Physical Sciences and Mathematics Commons^™

Diastereoselective Synthesis Of The Hiv Protease Inhibitor Darunavir And Related Derivatives Via A Titanium Tetrachloride-Mediated Asymmetric Glycolate Aldol Addition Reaction, Jordan M. Witte, Emmanuel Ayim, Christopher J. Sams, Jasmine B. Service, Caitlyn C. Kant, Lillian Bambalas, Daniel Wright, Austin Carter, Kelly Moran, Isabella G. Rohrig, Gregory M. Ferrence, Shawn R. Hitchcock

Faculty Publications – Chemistry

Darunavir is a potent HIV protease inhibitor that has been established as an effective tool in the fight against the progression of HIV/AIDS in the global community. The successful application of this drug has spurred the development of derivatives wherein strategic regions (e.g., P1, P1’, P2, and P2’) of the darunavir framework have been structurally modified. An alternate route for the synthesis of darunavir and three related P1 and P1’ derivatives has been developed. This synthetic pathway involves the use of a Crimmins titanium tetrachloride-mediated oxazolidine-2-thione-guided asymmetric glycolate aldol addition reaction. The resultant aldol adduct introduces the P1 fragment of …

Immobilization Of Thiol-Modified Horseradish Peroxidase On Gold Nanoparticles Enhances Enzyme Stability And Prevents Proteolytic Digestion, Faith E. Breausche, Annelise Somerlot, Jason Walder, Kwame Osei, Samuel Okyem, Jeremy D. Driskell

Faculty Publications – Chemistry

The specificity and efficiency of enzyme-mediated reactions have the potential to positively impact many biotechnologies; however, many enzymes are easily degraded. Immobilization on a solid support has recently been explored to improve enzyme stability. This study aims to gain insights and facilitate enzyme adsorption onto gold nanoparticles (AuNPs) to form a stable bioconjugate through the installation of thiol functional groups that alter the protein chemistry. In specific, the model enzyme, horseradish peroxidase (HRP), is thiolated via Traut’s reagent to increase the robustness and enzymatic activity of the bioconjugate. This study compares HRP and its thiolated analog (THRP) to deduce the …

Promoting Thermal Conductivity Of Alumina-Based Composite Materials By Systematically Incorporating Modified Graphene Oxide, Nawon Lee, Jinsol Park, Nayeon Jang, Sehui Lee, Dayeon Kim, Sanggin Yun, Tae Woo Park, Jun-Hyun Kim, Hyun-Ho Park

Faculty Publications – Chemistry

Small amounts of thermally conductive graphene oxide (GO) and modified GO are systematically introduced as a second filler to thermal interface materials (TIMs) consisting of alumina (Al2O3) particles and polydimethylsiloxane (PDMS). The surface of GO is covalently linked with an organic moiety, octadecylamine (ODA), to significantly improve the miscibility and dispersity of GO across the TIM matrix. Subsequently, two series of PDMS-Al2O3 composite TIMs are manufactured as a function of GO and ODA-GO content (0.25 wt%–2.5 wt%) to understand the effect of these second additives. The incorporation of GO into the Al2O3-PDMS composite materials generally increases the thermal conductivity (TC), …

Identifying Quantum Interference Effects From Joint Conductance–Thermopower Statistics, Justin P. Bergfield

Faculty Publications – Chemistry

Although quantum effects are thought to dominate the heat and charge transport through molecular junctions, large uncertainties in chemical structure, lead-molecule coupling strengths, and energy levels make it difficult to definitively identify these effects from the measured thermopower S and conductance G distributions alone. Here, we develop a simple statistical method to identify destructive quantum interference features (nodes) through the anticorrelation between simultaneously measured G and S values. We find these correlations can be used to unambiguously identify far-detuned nodes, even when G and S distributions alone cannot. As an example, we consider several para- and meta-configured systems, including benzenediamine …

Assessment Of Conjugation Pathways In N-Methylporphyrins That Are Fused To Acenaphthylene, Phenanthrene Or Pyrene: Evidence For The Presence Of Alternative Aromatic Circuits, Jared S. Salrin, Brian G. Carpenter, Deyaa Abusalim, Timothy D. Lash

Faculty Publications – Chemistry

Acenaphtho-, phenanthro-, and pyrenopyrrole esters, readily available from Barton-Zard reactions of ethyl isocyanoacetate with nitroarenes, were reacted with methyl iodide and KOH in DMSO to give N-methylpyrroles and subsequent cleavage of the ester moieties was accomplished with KOH in ethylene glycol at 200 °C. Condensation with two equiv of an acetoxymethylpyrrole in refluxing acetic acid-2-propanol afforded a series of annulated tripyrranes. Cleavage of the terminal tert-butyl ester groups with trifluoroacetic acid, followed by condensation with a diformylpyrrole and oxidation with FeCl3, gave N-methyl acenaphtho-, phenanthro-, and pyrenoporphyrins. The N-methyl substituent effectively freezes the tautomeric equilibria to maximize interactions between the …

The Oral-Microbiome-Brain Axis: A Thorough Review On The Relationship Between Periodontitis And Alzheimer’S Disease And A Proposed Innovative Application Of Biomagnetism As A Means Of Alternative Therapy., Taha Al Hassan, Noah Al-Hassan, Maria Quiñones-Peña, Juan Lopez-Alvarenga, Seratna Guadarrama-Beltran

MEDI 9331 Scholarly Activities Clinical Years

The relationship between periodontitis and Alzheimer's disease (AD) has garnered significant attention due to the potential influence of chronic oral inflammation on neurodegenerative processes. Our hypothesis is supported by the oral-microbiome-brain axis and highlights the possibility that chronic periodontitis contributes to cognitive decline by promoting systemic inflammation and neuroinflammation, mediated by specific pathogenic microorganisms within the oral microbiome. Our findings reveal a strong association between elevated levels of Porphyromonas gingivalis and Treponema denticola, red complex bacteria, and markers of systemic inflammation, such as C-reactive protein (CRP) and pro-inflammatory cytokines. Additionally studies have demonstrated that beta amyloid plaque in rat …

Reinforcement Learning: Applying Low Discrepancy Action Selection To Deep Deterministic Policy Gradient, Aleksandr Svishchev

College of Graduate Studies: Theses & Dissertations

Reinforcement learning (RL) is a subfield of machine learning concerned with agents learning to behave optimally by interacting with an environment. One of the most important topics in RL is how the agent should explore, that is, how to choose actions in order to rate their impact on long-term reward. For example, a simple baseline strategy might be uniformly random action selection. This thesis investigates the heuristic idea that agents will learn faster if they explore by factoring the environment’s state into their decision and intentionally choose actions which are as different as possible from what they have previously observed. …

Exploring The Consistency Of Flow Regimes Within And Among Ecoregions Of The Southeastern United States, Frank Paul Braun Iv

College of Graduate Studies: Theses & Dissertations

Human manipulation of river systems has long been a known contributor to the loss of freshwater biodiversity. By accounting for environmental causes of hydrologic variation among rivers, we can better understand how ecoregion mediates flow regimes and forecast species that may be at risk. Presumably, natural variation associated with ecoregion boundaries exerts strong influence on flow regimes, and may mediate relationships between other features (e.g., land use, dam operations) and hydrology. However, such between-ecoregion variation is poorly investigated, particularly at fine spatial and temporal scales. I characterized 10 hydrologic metrics, representing the five key dimensions of the flow regime (magnitude, …

Bringing Gans To Medieval Times: Manuscript Translation Models, Tonilynn M. Holtz

College of Graduate Studies: Theses & Dissertations

The Generative Adversarial Networks (GAN) recently emerged as a powerful framework for producing new knowledge from existing knowledge. These models aim to learn patterns from input data then use that knowledge to generate output data samples that plausibly appear to belong to the same set as the input data. Medieval manuscripts study has been an important research area in the humanities field for many decades. These rare manuscripts are often times inaccessible to the general public, including students in scholars, and it is of a great interest to provide digital support (including, but not limited to translation and search) for …

Assessing Performance Optimization Strategies In Cloud-Native Environments Through Containerization And Orchestration Analysis, Daniel E. Ukene

College of Graduate Studies: Theses & Dissertations

This thesis comprises three distinct, yet interconnected studies addressing critical aspects of web infrastructure management. We begin by studying containerization via Docker and its impact on web server performance, focusing on Apache and Nginx hosted on virtualized environments. Through meticulous load testing and analysis, we provide insights into the comparative performance of these servers, adding users of this technology know which webservers to leverage when hosting their webservice along alongside the infrastructure to host it on. Next, we expand our focus to examine the performance of caching systems, namely Redis and Memcached, across traditional VMs and Docker containers. By comparing …

Scattering Of Electromagnetic Radiation By Bianisotropic Spheres, Maxwell A. Wallace

College of Graduate Studies: Theses & Dissertations

Modern developments in materials science have led to the increased demand for the ability to control electromagnetic radiation at scales smaller than ever. One of the most important areas of research for controlling the manipulation of electromagnetic radiation, has been the studying of novel optical metamaterials, including the most general and complex form, bianisotropic metamaterials (BAMs). With modern developments in nano- engineering, paired with the advancement of more robust theoretical studies of BAMs, the demand for more novel BAM technologies has increased. With the advent of research of unbounded BAM media, as well as the recent extensions of Mie theory …

Characterization Of Carbon Nanotube/Polystyrene Composites Prepared Via Microwave-Induced Polymerization, Hubert Agamasu

College of Graduate Studies: Theses & Dissertations

Carbon nanotubes (CNTs), with their excellent mechanical properties, are well suited to the production of composites with good strength-to-weight ratio. However, the use of nanotubes as reinforcement is hampered by the lack of interaction between their inert surfaces and matrices. This, coupled with the van der Waal’s interactions between individual nanotubes, leads to agglomeration of CNTs in media. Functionalization is an efficient means to disperse nanotubes as well as increase their reactivity. The irradiation of CNTs with microwaves generates instantaneous, localized heating, being used in this work to trigger the rapid, thermal, free radical polymerization of styrene. Under microwaves, olefin-functionalized …

Enumeration Of Lattice Paths With Restrictions, Vince White

College of Graduate Studies: Theses & Dissertations

Lattice path enumeration, through the lens of Catalan numbers, plays a crucial role in combinatorics. This thesis delves into enumerations of some of the most common lattice paths – north-east paths, up-down paths, and Dyck paths – with restrictions applied. The first restriction is counting north-east lattice paths that only cross the diagonal line, y=x, once. The second form of lattice paths with restrictions is up-down paths that cross the x-axis exactly once and fall to a fixed depth of k. While working through this module, a novel proof for a known integer sequence was used, then applied to generate …

A Comparative Analysis Of A Family Of Advanced Iterative Optimization Methods In Nonlinear Regression, Tanmoy Kumar Debnath

College of Graduate Studies: Theses & Dissertations

Classical statistical supervised learning optimization techniques like the Gauss-Newton Iterative Method (GNIM), Weighted Gauss-Newton Iterative Method (WGNIM), Reweighted Gauss-Newton Iterative Method (RGNIM), and Levenberg-Marquart (LM) algorithm extend the nonlinear least squares method. The WGNIM improves model fitting by controlling heteroscedasticity in the linear and nonlinear models. A comparative analysis of the GNIM, WGNIM, RGNIM, and LM methods for fitting nonlinear models is presented. A step-wise diagnosis for structural multicollinearity in the reweighted linearized model is investigated via the Variance Inflation Factor (VIF) to determine variance inflation in the sequence of estimators for the model parameters. Under restricted multicollinearity levels in …

Mathematical Modeling Of Coupled Heat And Mass Transfer In Metal-Hydride Hydrogen Storage Systems, Muhammad Hasnain

College of Graduate Studies: Theses & Dissertations

As a promising clean energy carrier hydrogen has recently gained significant interest, but its efficient and safe storage is a major challenge. Compared to the gaseous state and liquid state, metal hydrides (MH) offer a potentially more effective storage approach for hydrogen. However, the main challenge in this approach is the low thermal conductivity of the MH bed that leads to low heat transfer and ultimately to higher charging and discharging times. The purpose of this work is to develop an in-house comprehensive heat and mass transfer model for hydrogen sorption in MH reactors to simulate the dynamic behavior of …

The De Rham Cohomology Of A Lie Group Modulo A Dense Subgroup, Brant Clark

College of Graduate Studies: Theses & Dissertations

Let $H$ be a dense subgroup of a Lie group $G$ with Lie algebra $\LG$. We show that the (diffeological) de Rham cohomology of $G/H$ equals the Lie algebra cohomology of $\LG/\LH$, where $\LH$ is the ideal \mbox{$\{Z\in\LG:\e{tZ}\in H \text{ for all } t\in\RR\}$}

Geoelectrical And Hydrochemical Characterization Of Submarine Groundwater Discharge In Florida Bay, Ifeanyi Emmanuel Eze

College of Graduate Studies: Theses & Dissertations

Florida Bay, situated at the southern tip of Everglades National Park and underlain by the Miami Limestone formation, is an ecosystem of global significance. Over the past century, the bay has faced threats such as droughts, seagrass mortality, and hypersalinity. Despite various studies and management efforts, the dynamics of submarine groundwater discharge (SGD) in the region remain underexplored. Given that SGD plays a significant role in the chemical dynamics of coastal ecosystems, it warrants thorough investigation. This study aims to characterize the spatial and temporal patterns of SGD in Florida Bay by surveying three basins – Rankin, Whipray, and Rabbit …

Concentration Effects Of Ytterbium(Iii) Ions On The Physical, Structural, Thermal, And Optical Properties Of Barium Phosphate Glasses, Richard Amesimenu

College of Graduate Studies: Theses & Dissertations

Ytterbium(III)-doped glasses are widely known for their application in near-infrared (NIR) lasers and nowadays attract attention for solar spectral conversion in photovoltaic cells. In this study, the effects of ytterbium(III) concentration on the physical, structural, optical, and thermal characteristics of Yb-doped phosphate glasses were investigated. The glasses were synthesized using the melt-quenching technique with nominal compositions of 50P₂O₅:(50 – xBaO):xYb₂O₃ (x = 0, 0.5, 1.0, 2.0, 3.0 and 4 mol%). The properties were then examined by density and related parameters, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform-infrared …

Investigating The Ultrafast Dissociation Dynamics Of Energetic Materials Using Femtosecond Time-Resolved Mass Spectrometry, Jacob M. Shusterman

Theses and Dissertations

Shock initiation of energetic materials produces cations and anions that can contribute to initial endothermic chemical reactions which lead to detonation. Hence, knowledge of the initial dissociation pathways of ionized energetic molecules is important for advancing the understanding of initiation mechanisms and meeting longstanding goals of the Department of Defense. Despite their potential importance, these transient charged species are difficult to detect in detonation experiments and are often ignored in molecular dynamics modeling of shocked energetic materials. However, the technique of pump-probe femtosecond time-resolved mass spectrometry (FTRMS) paired with complementary theoretical calculations can be used to elucidate initial unimolecular dissociation …

Graph Coloring Reconfiguration, Reem Mahmoud

Theses and Dissertations

Reconfiguration is the concept of moving between different solutions to a problem by transforming one solution into another using some prescribed transformation rule (move). Given two solutions s₁ and s₂ of a problem, reconfiguration asks whether there exists a sequence of moves which transforms s₁ into s₂. Reconfiguration is an area of research with many contributions towards various fields such as mathematics and computer science.
The k-coloring reconfiguration problem asks whether there exists a sequence of moves which transforms one k-coloring of a graph G into another. A move in this case is a type …

Redesign, Evaluation, And Validation Of A Commercially Viable High-Resolution Melt Based Mixture Screening Tool, Chastyn Smith

Theses and Dissertations

Analysis of evidentiary samples containing DNA from multiple contributors (“mixtures”) is a time intensive process for a forensic analyst and one where the contributor nature of a sample is not revealed until the end of the traditional forensic workflow. Often, at this stage, retesting or additional testing of mixture samples may not be possible, particularly if the DNA collection device did not preserve the DNA well enough; consequently leaving only trace amounts of a contributor’s DNA present. Thus, a new collection device that would allow for the increased preservation/integrity of evidentiary samples as well as a method that would allow …

Optimizing Deep Inspiration Breath Hold Technique For Personalized Breast Cancer Radiotherapy, Srinidhi Rajagopalan

Theses and Dissertations

The purpose of this research is entrenched in advancing the practice of 3D Conformal Radiation Therapy (3D CRT) for breast cancer patients by meticulously evaluating the impact of different Deep Inspiration Breath Hold (DIBH) techniques on dosimetric parameters. This study aims to ascertain the quantitative benefits of varied breathing techniques, primarily focusing on the 'Ultimate DIBH' method's efficacy in sparing critical organs such as the heart and lungs.

The comprehensive analysis of different DIBH techniques in this research is not merely an academic exercise but is geared towards substantiating the hypothesized advantages of these techniques with empirical data. By generating …

Illuminating Function And Enabling Inhibition At The Protein-Membrane Interface Of Glutathione Peroxidase 4., Courtney L. Labrecque

Theses and Dissertations

Membrane proteins act as gateways to cells and are responsible not only for signaling, lipid transport, and cellular homeostasis, but they are also integral in disease pathologies. One class of membrane proteins, peripheral membrane proteins (PMPs), reside in aqueous compartments of the cell until they are recruited to the membrane to perform their function. Glutathione peroxidase 4 (GPx4) is a PMP enzyme responsible for engaging the membrane and reducing lipid hydroperoxides, thereby preventing cellular death via ferroptosis. Due to its central function surrounding ferroptosis, GPx4 is an interesting drug target that has recently gained interest for inflammatory diseases as well …

Elucidation Of The Optical Properties Of Si And Si-Ge Alloy Nanostructures With Visible To Near-Ir Photoluminescence, Griffin Spence

Theses and Dissertations

Silicon and silicon-germanium alloy nanostructures have garnered increasing attention in the past 25 years due to their favorable optical properties, visible to near-IR luminescence, and inherently low toxicity. While many synthetic routes have been discussed in the literature, the high-temperature, solid-state disproportionation of hydrogen silsesquioxane (HSQ) has become the most popular way to produce highly crystalline, size-tunable Si and Si-based nanostructures (NCs). It has been shown in this work that maximum annealing temperature from 450°-1100°C and the addition of GeI₂or SnCl₄ precursors can be used to achieve different morphologies, alloying efficiency, and sizes. Directly annealing HSQ from …

Mathematical Modeling And Analysis Of Inflammation And Tissue Repair: Lung Inflammation And Wound Healing In Corals Under Stress, Quintessa Hay

Theses and Dissertations

A variety of insults, including tissue injury and/or exposure to pathogen, elicit an immune response in many organisms. An improperly regulated immune response can result in deleterious effects to the organism. Here we present models for lung injury in young and old mice and models for wound healing in coral reefs.

It is well known that the immune response becomes less effective in older individuals. This is of particular interest in pulmonary insults such as ventilator induced lung injury (VILI) or lung infection. We extended a mathematical model for the inflammatory response to VILI and used experimental data to select …

Large Language Models, Prompting, And Synthetic Data Generation For Continual Named Entity Recognition, Charles I. Cutler

Theses and Dissertations

With the ever-growing amount of textual data, the task of Named Entity Recognition (NER) is vital to Natural Language Processing (NLP), a field which focuses on enabling computers to understand and manipulate human language. NER enables the extraction of information from unstructured text. Accurate information extraction is crucial for applications ranging from information retrieval to systems for question-answering. To ensure that NER models are robust to changes in data distributions and capable of recognizing new entity types, one may consider expanding the capabilities of an existing model. Continual learning is a paradigm within machine learning. It studies the objective of …

Towards Effective Developer Communication In Open Source Software Via Emotional Awareness, Mia Mohammad Imran

Theses and Dissertations

Emotions play an integral yet understudied role in open-source software development, profoundly shaping critical collaborative processes such as knowledge sharing, decision-making, and team dynamics. However, accurately detecting and analyzing emotions in developer communications poses significant challenges due to the lack of visual and auditory cues in text-based interactions. This dissertation investigates techniques to enhance the understanding and modeling of emotions within the textual artifacts of open-source projects. We conduct an extensive evaluation of existing emotion classification tools using a novel dataset of annotated GitHub comments. An error analysis reveals deficiencies in handling implicit emotional expressions and figurative language. We demonstrate …

Problems In Graph Theory With Applications To Topology And Modeling Rna, Rayan K. Ibrahim

Theses and Dissertations

In this thesis, we explore four projects. In the first project, we explore $r$-neighbor bootstrap percolation on a graph $G$. We establish upper bounds for the number of vertices required to percolate in the case that $r=2$ for particular classes of graphs. In the second project, we study the structure of graphs with independence number two. We prove a lower bound on the number of edges of such graphs, related to an upper bound on the number of edges in a triangle-saturated graph, and give a sufficient forbidden induced subgraph condition for independence number two graphs. In the third project, …

Mathematical Analysis Of Eukaryotic Pericentromere, Puranjan Ghimire

Theses and Dissertations

The centromere is crucial for chromosomal stability and their proper segregation during cell division in eukaryotes. Surrounding the centromere are pericentromeres, made of repetitive DNA elements called pericentromeric repeats, varying from 10 in fission yeast to thousands in humans. These repeats form densely packed heterochromatin, where genes are usually silenced. The silencing mechanism across different pericentromeric repeats remains unclear.

Despite variations in sequence and length, pericentromeric repeats are conserved across eukaryotes, indicating their functional importance. This dissertation presents mathematical models to quantify gene silencing in fission yeast and humans. In fission yeast, my model predicts that silencing occurs only with …

Mathematical Modeling Of Phage-Bacteria Population Dynamics, John Lawrence D. Palacios

Theses and Dissertations

Bacteriophages are viruses that infect and replicate within bacteria. Lytic phages cause the bacterial cell to burst, killing the bacteria. These types of phages can be used to treat patients with antibiotic-resistant bacterial infections. As a step in developing successful treatment protocols, we aim to understand the population dynamics of phages and bacteria using an in vitro model. We model the dynamics using the Campbell model, which consists of a delay differential equation (DDE), as a base model. We extended the model by including the emergence of phage resistance. We then compared the DDE model with a parallel ordinary differential …