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Effects Of Secondary Stall And Unsteady Free-Stream On Blade Drag And Pitching Moments, Michael Malick

McKelvey School of Engineering Graduate Student Theses & Dissertations

Dynamic stall is a complex aerodynamic phenomenon occurring in helicopter rotors, limiting the flight envelope and causing control linkage damage and instabilities. The Peters-Modarres semi-empirical dynamic stall model is extended to simulate pitching moment and drag in unsteady freestream and yawed flow, including the effects of secondary stall. The aerodynamics are implemented as a state-space model, suitable for time-marching or aeroelastic analyses. With small modifications to the original stall model, secondary stall effects and unsteady freestream can be simulated without adding additional states. An optimization routine determines sets of parameters that minimize the error between the modeled solution and experimental …

Syntheses Of A Tin (Iv) Meso-Tetra(4-Pyridyl) Porphyrin Dichloride-Tetrachlorobis (Bipy)2 Ruthenium (Ii) Complex And Studies Of Photophysical Properties Of 1-Nitropyrene, Phillip Sharp

Electronic Theses and Dissertations

Development of a photosensitizer that can work in both aerobic and anaerobic environments would increase the robustness of the cancer treatment known as photodynamic therapy. The development of a photosensitizer was first attempted by synthesizing a tin (IV) meso-tetra (4-pyridyl) porphyrin dichloride-tetrachlorobis (Bipy)₂ ruthenium (II) complex. The synthesize of the tin porphyrin was done by a method from literature and had a percent error of 31.58 and 37.31 when comparing the theoretical percentages of carbon (55.39) and nitrogen (12.92) meaning that photosensitizer was not synthesized.

The second type of chromophore that was studied was 1-nitropyrene do determine if it …

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

McKelvey School of Engineering Graduate Student 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 …

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

McKelvey School of Engineering Graduate Student 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 …

Basis Vector Model Method For Proton Stopping Power Estimation Using Dual-Energy Computed Tomography, Shuangyue Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Accurate estimation of the proton stopping power ratio (SPR) is important for treatment planning and dose prediction for proton beam therapy. The state-of-the-art clinical practice for estimating patient-specific SPR distributions is the stoichiometric calibration method using single-energy computed tomography (SECT) images, which in principle may introduce large intrinsic uncertainties into estimation results. One major factor that limits the performance of SECT-based methods is the Hounsfield unit (HU) degeneracy in the presence of tissue composition variations. Dual-energy computed tomography (DECT) has shown the potential of reducing uncertainties in proton SPR prediction via scanning the patient with two different source energy spectra. …

Biosensing By “Growing” Antennas And Error-Correcting Codes, Mingquan Yuan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Food-borne disease outbreaks not only cause numerous fatalities every year but also contribute to significant economic losses. While end-to-end supply chain monitoring can be one of the keys to preventing these outbreaks, screening every food product in the supply chain is not feasible considering the sheer volume and prohibitive test costs. Fortunately, two converging economic trends promise to make this end-to-end supply chain monitoring possible. The first trend is that passive radio-frequency identification (RFID) tags and quick response (QR) codes are now widely accepted for food packaging. The second trend is that smartphones are now equipped with the capability to …

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

McKelvey School of Engineering Graduate Student 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) …

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

Arts & Sciences Graduate Student 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, …

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

Arts & Sciences Graduate Student 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 …

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

Arts & Sciences Graduate Student 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 …

Sequence Analysis Methods For The Design Of Cancer Vaccines That Target Tumor-Specific Mutant Antigens (Neoantigens), Jasreet Hundal

Arts & Sciences Graduate Student Theses and Dissertations

The human adaptive immune system is programmed to distinguish between self and non-self proteins and if trained to recognize markers unique to a cancer, it may be possible to stimulate the selective destruction of cancer cells. Therapeutic cancer vaccines aim to boost the immune system by selectively increasing the population of T cells specifically targeted to the tumor-unique antigens, thereby initiating cancer cell death.. In the past, this approach has primarily focused on targeted selection of ‘shared’ tumor antigens, found across many patients. The advent of massively parallel sequencing and specialized analytical approaches has enabled more efficient characterization of tumor-specific …

Mechanistic Characterization Of Resistome And Microbiome Dynamics Across Diverse Microbial Habitats, Andrew John Gasparrini

Arts & Sciences Graduate Student Theses and Dissertations

Increasing antibiotic resistance in pathogens is a serious public health challenge, with over two million antibiotic resistant infections in the United States leading to at least 23,000 deaths and an estimated $55 billion in excess healthcare and societal costs. Antibiotic resistance has risen steadily in both pathogenic and benign bacteria since antibiotics’ introduction to agriculture and medicine 70 years ago. A dramatic reduction in the number of antibiotics approved for human use has accompanied this rise in antibiotic resistance, leading to the alarming prospect of a post-antibiotic era. Understanding the evolutionary origins, genetic contexts, and molecular mechanisms of antibiotic resistance …

The Role Of Apolipoprotein E In Regulating Tau Pathogenesis And Neurodegeneration In A Tauopathy Mouse Model, Yang Shi

Arts & Sciences Graduate Student Theses and Dissertations

APOE4 is the strongest genetic risk factor for late-onset Alzheimer's disease (AD). APOE4 increases brain amyloid-β (Aβ) pathology relative to other APOE isoforms. However, whether APOE independently influences tau pathology, the other pathological hallmark of AD and other tauopathies, or tau-mediated neurodegeneration, is not clear. By generating P301S tau transgenic mice on either a human APOE knock in (KI) or APOE knockout (KO) background, we show that the presence of human APOE, regardless of APOE isoforms, leads to various degrees of brain atrophy in 9-month old P301S mice, whereas APOE ablation strongly protects against neurodegeneration. In particular, P301S/E4 mice develop …

Genetic Basis Of Thermal Divergence In Saccharomyces Species, Xueying C. Li

Arts & Sciences Graduate Student Theses and Dissertations

The genetic architecture of phenotypic divergence is a central question in evolutionary biology. Genetic architecture is impacted by whether evolution occurs through accumulation of many small-effect or a few large-effect changes, the relative contribution of coding and cis-regulatory changes, and the prevalence of epistatic effects. Our empirical understanding of the genetic basis of evolutionary change remains incomplete, largely because reproductive barriers limit genetic analysis to those phenotypes that distinguish closely related species. In this dissertation, I use hybrid genetic analysis to examine the basis of thermal divergence between two post-zygotically isolated species, Saccharomyces cerevisiae and S. uvarum. S. cerevisiae is …

The Role Of Fibrillin-1 In Eye Development And Disease, Wendell Brooks Jones

Arts & Sciences Graduate Student Theses and Dissertations

The ciliary zonule of the human eye consists of a circumferential array of fibers that connect the ocular lens to the nonpigmented ciliary epithelium (NPCE) located at the inner wall of the eye. Zonular fibers consist of bundles of beaded filaments called microfibrils. Microfibrils are major structural elements of the extracellular matrix and are present in pure form in the ciliary zonule. Microfibrils are composed principally of fibrillin-1 (FBN-1); a large extracellular matrix glycoprotein. In humans, mutations in FBN1 underlie Marfan syndrome; a pleiotropic connective tissue disorder that profoundly affects the eye. Ocular manifestations include ectopia lentis (dislocated lenses), cataracts, …

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

Arts & Sciences Graduate Student 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 is …

Protein Structure-Guided Approaches To Identify Functional Mutations In Cancer, Sohini Sengupta

Arts & Sciences Graduate Student Theses and Dissertations

Distinguishing driver mutations from passenger mutations within tumor cells continues to be a major challenge in cancer genomics. Many computational tools have been developed to address this challenge; however, they rely heavily on primary protein sequence context and frequency/mutation rate. Rare driver mutations not found in many cancer patients may be missed with these traditional approaches. Additionally, the structural context of mutations on tertiary/quaternary protein structures is not taken into account and may play a more prominent role in determining phenotype and function. This dissertation first presents a novel computational tool called HotSpot3D, which identifies regions of protein structures that …

The Splice Is Not Right: Splice-Site-Creating Mutations In Cancer Genomes, Reyka Glencora Jayasinghe

Arts & Sciences Graduate Student Theses and Dissertations

Accurate interpretation of cancer mutations in individual tumors is a prerequisite for precision medicine. Large-scale sequencing studies, such as The Cancer Genome Atlas (TCGA) project, have worked to address the functional consequences of genomic mutations, with the larger goal of determining the underlying mechanisms of cancer initiation and progression. Many studies have focused on characterizing non-synonymous somatic mutations that alter amino acid sequence, as well as splice disrupting mutations at splice donors and acceptors. Current annotation methods typically classify mutations as disruptors of splicing if they fall on the consensus intronic dinucleotide splice donor, GT, the splice acceptor, AG. Splice …

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

Arts & Sciences Graduate Student 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, …

The Effect Of Talker And Contextual Variability On Memory For Words In Sentences, Nichole Runge

Arts & Sciences Graduate Student Theses and Dissertations

Previous research has found that adding different forms of variability during study can affect later memory at test. For example, having words spoken by different talkers has been shown to improve recall of known and novel words (Goldinger et al., 1999; Barcroft & Sommers, 2005), and varying the cues in cue-target related word pairs has been found to improve recall of the targets (Glenberg, 1979; Bevan et al., 1966). It was unclear, however, whether benefits of variability would extend to more naturalistic stimuli, such as sentences, which have higher working memory demands. The present set of experiments investigated how talker …

Nanopower Analog Frontends For Cyber-Physical Systems, Kenji Aono

McKelvey School of Engineering Graduate Student 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 …

Neural Mechanisms Of Drosophila Circadian Rhythms, Xitong Liang

Arts & Sciences Graduate Student Theses and Dissertations

Animals show circadian rhythms in a variety of physiological functions and behaviors. In Drosophila melanogaster, behavioral rhythms are driven by circadian clock genes that are oscillating in ~150 circadian pacemaker neurons. To explain how circadian neurons encode time and regulate different behavioral rhythms, I performed 24-hour in vivo whole-brain calcium imaging using light-sheet microscopy. First, I found that different groups of circadian neurons show circadian rhythms in spontaneous neural activity with diverse phases. The neural activity phases of the M and E pacemaker groups, which are associated with the morning and evening locomotor activities respectively, occur ~4 hours before their …

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

Arts & Sciences Graduate Student Theses and Dissertations

ABSTRACT OF THE DISSERTATIONPhotophysical Characterization and Wavelength Tuning of Natural and Synthetic Oxobacteriochlorins and BiohybridsByDonald L. HoodDoctor of Philosophy in ChemistryWashington University in St. Louis, 2018Dr. Dewey Holten, ChairpersonHerein 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 oligomers. Synthetic oxobacteriochlorins provide simpler synthetic pathway …

Effects Of Secondary Stall And Unsteady Free-Stream On Blade Drag And Pitching Moments, Michael Malick

McKelvey School of Engineering Graduate Student Theses & Dissertations

Dynamic stall is a complex aerodynamic phenomenon occurring in helicopter rotors, limiting the flight envelope and causing control linkage damage and instabilities. The Peters-Modarres semi-empirical dynamic stall model is extended to simulate pitching moment and drag in unsteady freestream and yawed flow, including the effects of secondary stall. The aerodynamics are implemented as a state-space model, suitable for time-marching or aeroelastic analyses. With small modifications to the original stall model, secondary stall effects and unsteady freestream can be simulated without adding additional states. An optimization routine determines sets of parameters that minimize the error between the modeled solution and experimental …

Fast Objective Coupled Planar Illumination Microscopy, Cody Jonathan Greer

Arts & Sciences Graduate Student 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 …

A Mouse Model Of Börjeson-Forssman-Lehmann Syndrome Reveals A Potential Link With Autism Spectrum Disorder, Cheng Cheng

Arts & Sciences Graduate Student Theses and Dissertations

ABSTRACT OF THE DISSERTATIONA Mouse Model of Börjeson-Forssman-Lehmann Syndrome reveals a potential link with Autism Spectrum DisorderByCheng ChengDoctor of Philosophy in Biology and Biomedical SciencesDevelopmental, Regenerative and Stem Cell BiologyWashington University in St. Louis, 2018Dr. Azad Bonni, ChairIntellectual disability (ID) is a prevalent neurodevelopmental disorder that affects 1% to 3% of the general population. ID is characterized by developmental deficiencies in cognitive function and adaptive behaviors. Lacking effective treatments, ID currently presents an immense burden to affected families and the economy. Therefore, there is an urgent need to elucidate the pathogenesis of ID. Human genetic studies have associated ID with …

Intersecting Variables Of Second And Foreign Language Reading: Self-Assessment And Comprehension With Adolescents And Adults Across Languages, Haley Dolosic

Arts & Sciences Graduate Student Theses and Dissertations

Today, more individuals are seeking to learn a second language (L2) or foreign language (FL) than ever before. These individuals are language learners who intend to use their growing L2 knowledge to traverse linguistic and national boundaries in order to achieve their personal and professional goals (Callahan & Gándara, 2014). To realize these goals in the digital era, L2 learners must be more prepared than ever to use their knowledge with written media, making L2 reading a central skill to successful use of their L2 knowledge. Yet, when language learners attempt to use their L2 skills in their daily lives, …

Decoding Complexity In Metabolic Networks Using Integrated Mechanistic And Machine Learning Approaches, Tolutola Timothy Oyetunde

McKelvey School of Engineering Graduate Student Theses & Dissertations

How can we get living cells to do what we want? What do they actually ‘want’? What ‘rules’ do they observe? How can we better understand and manipulate them? Answers to fundamental research questions like these are critical to overcoming bottlenecks in metabolic engineering and optimizing heterologous pathways for synthetic biology applications. Unfortunately, biological systems are too complex to be completely described by physicochemical modeling alone.

In this research, I developed and applied integrated mechanistic and data-driven frameworks to help uncover the mysteries of cellular regulation and control. These tools provide a computational framework for seeking answers to pertinent biological …

Working Paper No. 29, Lina Khan, New Technologies, And Institutional Reform, Lillian Garcia

Working Papers in Economics

This inquiry seeks to establish that Lina Khan’s work brings to light the importance of reforming institutions in order to address the challenges of internet technology. As the dominance of a small number of technology giants has increased to unforeseen proportions, legal mind Lina Khan has emerged as a leading voice in the call for an updated legal framework, as well as a revision of current economic understanding, to address the new forms of monopoly power these firms practice. The first part of this inquiry examines Chicago School dominance over economic thought and its effect on antitrust enforcement over the …

España De La Guerra, By Brian Jeffery, Richard M. Long

Soundboard Scholar

A review of Brian Jeffery, España de la Guerra: The Spanish Political and Military Songs of the War in Spain, 1808 to 1814 (London: Tecla, 2017).