Physical Sciences and Mathematics Commons^™

"Reeling In" Juvenile Sportfish Through Coastal Habitat Restoration: Population, Community, And Trophic Responses In The Indian River Lagoon, Florida, Jennifer Loch

Electronic Theses and Dissertations, 2020-2023

Coastal habitats provide crucial nursery habitat for predatory fishes, but they are in decline worldwide, impacting economically important fisheries. Habitat restoration can simultaneously mitigate the effects of habitat loss and benefit predators (e.g., sportfish), although this relationship is understudied. Here, the response of juvenile sportfish to oyster reef and living shoreline restoration is compared to controls in the Indian River Lagoon, Florida prior to and following restoration for up to three years through examination of community (diversity, assemblage), population (abundance), biometric (size, body condition), ontogenetic, and trophic (gut contents, stable isotopes) dynamics. Stable isotopes were used to quantify dietary history, …

Development Of Holographic Phase Masks For Wavefront Shaping, Nafiseh Mohammadian

Electronic Theses and Dissertations, 2020-2023

This dissertation explores a new method for creating holographic phase masks (HPMs), which are phase transforming optical elements holographically recorded in photosensitive glass. This novel hologram recording method allows for the fast production of HPMs of any complexity, as opposed to the traditional multistep process, which includes the design and fabrication of a master phase mask operating in the UV region before the holographic recording step. We holographically recorded transmissive HPMs that are physically robust (they are recorded in a silicate glass volume), can handle tens of kilowatts of continuous wave (CW) laser power, are un-erasable, user defined, require no …

Graph Neural Networks For Improved Interpretability And Efficiency, Patrick Pho

Electronic Theses and Dissertations, 2020-2023

Attributed graph is a powerful tool to model real-life systems which exist in many domains such as social science, biology, e-commerce, etc. The behaviors of those systems are mostly defined by or dependent on their corresponding network structures. Graph analysis has become an important line of research due to the rapid integration of such systems into every aspect of human life and the profound impact they have on human behaviors. Graph structured data contains a rich amount of information from the network connectivity and the supplementary input features of nodes. Machine learning algorithms or traditional network science tools have limitation …

Balancing User Experience For Mobile One-To-One Interpersonal Telepresence, Kevin Pfeil

Electronic Theses and Dissertations, 2020-2023

The COVID-19 virus disrupted all aspects of our daily lives, and though the world is finally returning to normalcy, the pandemic has shown us how ill-prepared we are to support social interactions when expected to remain socially distant. Family members missed major life events of their loved ones; face-to-face interactions were replaced with video chat; and the technologies used to facilitate interim social interactions caused an increase in depression, stress, and burn-out. It is clear that we need better solutions to address these issues, and one avenue showing promise is that of Interpersonal Telepresence. Interpersonal Telepresence is an interaction paradigm …

Development Of An Hipsc-Cortical Neuron Long-Term Potentiation Model And Its Application To Alzheimer's Disease Modeling And Drug Evaluation, Kaveena Autar

Electronic Theses and Dissertations, 2020-2023

Alzheimer's disease (AD) is commonly characterized by a loss of cognitive function due to the deterioration of neuronal synapses from the presence of senile amyloid beta-42 (Aß42) plaques. Evaluating cognitive deficits caused by Aß42 using human cortical neurons poses a challenge due to sourcing difficulties, and the use of animal models to assess drug efficacy creates biological hurdles from lack of species translatability. Recent advances in induced-pluripotent stem cell technology have enabled the development of mature, human-based cortical neuron models. The development of an hiPSC-cortical neuron differentiation protocol facilitates the exploration of disease onset and functional analysis from a patient-derived …

The Site Evaluation Of Quercus Alba Metabolites, Zachary Alexander Byrd

Theses and Dissertations--Plant and Soil Sciences

Quercus alba has been the prominent tree species utilized in the spirits industry for decades. Of its many qualities, the ability to impart desirable flavors on spirits combined with its natural abundance makes it the ideal choice for barrels. Creating barrels is a uniform process, but variability still exists in aged spirits even when all other parameters are controlled. In this thesis, I explore how the origin of Quercus alba influences metabolite variability.

Quercus alba is a resilient species that can grow in many climates. This is seen through Quercus alba’s vast growing range, of which barrel quality white oak …

Surface Engineering For Controlled Growth And Deposition Of Nanomaterials - Assembly And Design At The Nano-Microscale, David Fox

Electronic Theses and Dissertations, 2020-2023

Materials with nanoscale dimensions offer several important benefits over bulk materials (e.g. increased surface area, low-cost, deviation from bulk properties, etc.). Such materials are critical components for next-generation energy storage materials, optoelectronic devices, and catalyst systems. However, these materials are often processed in liquid media, and their diminutive structures are fragile in the presence of capillary forces. As such, preparing uniform and stable nanomaterial coatings is a significant challenge. Herein, we discuss an approach where the substrate itself is factored into the assembly and growth of these materials. First, nanoporous surfaces were utilized to achieve a uniform deposition of one-dimensional …

Change Point Detection For Streaming Data Using Support Vector Methods, Charles Harrison

Electronic Theses and Dissertations, 2020-2023

Sequential multiple change point detection concerns the identification of multiple points in time where the systematic behavior of a statistical process changes. A special case of this problem, called online anomaly detection, occurs when the goal is to detect the first change and then signal an alert to an analyst for further investigation. This dissertation concerns the use of methods based on kernel functions and support vectors to detect changes. A variety of support vector-based methods are considered, but the primary focus concerns Least Squares Support Vector Data Description (LS-SVDD). LS-SVDD constructs a hypersphere in a kernel space to bound …

Genomic Analysis Of Pollen Grains For Forensic Applications, Luz Kelley

Electronic Theses and Dissertations, 2020-2023

With over 300,000 plant species on the planet and more than 90% of them relying on pollen for reproduction, palynology, the study of pollen grains plays a vital role in many research fields. One of them is forensic palynology, which uses pollen as a proxy to link individuals or objects to a location or instance. It relies on the fact that (1) pollen is an ever-present feature of the environment; (2) different locations have different pollen signatures, allowing for inference related to spatial tracking; (3) plants bloom at different times, allowing for temporal inference; and (4) pollen is exceptionally durable …

Translations To Support Loop Invariant Generation In Jml, Kohei Koja

Electronic Theses and Dissertations, 2020-2023

Software is used in many critical systems in the real world such as autonomous cars and medical devices. Such software must be reliable to protect the general public. One standard way to make reliable software is to use Hoare-style verification techniques. However, for Hoare-style verification of loop correctness, loop invariants are necessary but are difficult for people to write themselves. Since Java is one of the most popular programming languages in the world, it is useful to have a tool to generate loop invariants for Java programs. OpenJML is a widely used program verification tool for Java. However, it does …

Distance Perception Through Head-Mounted Displays, Sina Masnadi

Electronic Theses and Dissertations, 2020-2023

It has been shown in numerous research studies that people tend to underestimate distances while wearing head-mounted displays (HMDs). We investigated various possible factors affecting the perception of distance is HMDs through multiple studies. Many contributing factors has been identified by researchers in the past decades, however, further investigation is required to provide a better understanding of this problem. In order to find a baseline for distance underestimation, we performed a study to compare the distance perception in real world versus a fake headset versus a see-through HMD. Users underestimated distances while wearing the fake headset or the see-through HMD. …

Effficient Graph-Based Computation And Analytics, Bingbing Rao

Electronic Theses and Dissertations, 2020-2023

With data explosion in many domains, such as social media, big code repository, Internet of Things (IoT), and inertial sensors, only 32% of data available to academic and industry is put to work, and the remaining 68% goes unleveraged. Moreover, people are facing an increasing number of obstacles concerning complex analytics on the sheer size of data, which include 1) how to perform dynamic graph analytics in a parallel and robust manner within a reasonable time? 2) How to conduct performance optimizations on a property graph representing and consisting of the semantics of code, data, and runtime systems for big …

Computational And Experimental Studies Of Adsorption And Reactions On Molybdenum Nitride And Silica Covered Ruthenium Surfaces, Muhammad Sajid

Electronic Theses and Dissertations, 2020-2023

Fundamental studies of material surfaces are of continued interest to the development and improvement of many modern technologies, e.g. catalysis, energy efficient electronics, and high-capacity batteries etc. This dissertation targets two distinct sets of molecule-surface interactions relevant to the continued development of structure-property correlations using tools from Density Functional Theory with added verification from ultrahigh vacuum surface-science experiments. These include Haber-Bosch interactions at molybdenum-nitride surfaces and separation-dependent interactions between simple aromatics and Ru(0001) used to model a metal contact of Organic Electronic Devices (OEDs). In the first study, we focus on computational modelling of nitrogen fixation reactions on Mo- and …

Methods For Defending Neural Networks Against Adversarial Attacks, Sharvil Shah

Electronic Theses and Dissertations, 2020-2023

Convolutional Neural Networks (CNNs) have been at the frontier of the revolution within the field of computer vision. Since the advent of AlexNet in 2012, neural networks with CNN architectures have surpassed human-level capabilities for many cognitive tasks. As the neural networks are integrated in many safety critical applications such as autonomous vehicles, it is critical that they are robust and resilient to errors. Unfortunately, it has recently been observed that deep neural network models are susceptible to adversarial perturbations which are imperceptible to human vision. In this thesis, we propose a solution to defend neural networks against white box …

Optimization-Based Approaches To Low-Coherence Optical Diffraction Tomography, Seth Smith-Dryden

Electronic Theses and Dissertations, 2020-2023

Quantitative optical phase imaging techniques, such as optical diffraction tomography (ODT), are useful tools for refractive-index profiling. Many of them, however, rely on the weak-scattering assumptions, thus cannot be applied to multiple-scattering objects, or turbid media. In this thesis, I report several approaches for expanding the efficacy of ODT techniques and adapting them to new applications by use of low-coherence broadband illumination. First, I developed a method for ODT reconstruction using regularized convex optimization with a new phase-based fidelity criterion. The new criterion is necessary because objects with very different refractive-index distributions may produce similar diffracted fields (magnitude and principal-phase) …

Static Analysis Of The Build System To Accelerate Continuous Testing Of Highly Configurable Software, Necip Fazil Yildiran

Electronic Theses and Dissertations, 2020-2023

Continuous testing is widely used for facilitating fast and reliable software delivery. However, build-time configurability makes such testing harder for configurable software. As configurable software forms the basis of much of our computing infrastructure, there is even more need for better continuous testing for configurable software. In this dissertation, our goal is to improve the quality of configurable software. To this end, we tackle two, previously unsolved problems. The build system of configurable software is one of the biggest reasons why testing configurable software is hard. Therefore, in our solutions, we deal with the build system by using a comprehensive …

Synergistic Impacts Of Climate Change And Human Induced Stressors On The Apalachicola Bay Food Web, Kira Allen

Electronic Theses and Dissertations, 2020-2023

Apalachicola Bay, an estuary located in northwest Florida, is likely to experience an increase in climate change and human-induced stressors, such as sea level rise and changes in freshwater inflow, in the future. A coupled hydrodynamic and food web modeling approach was used to simulate future scenarios of low and high river flow and sea level rise in Apalachicola Bay from 2020 to 2049 and demonstrate the range of temporal and spatial changes in water temperature, salinity, fisheries species populations and the broader food web. Concurrent with model development, a survey of Apalachicola Bay stakeholders was conducted to assess stakeholder …

Towards Leveraging Sparse Infrared Datasets For Multiple View Synthesis, Few Shot Learning And Background Invariant Recognition, Maliha Arif

Electronic Theses and Dissertations, 2020-2023

This dissertation presents a study of various machine learning techniques for recognizing vehicular objects in infrared images. State of the art methods for computer vision have not been widely explored for this part of the electromagnetic spectrum (EM). Challenges that arise due to the dearth of infrared training images, terrain clutter, and thermal phenomenology have not been fully addressed. Infrared dataset collection and annotation is both difficult and expensive. What if there is a way we can generate infrared images and diminish the need for collecting data out in the field? Our first research study encompasses an encoder-decoder model that …

Third Order Nonlinear Optics In Solids, Nicholas Cox

Electronic Theses and Dissertations, 2020-2023

Nonlinear optical effects occur when strong electromagnetic waves induce changes in a medium that affect its own propagation or that of another wave. Third order optical nonlinearities scale linearly with irradiance and lead to effects like two-photon absorption and nonlinear refraction. This work focuses on the experimental and theoretical study of two-photon absorption in crystalline solids. We begin by detailing the quantum mechanical states of electrons in solids along with the computational approaches to calculate their band structure. Next, a theoretical model for the linear and nonlinear optical interaction of light with matter is presented in a many-body formalism. This …

Impacts Of Plastic Pollution On A Pelagic Marine Mammal, The Northern Elephant Seal, Lauren M. Kashiwabara

University of the Pacific Theses and Dissertations

As plastic pollution increases, top marine predators such as marine mammals are becoming increasingly susceptible to plastic particles and their additives. Plastic particles have been found in gastrointestinal tracts and scat of many marine mammals, and quantifying plastic pollution in those that are pelagic can provide insight into plastic pollution in mesopelagic ecosystems that are just beginning to be analyzed. Adapting well-developed laboratory techniques for microplastic (MP) isolation (i.e. density separation and chemical digestion), I isolated MPs from the scat of the deepest diving pinniped, the northern elephant seal (NES), and found that100% of scat samples (n=11) contained high counts …

Understanding The Impacts Of Urban Agriculture In Gentrifying Neighborhoods In Denver, Kate Johnson

Electronic Theses and Dissertations

Urban Agriculture is prominent in cities across the United States and has been studied in relation to food security, sustainability, and gentrification. Urban agriculture is context specific and can include individual gardens, community gardens, guerilla gardening, and urban farms. Urban agriculture is a product of the community it is based in, depending on politics, history, and social environments. For these reasons, the relationship between urban agriculture and the community is an area where more research is needed. This thesis explores the role visible gardens play in community building, sustainability, and food security in gentrifying neighborhoods in Denver. Through qualitative methods …

Investigating Spatiotemporal Kinetics, Dynamics, And Mechanism Of Exosome Release, Anarkali Mahmood

Electronic Theses and Dissertations

Exosomes are small lipid-based vesicles that can carry biomolecules from one cell to another. While exosomes are crucial to maintain homeostasis in healthy cells, they are exploited by unhealthy cells to aid disease progression. Exosomes likely facilitate disease progression via the transfer of disease-causing biomolecules from unhealthy to healthy cells. Exosomes are generated in Multivesicular endosomes (MVEs) and are then secreted into the extracellular space to travel to other cells. Despite being a crucial step, very little is known about exosomes release mechanism and dynamics. To further our understanding of exosomes, specifically their secretion, my work has focused on investigating …

Measurements Of Atmospheric Radicals, Heather L. Runberg

Electronic Theses and Dissertations

Atmospheric particulate matter (PM) is a global health concern. PM_2.5 is formed primarily through combustion processes such as automobile use and industrial activity. Natural sources of PM_2.5 result from events like volcanos and wildfires. Upon inhalation, PM_2.5 is small enough to travel deep into the lungs where it can form reactive oxygen species (ROS), such as hydroxyl radical (OH), causing oxidative damage to pulmonary tissues. PM_2.5 has been linked to cardiopulmonary diseases such as asthma, chronic obstructive pulmonary disease (COPD), and high blood pressure.

PM_2.5 is small enough to remain aloft and travel many hundreds …

Osiris-Rex Surface Imaging To Constrain Properties Of The Asteroid (101955) Bennu, Alicia Allen

Honors Undergraduate Theses

This study used images taken from the OSIRIS-REx spacecraft sample-return mission and projected onto a three-dimensional shape model to determine surface properties of the asteroid (101955) Bennu. Two major projects were completed. For the first project, images of the pre-sampled Nightingale site and post-sampled Nightingale were compared to determine how the TAGSAM sampling maneuver effected the surface of the asteroid directly at the sampling site and in the surrounding area. This analysis demonstrated how spacecraft can potentially affect a small body during this and future sample-return missions. For the second project, several craters on Bennu’s surface were selected and all …

Investigation Of Catalysis Of Nitration By Cytochrome P450s, Lannika Johnson

Honors Undergraduate Theses

TxtE is a protein related to cytochrome P450 enzymes, which catalyze a number of reactions that typically involve oxygen and not nitrogen. It has been discovered that TxtE can nitrate tryptophan through an unusual reaction in which it uses nitric oxide (NO) as a nitrogen donor to install the nitro group despite NO typically being considered toxic to bacteria. This project will determine if all cytochromes P450 can catalyze nitration as long as they are given NO. This will have an impact on understanding drug delivery and metabolism for which nitration is important.

Examining Cooperative System Responses Against Grid Integrity Attacks, Alexander D. Parady

Honors Undergraduate Theses

Smart grid technologies are integral to society’s transition to sustainable energy sources, but they do not come without a cost. As the energy sector shifts away from a century’s reliance on fossil fuels and centralized generation, technology that actively monitors and controls every aspect of the power infrastructure has been widely adopted, resulting in a plethora of new vulnerabilities that have already wreaked havoc on critical infrastructure. Integrity attacks that feedback false data through industrial control systems, which result in possible catastrophic overcorrections and ensuing failures, have plagued grid infrastructure over the past several years. This threat is now at …

Comparative Evaluation Of Assemblers For Metagenomic Data Analysis, Matheus Pavini Franco Ferreira

Honors Undergraduate Theses

Metagenomics is a cultivation-independent approach for obtaining the genomic composition of microbial communities. Microbial communities are ubiquitous in nature. Microbes which are associated with the human body play important roles in human health and disease. These roles span from protecting us against infections from other bacteria, to being the causes of these diseases. A deeper understanding of these communities and how they function inside our bodies allows for advancements in treatments and preventions for these diseases. Recent developments in metagenomics have been driven by the emergence of Next-Generation Sequencing technologies and Third-Generation Sequencing technologies that have enabled cost-effective DNA sequencing …

The Effects Of Viscous Damping On Rogue Wave Formation And Permanent Downshift In The Nonlinear Schrödinger Equation, Evelyn Smith

Honors Undergraduate Theses

This thesis investigates the effect of viscous damping on rogue wave formation and permanent downshift using the higher-order nonlinear Schrödinger equation (HONLS). The strength of viscous damping is varied and compared to experiments with only linear damped HONLS.

Stability analysis of the linear damped HONLS equation shows that instability stabilizes over time. This analysis also provides an instability criterion in the case of HONLS with viscous damping.

Numerical experiments are conducted in the two unstable mode regime using perturbations of the Stokes wave as initial data. With only linear damping permanent downshift is not observed and rogue wave formation is …

Instanton Counting, Matrix Models, And Characters, Spencer Tamagni

Honors Undergraduate Theses

In this thesis we study symmetries of quantum field theory visible only at the non-perturbative level, which arise from large deformations of the integration contour in the path integral. We exposit the recently-developed theory of qq-characters that organizes such symmetries in the case of N = 2 supersymmetric gauge theories in four dimensions. We sketch the physical origin of such observables from intersecting branes in string theory, and the mathematical origin as certain
equivariant integrals over Nakajima quiver varieties. We explain some of the main applications, including the derivation of Seiberg-Witten geometry for quiver gauge theories and the relations to …

Genetic Algorighm Representation Selection Impact On Binary Classification Problems, Stephen V. Maldonado

Honors Undergraduate Theses

In this thesis, we explore the impact of problem representation on the ability for the genetic algorithms (GA) to evolve a binary prediction model to predict whether a physical therapist is paid above or below the median amount from Medicare. We explore three different problem representations, the vector GA (VGA), the binary GA (BGA), and the proportional GA (PGA). We find that all three representations can produce models with high accuracy and low loss that are better than Scikit-Learn’s logistic regression model and that all three representations select the same features; however, the PGA representation tends to create lower weights …