VictorJuiz/thesis huggingface dataset:
Two studies of topological quantum field theory in two dimensions

Take powers of the determinant line bundles on the relative moduli spaces (or stacks) of principal G-bundles over relative curves C over a base space B, and then push them down to the base space B --- the resulting sheaves over B, which are in fact vector bundles, are known as the Verlinde bundles. They satisfy certain ``gluing'' properties and yield a structure known as (K-theoretic) cohomological field theory, which is a type of families 2-dimensional topological quantum field theory. In the first part of this thesis, we carry out an investigation of the higher twisted Verlinde bundles, as defined by Teleman--Woodward, for the case when G is C^*, the multiplicative group of complex numbers. In particular, we show that their Chern characters can be written in terms of tautological classes. This generalizes the known fact that the ordinary Verlinde bundles have tautological Chern characters; indeed we also include in our study an explicit computation of the Chern characters of the C^*-Verlinde bundles. From this computation we are able to explicitly demonstrate the gluing properties in action./nBy results of Costello and of Konstevich and collaborators, cohomological field theories can also arise from categories that are homologically smooth, proper, and Calabi--Yau. The state space of such a theory is given by the Hochschild (co)homology of the category. In the second part of this thesis, then, we study categories of matrix factorizations for Landau--Ginzburg models (X,W), where X is a complex variety. We show that when X is smooth and Calabi--Yau as a variety and W has a proper critical locus, the corresponding category of matrix factorizations is homologically smooth, proper, and Calabi--Yau as a category. Furthermore, we compute the Hochschild cohomology of these matrix factorization categories, and we get the result predicted by Kontsevich. These results, which are joint with Daniel Pomerleano, generalize the results of Dyckerhoff for the case when X is affine local and W has an isolated singularity./nWe conclude with some brief remarks on forthcoming work, also joint with Daniel Pomerleano, in which we propose mirror partners to certain Fano non-toric 3-folds which can be degenerated to nodal toric varieties. Using our results on matrix factorization categories, we are able to prove some homological mirror symmetry results for these proposed mirror pairs.

Advisor: Teleman, Constantin
Side Reactions in Lithium-Ion Batteries

Lithium-ion batteries store energy through two electrochemical reactions. In addition to these main reactions, many side reactions are possible. The causes and effects of battery side reactions are usually detrimental, sometimes positive, and almost always very complicated. We investigate here both fundamental and applied aspects of several side reactions using experiments and theory./nIn Part I, we develop a new method to characterize the solid-electrolyte-interphase (SEI), a passivating film that is the product of side reactions on the graphite electrode, using ferrocene, a redox shuttle. By comparing ferrocene kinetics in the presence and absence of passivating films, the shuttle functions as an electrochemical probe of the mechanism by which the SEI prevents reaction. We develop our method using a model system of a rotating-disk-electrode (RDE) and glassy carbon. Coupling experimental measurements with a physics-based model aids interpretation of the results. We develop both steady-state and transient methods in the model system before applying the methods to highly oriented pyrolytic graphite (HOPG), which more closely resembles the carbon found in an actual battery. We study the effects of the relative fraction of edge and basal planes, the formation voltage, and the electrolyte anion. We also attempt in-situ atomic-force microscopy to validate our electrochemical measurements./nIn Part II, we treat several different overcharge reactions theoretically to explain empirical observations, predict system behavior, and suggest considerations for battery design. We develop a two-dimensional model to explain why lithium deposition occurs preferentially at the edges of electrodes and suggest mitigation techniques. In a separate model, we implement a redox shuttle for overcharge protection. We study how the presence of a redox shuttle affects the macroscale current-potential relations of the battery and optimize the redox potential of the shuttle while considering the tradeoffs between current efficiency and overcharge protection.

Advisor: Newman, John S
Fluorescence Spectroscopy for Cell Membrane Biophysics at the Nanometer and Nanosecond Scales

Cell membranes organize and regulate a vital share of biological signaling. Fluorescence has become the main analytical tool with which to study such systems, and novel fluorescence techniques drive biological discovery at ever-smaller size and time scales. By exploiting the unique photophysics of fluorescent probes, I have advanced two parallel approaches to studying membrane systems: nanoengineered biointerfaces and time-resolved spectroscopy. Metallic nanostructures were engineered to precisely localize fluorescence emission, enhance label-free detection of lipid-protein interactions, and manipulate the diffusion landscapes of supported lipid bilayers. A platform for fluorescence spectroscopy at sub-nanosecond resolution combines fluorescence cross-correlation spectroscopy (FCCS) and time-resolved fluorescence anisotropy (TRFA) to characterize protein diffusion. These techniques have provided insight into the organization and structural flexibility of intercellular adhesion molecule-1 (ICAM-1), oligomerization of the small GTPase H-Ras, and the association of diverse lipid anchor domains in vitro and in vivo. Finally, I demonstrate progress toward single-molecule characterization of lipid-protein systems, and elaborate on its relevance to environmental biosensors for public health and biosecurity applications.

Advisor: Groves, Jay T
Grigoropoulos, Costas
Managing Intergroup Emotions: How Intergroup Ideologies and Emotion Regulation Can Stifle Positive Emotions and Intergroup Friendships

In interracial settings, a chief concern among majority group members is whether they appear prejudiced. These concerns often elicit feelings of anxiety and threat, which, ironically, run the risk of being interpreted as prejudice. One of the challenges majority group members face in intergroup interactions is the regulation of these negative emotions. Drawing on Gross's (1998, 2002) emotion regulation framework, I examine individual differences in how people manage negative emotions during intergroup encounters. I investigate whether a particular costly emotion regulation strategy, expressive suppression, is used by majority group members to limit intergroup emotional expressions, and in particular, used by individuals espousing colorblind ideologies that seek to avoid the perception, acknowledgement, and use of race. People endorsing more multicultural ideologies, on the other hand, accept group differences and thus should be less likely to rely on emotional suppression to manage interracial interactions. In Study 1a, I establish intergroup emotion regulation as distinct from global forms of emotion regulation. In Study 1b, I demonstrate the links between ideology and intergroup suppression. In Study 2, I examine of the social consequences of this ideology-suppression link, demonstrating that colorblind ideologies are associated with less positive, and multiculturalism with more positive, intergroup encounters and that these effects are mediated by intergroup suppression. Finally, in Study 3, I test this pathway experimentally, priming participants with multicultural or colorblind ideologies prior to an interracial interaction. Colorblind primes led to more suppression and less positive emotional expression, leading to less positive experiences for interaction partners.

Advisor: Mendoza-Denton, Rodolfo
Interactions among gene regulation and expression, sequence deletion, and purifying selection following whole genome duplications in flowering plants

Polyploidy, or whole genome duplication, is rampant among both extant and ancient flowering plant species. Whole genome duplications create simultaneous copies of all genes contained within a genome as well as associated regulatory sequences. These duplication and the subsequent deletions of redundant coding and noncoding sequence both shape the natural evolution of plant genomes and provide a unique opportunity for researchers to characterize the regulatory sequences which determine when, in which cells and in what quantities the mRNA encoded for by particular genes will be produced./nThis dissertation describes a model for explaining both bias in gene loss between parental subgenomes and the escape from preferential retention of duplicated genes between sequential whole genome duplications. Bias in gene deletion between individual duplicated segments had been previously observed by the publication of the sorghum and maize genomes provided an opportunity to demonstrate this bias was a consistent mark distinguishing whole pairs of ancestral chromosomes, and that ongoing gene loss remains consistently biased between high and low gene loss subgenomes millions of generations after a whole genome duplication. Bias in both ancestral and ongoing gene loss is shown to be correlated with biased gene expression between parental subgenomes with genes on the low gene loss subgenome tending to show higher expression levels than duplicate copies of the same genes on the high gene loss subgenome. This phenomena, originally referred to as genome dominance, although the literature has since become somewhat confused, provides an explanation both for biased gene loss between parental subgenomes and for the escape of deletion-resistant genes from the ratchet of ever increasing copy numbers through continued whole genome duplications./nThis dissertation also demonstrates the use of polyploid lineage - in this case maize - as a deletion machine to rapidly characterize the function of regulatory sequences shared by orthologous genes within a clade. It was possible to develop testable hypothesis about the specific function of individual regulatory sequences by combining conserved noncoding sequence sequence datasets, noncoding sequence deletions identified using comparative genomics with analysis and visualization of gene expression data from diverse organs, tissues, and cell types. As a test of the accuracy of this method, a putative pollen specific enhancer of expression identified using expression data from maize was cloned from the orthologous sorghum gene and used to drive the expression of a reporter construct in Brachypodium distachyon. Polyploid deletion machines have the potential to radically accelerate the characterization of noncoding regulatory sequences, an area of genetics previously largely untouched by advances next generation sequencing technologies.

Advisor: Freeling, Michael
Strategies for Sharing Bottleneck Capacity among Buses and Cars

In urban settings where space is at a premium, bus lanes can often only be created via the conversion of existing general-use lanes. This can be politically infeasible in cities where bus flows are low, because the converted lanes would be under-utilized and thereby squander road space. The roadway bottlenecks would then as a result create even greater delays and queuing for car traffic./nThe present thesis explores novel ways in which buses and cars might share lanes within select bottlenecks. Details of these shared-lane strategies vary, depending upon a bottleneck's local operating conditions. In all cases, cars would be inserted into a shared lane in ways that impart few delays to the buses. These insertions would allow for the unused space between buses to be used, lessening the damage otherwise incurred by car traffic at bottlenecks. Hence, by reducing the car delay at bottlenecks it may become feasible to deploy ordinary bus-lane conversions elsewhere throughout a city's road network. The ordinary lane conversions would enable buses to bypass the car queues that still form at bottlenecks./nAnalytical assessments unveil the wide range of bus flows for which these strategies increase a bottleneck's car-carrying capacity, in comparison to reserving one of its lanes for buses only. Simulations of a real case study indicate that significant reductions in car delays can result while increasing bus speeds as much as ordinary conversions.

Advisor: Cassidy, Michael J.
Demand for Environmentally-Friendly Durables

This thesis addresses several aspects of the demand for environmentally-friendly durable goods. Chapter 2 asks how technological obsolescence affects how we should think about how much to promote the adoption of environmentally-friendly durables. If the purely social benefits improve quickly but private benefits only improve slowly, then subsidizing adoption now may delay upgrading in the future. As an example, I consider the impact of subsidizing the replacement of short-lived incandescent bulbs with long-lived CFLs even though we know that much better LEDs will soon be on the market. In the process, I provide some of the first publicly-available estimates of the elasticity of demand for CFLs and energy-saving in lighting./nChapter 3 discusses the optimal timing of product introduction to market for goods that provide environmental benefits. Although a simple model argues for early introduction, if early-adopters have overly optimistic expectations about product quality, product launch decisions that are optimal for firms may be sub-optimal from a social point of view./nAt the firm level, capital stock can vary widely in the intensity with which it uses fuels. Newer vintages are often associated with increased input use efficiency, leading to emissions reductions through energy savings. Chapter 4 analyzes the impact of trade liberalization in India on the greenhouse gas emissions of that country's manufacturing firms. I document that over a period of 13 years within-industry reallocation of market share to favor more energy-efficient firms produced a larger savings in greenhouse gases than is expected from all of India's Clean Development Mechanism energy efficiency and renewable energy projects combined. Using 19 years of firm-level data from India's Annual Survey of Industries and industry-level variation in policy reforms, I estimate the relative contributions of tariffs on final goods, tariffs on intermediate goods, FDI reform, and delicensing on increasing energy efficiency within firms and on reducing market share of energy-inefficient firms. I observe that reductions in tariffs on intermediate inputs led to a 23% improvement in fuel efficiency, with the entire effect coming from within-firm improvements. Delicensing and FDI reform, not tariffs on final goods, drove the reallocation effect, with post-liberalization changes in licensing requirements improving fuel efficiency an additional 7%.

Advisor: Villas-Boas, Sofia
Controller Design and Implementation for a Powered Prosthetic Knee

Powered prosthetic knees offer many improvements over passive devices; however, the added actuation is difficult to control due to the lack of input from the user. A means of controlling a powered prosthetic knee is proposed by predicting the type of swing behavior the knee must perform based on the position of the foot relative to the person during toe-off. The software to accomplish this is implemented via a finite state machine which activates specific knee angle reference generators for each state. The reference generators serve as the input of a nonlinear feedback controller to ensure accurate positioning of the knee joint.

Advisor: Kazerooni, Homayoon
Function and regulation of the Super Elongation Complexes in HIV-1 transcription

In 2010, we discovered that the HIV-1 transactivator Tat interacts with a set of related transcription complexes containing two different classes of general transcription elongation factors, P-TEFb and ELL1/2, as well as the essential scaffolding protein AFF1/4. These complexes are called the Super Elongation Complexes (SECs). SECs are physically distinct from the two major P-TEFb complexes, the 7SK snRNP and the P-TEFb-Brd4 complex. In each SEC, AFF1/4 plays a scaffolding role in mediating the interaction between P-TEFb and ELL1/2. Our data show that the presence of Tat or AFF4 can significantly increase the half-life of ELL2, leading to significant elevation of levels of ELL2 and ELL2-P-TEFb-containing complex in cells. As a result of the increased amount of ELL2-P-TEFb-containing complex, both basal and Tat-dependent HIV-1 transcription is greatly enhanced in the presence of Tat or AFF4. In 2011, we found that ELL2 is targeted for polyubiquitination and degradation by the E3 ubiquitin ligase Siah1. Depletion of Siah1 promotes formation of SECs and SEC-dependent HIV transcription. The binding of AFF1/4 to ELL2 inhibits Siah1-mediated ELL2 polyubiquitination since Siah1 cannot access to and target ELL2 for polyuniquitination when ELL2 is being bound to AFF4. Together, our data illustrate that the control of ELL2 stability by Siah1 plays an important role in regulating SEC-dependent HIV-1 transcription and that Tat acts as a powerful activator of HIV-1 transcription by recruiting the stable, bifunctional elongation SEC complexes to the HIV-1 promoter. The link of the ubiquitination/proteolytic pathway to SECs will provide new opportunities for finding drugs and intervention strategies to modulate transcriptional elongation implicated in HIV/AIDS.

Advisor: Zhou, Qiang
Essays in Public Economics

This dissertation seeks to understand the determinants and effects of public policies and to understand how to use these results to improve policy. The first two parts consider government spending during recessions--the effects of the spending and how to spend most effectively./nIn "Does State Fiscal Relief During Recessions Increase Employment? Evidence from the American Recovery and Reinvestment Act," my co-authors and I measure the employment effects of spending during recessions. The American Recovery and Reinvestment Act (ARRA) of 2009 included $88 billion of aid to state governments administered through the Medicaid reimbursement process. We examine the effect of these transfers on states' employment. Because state fiscal relief outlays are endogenous to a state's economic environment, OLS results are biased downward. We address this problem by using a state's pre-recession Medicaid spending level to instrument for ARRA state fiscal relief. In our preferred specification, a state's receipt of a marginal $100,000 in Medicaid outlays results in an additional 3.8 job-years, 3.2 of which are outside the government, health, and education sectors./nIn "Labor Market Policy for Inefficient Job Rationing During Recessions," my co-author and I consider how to best design government spending during recessions. We consider a simple static model of labor markets during recessions where the allocation of scarce jobs to workers is resolved inefficiently. In our model, some of the unemployed have high surplus from employment (e.g., those with a mortgage, three children, and a non-working spouse), while some of the employed do not. This inefficient rationing increases the welfare costs of recessions. We propose three solutions: (i) subsidizing non-employment, (ii) taxing employees, and (iii) subsidizing employers. These policies make "space" for those who really need jobs./nIn "Why Fight Secession? Evidence of Economic Motivations from the American Civil War," I turn to the determinants of government policy. I ask why governments fight secession. This paper is a case study on this question, asking why the North chose to fight the South in the American Civil War. It tests a theoretical prediction that economic motivations were important, using county-level presidential election data. If economic interests like manufacturing wished to keep the Union together, they should have generated votes to do so. That prediction is borne out by the data, and explanations other than Northern economic concerns about Southern secession appear unable to explain the results, suggesting that economic motivations were important to support for fighting the South.

Advisor: Saez, Emmanuel
Gender, Ethnicity, and Drinking in Older Age: Understanding Mediators and Moderators of Risk

Background: Drinking among older adults might increase in the future due to relatively high rates of alcohol use in the "baby boomer" cohort and the rise in the proportion of older adults in the USA. Little is known, however, about potential moderation and mediation mechanisms determining risk or how these processes vary by gender or race/ethnicity. Guided by a cumulative inequality framework, three nationally representative analyses were conducted to help untangle the complicated relationships between risk factors for drinking and drinking related behaviors in older age, particularly for older women and older adults of color./nMethods: Logistic regression and path analysis models were used to examine drinking and related behaviors among adults aged 60 or older, using samples from the 2002-2010 National Health and Nutrition Epidemiologic Survey (NHANES)./nResults: Alcohol use in older adulthood may be even more problematic than previously thought due to the concurrent use of alcohol-interactive prescription drugs (AIPD), particularly for Mexican American men and Black women. Although no mediation effects were found, gender and race/ethnicity significantly modified several relationships between risk factors and drinking in older age. Older men who are impaired by depressive symptoms are at lower risk of heavy episodic drinking, while older women who are impaired by depressive symptoms are at higher risk of heavy episodic drinking. Gender and race/ethnicity also moderate the relationship between physical health and at-risk or heavy episodic drinking in old age, with highest risk for Mexican American men and Black older adults in poor health./nDiscussion: Drinking in older age is a not a monolithic behavior, instead there is considerable variation in which factors increase risk. Inconsistencies in the literature investigating drinking in older age are not just due to lack of research, but also to lack of research recognizing these important variations. Research efforts and social work practice with older adults must account for gender and racial/ethnic differences in order to help improve understanding, strengthen assessment efforts, and optimize treatment opportunities. Additionally, it is important to consider the role of AIPD use in older age drinking, as use is highly prevalent and could compound negative outcomes of a social problem poised to become a major public health concern in the 21st century.

Advisor: Midanik, Lorraine T