Physical Sciences and Mathematics Commons^™

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, …

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 …

Towards Engineering Advanced Nanomaterials: Elucidating Fundamental Particle Behavior In Water And Critical Sorption Dynamics, Changwoo Kim

McKelvey School of Engineering Theses & Dissertations

As advanced nanomaterials, inorganic-organic nano composites have received great interest as potential platform (nano) structures for sensor, catalyst, sorbent, and environmental applications. Here, my Ph.D. research has focused on the design, synthesis, and characterization of advanced water-stable engineered metal-oxide nanoparticles functionalized by organic frames for environmental applications. For the environmental applications, I have evaluated particleoptimized sorption processes for the remediation and separation of arsenic, chromium, and uranium under environmentally relevant conditions. More specifically, I have explored the critical role of organic coating on sorption mechanisms and performances using engineered iron oxide -based, manganese oxide -based, and manganese ferrite -based (core) …

Kcnq1/Kcne1 Interaction In The Cardiac Iks Channel And Its Physiological Consequences, Jiajing Xu

McKelvey School of Engineering Theses & Dissertations

Dynamic conformational changes of ion channel proteins during activation gating determine their function as carriers of current. The relationship between these molecular movements and channel function over the physiological timescale of the action potential (AP) has not been fully established due to limitations of existing techniques. We constructed a library of possible cardiac IKs protein conformations and applied a combination of protein segmentation and energy linearization to study this relationship computationally. Simulations reproduced the effects of the beta-subunit (KCNE1) on the alpha-subunit (KCNQ1) dynamics and function, observed in experiments. Mechanistically, KCNE1 increased the probability of “visiting” conducting pore conformations on …

Learning About Large Scale Image Search: Lessons From Global Scale Hotel Recognition To Fight Sex Trafficking, Abby Stylianou

McKelvey School of Engineering Theses & Dissertations

Hotel recognition is a sub-domain of scene recognition that involves determining what hotel is seen in a photograph taken in a hotel. The hotel recognition task is a challenging computer vision task due to the properties of hotel rooms, including low visual similarity between rooms in the same hotel and high visual similarity between rooms in different hotels, particularly those from the same chain. Building accurate approaches for hotel recognition is important to investigations of human trafficking. Images of human trafficking victims are often shared by traffickers among criminal networks and posted in online advertisements. These images are often taken …

Mechanisms Of Calcium Phosphate Mineralization On Biological Interfaces And Their Engineering Applications, Doyoon Kim

McKelvey School of Engineering Theses & Dissertations

All living organisms utilize phosphorus (P) as an essential component of their cell membranes, DNA and RNA, and adenosine triphosphate. Bones, in addition to bearing loads, play an important role in balancing P levels in our bodies. In bones, a network of collagen templates and calcium phosphate (CaP) nanocrystals builds hierarchical levels, from nano- to macroscale. Within this architecture, the thermodynamic properties of CaP minerals are influential. Despite the importance of nucleation, growth, and crystallization in collagen structures for tissue development, little kinetic study of these processes has been conducted due to the limited in situ techniques for monitoring these …

Nanopower Analog Frontends For Cyber-Physical Systems, Kenji Aono

McKelvey School of Engineering Theses & Dissertations

In a world that is increasingly dominated by advances made in digital systems, this work will explore the exploiting of naturally occurring physical phenomena to pave the way towards a self-powered sensor for Cyber-Physical Systems (CPS). In general, a sensor frontend can be broken up into a handful of basic stages: transduction, filtering, energy conversion, measurement, and interfacing. One analog artifact that was investigated for filtering was the physical phenomenon of hysteresis induced in current-mode biquads driven near or at their saturation limit. Known as jump resonance, this analog construct facilitates a higher quality factor to be brought about without …

Computational Explorations Of Information And Mechanism Design In Markets, Zhuoshu Li

McKelvey School of Engineering Theses & Dissertations

Markets or platforms assemble multiple selfishly-motivated and strategic agents. The outcomes of such agent interactions depend heavily on the rules, regulations, and norms of the platform, as well as the information available to agents. This thesis investigates the design and analysis of mechanisms and information structures through the ``computational lens'' in both static and dynamic settings. It both addresses the outcome of single platforms and fills a gap in the study of the dynamics of multiple platform interactions.

In static market settings, we are particularly interested in the role of information, because mechanisms are harder to change than the information …

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 …

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 …

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. …

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 …

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 …

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 …

Development And Application Of Hybrid Wray-Agarwal Turbulence Model And Large-Eddy Simulation, Xu Han

McKelvey School of Engineering Theses & Dissertations

Rapid development in computing power in past five decades along with the development and progress in building blocks of Computational Fluid Dynamics (CFD) technology has made CFD an indispensable tool for modern engineering analysis and design of fluid-based products and systems. For CFD analysis, Reynolds-Averaged Navier-Stokes (RANS) equations are currently the most widely used fluid equations in the industry. RANS methods require modeling of turbulence effect (i.e. turbulence modeling) based on empirical relations and therefore often produce low accuracy results for many flows. In recent years, the Large Eddy Simulation (LES) approach has been developed which has shown promise of …

Robust Engineering Of Dynamic Structures In Complex Networks, Walter Botongo Bomela

McKelvey School of Engineering Theses & Dissertations

Populations of nearly identical dynamical systems are ubiquitous in natural and engineered systems, in which each unit plays a crucial role in determining the functioning of the ensemble. Robust and optimal control of such large collections of dynamical units remains a grand challenge, especially, when these units interact and form a complex network. Motivated by compelling practical problems in power systems, neural engineering and quantum control, where individual units often have to work in tandem to achieve a desired dynamic behavior, e.g., maintaining synchronization of generators in a power grid or conveying information in a neuronal network; in this dissertation, …

In Vivo Vascular Imaging With Photoacoustic Microscopy, Hsun-Chia Hsu

McKelvey School of Engineering Theses & Dissertations

Photoacoustic (PA) tomography (PAT) has received extensive attention in the last decade for its capability to provide label-free structural and functional imaging in biological tissue with highly scalable spatial resolution and penetration depth. Compared to modern optical modalities, PAT offers speckle-free images and is more sensitive to optical absorption contrast (with 100% relative sensitivity). By implementing different regimes of optical wavelength, PAT can be used to image diverse light-absorbing biomolecules. For example, hemoglobin is of particular interest in the visible wavelength regime owing to its dominant absorption, and lipids and water are more commonly studied in the near-infrared regime.

In …

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 …

Self-Powered Time-Keeping And Time-Of-Occurrence Sensing, Liang Zhou

McKelvey School of Engineering Theses & Dissertations

Self-powered and passive Internet-of-Things (IoT) devices (e.g. RFID tags, financial assets, wireless sensors and surface-mount devices) have been widely deployed in our everyday and industrial applications. While diverse functionalities have been implemented in passive systems, the lack of a reference clock limits the design space of such devices used for applications such as time-stamping sensing, recording and dynamic authentication. Self-powered time-keeping in passive systems has been challenging because they do not have access to continuous power sources. While energy transducers can harvest power from ambient environment, the intermittent power cannot support continuous operation for reference clocks. The thesis of this …

Concurrency Platforms For Real-Time And Cyber-Physical Systems, David Ferry

McKelvey School of Engineering Theses & Dissertations

Parallel processing is an important way to satisfy the increasingly demanding computational needs of modern real-time and cyber-physical systems, but existing parallel computing technologies primarily emphasize high-throughput and average-case performance metrics, which are largely unsuitable for direct application to real-time, safety-critical contexts. This work contrasts two concurrency platforms designed to achieve predictable worst case parallel performance for soft real-time workloads with millisecond periods and higher. One of these is then the basis for the CyberMech platform, which enables parallel real-time computing for a novel yet representative application called Real-Time Hybrid Simulation (RTHS). RTHS combines demanding parallel real-time computation with real-time …

The Example Guru: Suggesting Examples To Novice Programmers In An Artifact-Based Context, Michelle Ichinco

McKelvey School of Engineering Theses & Dissertations

Programmers in artifact-based contexts could likely benefit from skills that they do not realize exist. We define artifact-based contexts as contexts where programmers have a goal project, like an application or game, which they must figure out how to accomplish and can change along the way. Artifact-based contexts do not have quantifiable goal states, like the solution to a puzzle or the resolution of a bug in task-based contexts. Currently, programmers in artifact-based contexts have to seek out information, but may be unaware of useful information or choose not to seek out new skills. This is especially problematic for young …

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. …

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 …

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 …

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. …