Physical Sciences and Mathematics Commons^™

Temperature Predictions With Zncuins/Zns Quantum Dots, Reu/Fri Program Physics And Astronomy, Amber Banks

Student Works

For hundreds of years, humans have built thermometers based on the principles of thermal expansion and contraction. In the modern world, there is a need to scale down our thermometers to monitor cellular reactions, both within the human body and within artificial organ chips. Lewis et al. (2020) introduces a nanoscale thermometer based on the thermal expansion of CdTe quantum dots. When ex panded, these dots exhibit systematic changes in photoluminescence (PL) which are recognized by a neural network as an increase in temperature. Our research builds upon the framework of Lewis et al. (2020), testing its feasibility with ZnCuInS/ZnS …

Synthetic Strategies For Bioactive Peptides: From Aggregation Inhibitors To The Total Synthesis Of Tunicyclin C, Stephanie Graciela Garcia Morin

Theses and Dissertations

In Alzheimer's disease (AD), a brain protein called "tau" abnormally clumps and forms neurofibrillary tangles (NFTs), causing damage to brain cells. Ac-PHF6-NH2 is a hexapeptide segment of tau protein that plays a dominant role in tau aggregation and is used as a model to design tau protein aggregation inhibitors. In this research we synthesized four dehydroamino acid (□AA) containing PHF6 analogues with △Abu (derived from L-threonine) and △Val (derived from □-OH-Valine) at position 2 or 3 via dehydrations or azlactone ring-openings as key reactions. We evaluated their proteolytic resistance, ability to inhibit aggregation of PHF6, and impact on the morphology …

Measuring Proteostasis Changes In Apolipoprotein E Mouse Models Using Quantitative And Kinetic Proteomic Methods, Ariel E.A. Denos

Theses and Dissertations

Alzheimer's Disease (AD) is a neurological disorder associated with brain mass loss and cognitive decline. It affects millions of elderly people and is currently uncurable. Since 1906, when the disease was first described, researchers have uncovered many components of AD pathology. However, it is now evident that curing Alzheimer's Disease will require intervention before the pathological onset of amyloid beta plaque deposition, tau neurofibrillary tangles, and associated neuronal loss. Studying AD from the perspective of early intervention requires special attention to small changes that may disrupt the normal processing of cells. Cells undergo a natural cycle of creation and destruction …

Multi-Band Extinction Modeling In Early-Type Galaxies With Circumnuclear Disks, Nonnie Bash

Theses and Dissertations

In this thesis, we present a spatially resolved, multi-band dust-attenuation method for correcting the stellar luminosity models used in dynamical supermassive black hole (BH) mass measurements. If uncorrected, dust extinction effects may dominate over other systematic uncertainties when determining the BH mass ($M_\mathrm{BH}$). We expand on a simple dust-attenuation method that treats the circumnuclear disk as a thin dust layer embedded in the galaxy midplane. Using a Multi-Gaussian Expansion, we create a three-dimensional stellar luminosity model to calculate the fractions of stellar light originating in front of and behind the disk along each line of sight. We infer the pixel-by-pixel …

Developing An Object Level Understanding Of Sine And Cosine As Ratios And A Coherent Trigonometry, Jeffrey Peter Nair

Theses and Dissertations

Solving right-triangle problems as well as integrating right-triangle and circular trigonometry into a coherent understanding are documented challenges for students. Prior research has deeply investigated students constructing ratio meanings for sine and cosine using a circle-first approach, which then can be extended to right triangles. Also, past work has separately documented distinct meanings that are useful for sine and cosine, in addition to the ratio meaning, including as lengths in a unit circle and coordinate points. This study took these existing ideas and put them together into one possible developmental progression, based on APOS theory, where students can learn length, …

Modifying Lta Zeolites For Reversible Hydrogen Sulfide Capture And Elucidating The Structure Of The Incorporated Metal And Sulfur Ions, Adeyemi D. Ojaide

Theses and Dissertations

Hydrogen sulfide (H2S) is a highly toxic and corrosive gas that poses significant environmental and industrial challenges, particularly within the wastewater treatment and oil and gas sectors. H2S leakage is among the deadliest industrial hazards, highlighting the urgent need for the development of highly efficient, non-corrosive adsorbents. This dissertation provides an in-depth examination of the use of metal-zeolites for H2S capture. We carefully investigate the impact of multiple divalent and one monovalent transition metals on LTA zeolites to optimize H2S removal. While Linde Type A (LTA) zeolites offer a robust structural framework for gas separation, a comprehensive understanding of how …

A Graphical Approach To Isospectral Unfoldings, Dallin Seyfried

Theses and Dissertations

Isospectral reductions are mathematical techniques used to shrink a matrix, or a graph, into a smaller, dimensionally reduced form while preserving its spectrum. Simple graphs that share isospectral reductions also share quantum walk properties. As such we further develop the inverse process, isospectral unfoldings, to find graphs that share isospectral reductions. We first prove many conditions relating to isospectral reductions and unfoldings. Afterwards, we define two new unfolding processes: general unfolding which unfolds the graph one vertex at a time, and equitable partition unfolding which excels at larger graph unfolding. In particular, through equitable partition unfolding, we discover many graphs …

Learning, Abstraction, And Creative Search For Interactive Agents, Jonathan Demke

Theses and Dissertations

Artificial intelligence systems are increasingly deployed as autonomous agents that interact directly with complex environments. Ensuring these agents remain reliable, adaptable, and useful presents an ongoing practical challenge. This dissertation studies agent-environment interactions through a progressive lens, examining behavior from foundational training stability and abstraction discovery to adaptation in unpredictable settings and open-ended creative search. The investigation begins by analyzing how hyperparameter settings affect early-stage Deep Q-Network performance, yielding practical guidelines for debugging reinforcement learning implementations. To address the challenge of long-horizon planning, the discovery of temporally extended options is formalized as the Minimum Shortcut Problem, demonstrating how agents can …

A Coupled Reaction-Diffusion Model Of Promoting And Suppressing Interactions Among Cancer Hallmarks In Endometrial Cancer, Jeddy Bennett

Theses and Dissertations

Spatial transcriptomics enables the scoring of Cancer Hallmarks at a high resolution across a tissue biopsy, yet current analyses of these data remain largely descriptive, treating each spot as a static, independent observation. This thesis develops a coupled system of advection-diffusion-reaction partial differential equations to model the hallmark landscape as the steady-state solution of an underlying spatial process, and casts the recovery of its physical parameters as a PDE-constrained inverse problem. The framework is implemented in FEniCSx on tissue-specific finite element meshes derived from two endometrial cancer biopsies provided by the Huntsman Cancer Institute, with subdomains, boundary interfaces, and an …

Sand Distribution On Titan And Implications For Sand Transport And Interconnectedness Of Sand Seas, Delaney Rose

Theses and Dissertations

The vast equatorial sand seas of Saturn's moon Titan are of particular interest for understanding surface processes and the budget of organic materials on Titan's surface. Previous studies have described sand dune morphology, transport, collection, and distribution patterns utilizing Cassini Imaging Science Subsystem (ISS), Visual and Infrared Mapping Spectrometer (VIMS), and Synthetic Aperture Radar (SAR) imagery. Studies have also shown evidence both for and against a global interconnected system of sand transport between Titan's major sand seas. This study worked both to create a higher resolution dataset of sand distribution using trimodal thresholding techniques applied to SAR images, as well …

Properties Of Enjoyable Mathematical Contexts From The Student Perspective, Emilie Nadine Hendrickson

Theses and Dissertations

Researchers continue to grapple with how to meaningfully engage students in mathematical content. Many students report disengagement due to perceptions that mathematics is difficult, irrelevant, boring, or anxiety-inducing. This study sought to understand how students interpret and respond to different mathematical problem contexts, with particular attention to the reasons students describe certain problems as enjoyable or unenjoyable. Using semi-structured interviews, this research examined student responses to a variety of mathematical problem types primarily across affective engagement. Students reflected on specific problem contexts and explained which features supported or hindered their enjoyment and engagement. Students described that contexts were enjoyable have …

Developing An Understanding Of Concavity Built On Covariation, Jade E. Gregg

Theses and Dissertations

This study investigated how six students developed a quantitative understanding of concavity founded in covariational reasoning through a series of task-based teaching interviews. A key finding was the importance of multivariational reasoning--the coordination of more than two variables--in helping students reason deeply about concavity in context. Common difficulties, including confusion about negative rates and overreliance on visual representations, served as productive opportunities for learning when addressed through carefully designed tasks and discussions. The findings extend existing frameworks of covariational reasoning and highlight instructional approaches that can support students in developing a robust, quantity-based understanding of concavity.

Religious Bias In Llms Is Significantly Understudied, Sheryl Carty, Nancy Fulda, Walter Reade

Faculty Publications

In the earlier years of development of LLMs, it was relatively easy to prompt an LLM to respond with toxic or biased statements about religion. Subsequent improvements in frontier models addressed many of the issues of bias and toxicity in general, including against religion. At the same time, the adoption and usage of these models has grown exponentially. Small and implicit biases, therefore, have a magnified overall impact. In this paper, we (1) briefly review previous efforts to measure religious bias in LLMs, (2) show, by reviewing over 12,000 papers dealing with bias in LLMs, that religious bias has been …

An Analysis Of Heat Spread Through Smoldering Pine Needles, Timothy Keith

Theses and Dissertations

The goal of this thesis is to calculate the average speed of flame spread through smoldering pine needles. We present two different models for doing this: the first is a very large system of ODEs meant to represent the spread of flame through individual needles, the second is a macroscopic model based on the porous medium PDE. Simulations are run for each of these models and compared to each other as well as to existing models and experimental results.

A Mathematical Model Of The Interactions Between A Collagen Lattice, Fibroblasts, And Fixed Surfaces With Varying Topographies, Mary Jenkins

Theses and Dissertations

Collagen is an important structural protein in the body, which plays a role in wound healing, particularly the contraction process. Collagen lattices have been studied for nearly 50 years to provide insight into wound contraction. In some cases, collagen interacts with surfaces that have fixed shapes, such as medical implants. Our model focuses on the interactions of a collagen lattice with such a fixed surface. We mathematically model a collagen lattice as a network of nodes connected by springs. We also model fixed surfaces that have various topographies. Our model includes fibroblast cells that connect to both surfaces and remodel …

Learning Trajectories Of Online Batch Selection Methods, Luke Green

Theses and Dissertations

Modern deep neural networks achieve strong performance on large-scale datasets, but often require substantial training time. Online batch selection methods seek to reduce this cost by updating models on informative subsets of each batch rather than on all available examples. Recently introduced methods leverage teacher models and report substantial speedups, particularly in noisy-label settings. However, comparisons are often based on the number of epochs required to reach a target test accuracy, a coarse metric that is sensitive to implementation details and may obscure important differences in learning dynamics. In this thesis, we implement several online batch selection methods in a …

Advancing Data Usability, Activity Modeling, And Stability Optimization In Computational Enzyme Design, Spencer Gardiner

Theses and Dissertations

A grand challenge of computational biology is to computationally design, in a single pass, a protein sequence that catalyzes an arbitrary chemical reaction at a high rate under specified conditions [1]. This work details advances in three essential areas on the path to that goal: data quality, activity prediction and modeling, and stability optimization. The structure and implementation of the Allotrope Simple Model (a FAIR data format for many scientific instruments) was examined in [2], setting the stage for training deep learning models on high-quality experimental datasets from diverse sources. In [3], the limits of physics-based and deep learning tools …

Beyond Single Images: A Comprehensive Benchmark For Album-Level Vision-Language Understanding, Shawn Huang

Theses and Dissertations

Automatic album organization has been studied extensively over the past decades due to significant progress in digital photography. Recent Vision-Language Models (VLMs) have shown strong performance on multi-image understanding, making them natural candidates for automating album organization workflows. While VLMs’ abilities in multi-image understanding have been widely studied, their performance on album organization remains underexplored. To bridge this gap, we introduce AlbumBench, the first comprehensive benchmark for automatic album organization. Specifically, we (1) define album organization tasks as photo selection for album-specific user objectives, photo rating according to how well user intents are fulfilled, and album-specific photo grouping given a …

Design Principle For Staple-Mediated Stabilization Of Peptides And Proteins, Samantha C. Hatfield

Theses and Dissertations

Macrocyclization, or stapling, has emerged as a powerful strategy to enhance the stability and function of peptides and proteins by constraining their conformational ensembles. Stapling can improve thermodynamic stability, increase resistance to proteolytic degradation, and enhance biomolecular recognition, making it particularly valuable for the development of peptide-based therapeutics. Despite these advantages, staple design remains largely empirical, relying on iterative screening of linker chemistries, lengths, and attachment sites. This trial-and-error approach limits scalability and hinders the rational design of stabilized peptide systems. In this work, we address this challenge by integrating large-scale experimental datasets with molecular dynamic simulations to develop predictive …

Tectonics: Supporting Information For Deformation Rates And Patterns Of The Emerging Banda Ranges Revealed By Uplifted Coral Terraces In Timor-Leste, Ron Harris, Nicole Cox, Megan Flexhaug, Dorothy Merritts, Chua-Chou Shen, Frederico Santos

ScholarsArchive Data

The supplementary information provided consist primarily of figures detailing coral terrace profiles and terrace inner margin elevation to MIS highstand correlations.

• a general overview of the kind of data files;
• a general description of processing steps used;
• any known imperfections or anomalies in the data.

Context-Sensitive Control-Flow Analysis For Non-Standard Language Semantics, Tim Whiting

Theses and Dissertations

Control-Flow Analysis (CFA) is a static technique for understanding the execution of higher-order programs without running the code. CFA aids in identifying bugs, assisting program comprehension, and exposing optimization opportunities. Constructing a CFA typically begins with an idealized evaluator--such as an abstract machine or interpreter--and proceeds by approximating components of evaluation to ensure that: (a) the analysis is sound (representing all possible behaviors), and (b) the analysis is guaranteed to terminate (finitely representable). These constraints necessitate a loss of precision, providing an approximation of the values that flow to program locations rather than exact execution traces. This imprecision causes the …

Data Science In The Utah Draft K-12 Standards Of Mathematics, Kate Webster Green

Theses and Dissertations

In today's data-driven world, the field of data science is becoming increasingly important. Research has shown that more job listings in Utah require applicants to have data science skills than ever before. Due to this growing demand, there is a push to begin data science instruction in grades K-12; however, what data science instruction is in grades K-12 is not yet clearly defined. Previous research has identified the skills and processes that make up data science in grades K-12, and several states and research groups have begun developing and implementing data science standards and learning progressions. This study analyzes the …

Spatiospectral Lobes And Radiation Modeling Of Partially Coherent Supersonic Jet Noise, Tyce Wayne Olaveson

Theses and Dissertations

Noise fields generated by high-performance military jets are known to contain acoustic structures that differ from their simulated and lab-scale counterparts. These differences may limit current noise control efforts, which are designed and tested at scale before being considered for full-scale aircraft. One such noise structure is the presence of spatiospectral lobes, which appear as multiple spectral peaks at single microphone locations and multiple radiation lobes in field reconstructions. This dissertation uses data collected from the T-7A jet noise measurement to characterize the spatial behavior of the spatiospectral lobes as well as their first time-domain description. A multiple wavepacket decomposition …

Panda-Plus-Bench: A Clinical Benchmark For Evaluating The Robustness Of Ai Foundation Models In Prostate Cancer Diagnosis, Joshua L. Ebbert, Dennis Della Corte

Faculty Publications

Artificial intelligence foundation models are increasingly deployed for prostate cancer Gleason grading, where GP3/GP4 distinction directly impacts treatment decisions (active surveillance vs. intervention). However, these models may achieve high validation accuracy by learning specimen-specific artifacts rather than generalizable biological features, limiting real-world clinical utility. We introduce PANDA-PLUS-Bench, a curated benchmark dataset derived from expertly annotated prostate biopsies designed specifically to quantify this failure mode. The benchmark comprises nine carefully selected whole slide images from nine unique patients containing diverse Gleason patterns, with non-overlapping tissue patches extracted at both 512 × 512 and 224 × 224-pixel resolutions across eight augmentation conditions. …

Real-Time Instruction Internalization For Large Language Models, Brenden Smith

Theses and Dissertations

For the end user, Large Language Models (LLMs) are programs that process natural language inputs into natural language outputs. In popular usage, this tends to take the form of conversation: a user asks a question, provides information, or gives instructions, and the LLM (hopefully) replies in a manner we would expect of an informed and compliant person. While convenient and intuitive for users, this natural conversational format encourages the misconception that LLMs are learning from conversations, when they do not. This work presents the benefits and practicality of a language model paradigm that meets this user expectation -- that is, …

A Comparative Study Of Tin Electrorefining In Molten Licl–Kcl–Cacl₂: Experimental Two-Electrode Current Control And Theoretical Three-Electrode Potential Control, Bryant Johnson, George Ankrah, Ander Fuller, Devin Rappleye

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

Molten salt electrorefining is a mature technology for metal recovery, yet conventional current‑controlled, two‑electrode operation provides limited electrochemical selectivity and restricted insight into electrode‑specific behavior. In this work, a simplified model is developed to compare current‑controlled two‑electrode electrorefining data with a potential‑controlled three‑electrode electrorefining simulation using tin in molten LiCl–KCl–CaCl₂ as a surrogate for plutonium processing. The model examines anodic and cathodic limitations under fixed‑potential operation and evaluates implications for selectivity, efficiency, and runtime relative to experimentally demonstrated two‑electrode performance. Results indicate that independent potential control enables operation closer to thermodynamic selectivity limits, with the potential to suppress impurity oxidation …

Mcgehee Blow Up And Collision Manifold Of Planar (2+2)-Body Problem, Nathaniel Scott Sill

Theses and Dissertations

This thesis analyzes the dynamics of the Planar (2+2)-Body Problem which consists of two asteroids moving under the gravitational force of each other and of two larger primaries. We use the McGehee blow up technique to remove the singularities in the dynamics associated with a triple collision with one of the primaries by introducing a new set of variables. Additional variables are introduced to reduce the dimension of the problem. We then derive the dynamics for these new variables. We then use the energy relation that comes from the original Hamiltonian to describe the collision manifold which is pasted in …

Differentiable Objectives For 3d Scene Relighting Via Gradient Descent On Olat Basis Coefficients, Anson Savage

Theses and Dissertations

Designing effective lighting is an iterative and often time-consuming process. This work contributes to automatic lighting design research by presenting a render-engine agnostic optimization routine: gradient descent on RGB multipliers of one-light-at-a-time (OLAT) basis images. We compare several objective functions to accomplish lighting tasks and show that our method is capable of quickly and effectively exploring different lighting styles using either text prompts or reference images. We also present several datasets specific to lighting tasks and show that fine-tuning on these datasets can improve performance.

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 …

Maximizing Uinta Basin Oil Well Yield Through Geochemical Fingerprinting Of Produced Water, Troy W. Day

Theses and Dissertations

The Uinta Basin is an unconventional oil play that has, since 2017, annually increased hydrocarbon extraction through modern drilling and fracing techniques with increased frac loading. The primary production target is the Uteland Butte Member of the Green River Formation, which consists of interbedded limestones, dolostones, and thick, organic-rich mudstones. Along with increased hydrocarbon production, volumes of produced water from the Uteland Butte Member have also risen. Water is co-produced with hydrocarbons and is an undesirable byproduct of hydrocarbon extraction. Large frac operations now consistently have highly variable percentages of recovered water volume relative to oil. This increase in water …