – when the impact of two gatekeepers is very different. Third, artificial delay may improve equilib- rium sorting and thereby enhance welfare. Finally, the bottom gatekeeper may endogenously specialize on a quality-irrelevant attribute./nIn other applications, there are no formal gatekeepers who regulate market access, yet endogenous access hurdles play a similarly selective role. In this vein of research, the second chapter studies the evolution of labor market composition under mentoring externalities. This chapter is joint work with Aniko Oery. We provide a continuous time, overlapping generations framework to analyze the costs and benefits of affirmative action policies if mentoring complementarities are present. Senior workers reduce the young population’s educational cost through mentoring, and thus act as ‘trailblazers’ for future generations. In such a framework, the main trade off is between using the most able workers and reducing mentorship misallocation. We identify conditions under which persistent market intervention is warranted to improve long-term surplus. We also contrast different channels through which the planner can affect market outcomes, and highlight the benefits of educational fellowships over hiring restrictions.

Advisor: Ergin, Haluk
Fuchs, William
Neural Circuits Underlying Mating Behavior in Drosophila

Reproduction is essential for the survival of animal species. Males and females exhibit innate sex-specific reproductive behaviors, which are established developmentally and do not require previous experience. Because mating can be energetically costly, animals have evolved mechanisms to distinguish between reproductively viable and futile conspecifics that rely largely on sex-specific pheromones. How these complex, often antagonistic cues are transmitted from the periphery to the higher brain, the neural circuits they activate, or the computational principles by which they are integrated remain unclear./nIn the first part of this dissertation, I investigate the neural circuits underlying mating behavior in the fruit fly Drosophila melanogaster, leading to a novel model of decision-making. I employ anatomical, calcium-imaging, optogenetic, and behavioral studies to demonstrate that sensory neurons that detect female pheromones, but not male pheromones, activate a novel class of neurons in the ventral nerve cord to cause activation of P1 neurons, male-specific command neurons that trigger courtship. In addition, I show that sensory neurons that detect male pheromones, as well as those that detect female pheromones, activate GABAergic mAL neurons to inhibit P1 neurons. These data support a model in which the balance of excitatory and inhibitory inputs onto central courtship-promoting neurons regulates the decision to court./nIn the second part of this dissertation, I develop methods to visualize the morphology of neurons in taste processing in the fly brain. I employ large-scale calcium imaging coupled to cell labeling to identify sweet- or bitter-responsive neurons in the subesophageal zone (SEZ), the primary taste relay in the fly brain. I successfully use this approach to label SEZ motor neurons and demonstrate that they are tuned to a single taste modality, arguing for labeled-line processing of taste from sensory input to motor output. Nonetheless, reliably labeling single, non-motor SEZ neurons using this strategy has been difficult. Using a modified approach incorporating a nuclear-localized calcium indicator, I reproducibly label a cluster of putative bitter-responsive SEZ neurons. Based on their morphology, these neurons appear to be inhibitory olfactory projection neurons (iPNs), which transmit information from the antennal lobe to the lateral horn, suggesting that taste inputs may modulate the processing of odors.

Advisor: Scott, Kristin
Engineering Dissipation to Generate Entanglement Between Remote Superconducting Quantum Bits

Superconducting quantum circuits provide a promising avenue for scalable quantum computation and simulation. Their chief advantage is that, unlike physical atoms or electrons, these ``artificial atoms'' can be designed with nearly-arbitrarily large coupling to one another and to their electromagnetic environment. This strong coupling allows for fast quantum bit (qubit) operations, and for efficient readout. However, strong coupling comes at a price: a qubit that is strongly coupled to its environment is also strongly susceptible to losses and dissipation, as coherent information leaks from the quantum system under study into inaccessible ``bath'' modes. Extensive work in the field is dedicated to engineering away these losses to the extent possible, and to using error correction to undo the effects of losses that are unavoidable./nThis dissertation explores an alternate approach to dissipation: we study avenues by which dissipation itself can be used to generate, rather than destroy, quantum resources. We do so specifically in the context of quantum entanglement, one of the most important and most counter-intuitive aspects of quantum mechanics. Entanglement generation and stabilization is critical to most non-trivial implementations of quantum computing and quantum simulation, as it is the property that distinguishes a multi-qubit quantum system from a string of classical bits. The ability to harness dissipation to generate, purify, and stabilize entanglement is therefore highly desirable./nWe begin with an overview of quantum dissipation and measurement, followed by an introduction to entanglement and to the superconducting quantum information architecture. We then discuss three sets of experiments that highlight and explore the powerful uses of dissipation in quantum systems. First, we use an entangling measurement to probabilistically generate entanglement between two qubits separated by more than one meter of ordinary cable. This represents the first achievement of remote entanglement in a superconducting qubit system, which will be a critical capability as quantum computers and simulators scale. We then use a nearly-quantum limited amplifier to unravel individual quantum trajectories of the system under that entangling measurement, performing the first systematic exploration of entangled trajectories in any physical implementation. We finally demonstrate deterministic entanglement by engineering a lossy quantum environment to efficiently generate and stabilize entangled states with both frequency and symmetry selectivity. These experiments provide evidence that explicitly building dissipation into an engineered quantum system can enable, rather than hinder, the study of fundamental quantum mechanics and complex many-body Hamiltonians.

Advisor: Siddiqi, Irfan
Anticipating Social Pleasure with Family, Friends, and New People: Conceptualization, Measurement, and Implications for Personality and Psychopathology

Individual differences in anticipatory pleasure have been studied primarily in physical or sensory domains, such as anticipating eating tasty food or the anticipating the excitement of riding a rollercoaster. The present studies were designed to extend this research to the social domain. We propose that, just as in nonsocial domains, people in social situations will orient and move toward those experiences they expect and predict will be pleasurable for them. Current self-report measures of social pleasure or its absence (i.e., anhedonia) tend to assess consummatory (in-the-moment) pleasure across one global, social domain. The current studies sought to define and assess individual differences that distinguish anticipatory pleasure in different kinds of social relationships. Conceptual, item-analytic, and factor-analytic work provided consistent evidence that self-reports of social pleasure anticipation can be distinguished across three relationship domains: Friends, Family, and New People. The Social Pleasure Anticipation (SPA) scales showed internal consistency and retest reliability, convergent and discriminant validity evidence when related to measures of social and nonsocial pleasure and to measures of personality and social functioning, as well as external validity based on peer reports. The SPA scales differentially predicted unique and replicated patterns of personality traits, psychological symptoms, and well-being. Discussion focuses on the implications of this tripartite taxonomy of the social domain for theories and measures of social functioning that so far have been conceptualized only at the global, undifferentiated level.

Advisor: Kring, Ann
The role of COPII coated vesicles in procollagen-1 trafficking

The coat protein complex II (COPII) achieves cargo sorting and vesicle formation at the endoplasmic reticulum (ER) and aids in protein trafficking by the early secretory pathway. The flexibility of the coat machinery to accommodate diverse size and shaped cargo in order to meet the demands of the cell is not well understood. An example of a large cargo protein is collagen, which is synthesized as 300nm precursor fibrils of procollagen in the endoplasmic reticulum (ER). The molecular mechanism by which large procollagen fibrils are accommodated in canonical COPII vesicles of about 70nm remains unclear. Genetic and biochemical evidence for the role of COPII in collagen trafficking has been established in several studies. Recent collaborative work has shown that mono-ubiquitylation of Sec31 by the ubiquitin ligase complex Cul3-Klhl12 leads to the formation of large COPII vesicles (200-500nm) that drive the secretion of collagen. Amongst the follow-up questions from this study were, whether these enlarged vesicles are bona fide transport carriers of procollagen and what might the three-dimensional ultrastructure be. This dissertation work aims to characterize the role of large COPII coated vesicles in intracellular procollagen-1 trafficking. Using a combination of in vivo imaging techniques and in vitro cell-free reconstitution assays, I present evidence that addresses this question.

Advisor: Schekman, Randy W
Poland on Trial: Postwar Courts, Sovietization, and the Holocaust, 1944-1956

This dissertation addresses the quandary of how the law can serve many different purposes and yet not the one we most closely associate it with – justice. Specifically, it examines how Poland, renowned as Europe’s only occupied country “without a Quisling,” confronted the paradox of otherwise upstanding citizens who betrayed, robbed, and murdered tens of thousands of their Jewish neighbors in hiding during the Nazi occupation. Far from being a footnote, the machinations over the fate of the defendants – in Poland and throughout Europe – were central to the negotiation of a new social contract in the wake of the war’s ethnic cleansing and property transfer./nAs a rare venue not corrupted by the Stalinization overtaking Poland, the judicial system held the trials in accordance with high European standards. But with the public awaiting absolution, the hated Soviet-backed government hoping to win a degree of legitimacy, and the few surviving Jewish voices marginalized by resurgent anti-Semitism, debates over the law gradually became vehicles for the expression of colonial anxieties and the establishment of a hierarchy of victimhood. Within the judiciary, the Right exploited the law’s weaknesses as a means of resistance, while the Left, fearful of undermining the rule of law, worked to restrict its ambit. In this atmosphere of cross-purposes, legality gradually gave way to the performance of legality, eclipsing the issue of justice for victims and survivors./nAlthough held under a dictatorial communist regime, the Polish trials ultimately experienced many of the same problems as their democratic analogues across Europe; the widespread inability to come to grips with native Holocaust perpetrators amounted to a tacit acknowledgment of the desirability of societies rendered ethnically homogeneous by war and genocide. Their example serves as a dystopian prefiguring of European unity and a lesson in the limitations of transitional justice at a time when, alongside the constant invocation of human rights, more and more people are looking to the supposed universality of justice, both international and domestic, to compensate for the failures of the political order in a world that seems frighteningly anarchic and de-centered.

Advisor: Connelly, John