Physical Sciences and Mathematics Commons^™

A Machine Learning Approach To Quantitative X-Ray Diffraction Analysis, Spencer Snow Chandler

Theses and Dissertations

X-ray Powder Diffraction (XRPD) is a powerful method in material sciences that gives insights into the atomical and crystallographic structure of a material, revealing information into the material's properties and suitability for industrial and scientific application. In geology, XRPD analysis is frequently leveraged to identify and quantify the present mineral phases in an unknown mixture. Despite it's widespread use, interpreting XRPD patterns requires highly-specialized knowledge, making the analysis largely dependent upon the background experience of the analyst. To assist experts, computational methods have been developed over the years. Some of these techniques involve fitting diffraction patterns using pseudo-Voigt functions, which …

Approximating Transport Maps Using Minibatch Optimal Transport Plans, Dawson Collins

Theses and Dissertations

Optimal Transport theory (OT) has gained much attention in the past decades due to its rich mathematical content and striking connections to other areas of math. It has also naturally found a place in data science as a way to compare and transform probability measures. Unfortunately, there remain significant computational burdens that restrict its effectiveness in large-scale data regimes. In this thesis, we consider Minibatch Optimal Transport (MiniOT), which breaks up the task of computing the optimal transport plan between datasets into several smaller tasks of computing the optimal transport plan between minibatches of the datasets. After obtaining the minibatch …

The Role Of The Cytosolic Chaperonin Cct In The Folding And Assembly Of G Protein Complexes, Mikaila I. Sass

Theses and Dissertations

All organisms depend on cellular signaling pathways to dictate cell growth, responses to stimuli, and all other cellular functions necessary to maintain health and survival. Many of these signals rely on G protein coupled receptors (GPCRs) and their associated heterotrimeric G proteins for signal detection and transduction. To perform this function, the three subunits of the G protein must be assembled after synthesis on the ribosome. This process requires additional proteins called molecular chaperones to assist in folding of the subunits and assembly into the G protein heterotrimer. Among these chaperones, the cytosolic chaperonin CCT plays an essential role in …

A New Approach To Stability Of Delay Differential Equations With Time-Varying Delays Via Isospectral Reduction, Quinlan Leishman

Theses and Dissertations

Understanding how time delays impact the stability of a delay differential equation is important for modeling many natural and technological systems that experience time delays. Here we introduce a new stability criterion for delay-independent stability of these equations, called intrinsic stability, showing global exponential stability for a large class of nonautonomous nonlinear systems. Our approach is able to incorporate bounded time-varying delays, including those with certain types of discontinuities. The approach we take to prove this result is novel, associating the delay differential equation with a sequence of finite-dimensional matrices of increasing size and using the graph-theoretic technique of isospectral …

Math 112 At Byu: Student Averages On Various Exam Questions, Makayla Mcleod

Theses and Dissertations

In Math 112 at BYU, exams play a crucial role in evaluating students' understanding of the course content. Traditionally, these exams are a combination of multiple-choice and free-response questions, with the latter serving as a means to assess a student's thought process while solving problems. Will students perform as well on a multiple-choice exam? Or will students' averages be higher on free-response exams? In this thesis, we test 7 hypotheses related to these questions to provide more insight into the answer. We examine other factors that may affect students' averages, including various Calculus 1 topics, modes of questioning, and difficulty …

Digital Infrastructure For The Regenerative Movement: A Case Study Of The Mycelium Learning Network, Abigail Karparis

Journal of Nonprofit Innovation

The regenerative movement is gaining momentum worldwide, driven by communities working to restore ecological and social systems through place-based, culturally rooted action. Yet many of the groups leading this work, especially in the Global South or in hyper-local contexts, remain digitally invisible due to structural barriers, including limited access to appropriate technology, funding constraints, and misalignment between available tools and local values. Conventional digital infrastructures often exclude or marginalize these efforts, leaving regenerative practitioners disconnected from each other and from potential sources of support.

This article explores these challenges and presents a case study response: the co-creation of accessible, relational …

Directivity And Sound Radiation Of Percussion Instruments And Harmonic Analysis Of The Alto Saxophone, Hanna Michelle Pavill

Theses and Dissertations

This thesis investigates how musical instruments radiate sound, with a focus on directional behavior under realistic performance conditions. High-resolution measurements using a rotating microphone array were used to study percussion and woodwind instruments, providing new insight into how design, excitation, and frequency content shape acoustic output. The first set of experiments analyzed the directivity of the bass drum, triangle, and open snare. Each instrument exhibited unique radiation patterns reflecting its structure and playing method. The bass drum showed dipole-like behavior at low frequencies, transitioning to omnidirectional spreading at mid frequencies, and increasingly irregular patterns at higher frequencies. The triangle, due …

Low Surface Brightness Features Of Edge-On Galaxies In Deep Sky Surveys, Kyle R. Adams

Theses and Dissertations

In this thesis, we present a comprehensive visual analysis of low surface brightness (LSB) structures in edge-on galaxies using two statistically complete samples: 838 galaxies from the SDSS Stripe 82 region (ES82) and 5,745 galaxies from the Edge-on Galaxies in SDSS (EGIS) catalog, both containing galaxies with spectroscopic redshifts out to 𝑧 ∼ 0.2. Using deep imaging data from the SDSS, SDSS Stripe 82, DESI Legacy Imaging Surveys, and the HSC-SSP, we construct RGB and coadded images for comparison and to improve feature detection. Average limiting photometric depth for each survey in the 𝑟 band for the surveys analyzed in …

Applying Ceragenins In Translational Medicine: Activating Mesenchymal Stem Cells And Preventing Healthcare-Associated Infections, Aaron L. Zaugg

Theses and Dissertations

Healthcare-associated infections are a major global concern. Increased infections among vulnerable populations lead to millions of deaths, annually, complicated by the emergence of multi-drug resistant pathogens. These infections are often facilitated by medical devices serving as abiotic surfaces that facilitate the formation of biofilms. Notably, colonization of prostheses and other bone-associated medical devices can lead to corrective procedures, revisions and death. To address these issues, inspiration can be drawn from natural sources of bone health and defenses against infection. Cathelicidins are endogenous peptides involved in both bone maintenance and infection control. Ceragenins are small molecule mimics of cathelicidins with broad …

Linking Static And Dynamic Structures And Properties Of Materials With Computational And Mathematical Models, (Enoch) Sin Hang Ho

Theses and Dissertations

Terahertz (THz) spectroscopy is an effective technique to study and manipulate the structural dynamics of materials, due to its frequency range being very similar to the vibrational frequencies of collective atom motions in a host of materials. High-field and broadband THz radiation can be generated via optical rectification (OR) in nonlinear optical (NLO) crystals. The efficiency of OR response in an NLO crystal is determined by many factors, including molecular hyperpolarizability (β), 2nd order electric susceptibility (χ(2)), crystal structure, primary growth orientation, refractive index, absorption and phase matching condition. In this dissertation, I will focus on using computation methods and …

The Cellular Mechanisms Of Alzheimer's Disease Protection By The Pilra G78r Variant, Wenhan Cheng

Theses and Dissertations

Microglial dysfunction is increasingly linked to Alzheimer’s Disease (AD). Immune receptors like TREM2 and CD33 play opposing roles in microglial activity. TREM2 activation triggers immunoreceptor tyrosine-based activation motif (ITAM) signaling to promote microglial activities, including amyloid-β clearance, but variants in TREM2 such as R47H that impair its function increase AD risk. In contrast, CD33 is an inhibitory receptor that contains an immunoreceptor tyrosine-based inhibitory motif (ITIM) which transmits signals that suppress microglial function. An AD-protective variant in CD33 alters CD33 activity, potentially enhancing TREM2 function. PILRA is another inhibitory immune receptor expressed by microglia that contains an ITIM. A naturally …

Quantum-Chemical Modeling Of Mechanisms And Selectivity In Open-Shell Organometallic Reactions, Michael T. Davenport

Theses and Dissertations

Quantum mechanical calculations have emerged as a powerful approach for directly evaluating reaction mechanisms and selectivity in transition metal-ligand complexes involving organometallic intermediates. Density functional theory (DFT) quantum mechanical methods enable the generation of potential energy surfaces and structures that define reaction mechanisms and allow for the evaluation of selectivity through statistical transition state theory. However, in certain cases, it is necessary to go beyond statistical treatments and incorporate atomic motion through molecular dynamics simulations. Additionally, many transition metal-mediated reactions involve unpaired electrons and spin state crossings. This dissertation focuses on the application of DFT-derived potential energy surfaces and molecular …

Structural Analysis Of The Aileu Metamorphic Complex And The Laclo Fault Of Timor Leste, Banda Arc-Continent Collision, Emma C. Morrison

Theses and Dissertations

This study presents a structural analysis of the brittle and ductile features within the Aileu Metamorphic Complex of Timor Leste, located in the active Banda Arc–Australian continental collision zone. The deformation history of the complex is interpreted from the Permian–Jurassic deposition of sediments and basalts into intra-arc basins of Gondwana, through to the present- day collision of the Australian continental margin. This collision led to the development of the Wetar Suture and subsequent back-thrusting of the Aileu metamorphic rocks northward over the Banda forearc. Field evidence confirms that the Laclo Fault is currently active, with the most recent movement exhibiting …

How Transitioning Autistic Adults Consciously Perform Neurotypical Communication, Makenna J. Allred

Theses and Dissertations

Using semi-structured interviews this research explored the experiences of transitioning autistic adults with online communication. Participants shared information about navigating online communication, highlighting specific challenges such as interpreting tone and sarcasm, managing unspoken social norms, like emoji use, and responding to ambiguous or unexpected interactions. Participants shared that misunderstandings do occur in their online communication and how they recognize those miscommunications and strategize around preventing and mitigating them. These findings reveal that while computer-mediated communication offers opportunities for connection, it also presents unique obstacles that can exacerbate feelings of frustration due to miscommunications or misunderstandings. To prevent these social frictions …

Semitic Root Encoding: Tokenization Based On The Templatic Morphology Of Semitic Languages In Nmt, Brendan T. Hatch

Theses and Dissertations

The morphological structure of Semitic languages like Arabic and Hebrew is based on non-concatenative roots and templates. This complex word structure used by humans is obscured to neural models that use traditional tokenization algorithms. In this work, I present and evaluate Semitic Root Encoding (SRE), a tokenization method that represents Semitic words with distinct root and template stem tokens, and apply it to neural machine translation (NMT). I evaluate whether tokenization with the SRE method leads to increases in translation quality, whether it allows NMT models to hypothesize unseen word forms needed at inference, and how impervious resulting NMT models …

Building And Demonstrating A Framework And Guide For Human-Centered Threat Modeling, Warda Usman

Theses and Dissertations

As researchers increasingly seek to understand threats faced by people rather than systems, there remains little consensus on how to study these threats in ways that are grounded in human experience. Traditional approaches to threat modeling are often designed for system vulnerabilities and offer limited guidance for eliciting or analyzing threats as understood by individuals in their social and cultural contexts. This dissertation addresses this gap by advancing human-centered threat modeling (HCTM) in security and privacy research as both a conceptual framework and through a set of empirical studies. The dissertation employs a mixed set of qualitative methods across four …

Refinement And Application Of The Absorption Cross-Section Of Molecular Bromine With Relevance To Atmospheric Chemistry, Callum Flowerday, Ryan Thalman, Jaron C. Hansen, Eric T. Sevy, Jason J. Sorensen, Matthew C. Asplund

ScholarsArchive Data

Defined Br2 XS - is the defined absorption cross-section using the UVvis spectrophotometer.

BBCEAS - This is raw absorption data measured using the BBCEAS (see article for details).

UVvis raw - This is the raw absorption data measured using the UVvis spectrophotometer.

Benchtop-Scale High Temperature Molten Salt Electrochemical Reactors: Experimental Setup And Considerations, Haley Hoover, Ivy Wu, Oluwatamilore Olushina, Robert Bell, Kerry Rippy

Reviews, Analyses, and Instructional Studies in Electrochemistry (RAISE)

Molten salt electrochemical reduction (MSER) is the dominant production method for aluminum and titanium, and emerging technologies for producing other commodity metals with these highly electrified techniques have demonstrated promising results. However, the scale up of MSER of materials such as iron and silicon are limited by the challenging issues of materials compatibility and impurity control. This work describes an experimental MSER setup using both chloride and carbonate salts. This setup is designed for operations outside of a glovebox, which is practical from an industrial perspective, but creates unique challenges. This work serves as a practical guide to discuss some …

From The University To The Universe: Byu’S West Mountain Observatory, Amber Zendejas, Dan Broadbent

BYU West Mountain Observatory Project

Brigham Young University’s West Mountain Observatory (WMO) is a research facility that offers primarily undergraduate students valuable mentoring and hands-on learning opportunities. Established in 1981, the observatory was built in response to increasing light pollution in Provo, Utah, which began affecting research at the Orson Pratt Observatory (OPO) atop the Eyring Science Center on the BYU main campus. Before WMO was created, OPO served as the primary observatory for astronomical research at BYU. Construction plans for a new observatory began in the late 1970s, as university planners and astronomers sought a location with minimal light pollution, favorable elevation, relatively easy …

The Conditioning Of Reservoir Computing And Ng-Rc For Forecasting And The Effects Of Temporal Overparameterization, Daniel Jensen

Theses and Dissertations

Reservoir computing and "Next-generation reservoir computing" built on nonlinear vector autoregression are algorithms for predicting time series given past observations. Both algorithms have been successful in predicting some chaotic dynamical systems, but this success is not theoretically well understood. This paper considers the conditioning of both algorithms and the nature of the solutions found. With either algorithm, the least squares problem which is solved to give parameters as a function of the time series data is ill-conditioned, leading to parameter non-identifiability. Both algorithms fall into the class of "sloppy models." Standard practice to regularize either algorithm includes a bias towards …

Gnn Convergence And Accuracy Analysis On Contextual Stochastic Block Models, Trevor Garrity

Theses and Dissertations

Contextual Stochastic Block Models (cSBMs) are simple generative graph models commonly used to benchmark the performance of Graph Neural Networks (GNNs). In this thesis, I prove how inducing symmetries on general, nonlinear GNNs improves their cross entropy on cSBMs, and I derive the limiting accuracy of linear Graph Convolutional Networks (GCNs) on cSBMs. I use these results to derive the functional form of cross-entropy optimal GCNs on cSBMs and compare them to accuracy optimal GCNs.

Exploring Representations And Inductive Bias For Machine Learning Tasks In Knot Theory, Nathaniel Driggs

Theses and Dissertations

Knot theory is a branch of mathematics that studies embeddings of the circle in $\mathbb{R}^3$ that are equivalent up to ambient isotopy. A link is a knot with one or more component. Knots and links have invariants, or functions from each knot to a set such as the integers or a family of polynomials. Predicting invariants can help us approximate them, understand them better, and find useful ways of representing knots and useful models for other machine learning tasks in knot theory. I perform many supervised learning experiments, predicting signature on a large, wide-ranging dataset using 5 different models and …

Power Series Rings Over Noncommutative Rings: Symmetry, Reversibility, And Semicommutativity, Nolan Ison

Theses and Dissertations

Let R be an associative, unital ring. One topic of interest is to assert R has some property, then determine what properties the polynomial ring R[x] and the power series ring R[[x]] are guaranteed to have. There are many relaxations of commutativity in rings. For example, a ring is said to be symmetric if abc = 0 implies acb = 0 for all a, b, c ∈ R. We discuss a certain construction of symmetric rings that we hope will yield the existence of a symmetric ring R such that the set of nilpotent elements in the power series ring …

Sample Preparation And Acquisition Strategies To Improve Accessibility And Proteome Depth In Single-Cell And Low-Input Proteomics, Sara Madisyn Johnston

Theses and Dissertations

Proteins are responsible for important cellular functions and processes including regulation, structural integrity, signaling, transport, and immune functions. Proteomics directly identifies these proteins and enables deeper characterization of the dynamic cellular environment beyond the capabilities of genomics and transcriptomics. Single-cell proteomics further enhances this approach by capturing cellular heterogeneity, which bulk proteomics obscures due to averaging protein expression across large cell populations. Despite significant advances in single-cell proteomics, continued innovation is necessary to increase workflow accessibility and throughput, minimize peptide losses, and achieve comprehensive coverage of the proteome. This dissertation addresses these challenges by developing improved sample preparation methods, two-dimensional …

Non-Destructive Testing Of Stressed Materials Using X-Ray Diffraction And Second-Harmonic Generation, Melissa Nguyen Lumogdang

Theses and Dissertations

A material in use, anywhere from a plastic bag to common infrastructure, will eventually fail from deformation. When strained, the material chemical structure can change, and that change is dependent on many factors, including the amount of strain and strain rate. Understanding the relationship between physical properties and structural changes due to deformation can allow structural manipulation to achieve the desired physical properties. Additionally, research into non-destructive testing (NDT) methods can be used as supporting evidence for replacing destructive testing methods and possible infield stress monitoring. In this dissertation, X-ray diffraction (XRD) and second-harmonic generation (SHG) are the main NDT …

Homomorphisms Of Peano Continua To Berbered Peano Continua, Logan Kennedy

Theses and Dissertations

The study of wild spaces, Peano continua that contain points that are not semi-locally simply connected, has been of integral importance in the study of low-dimensional wild topology. Mainly investigated from the view point of algebraic topology, the fundamental group has been found to be an indespensible tool in describing these spaces, and their local behavior. In particular, using methods developed by Cannon, Conner, Eda, and Kent demonstrated that all maps from Peano continua to planar or one-dimensional Peano continua are determined uniquely up to homotopy class by their induced homomorphisms on fundamental groups, and that fundamental groups are a …

Innovations In Sample Handling Automation To Increase Accessibility Of Sample-Limited Proteomics, Nathaniel Ben Axtell

Theses and Dissertations

Innovation is the vehicle that drives scientific research forward in virtually every field. Advances in genome sequencing propelled the human genome project to completion in 2003 and set the stage for the era of proteomics. Now decades of innovation in liquid chromatography (LC) and mass spectrometry (MS) have improved sensitivity sufficiently to enable single-cell proteomics and other sample-limited studies. Single-cell proteomics reveal patterns of gene expression that are often obscured by bulk-scale proteomics, leading to the identification of new protein biomarker candidates. Sensitive targeted proteomics is the key to successful translation of low-abundance protein assays into clinical applications. With a …

Influence Of The Duchesne Fault Zone On Oil Production In The Uinta Basin, Utah, Alan Matthew Ketring

Theses and Dissertations

The Duchesne Fault Zone (DFZ) is a series of east-west trending en echelon faults that developed synchronously above the neutral surface of the Duchesne Anticline during the Laramide Orogeny. The Duchesne Graben (DG) formed by decrease in displacement downward toward the neutral surface. Lake Canyon, a region that exposes the subsurface geology on the western portion of the DFZ, serves as an analog for fold formation within the saline facies of the lower Green River Formation, while Indian Canyon, an area created from the dip-slip faulting of the DG, provides clear exposures of the faulting within the sandstone-limestone facies of …

Improving Efficiency Of Wind Flow Modeling For Wildfire Applications Using Analytical Parameterization And Neural Networks, Laura Jane Housley

Theses and Dissertations

We model wind velocity fields for applications in wildfire modeling. We improve the accuracy of the mass-conserving WindNinja solver without compromising efficient temporal complexity. We consider two approaches: the parameterization method and the neural network method. In the parameterization method, we analyze eddies in the wake of obstacles by parameterizing cavity zones as inspired by the research by Kaplan & Dinar in 1996. Kaplan & Dinar parameterize cavity zones around rectangular buildings, and we approximate a continuous landscape with rectangular buildings in order to extend this parameterization to complex terrains. In the neural network method, we train a U-net CNN …

Inquiry-Style Planetarium Activities, Emma Rasmussen Groberg

Theses and Dissertations

Introductory astronomy students often face challenges in exploring their own ideas and investigating astronomical phenomena due to the limitations of nighttime observation and weather conditions. Planetariums overcome these barriers by simulating the night sky, making it accessible during class sessions regardless of external conditions. This provides an opportunity to engage students in inquiry-based activities, where they are presented with a scenario and encouraged to use their own reasoning to reach conclusions. In this study, we implemented inquiry-based activities in PHSCS 127 using the planetarium as an investigative tool. We developed four activities designed to help students explore their ideas and …