Physical Sciences and Mathematics Commons^™

Modeling The Bioactivation And Subsequent Reactivity Of Drugs, Tyler Brian Hughes

Arts & Sciences Electronic Theses and Dissertations

Metabolism can convert drugs to harmful reactive metabolites that conjugate to DNA and off-target proteins. Reactive metabolites are a significant driver of both drug candidate attrition and withdrawal from the market of already approved drugs. Unfortunately, reactive metabolites are difficult to study in vivo, because they are transitory and generally do not circulate. Instead, this work computationally models both metabolism and reactivity. Using deep learning, predictive models were developed for the metabolic formation of quinones and epoxides, which together account for about half of known reactive metabolites. Additionally, an accurate model of DNA and protein reactivity was constructed, which predicts …

Grammar And Variation: Understanding How Cis-Regulatory Information Is Encoded In Mammalian Genomes, Dana Michele King

Arts & Sciences Electronic Theses and Dissertations

Understanding how genotype leads to phenotype is key to understand both the development and dysfunction of complex organisms. In the context of regulating the gene expression patterns that contribute to cell identity and function, the goal of my thesis research is to how changes in genome sequence may impact impact gene expression by determining how sequence features contribute to regulatory potential. To accomplish this goal, I first leveraged the key regulatory role of pluripotency transcription factors (TFs) in mouse embryonic stem cells (mESCs) and tested synthetically generated and genomic identified combinations of binding site for four TFs, OCT4, SOX2, KLF4, …

Radiolabeled Nanohydroxyapatite As A Platform For The Development Of New Pet Imaging Agents, Stacy Lee Queern

Arts & Sciences Electronic Theses and Dissertations

Positron emission tomography (PET) imaging utilizes drugs labeled with positron emitters to target and evaluate different biological processes occurring in the body. Tailoring medicine to the individual allows for higher quality of care with better diagnosis and treatment and is a key purpose for advancing research into developing new platforms for PET imaging agents. A PET nuclide of high interest for the development of these agents is 89Zr. This can be attributed to the long half-life of 3.27 days and low positron energy of 89Zr.

In this work, we developed a production method for 89Zr using Y sputtered coins that …

Fast Objective Coupled Planar Illumination Microscopy, Cody Jonathan Greer

Arts & Sciences Electronic Theses and Dissertations

Among optical imaging techniques light sheet fluorescence microscopy stands out as one of the most attractive for capturing high-speed biological dynamics unfolding in three dimensions. The technique is potentially millions of times faster than point-scanning techniques such as two-photon microscopy. This potential is especially poignant for neuroscience applications due to the fact that interactions between neurons transpire over mere milliseconds within tissue volumes spanning hundreds of cubic microns. However current-generation light sheet microscopes are limited by volume scanning rate and/or camera frame rate. We begin by reviewing the optical principles underlying light sheet fluorescence microscopy and the origin of these …

Tunable Electronic And Optical Properties Of Low-Dimensional Materials, Shiyuan Gao

Arts & Sciences Electronic Theses and Dissertations

Two-dimensional (2D) materials with single or a few atomic layers, such as graphene, hexagonal boron nitride (h-BN) and transition metal dichalcogenides (TMDCs), and the heterostructures or one-dimensional (1D) nanostructures they form, have attracted much attention recently as unique platforms for studying many condensed-matter phenomena and holds great potentials for nanoelectronics and optoelectronic applications. Apart from their unique intrinsic properties which has been intensively studied for over a decade by now, they also allow external control of many degrees of freedom, such as electrical gating, doping and layer stacking. In this thesis, I present a theoretical study of the electronic and …

Photophysical Characterization And Wavelength Tuning Of Natural And Synthetic Oxobacteriochlorins And Biohybrids, Don Hood

Arts & Sciences Electronic Theses and Dissertations

ABSTRACT OF THE DISSERTATION

Photophysical Characterization and Wavelength Tuning of Natural and Synthetic Oxobacteriochlorins and Biohybrids

By

Donald L. Hood

Doctor of Philosophy in Chemistry

Washington University in St. Louis, 2018

Dr. Dewey Holten, Chairperson

Herein is discussed the theoretical and practical unpinnings of photophysical behaviors and kinetic constants for tetrapyrrole macrocycles, to wit, porphyrins, chlorins, and bacteriochlorins. Understanding the characteristic photophysical response of tetrapyrroles to changes in environment or substituents is important to designing synthetic chromophores with tunable absorption wavelengths and for preparing useful biohybrids of natural photosynthetic light antennas combined with unnatural chromophores attached to the light antenna …

Anodic Cyclization Reaction: Manipulation Of Reaction Pathway And Efforts To Radical Cation And Radical Intermediate, Ruozhu Feng

Arts & Sciences Electronic Theses and Dissertations

In recent years, synthetic chemists have been expressing significant interest in electro-organic synthetic methods. This interest is being fueled by the existence of an increasing number of successful methods in the literature and the availability of new electrochemical equipment that removes the barrier to attempting an electrolysis reaction for the first time. Yet while these developments have fueled growth in some areas of electro-organic synthesis (the recycling of chemical catalysts for example), other areas remain underdeveloped. One such area is the exploration of reactions that can be triggered directly as an electrode surface without the use of any chemical reagent. …

Linking Structure And Dynamics In Metallic Liquids: A Combined Experimental And Molecular Dynamics Approach, Robert Ashcraft

Arts & Sciences Electronic Theses and Dissertations

A major outstanding problem in condensed matter physics is the nature of the glass transition, in which a rapidly cooled liquid can bypass the transition into a crystalline state and the liquid structure is "frozen-in" due to kinetic arrest. To characterize the fundamental features behind this transition the liquid, both in the high temperature (equilibrium) and supercooled state, needs to be better understood. By examining the relationship between structure and dynamics a better characterization of the liquid state and a determination of the mechanisms that are ultimately important for the formation of the glass can be gained. In this dissertation, …

Synthesis And Integration Of Oligoviologens Into Hydrogel Actuators, Kevin Liles

Arts & Sciences Electronic Theses and Dissertations

Interest in the development of soft-material artificial molecular muscles has inspired scientists to pursue novel stimuli-responsive systems capable of undergoing change in the physical and mechanical properties of a material in response to external stimuli. This interest has been driven primarily by advances, or the desire for advances, in fields such as soft robotics, microfluidics, and bio-compatible drug-delivery systems. In this work, redox-responsive viologens and their ability to form stable radical-cation complexes were evaluated as a method of actuation in stimuli-responsive materials, specifically hydrogels.

First, a brief overview of hydrogel actuators is covered, with some examples given of the broad …

Different Estimation Methods For The Basic Independent Component Analysis Model, Zhenyi An

Arts & Sciences Electronic Theses and Dissertations

Inspired by classic cocktail-party problem, the basic Independent Component Analysis (ICA) model is created. What differs Independent Component Analysis (ICA) from other kinds of analysis is the intrinsic non-Gaussian assumption of the data. Several approaches are proposed based on maximizing the non-Gaussianity of the data, which is measured by kurtosis, mutual information, and others. With each estimation, we need to optimize the functions of expectations of non-quadratic functions since it can help us to access the higher-order statistics of non-Gaussian part of the data. In this thesis, our goal is to review the one of the most efficient estimation methods, …

Preventing Extinction Of At-Risk Plant Species In A Complex World, Holly Lee Bernardo

Arts & Sciences Electronic Theses and Dissertations

Earthճ current biodiversity crisis is now considered a true mass extinction event, with species level extinction rates well above background rates and population level extinction rates orders of magnitude more common that species extinctions. There are many threats driving this loss of biodiversity. How each threat impacts the viability of a species is highly context dependent, but all are anthropogenic in origin and so as the human population continues to increase, so too will the pressure of these threats on our natural systems. Ultimately, how much a threat decreases the viability of a species depends on how that threat influences …

Building On Nature: Spectroscopic Studies Of Photosynthesis-Inspired Pigments, Fused Light Harvesting Proteins, And Bacterial Reaction Center Mutants, Kaitlyn Faries

Arts & Sciences Electronic Theses and Dissertations

Photosynthesis is the dominant form of solar energy conversion on the planet, making it critical to understand the fundamentals of the process in order to effectively mimic and improve upon it for human energy needs. The initial stages of photosynthesis include light harvesting and chemical conversion of that harvested energy via electron transport, with both of these stages relying on pigments (or chromophores) such as chlorophyll and specific protein architectures for the processes. In this work, the fundamental underpinnings of photosynthetic light harvesting and electron transport are explored via spectroscopy of various photosynthetic systems with altered natural pigments and proteins. …

An Nmr Study Of Co2 Dynamics And Structural Characterization Of Porous Materials, Robert M. Marti

Arts & Sciences Electronic Theses and Dissertations

Nuclear magnetic resonance (NMR) has proven to be a versatile and powerful analytical tool to study many areas of interest to the scientific community, such as molecular dynamics and structural characterization. In this dissertation, NMR was used as a probe for CO2 dynamics in metal-organic frameworks. Variable temperature (VT) NMR was used to determine molecular dynamics of CO2, going as low as 8 K. In the fast motion regime, where the CO2 hopping rate is fast compared to the NMR experiment time, 13CO2 inside of Mg-MOF-74 still exhibits a chemical shift anisotropy (CSA) powder pattern. However, there is a certain …

Fundamental Controls On The Reactivity Of Aluminum Oxide And Hydroxide Surfaces: Contributions Of Surface Site Coordination States And Interfacial Water Structure, Tingying Xu

Arts & Sciences Electronic Theses and Dissertations

Chemical reactions at mineral-water interfaces are of great importance in many geological and environmental processes. Essential to many of these is adsorption because it directly controls contaminant fate and nutrient availability, promotes the nucleation and growth of minerals, initiates surface redox reactions, and plays a crucial role in carbon cycling and sequestration. These reactions occur at mineral surface sites having multiple possible coordination states that interact with both adsorbates and water. While general ion adsorption mechanisms and surface charging behaviors are well established, the roles of individual surface functional group types and water in affecting the structure and reactivity of …

Spin Alignment Generated In Inelastic Nuclear Reactions, Daniel Hoff

Arts & Sciences Electronic Theses and Dissertations

The spin alignment of inelastically excited 7Li projectiles, when the target remains in its ground state, was determined through angular-correlation measurements between the breakup fragments of 7Li_ (_ + t). It was found that 7Li_ is largely aligned along the beam axis (longitudinal) in this type of inelastic reaction, regardless of the target. This longitudinal alignment is well described by DWBA calculations, which can be explained by an angular-momentum-excitation-energy mismatch condition. These calculations also explain the longitudinal spin alignment of excited nuclei in several other systems, showing the phenomenon is more general. The experiment involving 7Li was performed at the …

Polarizable Force Field Development, And Applications To Conformational Sampling And Free Energy Calculation, Zhi Wang

Arts & Sciences Electronic Theses and Dissertations

The parameters of monovalent ions for the AMOEBA force field were revised. High level quantum mechanics results, relative solvation free energies of monovalent ions, lattice energies and lattice constants of salt crystals were used to calibrate the parameters. The revised parameters were validated against the quantum optimized structures and energies of ion-water dimers and ion-water clusters, and against thermodynamic properties of salt solutions at different concentrations measured in experiments, e.g. mean ionic activity coefficients, self-diffusion coefficients of water. In the simulations the sodium ion is found to qualitatively differ from larger cations in aqueous solution. Direct ionic interactions are predominant …

Simulation Of Black Hole Inner Accretion Disk-Corona And Optimization Of The Hard X-Ray Polarimeter, X-Calibur, Banafsheh Beheshtipour

Arts & Sciences Electronic Theses and Dissertations

Mass accreting stellar mass and supermassive black holes are strong sources of X-rays. The X- ray observations enable studies of the process of black hole accretion and give us information about the spacetime background. In the framework of my thesis work, I have continued the development of a general-relativistic ray-tracing code enabling the simulation of the Comptonization of photons in the hot accretion disk corona. I use the code to investigate the impact of various approximation schemes for modeling the Comptonization finding that a fully relativistic treatment is needed for accurate predictions in the soft and hard X- ray regimes …

Topics In Pt-Symmetric Quantum Mechanics And Classical Systems, Nima Hassanpour

Arts & Sciences Electronic Theses and Dissertations

Space-time reflection symmetry, or PT symmetry, first proposed in quantum mechanics by Bender and Boettcher in 1998 [2], has become an active research area in fundamental physics. This dissertation contains several research problems which are more or less related to this field of study. After an introduction on complementary topics for the main projects in Chap.1, we discuss about an idea which is originated from the remarkable paper by Chandrasekar et al in Chap.2. They showed that the (second-order constant-coefficient) classical equation of motion for a damped harmonic oscillator can be derived from a Hamiltonian having one degree of freedom. …

Index Theory For Invariant Elliptic Operators On Manifolds With Proper Cocompact Group Actions, Gong Cheng

Arts & Sciences Electronic Theses and Dissertations

In this thesis, we study G-invariant elliptic operators, and in particular Dirac operators, on the space of invariant sections of a Hermitian bundle over a (non-compact) manifold with a proper and cocompact Lie group action. We provide a canonical way to define the Hilbert space of invariant sections for proper and cocompact actions and prove that the G-invariant Dirac operators, and more generally, elliptic operators, are Fredholm for the Hilbert space we constructed. Using the framework developed in this thesis, we give a new proof of a generalized Lichnerowicz Vanishing Theorem for proper cocompact group actions as an application.

Spectral And Stratigraphic Mapping Of Layered Sulfate Deposits On Mars Using Advanced Crism Data Processing Techniques, Kathryn Elizabeth Powell

Arts & Sciences Electronic Theses and Dissertations

We apply orbital remote sensing of Mars to analyze the mineralogy and geologic setting of two areas near rover landing sites. We use the Compact Reconnaissance Orbiter for Mars (CRISM) observations, modeled to single scattering albedo, to identify and map hydrated sulfates in layered sedimentary sequences in these two locations. In Meridiani Planum, the Opportunity rover has characterized a ~10 m section of sulfate-bearing deposits known as the Burns formation. At our study area in ~20 km to the south at Iazu Crater, we found that the crater walls have strong spectral signatures of polyhydrated sulfate, strongly correlated with a …

Instrumentation For Cryogenic Dynamic Nuclear Polarization And Electron Decoupling In Rotating Solids, Faith Joellen Scott

Arts & Sciences Electronic Theses and Dissertations

Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) using the higher polarization of electron radical spins compared to nuclear spins. The addition of electron radicals for DNP to the sample can cause hyperfine broadening, which decreases the resolution of the NMR resonances due to hyperfine interactions between electron and nuclear spins. Electron decoupling has been shown to attenuate the effects of hyperfine coupling in rotating solids. Magic angle spinning (MAS) DNP with electron decoupling requires a high electron Rabi frequency provided by a high-power microwave source such as a frequency-agile gyrotron. This dissertation describes the development …

Dualities, Topological Properties, And Degeneracies Of Classical And Quantum Lattice Models, Seyyed Mohammad Sadegh Vaezi

Arts & Sciences Electronic Theses and Dissertations

We study various nontrivial facets of Ҥegeneracyӭ a concept of paramount importance in numerous physical systems.

In the first part of this thesis, we challenge the folklore that if the ground state degeneracy of a physical system depends on topology then this system must necessarily realize an unconventional, so-called Ҵopological quantumӬ order. To this end, we introduce a classical rendition of the Toric Code model that displays such a topological degeneracy yet exhibits conventional Landau order. As the ground states of this classical system may be distinguished by local measurements, this example illustrates that, on its own, topological degeneracy is …

Seismic Structure Near The Mariana Trench And Deep Earthquake Triggering In The Tonga Flat Slab, Chen Cai

Arts & Sciences Electronic Theses and Dissertations

This dissertation utilizes multiple techniques of earthquake location and seismic tomography to investigate deep seismicity in the Tonga flat slab region and the upper mantle structure of the Mariana subduction zone. I study the rupture property and aftershock distributions of the largest earthquake ever recorded in the Tonga flat slab region, defined by scattered seismicity and velocity anomalies. These, along with background seismicity, regional 3-D seismic velocity model and tectonic reconstructions of relict Vitiaz subduction zone, suggest the earthquakes are occurring in the final portion of the slab subducted at the now inactive Vitiaz trench. The associated Coulomb stress change …

Generalized Non-Inferential Approach To Modeling Restricted Discrete Choice For The Case Of The Spatial Random Utility, Elena Labzina

Arts & Sciences Electronic Theses and Dissertations

Multinomial logistic regression model (MNL) is a powerful and easily tractable way for measuring the probabilistic impact of input variables on individual categorical choices. Crucially, the standard MNL assumes that all subjects of the study have the same choice sets. In the meanwhile, especially in political science and economics, this condition is frequently violated. Probably, the most graphical example of varying choice sets (VCS) is partially contested elections. Furthermore, the MNL implicitly implies the Independence of the Irregular Alternatives (IIA) assumption by requiring i.i.d errors that contrasts the MNL and the multinomial probit (MNP) and mixed logit (MXL) models. In …

Algorithmic Trading With Prior Information, Xinyi Cai

Arts & Sciences Electronic Theses and Dissertations

Traders utilize strategies by using a mix of market and limit orders to generate profits. There are different types of traders in the market, some have prior information and can learn from changes in prices to tweak her trading strategy continuously(Informed Traders), some have no prior information but can learn(Uninformed Learners), and some have no prior information and cannot learn(Uninformed Traders). In this thesis. Alvaro C, Sebastian J and Damir K \cite{AL} proposed a model for algorithmic traders to access the impact of dynamic learning in profit and loss in 2014. The traders can employ the model to decide which …

Variable Selection Via Lasso With High-Dimensional Proteomic Data, Hongxuan Zhai

Arts & Sciences Electronic Theses and Dissertations

Multiclass classification with high-dimensional data is an applied topic both in statistics and machine learning. The classification procedure could be done in various ways. In this thesis, we review the theory of the Lasso procedure which provides a parameter estimator while simultaneously achieving dimension reduction due to a property of the L1 norm. Lasso with elastic net penalty and sparse group lasso are also reviewed. Our data is high-dimensional proteomic data (iTRAQ ratios) of breast cancer patients with four subtypes of breast cancer. We use the multinomial logistic regression to train our classifier and use the false classification rates obtained …

Deep Learning Analysis Of Limit Order Book, Xin Xu

Arts & Sciences Electronic Theses and Dissertations

In this paper, we build a deep neural network for modeling spatial structure in limit order book and make prediction for future best ask or best bid price based on ideas of (Sirignano 2016). We propose an intuitive data processing method to approximate the data is non-available for us based only on level I data that is more widely available. The model is based on the idea that there is local dependence for best ask or best bid price and sizes of related orders. First we use logistic regression to prove that this approach is reasonable. To show the advantages …

Lattice Scales From Gradient Flow And Chiral Analysis On The Milc Collaboration's Hisq Ensembles, Nathan Joseph Brown

Arts & Sciences Electronic Theses and Dissertations

The interactions of quarks and gluons form most of the visible matter around us. Yet, extracting precise predictions from the field theory describing them, Quantum Chromodynamics (QCD), is notoriously difficult. By simulating the QCD interaction on a Euclidean space time lattice, the field theory can be regularized non-perturbatively and familiar statistical techniques from classical statistical mechanics can be applied. Then, by systematically improving each component of the process, high precision results can be obtained. Some of the possible components to be improved include the discretization of the continuum action, the determination of the lattice scale(s), the generation of gauge field …

Wild Primates In Documentary Films: Biodiversity, Behavior, And Pedagogical Applications, Crystal Marie Riley Koenig

Arts & Sciences Electronic Theses and Dissertations

The representation of wild primates in the nature documentary genre could have important implications for conservation and education. However, no prior research has looked at the content of this genre or its use in education. To fill this gap, the current research included a content analysis of all available documentaries focused on wild primates (n = 210) and a survey of 219 college-level anthropology instructors, with an emphasis on determining how primate biodiversity was portrayed, whether primate behavior was realistically depicted in documentaries, whether mistakes and inaccuracies were common, and how college instructors use primate documentaries as resources in their …

Dying Worlds: Environment, Ecology, And Empire In British Literature 1878-1919, Susanna Williams

Arts & Sciences Electronic Theses and Dissertations

This dissertation argues that models of approaching environmental crisis in late-nineteenth- and early-twentieth-century British literature have been obscured by a false, mid-twentieth century, American-centered genealogy of environmentalism. As Victorian scientists made discoveries about deep time, entropy, and tidal drag, scientific and popular writers in the following decades came to terms with ideas about an earth made unfit for human existence and humans’ imminent extinction. Writers grappled with feelings of loss and grief, and they felt disoriented by time scales and energetic processes that were beyond the scope of a single human life. This overwhelming information required them to take a …