VictorJuiz/thesis huggingface dataset:
A new construction of virtual fundamental cycles in symplectic geometry [electronic resource]

We develop techniques for defining and working with virtual fundamental cycles on moduli spaces of pseudo-holomorphic curves which are not necessarily cut out transversally. Such techniques have the potential for applications as foundations for invariants in symplectic topology arising from "counting" pseudo-holomorphic curves. We introduce the notion of an implicit atlas on a moduli space, which is (roughly) a convenient system of local finite-dimensional reductions. We present a general intrinsic strategy for constructing a canonical implicit atlas on any moduli space of pseudo-holomorphic curves. The main technical step in applying this strategy in any particular setting is to prove appropriate gluing theorems. We require only topological gluing theorems, that is, smoothness of the transition maps between gluing charts need not be addressed. Our approach to virtual fundamental cycles is algebraic rather than geometric (in particular, we do not use perturbation). Sheaf-theoretic tools play an important role in setting up our functorial algebraic "VFC package". We illustrate the methods we introduce by giving definitions of Gromov--Witten invariants and Hamiltonian Floer homology over $\QQ$ for general symplectic manifolds. Our framework generalizes to the $S^1$-equivariant setting, and we use $S^1$-localization to calculate Hamiltonian Floer homology. The Arnold conjecture (as treated by Floer, Hofer--Salamon, Ono, Liu--Tian, Ruan, and Fukaya--Ono) is a well-known corollary of this calculation. We give a construction of contact homology in the sense of Eliashberg--Givental--Hofer. Specifically, we use implicit atlases to construct coherent virtual fundamental cycles on the relevant compactified moduli spaces of holomorphic curves.

Keywords: Mathematics.
Advisor: Eliashberg Y.
Galatius Søren
Ionel Eleny advisor. Thesis advisor
New insights into neuronal polarity [electronic resource] : actin waves and dynamic microtubule-based transport

Neuron polarization is a fundamental process in the development of the nervous system. In vivo and in vitro, many types of neurons, including hippocampal neurons, transition from a multi-polar state with relatively identical, immature neurites, to a single axon state. During the multi-polar state, neurites seemingly stochastically retract and elongate while receiving different amounts of growth promoting factors via microtubule-based transport. A long-standing, unanswered question in the field is what controls fluctuating microtubule-based transport during neuronal polarity. In this thesis, we address this problem in several parts. First, we note that actin waves, waves of F-actin that move through neurites to promote neurite extension, are tightly linked to the fluctuating neurite lengths observed during the multi-polar phase. We performed further characterization of actin waves, showing that actin waves are under the control of small Rho GTPase activity and are composed of actively polymerizing actin. Because of the role of actin waves in controlling neurite length during the multi-polar phase, we then examined their role in mediating microtubule-based transport. Indeed, we found that actin waves serve to transiently increase microtubule-based transport by transiently increasing microtubule polymerization and number. We propose that actin wave promote microtubule polymerization by widening the neurite to create more space for already polymerizing microtubules. Finally, we offer preliminary data that suggests that retrograde movement of cargo during the multi-polar phase, which decreases a neurite's probability of becoming an axon, is driven by an increase in retrograde microtubule polymerization. As a whole, this thesis offers novel mechanisms for how dynamic microtubule-based transport is controlled during the multi-polar phase. It also proposes a new function for actin waves: in addition to mediating neurite outgrowth during the multi-polar phase, they also control anterograde microtubule-based transport, ensuring neurites grow out to explore their extracellular space to look for axon-promoting cues, as well as receive axon-promoting factors.

Advisor: Meyer Tobias primary advisor. Thesis advisor
Garner Craig advisor. Thesis advisor
Nelson William advisor. Thesis advisor
New methods and models for interrogating cell assembly, projection, and whole brain functional data during motivated behavior [electronic resource]

While it is accepted that coordinated activity among populations of neurons in three-dimensional brain structures is critical to animal behavior, our understanding of such systems and their dynamics is circumscribed by available recording and intervention technologies. In particular, the ability to optically record and perturb dynamics in long-range, connectivity- and genetically-specified projections is needed to understand the roles that such inter-regional projections play in behavior, and fast methods to record and perturb population dynamics at cellular resolution across brain volumes are necessary to understand how cell assemblies coordinate across areas to encode and generate behavior. Finally, interpretable statistical techniques able to accurately capture the trends and dynamics in these complex data are required to turn observations into comprehensible descriptions, models, and theories. This work seeks to address these needs by developing (1) fiber photometry, a minimally-invasive method for recording bulk activity in connectivity-targeted and genetically-targeted cell bodies and projections during behavior, (2) SWIFT volume imaging, a method for synchronous recording and identification of cell assemblies across large volumes of tissue at high frame rates during behavior, and (3) interpretable statistical methods appropriate for high dimensional, potentially nonlinear neuroimaging data including those that are produced by SWIFT but also applicable to other whole-brain imaging data such as those generated by functional magnetic resonance imaging (fMRI). These approaches are applied and validated in several examples of motivated behavior including social approach behavior in mice, prey approach behavior in zebrafish, reward-based learning in mice, modulation of reward-seeking behavior by prefrontal cortex in rats, and incentivized decision making in humans.

Keywords: Neurosciences.
Advisor: Deisseroth Karl primary advisor. Thesis advisor
Boyd Stephen P. advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Shenoy Krishna V. (Krishna Vaughn) advisor. Thesis advisor
No Negative Modes About the Axionic Wormhole Instanton

The axion is a hypothetical elementary particle originally proposed as a solution to the strong CP problem. Because the axion is associated with a pseudo-scalar field instead of a scalar field, it has a nontrivial instanton solution, which has the form of a spherically symmetric wormhole. We examine the perturbations about this instanton using a scalar-vector-tensor decomposition. The vector modes are pure gauge, and therefore may be directly integrated. We compute the action for the tensor modes and the spectrum is shown to be non-negative. We obtain the action of the scalar modes using a transformation from the known action of a scalar field coupled to gravity. The scalar mode spectrum is also shown to be non-negative, so the axionic wormhole instanton has no negative modes. This discourages the interpretation of this instanton as a decay rate, and instead supports the Coleman interpretation of this instanton as showing that the ground state is a superposition of many-universe states.

Keywords:  Department of Physics
axion
instanton
wormhole
Thesis
Advisor: Hartnoll Sean
Kachru Shamit
Non-Abelian Lefschetz hyperplane theorems [electronic resource]

Let X be a smooth variety over the complex numbers, and let D be an ample divisor in X. For which spaces Y does every map from D to Y extend uniquely to a map X to Y? Our main result, proved via positive characteristic methods, is the following: if dim(X) > 2, Y is smooth, the cotangent bundle of Y is nef, and dim(Y) < dim(D), every such map extends. Taking Y to be the classifying space of a finite group BG, the moduli space of pointed curves M_g, n, the moduli space of principally polarized Abelian varieties A_g, certain period domains, and various other moduli spaces, one obtains many new and classical Lefschetz hyperplane theorems. We also prove many other such extension theorems, and develop general techniques for recognizing spaces Y for which these sorts of Lefschetz theorems hold.

Keywords: Mathematics.
Advisor: Vakil Ravi primary advisor. Thesis advisor
Conrad Brian
Galatius Søren
Non-equilibrium population genetics [electronic resource] : sex-biased demography and mutational load

Elucidating the relationship between a population's history and its genetic data is a central goal of population genetics. The recent deluge of genetic sequence data makes it possible to test long-standing hypothesis about human demographic history and evolution, and to assess the validity of commonly-used equilibrium assumptions. In this thesis, I focus on questions in human population genetics concerning deleterious mutational load and sex-biased demography. In Chapter 2, I test the hypothesis that the load of deleterious alleles varies across populations and find evidence that it does, possibly due to differing demographic histories. In Chapter 3, I present a new method to estimate the female fraction of the effective population size and apply it globally distributed data. I find evidence for a pervasive female bias and a male-biased bottleneck during the Out-of-Africa migration. In Chapter 4, I study more recent demographic events which led to the peopling of Central and South America and the formation of admixed populations. I apply a novel test for sex-biased admixture to genomic data and find support for varying, sex-biased histories among populations. These chapters highlight the importance of modeling demographic history in hypothesis testing, and demonstrate ways in which current population genetic inference can be extended. This thesis sheds light on the non-equilibrium nature of human populations genetics and its results give insight into our shared history.

Advisor: Bustamante Carlos (Carlos D.)
Feldman Marcus W.
Montgomery Stephen
Petrov Dmitri Alex
Tang Hua (Geneticist)
Nonlytic spread of a naked virus [electronic resource]

How do viruses spread from cell to cell? Enveloped viruses acquire their surrounding membranes by budding either through the plasma membrane or an internal membrane of infected cells. Thus, a newly budded enveloped virus finds itself either in the extracellular milieu or in a lumenal compartment from which it can exit the cell by conventional secretion. On the other hand, naked viruses such as poliovirus lack an external membrane. They are simply protein-nucleic acid complexes within the cytoplasm or nucleus of the infected cell, and thus would seem to have no other exit route than cell lysis. Poliovirus is a lytic virus, although a few examples of apparently nonlytic spread have been documented. Real demonstration of nonlytic spread for poliovirus or any other cytoplasmic constituent requires demonstration that a small amount of lysis in the cellular population is not responsible for the release of cytosolic material. The work in this thesis has demonstrated, for the first time, definitive nonlytic cell-to-cell spread of poliovirus. We have also shown a link between this type of spread and components of a conserved pathway called autophagy. Chapter 1 contains a review of the cell biology of poliovirus infection that has led to the hypothesis for nonlytic spread. In Chapter 2, we describe the time-lapse microscopy setup used to monitor real time cell-to-cell spread of poliovirus and some of the unique early observations of how the virus spreads. In Chapter 3, we dive into the role the autophagy pathway or its components play on the spread of poliovirus. Chapter 4 moves to the mouse model of poliomyelitis where we investigate how perturbing the autophagy pathway affects the pathogenesis of poliovirus. In Chapter 5, we demonstrate nonlytic spread of poliovirus in tissue culture and begin to dissect the mechanism for this type of spread. Finally, in Chapter 6, we draw conclusions about the possible role of nonlytic spread in the life cycle of poliovirus and why studying the role of autophagy in acute viral infections may be important.

Keywords: Microbiology and Immunology.
Advisor: Kirkegaard Karla primary advisor. Thesis advisor
Covert Markus advisor. Thesis advisor
Monack Denise M. advisor. Thesis advisor
Sonnenburg Justin
Nonproliferation Sanctions: Taking the "Profit out of Proliferation?"

How do sanctions impact national decisions to go nuclear? Sanctions have emerged as a frequently employed tool of statecraft and as a go-to tool in U.S. nonproliferation policy. However, the outcomes of proliferation and nonproliferation in cases of sanction imposition beg a closer examination of their efficacy- when and how are sanctions effective?
This thesis finds that the efficacy of nonproliferation sanctions depends on their ability to impact domestic politics and change the calculus in the nuclear decision-making process. The causal mechanisms behind national decisions to go nuclear reveal that the efficacy of sanctions depends on domestic political conditions. These conditions include regime type, the structure of the economy, and domestic political coalitions.
In order to understand the causal mechanisms of sanctions, this thesis examines the empirical evidence of nonproliferation sanctions imposition. The cases are divided into two categories: North Korea, Pakistan, and India constitute the proliferation outcome cases, and South Africa, Argentina, Brazil, and Libya constitute the nonproliferation outcome cases. By analyzing the causal mechanisms of sanctions and applying the relevant theoretical frameworks of sanction efficacy in these cases, this thesis gleans insights on the conditions that render sanctions effective in dissuading states from proliferation. Ultimately, this thesis seeks to understand how sanctions can be effectively maximized as a tool of nonproliferation policy and to contribute to the literature on nonproliferation sanctions.

Keywords: nonproliferation sanctions
Center for International Security and Cooperation
Interschool Honors Program in International Security Studies
Thesis
Advisor: Krasner Stephen
Norms, Latinos, and political attitudes in the United States [electronic resource]

This dissertation investigates the that role norms play in structuring attitudes toward Latinos and immigrants in the United States, and on a variety of policies. Norms are defined as standards of conduct dictated by a person's identity. While previous research does focus on the role of cultural integration in structuring attitudes, this project takes the next step by breaking down the category of cultural integration into two primary components, norms of propriety (p-norms) and norms of culture (c-norms). P-norms are related to "good" behavior, where "good" refers to actions associated with an upstanding member of society, such as seeking or retaining employment and following the law. C-norms are markers of American cultural identity. Speaking Spanish and flying a Mexican flag are examples of c-norm violations. Survey experiments are used to compare and contrast the effects of violating p- and c-norms on attitudes toward immigrants, Latinos, and on policy stances. Respondents react negatively to p- and c-norm violations by Latinos and immigrants. Even when respondents are primed to view Latinos and immigrants as upstanding members of society (p-norm followers), c-norm violations negatively impact respondents' assessments of Latinos and immigrants. Moreover, the perception of Latinos as norm violators is related to support for restrictive immigration policies and English language laws. Norms are pervasive and targeting them for inquiry brings into view the societal structure of opposition to immigration. Additionally, this research uncovers the conditions under which norms matter more or less. Ideology greatly influences the lens by which people view norm violations by Latinos and immigrants, and the perceptions people hold about groups.

Keywords: Political Science.
Advisor: Sniderman Paul M. primary advisor. Thesis advisor
Laitin David D. advisor. Thesis advisor
Segura Gary M.
Novel low-cost tools for science, diagnostics, and education [electronic resource]

Scientific research and discovery have played a crucial role in the development of modern society. The technological innovations of the past few centuries offer multifarious benefits that many of us enjoy every day; yet, nearly half the world's population lives in poverty with inadequate resources to serve their basic needs. The methods, technologies, and tools engineered for the developed world often do not translate well as solutions for the idiosyncratic needs of developing regions. Accordingly, this thesis work aims to expand the impact of available funding by exploring the design space of "frugal science", or science practiced in a context of limited resources. My frugal innovations target simultaneous optimization of performance, cost, and scalability. The Foldscope, a

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Prakash Manu primary advisor. Thesis advisor
Baer Thomas
Numerical investigation of breaking internal waves on slopes [electronic resource] : dynamics, energetics, and transport

Over the past fifty years, advancements in ocean instrumentation have led to fascinating observations of internal waves propagating, shoaling, and breaking in the coastal ocean. These observations have shown that breaking internal waves are likely important contributors to transport and mixing in coastal ecosystems, as well as to turbulent dissipation and mixing in the global ocean energy budget. However, much of the physics of internal waves, especially the process of breaking on slopes, remains poorly understood. Due to the limited spatial and temporal resolution of field observations in the ocean, many idealized laboratory and numerical experiments have also been used study internal waves. The primary goal of this dissertation is to use high-resolution, laboratory-scale numerical simulations to increase the current understanding of breaking internal waves on slopes. I take advantage of high-performance, parallel computing to resolve turbulent effects using direct numerical simulations (DNS), and focus on three specific aspects of internal wave breaking: dynamics, energetics, and transport.

Keywords: Civil and Environmental Engineering.
Advisor: Fringer Oliver B. (Oliver Bartlett) primary advisor. Thesis advisor
Koseff Jeffrey Russell advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Numerical investigations of turbulent duct flows using wall-modeled large-eddy simulation [electronic resource]

The challenges posed by shock wave-turbulent boundary layer interactions (STBLIs) remain one of the primary considerations in the design and operation of air-breathing hypersonic vehicles. The internal flow within the isolator of a scramjet engine involves a series of coupled STBLIs. In order to study these phenomena, the interaction of a turbulent boundary layer with a shock train in a constant area duct (STCAD) is used as a model problem. Calculations of a STCAD are performed using wall-modeled Large-Eddy Simulation (WMLES). This approach reduces the computational cost of a simulation by modeling the inner portion of the boundary layer and thereby enables the calculation of high Reynolds number flows. The equilibrium formulation of the wall-model, which neglects the pressure gradient and convective terms in the thin boundary layer equations (TBLEs), is evaluated for a class of flows where the non-equilibrium characteristics are primarily exhibited outside of the wall-modeled region. Several modifications to the framework of the WMLES are also developed and tested in order to improve predictions for turbulent, non-circular duct flows. Results from calculations of a STCAD at lower Reynolds number are compared with previous wall-resolved LES investigations to establish confidence in the approach. The WMLES is then applied to a STCAD at the higher Reynolds number conditions from experiments where wall-resolved calculations were prohibitively expensive. A parameter study related to the physical characteristics of the interaction is performed to address the uncertainty created by the lack of experimental data with respect to the side wall boundary layers. The equilibrium WMLES is shown to provide accurate predictions in comparison with the experimental data measured in the spanwise center plane. The physics of the STCAD are shown to be strongly dependent on the three-dimensional confinement of the mean flow by the boundary layer as well as the pressure ratio across the interaction. Further studies explore the effects that the side wall boundary layers and variations in the Reynolds number have on the properties of the interaction. An investigation into the potential applicability of a reduced-order model to predict the general trends exhibited by the three-dimensional STCAD is also conducted.

Keywords: Aeronautics and Astronautics.
Advisor: Lele Sanjiva K. (Sanjiva Keshava)
Alonso Juan José
MacCormack R. W. (Robert William)
Numerical optimization and modeling techniques for power system operations and planning [electronic resource]

In modern societies, electricity is ubiquitous and its availability and reliability are often taken for granted. However, the reality is that these properties rely on the proper operation of one of man's most complex creations: electric power grids. These systems transport electric energy across wide geographical regions from places where it is produced to places where it is consumed. They do so in many cases with virtually no storage. To ensure an efficient and reliable operation of these complex machines, numerical optimization algorithms are applied at almost every level of the operations and planning spectrum. For example, they are used for planning network expansions, scheduling generators, adjusting control devices, determining system state, computing security margins, and for many other crucial tasks. However, many of the algorithms currently used by system operators and planners are based on heuristics and have severe limitations. For example, common power flow algorithms, which are used for scenario analysis, typically fail to provide useful system information in the absence of accurate estimates of system state. Optimal power flow algorithms, which are used for planning system adjustments, typically use inadequate techniques for handling discrete variables and identifying key control actions. Security assessment algorithms typically require expensive system simulations that prevent frequent security analyses. These deficiencies may compromise system performance as grids become more complex, variable and unpredictable, and are operated closer to their limits. In this work, modeling and numerical optimization techniques are explored for overcoming many of the limitations associated with the algorithms used for scenario analysis, planning and control, and online security assessment. The proposed techniques have been tested on mid to large-scale real power networks obtained from South American, North American, and European electric institutions. The results demonstrate the potential benefits of the proposed techniques for improving the tools used by operators and planners for maintaining system reliability and efficiency.

Keywords: Electrical Engineering.
Advisor: Murray Walter primary advisor. Thesis advisor
Entriken Robert advisor. Thesis advisor
Glynn Peter W. advisor. Thesis advisor
Rajagopal Ram advisor. Thesis advisor