VictorJuiz/thesis huggingface dataset:
Modeling 3D Laplace-Fourier domain acoustic wave equation with free-surface topography using finite-difference

We develop embedded boundary methods to handle arbitrarily shaped topography to ac- curately simulate acoustic seismic wave propagation in Laplace-Fourier (LF) domain. The purpose is to use this method to enhance accurate wave simulation near the surface. Unlike most existing methods such as the ones using curvilinear grids to fit irregular surface topography, we use regular Cartesian grid system without suffering from staircasing error, which occurs in the conventional implementations. In this improved embedded-boundary method, we account for an arbitrarily curved surface by imposing ghost nodes above the surface and approximating their acoustic pressures using linear extrapolation, quadratic interpolation, or cubic interpolation. Implementing this method instead of using curvilinear grids near the boundaries greatly reduces the complexity of preprocessing procedures and the computational cost. Furthermore, using numerical examples, we show the accuracy gain and performance of our embedded-boundary methods in comparison with conventional finite-difference (FD) implementation of the problem./nIn realistic 3D geological settings underlying topography surfaces with a large velocity contrast between shallow and deep regions, simulation of acoustic wave propagation in LF domain using a spatially uniform grid can be computationally demanding, due to over-discretization of the high-velocity material. We introduce a discontinuous mesh (DM) method that exchanges information between regions, discretized with different grid spacings, to improve efficiency and convergence. We present a 3D second- and fourth-order velocity- pressure staggered-grid FD DM acoustic wave propagation method in LF domain for acoustic wave estimation using any spatial discretization ratio between meshes. We evaluate direct and iterative parallel solvers for computational speed, memory requirements and convergence. Benchmarks in realistic 3D models with extreme and realistic topography examples show more efficient and stable results for DM with direct solvers relative to uniform mesh with iterative solvers.

Advisor: Rector, James
Computational Methods and Epidemiologic Approaches for Revealing the Etiology of Autoimmune Diseases

Autoimmune diseases, in which normal tissues are inappropriately attacked by the immune system, are complex diseases driven by a combination of genetic and environmental factors. Most are chronic inflammatory diseases with some treatments available but no known cures, and the disease mechanisms are not completely understood. Epigenetic factors, such as DNA methylation and microRNAs, are affected by genetic and environmental exposures and in turn affect gene expression and thus may play a role in autoimmune disease pathogenesis. In this dissertation, I employ a combination of computational, bioinformatic, statistical, and epidemiologic methods to study the role of epigenetics in autoimmune diseases in humans, and to characterize inflammatory changes in human cell lines./nChapter one introduces some complexities of studying autoimmune diseases in humans and introduces concepts of epigenetics. Chapter two shows that naïve T cells from rheumatoid arthritis patients share DNA methylation sites with fibroblast-like synoviocytes, cells that line joints and are involved in joint inflammation. Chapter three shows that there are differences in DNA methylation in CD4+ and CD8+ T cells from multiple sclerosis patients compared to cells from healthy controls. Chapter four uses genome-wide association study results to implicate specific microRNAs and tissues in pediatric-onset multiple sclerosis. Chapter five shows that the inflammatory cytokine tumor necrosis factor alpha drives DNA methylation and transcriptional changes and activates autoimmune disease genes in endothelial cells. Chapter six is a summary of conclusions and key findings.

Advisor: Barcellos, Lisa F
Multimodal Assessment of Structure and Function in Inherited Retinal Degenerations

Inherited retinal degenerations (IRDs) affect approximately 1:4,000 people worldwide and are currently the leading cause of vision loss of people between the ages of 15-45. The mechanisms of degeneration in many IRDs remain unclear. It is vital to establish relationships between retinal structural and functional measures in order to better understand the relationship between the genetic mutations and the phenotypes they cause in these diseases. For example, retinitis pigmentosa (RP), the most prevalent IRD, and choroideremia (CHM), an X-linked degeneration that affects choroidal, RPE and photoreceptor cells, both progress over time due to rod, then cone, photoreceptor loss. Greater understanding of disease progression may clarify the underlying mechanisms of retinal degenerations. Furthermore, the development of novel outcome measures could accelerate clinical trials of treatments designed to treat these relentless, sight-threatening diseases. The experiments and research described in this document use multimodal state-of-the-art, novel, high-resolution techniques in addition to standard technologies used in the clinical setting to study the relationship between structure and function of the retina including rod and cone photoreceptors, retinal pigment epithelium, choriocapillaris and other retinal layers affected in the eyes of patients with retinal degeneration.

Advisor: Roorda, Austin
Towards Grid-independent Dynamics in High-resolution Numerical Weather Prediction Models

Since the beginning of numerical weather prediction (NWP), which was performed on O(700 km) grids, advances in computing technology have driven corresponding advances in model resolution. In recent years, operational NWP efforts have reached O(1 km) horizontal resolutions, leading to the use of large-eddy simulation (LES) to simulate the atmospheric boundary layer (ABL). However, the available turbulence closure models for atmospheric LES were designed to model the smallest scales of atmospheric turbulence, leaving operational forecasters and researches in many diverse fields alike without a turbulence model fit for the computing power available to them. This range of resolutions is known as the "gray zone" or "terra incognita" in the atmospheric turbulence literature, and will be the focus of much discussion in this dissertation. Further, the results will be presented in a way that is visual and digestible to a user of LES whose expertise is not necessarily in theoretical turbulence./nHere, the Weather Research and Forecasting (WRF) model is used to give a thorough and visual demonstration of the inadequacies of the more popular LES turbulence closure models, the Smagorinsky-Lilly and TKE-1.5 models, at gray-zone resolutions, and an explanation of the behavior is offered. Two alternatives, both with multiple flavors, the dynamic reconstruction model (DRM) and an alternative-anisotropic formulation of the classical eddy-viscosity models, are presented as potential remedies to the gray-zone issue. Studies are conducted first for an idealized free-convection case with constant surface heat flux and zero mean wind. A more realistic initial profile with an initial wind and geostrophic forcing is then considered. Finally, three more cases are considered with various surface heat flux values and initial wind profiles./nBoth the DRM and alternative-anisotropic eddy-viscosity models are able to deliver much more consistent results at coarse resolutions when considering planar-averaged profiles of potential temperature and velocity, resolved velocity fields and resolved turbulent kinetic energy, and their performance inspires interesting topics of future work regarding the representation of scales of energy in the atmosphere. The implementation of the anisotropic eddy-viscosity model in general, as well as the anisotropic Smagorinsky-Lilly model specifically, in the WRF model is also considered, resulting in a change in the WRF turbulent diffusion routines and a demonstration of improvement seen at coarse resolutions by reformulating the anisotropic Smagorinsky-Lilly model to partition stress terms into horizontal and vertical components. An additional chapter presents the gray zone problem as it relates to complex terrain.

Advisor: Chow, Fotini K
Holography beyond AdS/CFT

Physicists have long sought to fully understand how gravity can be fully formulated within a quantum mechanical framework. A promising avenue of research in this direction was born from the idea of holography - that gravitational physics can be recast as a different theory living in fewer dimensions. Evidence of this phenomena was first observed in the arena of black hole physics, where the entropy of a black hole was calculated to scale with its area, not its volume. The advent of the Anti-de Sitter/Conformal Field Theory (AdS/CFT) correspondence provided an explicit realization of holography for gravitational theories in AdS space. This brought a flurry of activity dedicated to dissecting this correspondence. Ultimately, however, it will be necessary to move beyond the confines of AdS/CFT in order to understand our universe, as we live in a de Sitter type universe. The research presented in this dissertation attempts to broaden the scope of holgraphic theories to include more phenomenologically relevant universes. To do so, we utilize a top-down approach and take results from AdS/CFT that appear to be general holographic results and see how they can be applied in spacetimes other than AdS. In particular, we take the Ryu-Takayanagi (RT) formula, along with its related results, and investigate what we can learn by applying it to general spacetimes. Doing so naturally forces us to utilize holographic screens, as these are the largest such surfaces where the RT formula can be self-consistently applied. This approach allows us to examine properties of the purported boundary theory for general spacetimes, including the entanglement structure and propagation speeds of excitations dual to bulk excitations. This is done in chapters 2 and 3. In chapters 4 and 5, we use this lens of generalized holography to elucidate the nature of the relationship between entanglement and emergent geometry. Finally, in chapter 6, we revisit one the important underlying assumption that the RT formula is general and demonstrate the validity of this assumption.

Advisor: Nomura, Yasunori
Mothers’ Perceptions of Stress, Parenting Self-Efficacy, and Permissive and Inconsistent Discipline: Insights from China, Japan, and the United States

Decades of parenting research has shown that heightened stress may interrupt the parenting process and negatively affect the child and the family. However, most existing studies have primarily focused on how stress can undermine parenting, and relatively few have attended to the role of cognitive appraisal in shaping the interpretation and ultimate effects of stressful conditions on parenting behavior. Following theoretical recommendations associated with social cognitive theory as well as transactional theory of stress and coping, the current study examined the association of psychological stress to mothers’ use of inconsistent and permissive discipline, focusing particularly on the mediating role of parenting self-efficacy (PSE) in the link between perceived stress and parental discipline. Separate path analyses were conducted with survey data collected from a total of 540 mothers of young children in China (n = 113), Japan (n = 262) and the United States (n = 165). Results indicated significant associations among mothers’ perceived stress, PSE, as well as permissive and inconsistent discipline in all three samples, with exceptions in the Chinese sample. Furthermore, path models supported the mediating effect of PSE in the link between mothers perceived stress and the inconsistent parenting in all three samples. In the US and Japanese samples, PSE also mediated the relationship between stress and permissiveness. Overall, these findings suggest the important role of PSE in parents’ stress and coping processes across diverse contexts as well but also underscore the importance of examining relevant sociocultural factors that might also contribute to the salience and strength of certain associations.

Advisor: Holloway, Susan D
Low Regularity Solutions for Gravity Water Waves

The gravity water waves equations are a system of partial differential equations which govern the evolution of the interface between a vacuum and an incompressible, irrotational fluid in the presence of gravity. In the case of two dimensions, these equations model non-breaking waves at the surface of a body of water, such as a lake or ocean, while in one dimension, they model non-breaking waves propagating in a channel./nWe are concerned with the well-posedness of the Cauchy problem for the gravity water waves equations: We seek to show that given an initial configuration of the vacuum-fluid interface and an initial fluid velocity field beneath the interface, there is a unique solution to the gravity water waves equations which matches the given initial data. In particular, we are concerned with the situation where the initial data has low regularity, corresponding to surface waves which are not necessarily smooth./nThe classical regularity threshold for the well-posedness of the water waves system requires initial velocity field in $H^s$, with $s > \frac{d}{2} + 1$, and can be obtained by proving standard energy conservation estimates. On the other hand, it has been shown that for dispersive equations (equations describing phenomena which disperse waves of different frequencies), one can lower well-posedness regularity thresholds below that which is attainable by energy conservation alone. This was first realized for the nonlinear wave equation via dispersive estimates known as Strichartz estimates, and was first applied toward the well-posedness of gravity water waves by Alazard-Burq-Zuily./nHowever, this approach was implemented as a partial result, using Strichartz estimates with loss relative to what one expects based on the corresponding linearized model problem. In this dissertation, we prove well-posedness with initial velocity field in $H^s$, $s > \frac{d}{2} + 1 - \mu$, where $\mu = \frac{1}{10}$ in the case $d = 1$ and $\mu = \frac{1}{5}$ in the case $d \geq 2$, extending the previous result of Alazard-Burq-Zuily. In the case of one dimension, using a further refined argument, we establish the well-posedness for $s > \half + 1 - \frac{1}{8}$, corresponding to proving lossless Strichartz estimates. This provides the sharp regularity threshold with respect to the approach of combining Strichartz estimates with energy estimates.

Advisor: Tataru, Daniel
The Trilingual Ideal in Quintana Roo, Mexico: The Metapragmatics and Embodiments of Yucatec Maya, Spanish, and English

In Quintana Roo, Mexico, discourses of cultural loss, linguistic revitalization, and economic opportunity exist within the context of the neoliberal tourism industry, an economic force which necessitates specific engagements with national and transnational systems of capital and governance. This region, the ‘Zona Maya’, is also powerfully shaped by historical narratives and acts of resistance and negotiation with colonial, assimilating forces. I argue that within this complex contemporary social world, trilingualism in Yucatec Maya, Spanish, and English has emerged as an educational and social ideal, which speaks to the political economic and social situation at hand through an embodiment of three distinct voices. Differently mediatized communicative practices, in particular the use of social media, among young people who come from communities of Maya speakers (though they may not consider themselves to be ‘speakers’ per se) serve to produce new political-linguistic subjectivities, intersubjectivities, and collectivities. I demonstrate that these social formations embody the seemingly distinct, if not contrary, projects of Maya language revitalization and English language promotion and teaching. Meanwhile, communicative privilege emerges as an effect of efforts to standardize and evaluate each language; this privilege marginalizes people who use language in a non-standard way, and such usages can also be targeted as illegitimate by Maya or English language education. Finally, I argue that those who embody the trilingual ideal use the voices and mediatized modalities at hand to contest neoliberal educational and political-economic paradigms and fight for new forms of emplaced and cosmopolitan belonging and participation.

Advisor: Briggs, Charles
Hanks, William
Manipulating 1D Conduction Channels; from Molecular Geometry to 2D Topology

This dissertation is divided into two segments, both of which focus on creating and manipulating one-dimensional (1D) conduction channels in novel 1D and two-dimensional (2D) systems, characterized by scanning tunneling microscopy (STM)./nThe first half describes how the electronic properties of quasi-1D graphene nanoribbons (GNRs) are manipulated by controlling their width and edge geometry at the atomic scale. A bottom-up approach is used for fabricating three different armchair GNR (AGNR) systems, allowing the geometry and hence the electronic properties of resultant AGNRs to be controlled. Successful molecular bandgap engineering in 1D AGNR heterojunctions is described, as well as the electronic and topographic characterization of the concentration dependence of boron-doped AGNRs. The discovery of two new in-gap dopant states with different symmetry is described. The successful fabrication and characterization of S-AGNRs having sulfur atoms substitutionally doped at the AGNR edges is also described. Our results indicate that S-doping induces a rigid shift of the energies for both the valence and conduction bands./nThe second half of this thesis describes how the 1T’ phase of monolayer transition metal dichalcogenides (TMDs) can be used as a platform to create 2D topological insulators (TIs). These novel TI systems are characterized in great detail. The successful growth and characterization of single-layer 1T’–WTe2 is described. This material is shown to host a bulk bandgap and helical edge states at the 1T’–vacuum interface. The growth and characterization of mixed phase-WSe2 is described. New techniques for creation and manipulation of edge conduction channels at interfaces between materials of different topologies are described.

Advisor: Crommie, Michael F.
Computational Investigations of Coordination Bonding and Adsorbate Properties in Metal-Organic Frameworks

In this thesis, I have used computational methods to the study of flexibility in metal-organic frameworks (MOFs) and the behavior of adsorbed gases and liquids in MOFs. Among nanoporous materials, MOFs are of particular interest for adsorption-based applications for reasons that include (1) their huge chemical space, which raises the possibility of tuning them for specific industrial processes and (2) the ability of the under-coordinated metals present in some MOFs to endow their respective materials with impressive adsorbate binding energies./nChapters 2 and 4 relate to analogs of a series of MOFs with under-coordinated metals (the M-MOF-74 series). In Chapter 2, I report the discovery of a novel argon adsorbate-induced deformation pattern for this framework series. This result was arrived at using a flexible framework model, and is presented as an explanation for an intriguing signal observed in experimental small-angle X-ray scattering profiles upon argon adsorption. This hypothesis is supported by a complementary investigation of an alternative explanation for the X-ray signal, in which argon atoms are proposed to adsorb at different densities in adjacent pores./nIn Chapter 3, I studied the dynamics of adsorbed xylene isomers in MOF-5. I compare the translational and rotational motion of the xylene isomers, and explain the differences based on molecular geometries. The most rod-like molecule, para-xylene, is more rotationally constricted in the pore due to its intermolecular interactions with the aromatic group of the MOF linker. This finding has implications for the rational design of MOFs, as a process that can take advantage of the MOF-induced variations in xylene isomer dynamics could be used for lucrative liquid-phase xylene separations./nIn Chapter 4, I present a method for parameterizing the type of flexible framework model used in Chapter 2 from ab initio quantum chemistry calculations. The goal of this work is to facilitate the rapid development of flexible, versatile MOF models that can capture changes in the coordination bonding of metals in MOFs. This type of model can be used to study structural transitions and may be extended to study MOF formation. We demonstrated that our approach yields models for the M-MOF-74 series that are stable and have simulated structural properties in good agreement with quantum chemistry calculations.

Advisor: Smit, Berend
Unraveling the structure-property relationships in perovskite oxides

This dissertation focuses on the manipulation of the lattice degree of freedom in perovskite oxide thin films, and explores the fundamental structure-property relationships. Epitaxial thin-film engineering and state-of-the-art thin-film characterization techniques are employed to achieve an effective and quantifiable control over a number of structural features including lattice expansion/compression, lattice tilting, octahedral rotations, and surface structures. Henceforth, the detailed correlation between structural features and/ncorresponding physical properties are established and exemplified in several model perovskite systems. The key findings in this work include that, first, the interfacial structural coupling effect is explored and demonstrated in SrRuO3 thin films where the lattice symmetry,/nmagnetic anisotropy, and electrical transport can be readily controlled. Moreover, growth-mediated antisite defects are found to be responsible in determining the energy competition between the low-symmetry antiferroelectric and the high-symmetry ferroelectric phases in PbZrO3 thin films, and the metastable ferroelectric phase can be stabilized. In addition, detailed relationships between ionic charge transport and lattice structure is explored in LSGM, and in turn, an optimal design of perovskite structure for high ionic conduction is successfully demonstrated through epitaxial strain and interfacial engineering. And lastly, surface engineering via growth-orientation control is explored in LSCF to establish the correlation between surface structure and electrochemical activities.

Advisor: Martin, Lane