Physical Sciences and Mathematics Commons^™

Probing The Disequilibrium Chemistry Of Two Late T-Dwarfs Using Planetary Intensity Code For Atmospheric Scattering, Crystal-Lynn Jacqueline Bartier

Theses and Dissertations

We have performed a detailed analysis of the atmospheric properties of two late-T type brown dwarfs, 2MASSI J0415195-093506 and 2MASS J05591914-140448. For each brown dwarfs, we combined the spectra of each brown dwarf from the ground at 1-2.5 µm, AKARI at 2.5-5 µm, and from the Spitzer Space Telescope at 5-15 µm. For this project, we are particularly interested in probing the extent of vertical mixing. For this analysis, we used the Planetary Intensity Code for Atmospheric Scattering (PICASO), which is a code that creates a radiative transfer model for a given set of atmospheric parameters. With PICASO we find …

A Masked-Perturbation Model For Destabilization Security Games In Feedback Systems, Gabriel Michael Perry

Theses and Dissertations

In this thesis, we present a mathematical formulation for increasing cyberphysical system security. This model allows a system administrator to use assumptions about exposed signals to derive defense strategies meant to mitigate the system's vulnerability to feedback perturbation attacks. We begin with a survey of game theory with the goal of building the concepts of resource and security games. We then introduce our model, which is a security game; targets in this game are exposed signals in the model map of the system, and resources are perturbed or introduced dynamical relationships between these signals. This formulation, called the masked-perturbation model, …

Theoretical Expressivity Of Self-Attention As A Model Of Binary Sequence-To-Sequence Functions And Other Explorations, Dustin Angerhofer

Theses and Dissertations

The self-attention mechanism lies at the heart of modern sequential modeling with deep neural networks, especially in the context of Large Language Models (LLMs). The basic role of self-attention is to capture pairwise interactions between tokens in a sequence. This allows token embeddings to be endowed with context-dependent information before further processing. Despite its widespread use, our theoretical understanding of self-attention is still nascent. In this work, we examine self-attention as a model of binary sequence-to-sequence (seq2seq) functions, which is the simplest non-trivial case to analyze. We find, using VC dimension and the Sauer-Shelah lemma, that in the limit of …

The Lookahead Transformer, Justin P. Olcott

Theses and Dissertations

Large Language Models (LLMs) are transformer models that generate text autoregressively in two stages: prefill and decode. The prefill stage processes all input tokens in parallel and caches them into the KV cache. The decode stage uses the KV cache, processes a single token at a time, and is generally memory-bandwidth constrained. Each decode step generates a token probability distribution, samples from it, appends the token to the cache, and repeats. This left-to-right, one-at-a-time generation paradigm has proven effective for language modeling in many domains; however, it also has limitations such as token permanence, constant compute per token generation, constant …

Detection Of The Presence And Growth Of E. Coli Bacteria In A Droplet-Based Microfluidic System Using Laser Induced Fluorescence, Oshira Peiris

Theses and Dissertations

Antimicrobial resistance is a biomedical event, wherein an infectious microbe becomes non-responsive to the dosage of a particular antibiotic due to previous overuse or overexposure. Currently, agar plate disc diffusion is used as the gold standard for detecting antimicrobial resistance. The possibility of miniaturizing and speeding up detection techniques for antimicrobial resistance is investigated in this thesis. Microfabrication techniques were used in developing two droplet microfluidic systems interfaced with laser induced fluorescence detection. Microfluidic devices were manufactured with different droplet generating geometries using poly-dimethyl siloxane, soft lithography and hydrophobic surface treatment. The microfluidic devices were tested for droplet quality using …

Model Unification: A Systematic Approach For The Cluster Expansion, Kolten Barfuss

Theses and Dissertations

A systematic approach for model unification of cluster expansion models is developed and demonstrated. The method builds on previous work with the Manifold Boundary Approximation Method (MBAM) to identify supremal models. The work is motivated by the exercise of unifying cluster expansion models – characterized by Π matrices – for two binary alloys that share one atomic species to form a model for the ternary alloy. The result is the Supremal Π Algorithm, a systematic unification algorithm that relies on an MBAM-informed understanding of models and on the singular value decomposition. The algorithm yields ΠΛ, a Π matrix for the …

Some Closure On The Relation Between Cfg And Peg, Nathan J. Bulloch

Theses and Dissertations

We work toward a practical, unified language formalism for structurally recursive languages by expressing the mathematical theories underlying context-free grammars with lookahead (CFGLA) in the Rocq theorem prover and leveraging CFGLA semantics to analyze interactions between between recursion and negative lookahead. We give examples of grammars with left-recursive negation cycles for the parsing expression grammar (PEG) variant due to Medeiros et al. and for the translation from PEG to CFGLA due to Miyazaki and Minamide. To study the interaction between left recursion and negative lookahead in a PEG context, we introduce FPEG, a left-recursive extension of PEG with Fitting semantics.

Asymptotic Sensitivity And Adjoint Methods For Equation Discovery With Open-Source Implementation, Nathan Schill

Theses and Dissertations

The "on-the-fly" (OTF) method is a gradient-based approach to equation discovery. It makes use of (potentially limited) observational data, a data assimilation technique such as continuous data assimilation (also called nudging), and an error metric. From these it computes an asymptotic approximation of a simulated system's error sensitivity with respect to unknown parameters and utilizes any gradient-based optimization algorithm to perform parameter updates. These parameter updates may be done online or offline, and the model may be of a precisely specified form or simply a library of possible terms with potentially nonlinear parameters. We have applied the adjoint method to …

Sonic Booms From Rockets: Measurements And Modeling, Mark Charles Anderson

Theses and Dissertations

Rocket sonic booms are produced when launch vehicles or boosters travel faster than the local speed of sound in the atmosphere, generating systems of conical shock waves. The purpose of this dissertation is to perform high-fidelity measurements of rocket sonic booms and to explain the physics behind the unique phenomena observed. After a thorough literature review on sonic booms produced during spaceflight operations, Part I of this dissertation deals with measurement and analysis challenges. One challenge is reducing contaminating noise effects on sonic boom perception metrics, addressed using a low-pass filtering method tied to the noise floor. A second challenge …

Unlocking Inexpensive Training Through Overcoming Weaknesses In Dataset Distillation, Connor Wilhelm

Theses and Dissertations

Dataset distillation is a nascent technique that promises accelerated neural network training. In particular, distillation produces a highly compressed dataset that can train a neural network in as little as a single optimization step. However, distillation has not been adopted for real-world use cases due to weaknesses, such as poor approximation of the original task, unclear interpretability, high costs of the initial distillation, and poorly elaborated use cases. Here, we present five papers that advance task distillation towards real-world adoption. The papers focus on: distilling reinforcement learning environments, interpreting distillation-produced datasets, improving distillation performance using ensembling, examining distillation's generalization to …

Understanding The Role Of Tiktok As A Source Of Support For Cyberbullying Victims, Saba Iqbal

Theses and Dissertations

Cyberbullying poses a significant threat to teenagers and young adults, who often seek support and advice online. Little is known about the support and advice shared online for victims of cyberbullying and whether it is helpful. In this study, we used qualitative thematic analysis to examine a sample of 150 TikTok videos that give support or advice for cyberbullying victims. We identify 33 unique pieces of support and advice across 5 categories, with differences in tone and delivery among different types of videos. We then evaluated the quality of 33 unique pieces of cyberbullying advice in a user study with …

Advancing Cyclic Ion Mobility Mass Spectrometry For Structural Characterization, Isomer Discrimination And Gas-Phase Ion Chemistry, Sudam Shivaji Mane

Theses and Dissertations

This dissertation focuses on the development and application of high-resolution ion mobility-mass spectrometry (IMS-MS) methodologies for gas-phase separation and structural characterization of small molecules, with particular emphasis on epimers, positional isomers, and protomers. In addition to structural separations, this work investigates fundamental aspects of gas-phase ion chemistry using IMS-MS in combination with collision-induced ion activation and dissociation techniques. Advanced separations were performed using cyclic traveling-wave ion mobility spectrometry (cyclic TWIMS), implemented in a commercial cyclic ion mobility-mass spectrometry (cIMS) platform, to systematically evaluate both the capabilities and limitations of high-resolution IMS in resolving subtle structural differences. Initial studies demonstrated that, …

Practical, Scalable, And Cost-Effective Nanolc-Ms Workflow For Single-Cell Proteomics, Siqi Huang

Theses and Dissertations

Single-cell proteomics provides a novel research strategy for decoding cellular heterogeneity, revealing the molecular mechanisms of rare cell subpopulations, and studying the dynamic responses of cells to external stimuli. However, compared to transcriptomics, single-cell proteomics faces even more challenging technical challenges: extremely low protein amount in single cells, wide dynamic range, significant adsorptive losses during sample preparation, and the complex matrix and trace sample injection demanding extremely high stability and sensitivity from the separation and detection systems. Mass spectrometry-based bottom-up proteomics has become an important tool for analyzing complex biological systems, and nano-flow liquid chromatography-mass spectrometry (nanoLC-MS) exhibits unique advantages …

Differentials As Models: Constructing A Differentials-Within-Limits Framework For First-Year Calculus And Examining Students' Understanding Of Limits, Differentials, And Derivatives Within It, Alexander A. Swindler

Theses and Dissertations

Work in first-year calculus has clearly shown the power that treating differentials (such as dx) as tiny quantities affords for first-year calculus learning, yet a traditional limits-based approach leaves no room for them. While some researchers have loosely described informal differentials and limits within the same paradigm, their actual conceptual definitions and relationships have not been explicitly constructed. Continued progress in this area could benefit from theoretical consideration of (a) providing clearer intuitive definitions for differentials inside a limits-based approach to calculus, and (b) defining more exactly the relationships between differentials and limits. In this study, I propose a theoretical …

Observational Diagnostics And Spectroscopic Detection Of Tropospheric Trace Gases And Oxidation Processes, Callum E. Flowerday

Theses and Dissertations

The troposphere is governed by photochemical and radical-mediated processes that control atmospheric oxidation capacity, secondary pollutant formation, and the chemical lifetime of gases. Quantitative understanding of these processes requires both robust observational frameworks capable of resolving complex precursor–product relationships and instrumentation with sufficient sensitivity and selectivity to detect reactive and low-concentration species. This dissertation advances atmospheric chemistry through the parallel development of quantitative observational methodologies and refined spectroscopic measurement techniques. The first component of this work evaluates atmospheric oxidation systems using long-term monitoring data and empirical diagnostics. Multi-year analyses of ozone and particulate matter trends were conducted to characterize variability …

Objective Conditioning Via Latent-Factor Modeling, Kalman-Smoothing, And Hidden Markov Clustering: An Application To Empirical Asset Pricing, Melanie R. Neller

Theses and Dissertations

Empirical asset pricing relies heavily on conditioning sets--industry groupings, size buckets, valuation screens, and other researcher-defined partitions--to structure cross-sectional tests and portfolio construction. While intuitive, such partitions risk blending heterogeneous firms, masking latent exposures, and introducing omitted-variable bias. This thesis develops an objective, mathematically grounded conditioning pipeline that replaces subjective groupings with latent-factor extraction, Kalman-based data techniques, and probabilistic clustering via Gaussian hidden Markov models (HMMs). Using CRSP monthly returns, the framework stabilizes noisy return data, extracts systematic structure through principal component analysis (PCA), identifies homogeneous stock cohorts through HMM clustering, and models regime persistence using Markov transition matrices. These …

Improving Surface Analysis Through The Correct Use Of Low Energy Ion Scattering And X-Ray Photoelectron Spectroscopy: Best Practices, Common Errors, And Multimodal Approaches For Material Development, Joshua W. Pinder

Theses and Dissertations

Surface analysis is the study of the atoms at surfaces and their connectivity, including their relative depth distribution, concentration, chemical state, and crystallinity. These characteristics govern many important material properties. X-ray photoelectron spectroscopy (XPS) is one of the most widely used surface analysis techniques. Proper interpretation of XPS spectra including the appropriate use of backgrounds, peak shapes, peak positions, and charge compensation, with appropriate constraints on fitting parameters provide valuable information about elemental composition, concentration, depth distribution, and chemical speciation of surface atoms. However, despite widespread use, much of the XPS literature contains poor interpretations and irreproducible results which undermine …

Guitar Amplifier Directivity, Rachel C. Edelman, Brian E. Anderson, Samuel D. Bellows, Timothy W. Leishman

Directivity

No abstract provided.

Panda-Plus: Improved Dataset Of Prostate Whole Slide Images From Panda Challenge With Pixel-Level Expert Annotations, Spencer Hopson, Carson Mildon, Corbyn Kubalek, Joshua L. Ebbert, Ryan Vance, Lauren Laverty, Paul Urie, Dennis Della Corte

Faculty Publications

Artificial intelligence (AI)-based prostate cancer detection through whole slide images (WSIs) offers promising potential to address the global pathologist shortage while improving clinical consistency. Digital slides and improving image analysis methods encourage the creation of tools to aid in WSI classification. Despite promising advances, these tools are still limited by available training data. Current publicly available datasets, such as Kaggle's PANDA Challenge, while large in scale, rely on slide-level labels that may introduce noise and limit model reliability. Others contain detailed annotations, but are smaller in size due to manual processing efforts. In this work, we introduce PANDA-PLUS, a 546-image …

Structural Framework And Tectonic Implications From Field Investigations In The Ramelau Mountains, Timor-Leste, Tanner A. Nielsen

Theses and Dissertations

Recent advances in petroleum exploration off the southern coast of Timor-Leste and emerging mineral discoveries onshore have underscored the need for a more comprehensive structural understanding of the nation's geology. Although new structural models have been proposed for other parts of Timor, limited progress has been made toward developing detailed models for the Ramelau Mountains, which presents the highest structural relief of the Timor Ranges. Previous mapping in this area has been largely reconnaissance in nature and focused primarily on surface bedrock geology. This study presents a new 1:62,500-scale geologic map and a geometric structural analysis of the Ramelau region …

A Systematic Study Of Passkey User Experience Consistency, Bernhardt Ramat

Theses and Dissertations

Passkeys have emerged as a more secure authentication method than passwords, providing a passwordless alternative resistant to phishing and credential theft attacks. Despite their growing adoption, a systematic study into the user experience of passkeys across various websites has yet to be conducted. Usability heuristics suggest that users transfer their expectations from one product to another, and therefore, inconsistencies in passkey deployments can increase cognitive load, resulting in frustration and possible rejection. To address this knowledge gap, this paper presents a comparative analysis of the external functional consistency of the passkey user experience across 111 websites. Our research reveals that …

The Role Of Dust Inputs And Sediment Phosphorus Diffusion Into Utah Lake, Utah, United States Of America, Kristen E. Smith

Theses and Dissertations

Human activities have led to excessive nutrient enrichment which is greater than lake systems can naturally assimilate. This process is known as eutrophication and it is driving significant algae growth resulting in the more common release of harmful toxins. Utah Lake, located in Utah County, UT is one such water body that even after major reductions in anthropogenic phosphorus influent, continues to experience frequent, harmful algal blooms. The extent to which natural processes, like atmospheric dust deposition and sediment recycling, contribute to the lake's phosphorus budget is still poorly understood.

To address this gap of knowledge, this study quantified phosphorus …

Enhancing Silicon Sampling In Large Language Models: Fine-Tuning Techniques Using Survey Data, Davis P. Forster

Theses and Dissertations

Large language models (LLMs) are increasingly used to simulate responses of human demographic groups, a task known as silicon sampling. This paper investigates whether supervised fine-tuning can improve algorithmic fidelity in such settings. We construct a dataset from the General Social Survey (GSS), converting demographic attributes into natural-language backstories and randomly selecting one attribute as a held-out target. Fine-tuning a LLaMA-3.1-70B model on this dataset yields significant improvements on two tasks: (1) imputing missing attributes at the individual level, and (2) reproducing response distributions for demographic slices, such as racial and age groups. Notably, these improvements are achieved with minimal …

Modeling Network Growth Via Generalized Isospectral Reductions, David Thomas Litster

Theses and Dissertations

Many real-world networks also exhibit a variety of symmetries. In this thesis we study equitable partitions and isospectral reductions, both of which are generalizations of symmetries. We formalize the relationship between these two types of generalized symmetry through the study of invariant subspaces. We then use recent results about the presence of equitable partitions in real-world networks to develop a network growth model that introduces similar structures, thereby introducing symmetries similar to those in real world networks.

Intrinsic Stability Of Controlled Systems Via Gershgorin-Type Estimates, David Friedbaum

Theses and Dissertations

Time delays are an inherent feature of real-world dynamical systems, arising whenever information, matter, or energy requires non-negligible time to propagate. Even small delays can destabilize systems that are otherwise well behaved, yet most standard control designs--such as PID or LQR--do not explicitly account for them and may fail when delays are present. This thesis investigates the stability of controlled dynamical systems subject to arbitrary time delays and develops new tools to determine when such systems remain stable. Our approach builds on the notion of intrinsic stability, a strong form of global stability introduced by Webb and Bunimovich, which guaranties …

Game-Theoretically Optimal Strategies In Baseball, William Michael Melville

Theses and Dissertations

Baseball players and their managers make numerous decisions that can have a significant effect on the result of the game. The effectiveness of their decision-making strategies depend on the strategies played by their opponents. For example, throwing a first-pitch fastball down the middle is a good strategy against a hitter who always takes the first pitch, but it is a risky strategy against a hitter who likes to swing at the first pitch and who is good at hitting fastballs. Additionally, any payoff a player receives from playing a strategy comes at the expense of their opponent. A batter cannot …

Play-Based Assessment Of The Cardinal Principle, Allyssa Sonnefeld Leavitt

Theses and Dissertations

Gelman and Gallistel (1986) determined five counting principles that are essential for successful counting, including the cardinal principle where children understand that the last number counted represents the quantity of a set of objects. The traditional How many? task and the Give-n task are the most common tasks that have been used to assess whether children understand the cardinal principle. However, many researchers claim that these tasks either overestimate or underestimate children's understanding of the cardinal principle. Some researchers (Baroody & Pellegrino, 2023) suggest that embedding the traditional How many? task in a game may improve its validity. In this …

An Analysis Of Student Performance In Elementary Linear Algebra At Brigham Young University, Adrienne Irene Christensen

Theses and Dissertations

This study investigates different factors that influence performance in the Elementary Linear Algebra (ELA) course taught at Brigham Young University. These factors include student characteristics such as true freshman status and college enrollment, and content-specific factors such as how performance on essential topics affects overall performance in the course. To analyze the various research questions posed in the study, I used robust linear mixed effects models with random effects controlling for the hierarchical structure of the data. The statistically significant results from these models indicate that (i) true freshmen perform better than other students on exams and in the ELA …

Bayesian Alignment Prior To Connectionist Temporal Classification Loss, Lawry Sorenson

Theses and Dissertations

We propose revisions of Connectionist Temporal Classification (CTC) loss and forced alignment to support longer input sequences. CTC loss is normally used for training in speech and handwriting recognition tasks when the labels are not fully aligned with the data, while forced alignment is a downstream task that finds the optimal path for segmentation purposes. The current implementations consider all possible alignments between the input and label, which grows exponentially with the size of the input. We show that in cases when silence is removed and speaking rate is consistent, the true alignment is a mostly straight line across time …

Commutative Schur Rings Over Characteristic 2 Special Orthogonal Groups, Andrew Haviland

Theses and Dissertations

We study commutative Schur rings over the special orthogonal groups $\mathrm{SO}^{\pm}(n,2)$ that contain the class $\mathcal{C}$ of transvections. We show that the partition of $\mathcal{C}$ determined by a commutative Schur ring has either one or two parts. We classify all remaining partitions of $\mathcal{C}$ that could be determined by a commutative Schur ring.