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 …

Volumetric Imaging Using The Pupil-Matched Remote Focusing Technique In Light-Sheet Microscopy, Sayed Hassan Dibaji Foroushani

Optical Science and Engineering ETDs

ABSTRACT

The dissertation explores innovative techniques in light sheet microscopy, a pivotal tool in biomedical imaging, to enhance its speed, resolution, and efficiency in capturing dynamic biological processes. Light sheet microscopy allows for quick 3D imaging of biological specimens ranging from cells to organs with high spatiotemporal resolution, large field-of-view, and minimal damage, making it vital for in vivo imaging.

The first project introduces a novel optical concept designed to optimize Axially Swept Light Sheet Microscopy (ASLM). This technique is crucial for imaging specimens ranging from live cells to chemically cleared organs due to its versatility across different immersion media. …

Modeling Lithographic Quantum Dots And Donors For Quantum Computation And Simulation, Mitchell Ian Brickson

Physics & Astronomy ETDs

Our first focus is on few-hole quantum dots in germanium. We use discontinous Galerkin methods to discretize and solve the equations of a highly detailed k·p model that describes these systems, enabling a better understanding of experimental magnetospectroscopy results. We confirm the expected anisotropy of single-hole g-factors and describe mechanisms by which different orbital states have different g-factors. Building on this, we show that the g-factors in Ge holes are suciently sensitive to details of the device electrostatics that magnetospectroscopy data can be used to make a prediction of the underlying confinement potential. The second focus is on designing quantum …

Radio Insights Into Gamma-Ray Mysteries, Seth M. Bruzewski

Physics & Astronomy ETDs

In the time since its launch, the \textit{Fermi Gamma-Ray Space Telescope} has provided new and unparalleled views of the $\gamma$-ray sky, dramatically increasing our understanding of sources of high-energy radiation. During that same time, however, its ``unassociated'' sources have provided a consistent mystery: approximately one third of the modern gamma-ray sky remains completely unaccounted for in other electromagnetic regimes. While some of the fainter sources simply pose challenges in achieving the necessary signal-to-noise ratio, others are well constrained and have resisted traditional investigations for years, and in some cases, for over a decade. Radio astronomy has traditionally been the best …

Computational Fluid Dynamics Modeling Of Internal Wave Interactions On Conch Reef, Florida Keys, Megan Miller

All HCAS Student Capstones, Theses, and Dissertations

Internal waves breaking on continental shelves play a significant role in mixing and nutrient delivery to coral reef ecosystems. As internal solitary waves, or solitons, propagate shoreward onto continental slopes, they can become unstable and break into turbulent bores that bring cool, nutrient-rich sub-thermocline water shoreward onto coral reefs. The propagation of turbulent bores generated by internal waves interacting with a complex surface creates high-frequency variabilities in the thermal and nutrient environment of Conch Reef in the Florida Keys, which has been studied previously. Here, I have created a three-dimensional model using ANSYS Fluent Computational Fluid Dynamics (CFD) software to …

Characterization Of Isomeric States In Neutron-Rich Nuclei Approaching N = 28, Timilehin Hezekiah Ogunbeku

Theses and Dissertations

The investigation of isomeric states in neutron-rich nuclei provides useful insights into the underlying nuclear configurations, and understanding their occurrence along an isotopic chain can inform about shell evolution. Recent studies on neutron-rich Si isotopes near the magic number N = 20 and approaching N = 28 have revealed the presence of low-lying states with intruder configurations, resulting from multiple-particle, multiple-hole excitations across closed shell gaps. The characterization of these states involves measuring their half-lives and transition probabilities.

In this study, a new low-energy (7/2⁻₁) isomer at 68 keV in ³⁷Si was accessed via beta decay …

Investigating The Effects Of A Southward Flow In The Southeastern Florida Shelf Using Robotic Instruments, Alfredo Quezada

All HCAS Student Capstones, Theses, and Dissertations

We deployed a Slocum G3 glider fitted with an acoustic Doppler current profiler (ADCP), a Conductivity-Temperature-Depth sensor (CTD), optics sensor channels, and a propeller on the Southeastern Florida shelf. The ADCP and CTD provide continuous measurements of Northern and Eastern current velocity components, salinity, temperature, and density, throughout the water column in a high-current environment. The optics sensor channels are able to provide measurements of chlorophyll concentrations, colored dissolved organic matter (CDOM), and backscatter particle counts. Additionally, for one of the glider deployments, we deployed a Wirewalker wave-powered profiling platform system also fitted with an ADCP and a CTD in …

Thermocatalytic Plasma-Assisted Dry Reforming Of Methane Over Ni/Al2o3 Catalyst, Tyler Wong

Seton Hall University Dissertations and Theses (ETDs)

Plasma catalysis is an advantageous approach that combines the effects of plasma with the enhancements of a catalyst. By utilizing a nickel catalyst in the plasma discharge zone of a dielectric barrier discharge (DBD), it can give an enhancement to the electrical field, boost microdischarges, and increase conversion and selectivity rates of CH₄ and CO₂ in the dry reforming of methane (DRM) reaction.

Industrial application of nickel catalysts in DBD Plasma DRM process are limited by poor stability, which is caused by the sintering of active metal particles and coke deposition on the catalyst surface. In this work, …

High-Performance Computing In Covariant Loop Quantum Gravity, Pietropaolo Frisoni

Electronic Thesis and Dissertation Repository

This Ph.D. thesis presents a compilation of the scientific papers I published over the last three years during my Ph.D. in loop quantum gravity (LQG). First, we comprehensively introduce spinfoam calculations with a practical pedagogical paper. We highlight LQG's unique features and mathematical formalism and emphasize the computational complexities associated with its calculations. The subsequent articles delve into specific aspects of employing high-performance computing (HPC) in LQG research. We discuss the results obtained by applying numerical methods to studying spinfoams' infrared divergences, or ``bubbles''. This research direction is crucial to define the continuum limit of LQG properly. We investigate the …

Atomic-Level Mechanisms Of Fast Relaxation In Metallic Glasses, Leo W. Zella

Doctoral Dissertations

Glasses are ubiquitous in daily life and have unique properties which are a consequence of the underlying disordered structure. By understanding the fundamental processes that govern these properties, we can modify glasses for desired applications. Key to understanding the structure-dynamics relationship in glasses is the variety of relaxation processes that exist below the glass transition temperature. Though these relaxations are well characterized with macroscopic experimental techniques, the microscopic nature of these relaxations is difficult to elucidate with experimental tools due to the requirements of timescale and spatial resolution. There remain many questions regarding the microscopic nature of relaxation in glass …

A Measurement Of Neutron Polarization And Transmission For The Nedm@Sns Experiment, Kavish Imam

Doctoral Dissertations

The D.O.E Nuclear Science Advisory Committee Long Range Plan has called for experimental programs to explore fundamental symmetry violations and their implications in nuclear, particle and cosmological physics. The neutron electric dipole moment experiment at the Spallation Neutron Source (nEDM@SNS) aims to search for new physics in the Time-reversal (T) and Charge-Parity (CP) symmetry violating sector by setting a new limit on the nEDM down to a few x 10^-28 e·cm using a novel cryogenic technique, which combines the unique properties of polarized Ultracold Neutrons (UCN), polarized ³He, and superfluid ⁴He. The experiment will employ a cryogenic …

Effect Of Self-Interaction Correction On Molecular Polarizabilities And Core Ionization Energies, Sharmin Akter

Open Access Theses & Dissertations

Density Functional Theory (DFT) is one of the most successful and popular computational Quantum Mechanical approaches to understanding materials. DFT allows the prediction of material properties from the electron density. Although in principle, density functional theory is exact, it, however, relies on approximate functional for exchange-correlation energy. Due to the approximate nature of the exchange-correlation functional, the self-Coulomb energy of the electrons is not exactly canceled out by the self-exchange, leading to the spurious self-interaction error (SIE). Due to this error, the potential shows incorrect behavior which leads to errors in calculated properties such as ionization energies, electron affinities, polarizabilities, …

Intercomparison Of Planetary Boundary Layer Over El Paso-Juarez Region Using Vaisala Ceilometers, Vianey Arvilla

Open Access Theses & Dissertations

Vaisala ceilometers (models CL 31 and Cl 51) were used to monitor and study the planetary boundary layer (PBL). There were four ceilometer stations that we connected to create the Paso del Norte ceilometer network. These stations are located at: UTEP, Socorro, Ivanhoe, and Juarez. This network has been automatized and its hourly averaged mean boundary layer height data is being downloaded into a computer accessible to TCEQ (Texas Commission on Environmental Quality) and to the public. In this study, data from each ceilometer was used to produce scatter plots. These scatter plots were analyzed to obtain the PBL heights …

Co2-Dependent Nanoscale Organization In Bulk And Interfacial Carbon Dioxide Capture Liquids Elucidated Using X-Ray Scattering, Daniel Eduardo Moran

Open Access Theses & Dissertations

The pressing need to control carbon dioxide emissions has propelled extensive research efforts employing a variety of approaches across the globe. In flue-gas recovery of CO2, the water-lean amine-based solvent N-(2-ethoxyethyl)-3-morpholinopropan-1-amine (2-EEMPA), has shown exceptional performance. Recent studies show that 2-EEMPA exhibits intermediate-range order (IRO), beyond the first nearest neighbor length scale, consisting of tetrameric clusters. In view of the need to find solutions for direct air capture (DAC) of CO2, this system may represent a critical linkage in a DAC strategy, yet structural insights on EEMPA's behavior at solid surfaces are still lacking. To this end, we applied the …

Biomolecular Function From Structural Snapshots, Roshanak Etemadpour

Theses and Dissertations

Biological molecules can assume a continuous range of conformations during function. Near equilibrium, the Boltzmann relation connects a particular conformation's free energy to the conformation's occupation probability, thus giving rise to one or more energy landscapes. Biomolecular function proceeds along minimum-energy pathways on such landscapes. Consequently, a comprehensive understanding of biomolecular function often involves the determination of the free-energy landscapes and the identification of functionally relevant minimum-energy conformational paths on these landscapes. Specific techniques are necessary to determine continuous conformational spectra and identify functionally relevant conformational trajectories from a collection of raw single-particle snapshots from, e.g. cryogenic electron microscopy (cryo-EM) …

Wavelet Compression As An Observational Operator In Data Assimilation Systems For Sea Surface Temperature, Bradley J. Sciacca

University of New Orleans Theses and Dissertations

The ocean remains severely under-observed, in part due to its sheer size. Containing nearly billion of water with most of the subsurface being invisible because water is extremely difficult to penetrate using electromagnetic radiation, as is typically used by satellite measuring instruments. For this reason, most observations of the ocean have very low spatial-temporal coverage to get a broad capture of the ocean’s features. However, recent “dense but patchy” data have increased the availability of high-resolution – low spatial coverage observations. These novel data sets have motivated research into multi-scale data assimilation methods. Here, we demonstrate a new assimilation approach …

Short Range Correlation Measurements In The Quasielastic Region With An 11 Gev Beam, Casey Morean

Doctoral Dissertations

Electron scattering is a significant means of studying internal high momentum
nucleon and quark distributions in nuclei. Thomas Jefferson National Accelerator
Facility (JLab) with its 11GeV beam is capable of studying high momentum nucleons
with unmatched precision. The role of short range nucleon configurations and
quark distributions is significant for understanding the dynamics of nuclei and their
underlying components. Scattering cross section measurements in the kinematic
regime x > 1, where the free nucleon is forbidden, are sensitive to high momentum
nucleons, which are believed to come from short range correlations (SRCs). SRCs are
strongly interacting, high momentum nucleons with a …

Radiation Exposure Calibration Of The Al2o3:C With Radium-226 And Cesium-137 Using The Osl Method, Selma Tepeli Aydin

All Theses

Optically stimulated luminescence (OSL) dosimetry was utilized to calibrate Al₂O₃:C powder dosimeters, available commercially as the nanoDot® from Landauer Inc., and compare the dosimeter response to radium-226 (²²⁶Ra) and cesium-137 (¹³⁷Cs). The signal from the OSL was quantified using a microSTARii^® OSL reader also produced by Landauer Inc. Dose-response curves were developed for ²²⁶Ra and ¹³⁷Cs experiments (5 dosimeters each) at thirteen absorbed doses. Individual dosimeter response was tracked by serial number. Linear regression analysis was performed to determine if there were significant differences between the intercepts of the …

Measuring The Lengths Of Sperm Whales Of The Northern Gulf Of Mexico By Wavelet Analysis Of Their Usual Clicks, George Drouant

University of New Orleans Theses and Dissertations

Abstract

Acoustic recordings of underwater sounds produced by marine mammals present an attractive alternative to costly and logistically complex ship based visual surveys for collecting population data for various species.

The first reported use of underwater acoustic recordings in the long-term monitoring of sperm whale populations was by Ackleh et al. (Ackleh et al., 2012). The paper describes counting sperm whale clicks at different locations to track population changes over time.

Analysis of sperm whale clicks offers additional insight into sperm whale populations. The echo location clicks (usual clicks) of sperm whales can be used to give an estimate of …

Viability Of Magnetic Nanoparticles For Magnetic Hyperthermia Cancer Therapy, Marcos Adrian Garcia

Open Access Theses & Dissertations

Over the last few decades magnetic nanoparticles have gained an extraordinary amount of attention in the science community. Their versatile use in many different research areas such as medicine, engineering and technology and many other areas has made them a popular subject. In this thesis, the synthesis of different systems of magnetic nanoparticles will be explored along with the potential use of the MNP's as viable candidates for Magnetic Hyperthermia Cancer Therapy. With values of over 200 emu/g for Iron-Silver magnetic nanoparticles with particle sizes ranging from 30-70nm and their heating properties under an AC magnetic field. As well of …

Development Of Back-Scatter And Pile-Up Identification For Ucna+, Amelia Greathouse

Undergraduate Honors Theses

The UCNA Experiment at the Los Alamos Neutron Science Center (LANSCE) uses

an electron spectrometer to observe angular correlations between the neutron spin and the momenta of beta particles emitted during the process of beta (β) decay. Combined with neutron lifetime measurements, these observations probe physics beyond the standard model. In recent years there has been an effort to modernize the equipment to reduce the physical limitations of the experiment. The new prototype helps to reduce error via use of silicon photo-multipliers (SiPMs) and the SiPMs also have a greater quantum efficiency than the photomultiplier tubes (PMTs). However, there is …

Analyzing The Effects Of Ultrafast Laser Processing On Mechanical Properties Of 3d-Printed Pla Parts, Darshan Pramodbhai Yadav

Theses and Dissertations

Recent advances in additive manufacturing technologies have already led to wide-scale adoption of 3D-printed parts in various industries. The expansion in choice of materials that can be processed, particularly using Fused Deposition Modeling (FDM), and the steady advancements in dimensional accuracy control have extended the range of applications far beyond rapid prototyping. However, additive manufacturing still has considerable limitations compared to traditional and subtractive manufacturing processes. This work addresses limitations associated with the as-deposited surface roughness of 3D-printed parts. The effects of roughness-induced stress concentrations were studied on ultimate tensile strength and fatigue life. The samples were manufactured using a …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Controlled Manipulation And Transport By Microswimmers In Stokes Flows, Jake Buzhardt

All Dissertations

Remotely actuated microscale swimming robots have the potential to revolutionize many aspects of biomedicine. However, for the longterm goals of this field of research to be achievable, it is necessary to develop modelling, simulation, and control strategies which effectively and efficiently account for not only the motion of individual swimmers, but also the complex interactions of such swimmers with their environment including other nearby swimmers, boundaries, other cargo and passive particles, and the fluid medium itself. The aim of this thesis is to study these problems in simulation from the perspective of controls and dynamical systems, with a particular focus …

Interactive Water Vortex Exhibit, Simon Way, Emily Laing, Roqaya Naseri, Makenzie Kan

Mechanical Engineering

The San Luis Obispo Children’s Museum requested an interactive water vortex exhibit to both engage and entertain inquisitive guests, ages two to eight. The goal was to design and manufacture an exhibit that would educate its users on the fluid mechanics behind water vortices. They activate the mechanics by spinning a wheel, which is perceived as the catalyst to manipulate the flow of water to successfully create a whirlpool. Our team has created an interactive display that will enlighten young minds, providing the museum with an educational exhibit which shares a concept not currently taught by any other. Our project …

Generative Adversarial Game With Tailored Quantum Feature Maps For Enhanced Classification, Anais Sandra Nguemto Guiawa

Doctoral Dissertations

In the burgeoning field of quantum machine learning, the fusion of quantum computing and machine learning methodologies has sparked immense interest, particularly with the emergence of noisy intermediate-scale quantum (NISQ) devices. These devices hold the promise of achieving quantum advantage, but they grapple with limitations like constrained qubit counts, limited connectivity, operational noise, and a restricted set of operations. These challenges necessitate a strategic and deliberate approach to crafting effective quantum machine learning algorithms.

This dissertation revolves around an exploration of these challenges, presenting innovative strategies that tailor quantum algorithms and processes to seamlessly integrate with commercial quantum platforms. A …

Microscale To Mesoscale Modeling Of The Ocean Under Tropical Cyclones: Effects Of Sea Spray And Surfactants On Tropical Cyclone Intensity And Air-Sea Gas Exchange, Breanna Lynn Cain Vanderplow

All HCAS Student Capstones, Theses, and Dissertations

Tropical cyclone intensity prediction remains a challenge despite computational and observational developments because successful intensity forecasting requires implementing a multitude of atmospheric and oceanic processes. Hurricane Maria 2017 and Hurricane Dorian 2019 serve as prime examples of rapidly intensifying storms that devastated communities in the Caribbean. A lack of understanding and parameterization of crucial physics involved in tropical cyclone intensity in existing forecast models may have led to these and other forecasting errors.

Microscale physical processes at the air-sea interface are a major factor in intensification of tropical cyclones that are often unaccounted for in forecasting models since they are …

Patterned Heating Induced Propulsion, Saajid A. Aman

Electronic Thesis and Dissertation Repository

This study explores propulsion effects generated by patterned heating acting on smooth and corrugated surfaces. The model problem assumes that the upper plate moves freely, and the lower plate is stationary, equipped with grooves, and exposed to spatially distributed heating. Our findings identify two distinct propulsion effects: thermal streaming and thermal drift. Thermal streaming occurs when given sufficient heating intensity with net flow in the left or right direction characterized by a pitchfork bifurcation. The efficiency of this technique can be controlled using the wavelength of heating. Thermal drift represents a pattern interaction effect. Its strength depends on the relative …

When To Hold And When To Fold: Studies On The Topology Of Origami And Linkages, Mary Elizabeth Lee

Doctoral Dissertations

Linkages and mechanisms are pervasive in physics and engineering as models for a
variety of structures and systems, from jamming to biomechanics. With the increase
in physical realizations of discrete shape-changing materials, such as metamaterials,
programmable materials, and self-actuating structures, an increased understanding
of mechanisms and how they can be designed is crucial. At a basic level, linkages
or mechanisms can be understood to be rigid bars connected at pivots around which
they can rotate freely. We will have a particular focus on origami-like materials, an
extension to linkages with the added constraint of faces. Self-actuated versions typ-
ically start …

Search For Exotic Higgs Boson Decay To Multiple B-Quarks With The Atlas Detector At Lhc Using Machine Learning Methods, Yuan-Tang Chou

Doctoral Dissertations

The discovery of the Higgs boson has opened up new possibilities for investigating physics beyond the Standard Model (SM). New particles may interact with the SM through the Higgs boson, and deviations from SM predictions can indicate the presence of new physics. This dissertation focuses on the search for exotic Higgs decay, $H\rightarrow aa \rightarrow (b\bbar)(b\bbar)$ where a is a new scalar boson and focuses on the case where the Higgs boson is produced in association with a Z boson. The data were collected by the ATLAS detector at the Large Hadron Collider at center-of-mass energy $\sqrt{s} =~13~\TeV$ from 2015 …