Physical Sciences and Mathematics Commons^™

Information-Rich 6d Single-Molecule Imaging Design Using Optimization, Tingting Wu

McKelvey School of Engineering Theses & Dissertations

When studying biochemical processes, localizing the targets alone will not paint a complete picture. We also need techniques to probe how biomolecules interact with one another, including how molecules are organized into larger structures, how they are oriented with respect to surrounding molecules, and how local chemical parameters, like pH and hydrophobicity, vary spatially and temporally. My dissertation focuses on single-molecule orientation localization microscopy (SMOLM, Chapter 1). The objective is to develop imaging techniques for measuring how molecules are oriented with respect to their surrounding molecules, namely, 3D orientation. Achieving optimal imaging performance requires careful design of both the forward …

Lepton Flavor Violation And Lepton Flavor Universality Violation: Opportunity For New Physics Beyond The Standard Model, Fang Xu

Arts & Sciences Electronic Theses and Dissertations

The Standard Model (SM) of Particle Physics has been remarkably successful in explaining the fundamental forces and classifying elementary particles. However, there are various experimental and theoretical indications that suggest the need to go beyond the SM (BSM) and expand our understanding of the fundamental nature of the universe. From a theoretical perspective, there are several limitations of the SM that suggest the existence of a more fundamental theory. For example, the SM does not incorporate gravity, and it fails to explain the hierarchy problem. Additionally, the nature of dark matter and the origin of the mass hierarchy of elementary …

The Quantitative Microanalysis Explorer: Introducing Web-Based Visualization For Optical, Electron, And Quantitative X-Ray Maps For Studying Lunar Samples, Angelina Minocha

Senior Honors Papers / Undergraduate Theses

Modern sample imaging techniques produce data in the form of large mosaics, wherein every pixel contains valuable mineralogical information. These heavy data files are challenging for most computers to load and process, furthermore access to lunar and other extraterrestrial samples is limited. We developed the QME Tool to display optical, electron, and quantitative x-ray maps in conjunction with one another to overcome these challenges and advance mineralogy data presentation and analysis. The images and quantitative data was collected using specialized techniques, followed by an extensive image co-registration process. The interface was developed using OpenSeadragon, “An open-source, web-based viewer for high-resolution …

The Physics Of Associative Polymers And Applications To Biomolecular Condensates, Furqan Dar

Arts & Sciences Electronic Theses and Dissertations

Biomolecular condensates represent a new and ubiquitous class of membraneless organelles (MLOs) that are essential for healthy cellular functioning. The constituent molecules of such condensates span a vast bio-macromolecular gamut from intrinsically disordered regions and proteins (IDPs/IDRs), to RNA and RNA-binding proteins (RNPs), to polymerases and DNA etc. Apart from being part of the regular healthy cell cycle, these condensates are also implicated in many diseases, most notably progressive neurodegenerative diseases like Amyotropic Lateral Sclerosis (ALS) and Huntingtin's Disease (HD). Since the constituent molecules of these condensates span a broad range of length scales and modes of interaction, uncovering a …

The Effect Of Ionization Density In Applications Of Radiation Detection, Dosimetry, And Therapy, Daniel Mulrow

Arts & Sciences Electronic Theses and Dissertations

This dissertation covers a wide range of topics but is linked by the common theme of radiation interacting with materials and studying the result of those interactions. The introduction describes the fundamentals of how radiation interacts with material and how we are able to detect that radiation and the application of how we use those interactions in radiation oncology. The thesis starts with a chapter detailing the temperature dependence of the photophysics in two organic scintillators. This chapter is the foundation for a future study that will look the degree to which these scintillators can distinguish between gammas and neutrons …

Quasiparticle And Excitonic Effects In Two-Dimensional Van Der Waals Materials, Linghan Zhu

Arts & Sciences Electronic Theses and Dissertations

Since their discovery, low dimensional van der Waals materials have attracted increasing research interests. They serve as ideal platforms to study novel physics in reduced-dimensional systems, and are critical in nowadays’ nanotechnology applications. Due to the reduced dielectric screening in low dimensions, strong excited state properties dictate their electronic, transport and optical properties, the study of which calls for a description of the many-particle interactions beyond the traditional density functional theory. This is where the many-body perturbation theory comes into play. In this thesis, I will present a comprehensive study of the quasiparticle and excitonic properties of a variety of …

Systems Level Analysis Of Organelle Biogenesis In Saccharomyces Cerevisiae, Kiandokht Panjtan Amiri

Arts & Sciences Electronic Theses and Dissertations

Eukaryotic cells contain hundreds of subcellular structures that serve different functions to maintain cellular homeostasis. A hallmark of Eukaryotic cells is its compartmentalization into membrane-bound organelles. One of the grand challenges in quantitative cell biology is understanding the precision with which cells assemble and maintain subcellular organelles. Despite identification of numerous molecular factors that regulate organelle sizes we lack insight into the quantitative principles underlying organelle size control. We examine organelle sizes from Saccharomyces cerevisiae and human iPS cells with mathematical theory to show that cells can robustly control average fluctuations in organelle size. By demonstrating that organelle sizes obey …

Plasmonic Nanomaterials-Based Point-Of-Care Biosensors, Rohit Gupta

McKelvey School of Engineering Theses & Dissertations

Point-of-care (POC) biosensors, although rapid and easy-to-use, are orders magnitude less sensitive than laboratory-based tests. Further they are plagued by poor stability of recognition element thus limiting its widespread applicability in resource-limited settings. Therefore, there is a critical need for realizing stable POC biosensors with sensitivity comparable to gold-standard laboratory-based tests. This challenge constitutes the fundamental basis of this dissertation work– to expand access to quality and accurate biodiagnostic tools. At the heart of these solutions lies plasmonic nanoparticles which exhibit unique optical properties which are attractive for label-free and labelled biosensors.Firstly, we improve the stability and applicability of label-free …

Evaluation And Clinical Implementation Of A Dual-Energy Ct Stopping-Power Ratio Mapping Technique For Proton-Therapy Treatment Planning, Maria Jose Medrano Matamoros

McKelvey School of Engineering Theses & Dissertations

Proton radiotherapy has the potential to treat tumors with better conformal dose distribution than competing modalities when the rapid dose falloff at the end of the proton-beam range is correctly aligned to the edge of the clinical target volume (CTV). However, its clinical potential is dependent on the accurate localization of the Bragg-peak position from predicted stopping-power ratio maps. The method that is most commonly used in today’s clinical practice for predicting stopping-power ratio (SPR) consists of a stoichiometric calibrationtechnique based on single-energy CT (SECT) for direct estimation of patient-specific SPR distribution from vendor-reconstructed Hounsfield Unit (HU) images. Unfortunately, this …

Exploring The Solar System Through Space And Time Via Laboratory Investigations Of Extraterrestrial Material, Kainen Lee Utt

Arts & Sciences Electronic Theses and Dissertations

This dissertation reports the results of laboratory studies of lunar soil samples, gas-to-solid filamentary enstatite grains from a likely-cometary interplanetary dust particle (IDP), and exogenous clasts in the CH3 chondrite Acfer 182 that likely originated from a differentiated basaltic planetesimal. These studies were performed using multi-instrument analyses involving high-resolution scanning and transmission electron microscopy (SEM/TEM) techniques, nanoscale secondary ion mass spectrometry (NanoSIMS), synchrotron infrared nanospectroscopy (SINS), electron probe microanalysis (EPMA), and Raman spectroscopy. The results of these analyses are used to examine space weathering phenomena, energetic processing and radial transport in the protoplanetary disk, and the origins of igneous inclusions …

Electronic, Optical, And Thermal Probes Of The Layered Mott Insulator Α-Rucl3 In The Atomically Thin Limit, Jesse Balgley

Arts & Sciences Electronic Theses and Dissertations

Alpha-ruthenium(III) chloride (α-RuCl3) is a layered Mott insulator and van der Waals material that can be cleaved down to a single atomic layer. This material is a promising candidate to realize the Kitaev quantum spin liquid, a strongly correlated phase of matter expected to host fractionalized quasiparticles and a potential platform for topological quantum computation. When α-RuCl3 is placed in direct contact with the layered semimetal graphene we observe a strong charge transfer between the two materials despite the electrically insulating nature of α-RuCl3, which absorbs ≈ 4 × 10^13 electrons/cm^2 from the graphene. Remarkably, this charge transfer persists and …

Design & Analysis Of Mixed-Mode Integrated Circuit For Pulse-Shape Discrimination, Bryan Orabutt

McKelvey School of Engineering Theses & Dissertations

In nuclear science experiments it is usually necessary to determine the type of radiation, its energy and direction with considerable accuracy. The detection of neutrons and discriminating them from gamma rays is particularly difficult. A popular method of doing so is to measure characteristics intrinsic to the pulse shape of each radiation type in order to perform pulse-shape discrimination (PSD).

Historically, PSD capable systems have been designed with two approaches in mind: specialized analog circuitry, or digital signal processing (DSP). In this work we propose a PSD capable circuit topology using techniques from both the analog and DSP domains. We …

Computational Methods For Analysis Of Data For Conformational And Phase Equilibria Of Disordered Proteins, Jared Michael M Lalmansingh

Arts & Sciences Electronic Theses and Dissertations

Intrinsically disordered proteins and regions (IDPs / IDRs) are a class of proteins with diverse conformational heterogeneity that do not fold into a tertiary structure due to the lack of a native structural state. Consequently, disordered proteins are remarkably flexible and exhibit multivalent properties that enable them to adopt myriad functional roles within the cell such as: signaling transduction, transcription, enzymatic catalysis, translation, and many more. Due to their multivalency, some IDPs undergo monomeric and heterotypic interactions which can drive phase separation. Such IDPs can form membraneless organelles with specific regulatory roles within the cell which include, but are not …

Probing New Physics Beyond The Standard Model Via New Neutrino Interactions, Garv Chauhan

Arts & Sciences Electronic Theses and Dissertations

The Standard Model (SM) of Particle Physics provides a self-consistent quantum field theoretic framework to explain three of the four known fundamental forces (electromagnetic, weak, strong) along with classifying all known elementary particles. Since its conception in the 1960s, the SM has been one of the most tested theories of physics and has withstood all experimental batterings. In spite of these successes, there are compelling indications, both experimental and theoretical, that require us to expand our understanding of the nature beyond the SM (BSM). Arguably the most glaring indication of BSM physics is the observation of neutrino oscillations, which implies …

A Systematic Study Of Neutron Production In Two Versions Of The Mevion Proton-Therapy System, Nima Tatari

Arts & Sciences Electronic Theses and Dissertations

This thesis presents a study of neutron production in two types of proton-therapy systems: passive scattering Mevion S250, and active scanning Mevion S250i. The scattering system has been operating at Washington University in St. Louis since 2013. The scanning system was installed in the same building in 2020. The scanning system has the advantage of producing fewer neutrons due to a focused scanned beam and the absence of beam scatterers, collimators, and a static brass aperture. A systematic particle transport Monte Carlo analysis using the Geant4 toolkit has been performed to track the neutrons produced in various components of each …

Electronic, Optical, And Magnetic Properties Of Novel Two-Dimensional Materials, Xiaobo Lu

Arts & Sciences Electronic Theses and Dissertations

The field of two-dimensional(2D) materials is experiencing rapid growth and attracting tremendous research interests within the condensed matter community due to its ultimate thickness dimension and unique physical properties. The consistently emerging novel 2D materials not only provide extraordinary intrinsic properties of their single layer and multi- layer structures but also exhibit fascinating responses to the tunable external conditions. The fertile contents and boundless possibilities of novel 2D materials make it one of the pivots of modern nanotechnology towards deepening the physics understanding and promising practical applications.

In the first part of the thesis, we reveal the distinct Stark effects …

Neural Representation In The Primary Visual Cortex Amid High Neural Variability, Ji Xia

Arts & Sciences Electronic Theses and Dissertations

Animals process high-dimensional sensory information constantly. How does neural activityin sensory cortices represent this information? Recent advances in large-scale recordings allow us to monitor activity of hundreds or thousands of neurons simultaneously across a long period of time. Population recordings showed that cortical neuronal responses to repeated sensory stimulation is highly variable from trial to trial. However, how neurons in neocortex represent sensory information amid high neural variability is not well understood. To answer this question, we used two-photon calcium imaging to record from hundreds of excitatory neurons simultaneously from mouse primary visual cortex. We analyzed neural responses to repeated …

Non-Hermitian Physics And Engineering In Whispering Gallery Mode Microresonators, Changqing Wang

McKelvey School of Engineering Theses & Dissertations

Non-Hermitian physics describes the behaviors of open systems which have interactions with the environment. It can be applied to a wide range of classical and quantum systems. Exotic physical phenomena are unveiled in such non-Hermitian systems, especially around a singular point in the parameter space, i.e., the exceptional point (EP), where the eigenvalues and the associated eigenvectors are degenerate. A plethora of demonstrations have been found in optics and photonics, where the non-Hermitian effects are ubiquitous due to the existence of optical dissipation or amplification. In particular, whispering gallery mode (WGM) resonators are ideal candidates for studying light-matter interactions in …

Community Detection In Complex Networks, Zhenqi Lu

McKelvey School of Engineering Theses & Dissertations

Network science plays a central role in understanding and modeling complex systems in many disciplines, including physics, sociology, biology, computer science, economics, politics, and neuroscience. By studying networks, we can gain a deep understanding of the behavior of the systems they represent. Many networks exhibit community structure, i.e., they have clusters of nodes that are locally densely interconnected. These communities manifest the hierarchical organization of the objects in systems, and detecting communities greatly facilitates the study of the organization and structure of complex systems.

Most existing community-detection methods consider low-order connection patterns, at the level of individual links. But high-order …

Modeling Hyperpolarized Nmr Phenomena In Optically Pumped Semiconductors, Michael Eric West

Arts & Sciences Electronic Theses and Dissertations

Nuclear magnetic resonance (NMR) is a widely-used technique that measures the local environments of nuclei. It is able to detect small differences in energy, making it a highly-valued tool. However, the technique is challenged by inherently low sensitivities, requiring either large sample volumes or long periods of time to overcome this. In semiconductors, optical pumping (OP) can overcome this low sensitivity by creating incredibly large and dynamic nuclear spin polarizations (``hyperpolarization''), which is detectable as a large NMR signal. The combined technique of optically-pumped NMR (OPNMR) is a valuable tool that can explore electronic and nuclear phenomena within semiconductors. In …

Development Of A Diamond Defect Quantum Sensing Platform For Probing Novel Quantum Magnetic Phases, Jeffrey Ahlers

Senior Honors Papers / Undergraduate Theses

Nitrogen vacancy centers in diamond are highly effective quantum sensors due to their high spatial resolution and high magnetic field sensitivity. We present the construction of an optically detected magnetic resonance platform in order to facilitate the probing of magnetic phases in two-dimensional heterostructures. This includes the characterization of the required microwave voltage controlled oscillator and amplifier. In the presence of crystal strain, we measure ensemble nitrogen vacancy spin transitions with and without an applied magnetic field, and observe frequency shifts consistent with sample heating.

Assessment And Diagnosis Of Human Colorectal And Ovarian Cancer Using Optical Imaging And Computer-Aided Diagnosis, Yifeng Zeng

McKelvey School of Engineering Theses & Dissertations

Tissue optical scattering has recently emerged as an important diagnosis parameter associated with early tumor development and progression. To characterize the differences between benign and malignant colorectal tissues, we have created an automated optical scattering coefficient mapping algorithm using an optical coherence tomography (OCT) system. A novel feature called the angular spectrum index quantifies the scattering coefficient distribution. In addition to scattering, subsurface morphological changes are also associated with the development of colorectal cancer. We have observed a specific mucosa structure indicating normal human colorectal tissue, and have developed a real-time pattern recognition neural network to localize this specific structure …

Computational Design Of Two-Dimensional Transition Metal Dichalcogenide Alloys And Their Applications, John Douglas Cavin

Arts & Sciences Electronic Theses and Dissertations

The discovery of bronze as an alloy of copper and tin is arguably the earliest form of material design, dating back thousands of years. In contrast, two-dimensional materials are new to the 21st century. The research presented in this dissertation is at the intersection of alloying and two-dimensional materials. I specifically study a class of two-dimensional materials known as transition metal dichalcogenides (TMDCs). Because of the large number of transition metals, there are many combinations of TMDCs that can be alloyed, making experimental exploration of the phase space of possible alloys unwieldly. Instead, I have applied first-principles methods to study …

Partial Measurements Of Quantum Systems, Jonathan Tyler Monroe

Arts & Sciences Electronic Theses and Dissertations

Projective measurement is a commonly used assumption in quantum mechanics. However, advances in quantum measurement techniques allow for partial measurements, which accurately estimate state information while keeping the wavefunction intact. We employ partial measurements to study two phenomena. First, we investigate an uncertainty relation—in the style of Heisenberg’s 1929 thought experiment—which includes partial measurements in addition to projective measurements. We find that a weak partial measurement can decrease the uncertainty between two incompatible (non-commuting) observables. In the second study, we investigate the foundation of irreversible dynamics resulting from partial measurements. We do so by comparing the forward and time-reversed probabilities …

Mutual Interaction Induced Multi-Particle Physics In Qed Systems – Cooperative Spontaneous Emission And Photonic Dimer Enhanced Two-Photon Excitation, Yao Zhou

McKelvey School of Engineering Theses & Dissertations

In recent years, the study of quantum electrodynamics (QED) in light-matter interactions has discovered various interesting phenomenons that orient many applications. However, due to the ambient entanglement among photons and atoms, few-particle dynamics remains challenging to analyze precisely and limits the progress in several fields. In few-particle systems, different number of atoms interacting with the light field generates drastically different results, even when there is only a single photon involved in the system. The interference between individual atom’s spontaneous emission wavefunctions can cooperatively alter the effective atom-light coupling strength. Depending on the spatial distance between individual of atoms and the …

Toward An Understanding Of High-Mass Gamma-Ray Binaries: An Investigation Using Current Observatories And The Development Of A Future Gev Instrument, Zachary Daniel Hughes

Arts & Sciences Electronic Theses and Dissertations

The current generation of gamma-ray instruments have produced a treasure trove of astrophysical discoveries. Among them are a new class of objects tentatively designated high-mass gamma-ray binaries (HMGBs). Thought to be systems containing the colliding wind of a massive star and a young pulsar, these objects are distinguished by emission >1 MeV dominating their spectral energy distributions. We present a multiwavelength study of a newly detected gamma-ray source, HESS J1844-030, utilizing Chandra, Fermi, and VERITAS to show that its spatial, spectral, and flux variability properties are compatible with a classification as a HMGB. The current generation of instruments have identified …

Structural Organization And Chemical Activity Revealed By New Developments In Single-Molecule Fluorescence And Orientation Imaging, Tianben Ding

McKelvey School of Engineering Theses & Dissertations

Single-molecule (SM) fluorescence and its localization are important and versatile tools for understanding and quantifying dynamical nanoscale behavior of nanoparticles and biological systems. By actively controlling the concentration of fluorescent molecules and precisely localizing individual single molecules, it is possible to overcome the classical diffraction limit and achieve 'super-resolution' with image resolution on the order of 10 nanometers.

Single molecules also can be considered as nanoscale sensors since their fluorescence changes in response to their local nanoenvironment. This dissertation discusses extending this SM approach to resolve heterogeneity and dynamics of nanoscale materials and biophysical structures by using positions and orientations …

Growth Of Small Particles In Nonequilibrium Plasmas, Necip Berker Üner

McKelvey School of Engineering Theses & Dissertations

Nonequilibrium plasma (NEP) is an extraordinary environment for material synthesis. NEP is comprised of hot electrons with temperatures greater than 10000 K and of cold ions and neutrals that are usually at few hundred kelvins above room temperature. Due to this large difference in species’ temperatures, the assumption of local thermal equilibrium does not hold in NEP. Therefore, NEP can act as a unique processor of mass, and it can transform materials along pathways that are not accessible by methods wherein local thermal equilibrium is valid. For decades, NEPs have been employed in the semiconductor industry to manufacture many thin …

Production Of Medical Radioisotopes Using Titanium Accelerator Targets, Christopher Shaun Loveless

Arts & Sciences Electronic Theses and Dissertations

Theranostic radiopharmaceuticals enable diagnostic imaging and radionuclide therapy in patients using a single molecular agent labeled with a diagnostic-therapeutic pair (e.g., 68Ga/177Lu) or a theranostic radionuclide (e.g., 131I). This theranostic approach can help inform patient-specific treatment plans and improve clinical outcomes. Radionuclide pairs used in theranostic agents fall into two categories: pseudo matched-pairs (e.g., 68Ga/177Lu) and matched-pairs (e.g., 124I/131I). Pseudo matched-pair radionuclides have similar chemistries and pharmacokinetics when bound to the same bioconjugate molecule. In contrast, identical chemistries and pharmacokinetics can be obtained by using the matched-pair radionuclides.

The isotopes of Sc include two diagnostic radioisotopes, 43Sc & 44Sc, and …

Peer-Led Team Learning In Calculus-Based Introductory Physics: Implementation And Evaluation, Siera Maia Stoen

Arts & Sciences Electronic Theses and Dissertations

Robust evidence shows that Peer-led Team Learning (PLTL) improves the academic success of college students in introductory Science, Technology, Engineering, and Mathematics (STEM) courses. However, further research is needed to gain a fuller understanding of the benefits of PLTL and the aim of this dissertation is to explore two key and understudied questions surrounding the effects of PLTL. First, does deviating from the optimal implementation of PLTL change its effectiveness? Second, what specific outcomes, in addition to academic success (e.g., exam scores), does PLTL improve? This dissertation will provide a fuller picture of the impact of PLTL by examining its …