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Effects Of O-Glcnacylation And Phosphorylation On Tau Aggregation By Cd And Tem, Andrew Whyte Jr.

Electronic Theses and Dissertations

Alzheimer’s disease (AD) is characterized by the accumulation of extracellular amyloid-β (Aβ) plaques and intracellular neurofibrillary tangles composed of aggregated tau protein. Among the numerous post-translational modifications that regulate tau function, phosphorylation and O-GlcNAcylation have emerged as key modulators of tau aggregation and pathology. While phosphorylation is generally associated with tau misfolding and fibril formation, O-GlcNAcylation has been proposed to exert protective effects through its interplay with phosphorylation. However, the site-specific structural consequences of these modifications remain incompletely understood.

The objective of this work was to develop synthetic tools for the site-specific incorporation of O-GlcNAc and phosphate …

In-Situ Stm Visualization Of Molecular Structural Evolution During Electrochemical Oxidation Coupling Of Para-Aminothiophenol On Au(111), Zi-Wei Ma, Tai-Rui Wu, An-Ni Zheng, Lai-Ke Chen, Yuan-Hui Xiao, Zhao-Bin Chen, Qing-Na Zheng, Jian-Zhang Zhou, Jia-Wei Yan, De-Yin Wu

Journal of Electrochemistry

Para-aminothiophenol (PATP) is not only a widely-used probe molecule in the field of surface-enhanced Raman spectroscopy (SERS), but also an important model molecule for interfacial reactions, exhibiting distinct photo- and electro-oxidation pathways, so that PATP is selectively activated under different external fields. The evolution of products and intermediates during electrochemical oxidative coupling remains unknown. In this study, we have investigated the dynamic electrochemical oxidation process of PATP on the Au(111) surface using cyclic voltammetry, electrochemical (EC)-SERS, and in situ electrochemical scanning tunneling microscopy (EC-STM). The results showed that PATP forms an unsaturated adsorption coverage on Au(111) in an acidic solution. …

Boundary Integral Method For A Modified Mullins–Sekerka System, Ly Le

Mathematics & Statistics ETDs

This thesis develops a boundary integral method for a modified Mullins–Sekerka system arising as the sharp-interface limit of a nonreciprocal Cahn–Hilliard model. Nonreciprocal coupling changes the classical Cahn–Hilliard structure by introducing an additional conserved field, leading to coupled elliptic and parabolic dynamics at the interface. Using matched asymptotic expansions, we formally derive the modified Mullins–Sekerka model and then apply the boundary integral method to rewrite it on the moving interface. The elliptic component is represented using the periodic Green’s function for the Laplace equation, while the parabolic component is represented using the periodic heat kernel. This method reduces the bulk …

Nerve Constructions And Mapper, Alexander Bram Fritschi

Mathematics & Statistics ETDs

Mapper is a data visualization tool commonly used in topological data analysis to study large, often high-dimensional datasets. Mapper operates through the selection of a lens function, a clustering algorithm, and a cover. The Mapper graph is constructed using the nerve of the cover after the clustering algorithm is performed; it is therefore useful to study nerves to better understand Mapper. In this thesis, we will utilize the properties of nerves to find the minimal point set that produces a given graph. We will then extend this to Mapper to determine what Mapper graphs may be constructed over a given …

Interpretable Case-Control Inference Through Log-Linear General Location Models, Zacharia Stuart

Mathematics & Statistics ETDs

This dissertation analyzes one of the few publicly available NFL injury datasets to study field type and non-contact lower-limb injuries. Field type is studied jointly with other risk factors to understand how these factors interact to affect injury risk. The data were gathered through a case-control sampling scheme, which limits direct inference on absolute injury probabilities. While not the most common approach for case-control data, this dissertation models the retrospective distribution directly through Log-Linear General Location Models (Log-Linear GLOMs). Through a log-linear structure placed on a log-odds-ratio reparameterization, the model provides directly interpretable marginal and interaction contributions to injury log-odds …

The Uncertainty Principles, Lee Michael Felicetti

Mathematics & Statistics ETDs

The Heisenberg uncertainty principle is a central aspect of quantum mechanics, but also illustrates an essential quality of the Fourier transform. After Heisenberg, a variety of uncertainty inequalities emerged in the fields of physics and mathematics. In this thesis we will analyze the Heisenberg uncertainty principle in both the setting of quantum mechanics and Fourier analysis. We will then look at how the work of Heisenberg has been expanded upon in both physics and mathematics. Particularity, we will see how uncertainty principles can be applied to signal recovery and explore current research in this field.

Mining Legacy And Wildfires: Interfacial Reactions Affecting Metal Mobility, Eresay Alcantar-Velasquez

Earth and Planetary Sciences ETDs

We identified water labile interfacial reactions between laboratory burned pinewood ash and mine waste solids that influence metal mobilization. The Upper Gallinas Creek Watershed in New Mexico is affected by wildfires and mining legacy. Pinewood and mine waste sediments were sampled from the area, and the pinewood was burned at 350°C to simulate medium burn intensity ignition. Rapid desorption and gradual dissolution of Mn and Fe was detected by ICP-MS as pH decreased over time. After reacting 18 MΩ ultra-pure water with a mixture of pinewood ash and mine waste sediments Fe (143%) and Mn (89.2%) concentrations increased over time. …

Mapping Along-Strike Changes In Shallow Subduction Zone Geometry At The Alaska Subduction Zone Using Seismic Reflection And Tectono-Geomorphic Analysis, Madelyn K. Hurd

Earth and Planetary Sciences ETDs

The Alaska subduction zone, where the oceanic Pacific plate subducts beneath the continental North American plate at a rate of 60-66 mm/yr, has hosted more >M8 earthquakes over the last century than any other subduction zone globally. The largest of these, the 1964 M9.2 Alaska earthquake, ruptured 800 km of the margin, including a high slip patch near the trench offshore Kodiak Island. The 1964 rupture area may have overlapped with the 1938 M8.3 Semidi earthquake rupture zone that lies to the west. Slip propagation near the subduction trench during large earthquakes can control tsunamigenesis, and differences in wedge geometry …

Information Theory Analysis Of Water Vapor Stable Isotopes From The Sail Campaign, Matthew John Rybecky

Earth and Planetary Sciences ETDs

Understanding the processes that control water vapor isotopic composition in mountain environ- ments is essential for interpreting isotope records and predicting water resource responses to cli- mate change. This thesis applies information theory to continuous, high-resolution water vapor stable isotope measurements from the Surface Atmosphere Integrated Field Laboratory (SAIL) campaign in the East River watershed of Colorado’s Upper Gunnison Basin, spanning the winter- to-spring transition of 2022–2023. The analysis employs Shannon entropy, mutual information, transfer entropy, and joint transfer en- tropy (JTE) to quantify how environmental variables, including surface meteorology, radiation, tur- bulent fluxes, and ERA5 reanalysis products, transfer information …

Gradients Of Abandonment, William Tatman

Geography ETDs

As urban-rural disparities drive depopulation in rural areas worldwide, local strategies emerge as pathways for resilience. Research on Ojika, a Japanese island that has lost 75% of its population since the 1960s, reveals an Abandonment Gradient: a nuanced pattern of disuse adapted to modern polycrises. Extending the concept of "lying fallow" to homes and infrastructure, this thesis focuses on abandonment practices that reflect complex realities of labor, capital, and climate uncertainty. Rather than viewing depopulating communities as passive victims of out-migration, this paper argues they are critical sites for generating crisis response. Communally crafted attitudes toward unused space and more-than-human …

Ai-Powered Resume Screening, Sang Suh, Numery Zaber

Faculty Publications

Traditional resume screening is manual, slow, and susceptible to bias, and it struggles to keep pace with today’s application volumes. This paper presents a dual-engine, AI-powered resume screening system designed for transparency and reproducibility. The primary (classical) pipeline encodes resumes and job descriptions using Sentence-BERT (SBERT), computes a resume–job match score via cosine similarity, classifies candidates into 25 job categories using XGBoost, and provides model interpretability through SHAP. In parallel, a prompted large language model (LLM) baseline (GPT-4o/4o-mini) outputs a match score and predicted category for comparative analysis. A Streamlit-based interface integrates both engines to support recruiter workflows and human-in-the-loop …

Timelines Over Tokens: Summarization, Prompting, And Explainable Fine-Tuning For User-Level Suicide Risk Detection, Aditya Tekale

Master's Theses

This research presents a two-stage pipeline for user-level suicide risk detection from Reddit: first, inference-only prompting with summarization; second, fine-tuned encoder classification with explainability and expert validation. The data are user-level: each of the 500 C-SSRS Reddit items is one user’s chronologically concatenated posts and comments (a user timeline), annotated by psychiatrists. Stage one: six prompting strategies zero-shot, few-shot, chain-of-thought, tree-of-thought, least-to-most, and self-consistency are evaluated across six LLMs on multi-class and binary formulations; simple zero-shot achieves the highest balanced accuracy (0.53 multi-class). Error analysis shows longer inputs associate with misclassification (p = 0.002); domain-specific summarization (timelines >2,000 tokens) reduces …

Butte Priority Soils Operable Unit Final 2022 Unreclaimed Sites Sampling: Ur-27 Site Evaluation Summary Report, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Elucidation Of Spin-Hamiltonian Parameters Via Spectroscopy, Magnetization, And Computation, Joshua C. Mengell

Chemistry and Chemical Biology ETDs

Molecular Quantum Information Science (QIS) is fundamentally concerned with using spin-systems as quantum bits (qubits) or as sensors. Prerequisite to using molecular systems for QIS applications, it must be understood how one can design molecules with bespoke magnetic characteristics. Herein we study various paramagnetic molecular compounds, describing their complex magnetic characteristics using a spin-Hamiltonian formalism. We utilize various (sometimes novel) methods for determining these spin-Hamiltonian parameters. Many of these molecules possess magnetic characteristics, which make them attractive as qubits or for sensing applications. These characteristics include higher total spin-states (qudits—S_T>1/2), forbidden interstate electronic transitions, systems of spatially distant …

Exploring The Nature And Role Of Local Cation Ordering In Disordered Rock Salt Cathodes For Li- And Na-Ion Batteries, You Wang

Chemistry and Chemical Biology ETDs

Cation-disordered rock-salt (DRX) cathodes provide a highly tunable platform for next-generation Li- and Na-ion batteries, but their electrochemical behavior is strongly influenced by local structural features hidden in average crystal structures. This dissertation systematically investigates local cation ordering in Li- and Na-based DRX cathodes to understand its effects on Li+/Na+ transport, redox activity, structural evolution, and electrochemical performance. In Li-based systems, Raman spectroscopy and electrochemical analysis reveal that local layered cation ordering in Mn- and Fe-based DRX cathodes is closely correlated with electrochemical behavior. Over-stoichiometric Li-based DRX oxyfluorides further demonstrate that excess Li can regulate local cation ordering, improve Li+ …

Mapping And Modeling Threat-Evoked Brain States After Early Life Adversity, Taylor W. Uselman

Biomedical Sciences ETDs

Early life adversity (ELA) increases lifelong neuropsychiatric vulnerability. Yet how ELA reorganizes brain-wide activity and circuit coordination across later experience remains unclear. This dissertation tests the hypothesis that ELA alters adult brain-wide activity and responses to threat through disrupted coordination among neural systems that regulate emotional experience, including prefrontal-limbic and monoaminergic systems. Longitudinal manganese-enhanced MRI of adult mice exposed to standard or fragmented early care, combined with computational processing and statistical modeling, quantified brain states before, during, and long after innate predator threat. These studies established that acute threat evokes large-scale, distributed brain activity that evolves over time. ELA potentiates …

Multiscale Network Modeling Of Native And Modified Photosynthetic Light-Harvesting Complexes, Zane E. Armijo

Chemical and Biological Engineering ETDs

Photosynthetic light-harvesting complexes harvest solar energy and direct electronic excitations toward reaction centers with exceptional efficiency. This dissertation models the Fenna--Matthews--Olson complex of green sulfur bacteria, coupled to the PscA1 reaction center, as a chromophoric network. Forster resonance energy transfer theory, validated against numerically exact hierarchical equations of motion, was implemented in kinetic Monte Carlo simulations to resolve fine-grained excitation-transport pathways. The predicted charge-transfer efficiency of 77\% agrees with experiment, with the FMO2 monomer and its gateway pigment governing interfacial transfer. Systematic single, multi, and symmetry-preserving site removals, interpreted through Mobius inversion, identify critical pigments and show that cooperative effects …

Wildfire Impacts On Fluvial Hydrology From Watershed To National Scales, Paige G. Tunby

Civil Engineering ETDs

Wildfires alter the water quantity and quality in downstream river networks. Fires promote biodiversity, maintain habitat, and provide many ecosystem services in a fire-adapted landscape. However, changes in the natural fire regimes can alter ecosystem function and threaten the water security of impacted downstream communities. The magnitude, timing, and persistence of these impacts are difficult to predict due to the lack of high-resolution datasets with adequate coverage to evaluate spatiotemporal trends after a fire. This dissertation moves us beyond the status quo to evaluate post-fire fluvial responses across scales, from the event-scale impacts after the Hermit’s Peak-Calf Canyon wildfire in …

Surveyception: An Exploration Of Deceptive Survey Forms, Muhammad Danish

Computer Science ETDs

Survey platforms such as Google Forms and Microsoft Forms are widely used for feedback, data collection, and engagement, but scammers increasingly exploit them to distribute phishing and deceptive attacks. This thesis presents a large-scale study of survey-form abuse across ten major providers. We collected 140,000 forms from three sources: public posts on X, search-engine results, and web pages from the top 10 million DomCop-ranked domains. Using automated filtering and manual qualitative review, we identified 2,645 forms requesting sensitive information and classified 566 as scams. These forms used techniques including phishing, private-secret theft, account and personal-data harvesting, financial deception, and psychological …

New Distance Distributions Of Asymptotic Giant Branch Stars And Their Role In Tracing Galactic Structure, Rajorshi Bhattacharya

Physics & Astronomy ETDs

Asymptotic giant branch (AGB) stars are among the final evolutionary stages of low- and intermediate-mass stars and among the most luminous cool stellar populations in the Milky Way (MW). Their strong infrared emission allows them to be observed through regions of high interstellar extinction, making them useful tracers of the inner MW. However, their use is limited by unreliable distances because many are dust-obscured and variable, while geometric parallaxes are often unavailable or uncertain. This thesis develops statistical distance-estimation methods for large samples of oxygen-rich AGB stars. The resulting distances broadly agree with literature estimates, supporting their statistical reliability for …

Extending The Discovery Space Of Tess: Probing Underexplored Exoplanet Populations, Mallory L. Harris

Physics & Astronomy ETDs

This dissertation investigates how cold exoplanets can be identified despite the strong observational bias of exoplanet surveys toward short-period systems. Planets at wider orbital separations remain comparatively poorly constrained, limiting tests of planetary-system formation and the prevalence of outer architectures beyond compact systems. To address this gap, I use two complementary approaches. First, I develop a transit-search pipeline for TESS Full-Frame Images that identifies both isolated and repeated transit-like signals around nearby M dwarfs and characterizes the dominant false-positive classes that limit sensitivity in this regime. I then present TOI-904 c, the coldest planet discovered by TESS around an M …

An Investigation Of Tess M&Ms And The Occurrence Rate Of Transiting Circumbinary Planets, Dominic Oddo

Physics & Astronomy ETDs

Circumbinary planets (CBPs) are worlds which orbit two stars simultaneously. CBPs are excellent tests of the tenacity of planet formation, but are difficult to detect. The space-based NASA Transiting Exoplanet Survey Satellite (TESS) mission is a nearly all-sky survey designed to detect exoplanets transiting nearby stars. In this dissertation, I analyze the performance of TESS by comparing to the photometric precision of the ESA CHEOPS mission. Then, I define a catalog of low-mass eclipsing binaries (M&Ms), which are the best sources to search for CBPs. I describe my custom transit search methodology and apply it to the M&M catalog. I …

Simulating Quantum Field Theories On Fault-Tolerant Quantum Computers, Mason L. Rhodes

Physics & Astronomy ETDs

Quantum field theories are an essential framework in modeling fundamental interactions in nature, yet reliable simulations consume large portions of the world's most powerful supercomputers. In this Dissertation, we explore an alternative simulation paradigm on fault-tolerant quantum hardware, discussing both algorithmic and model advancements. In the former, we construct state-of-the-art algorithmic subroutines that take advantage of useful properties of the Hamiltonian describing the theory to achieve an exponential improvement in resources over prior quantum algorithms. In the latter, we simplify the structure of the Hamiltonian, making it more amenable to quantum simulation. First, we present an improved regularization of the …

Strategies For Large Dynamic Range, Entanglement-Enhanced Quantum Metrology With Experimentally Demonstrated Resources, Tyler G. Thurtell

Physics & Astronomy ETDs

Quantum metrology studies the use of quantum mechanical systems as measurement devices or sensors. Surprisingly, preparing a sensor in an entangled state can enhance measurement precision. The simplest protocols for entanglement enhancement sense only small changes in a quantity. The range of values over which a measurement protocol works is called its dynamic range. For many types of sensors we require end-to-end protocols that describe how to use entanglement to achieve enhanced precision over a large dynamic range. In this dissertation, we describe two approaches to achieving entanglement-enhanced sensing over a large dynamic range. The first approach uses entangling resources …

Quantum Control Of Qubits And Qudits In Neutral Atom Systems, Sri Datta Vikas Buchemmavari

Physics & Astronomy ETDs

This dissertation explores control of neutral atom quantum systems across multiple levels of abstraction, from atomic physics to system-level fault tolerance, using optimal control to improve performance. First, we propose a Rydberg entangling gate based on dressing with only the qubit control field; an interaction energy near the Rabi frequency benefits both gate speed and Rydberg decay. Second, with Sandia National Laboratories, we show that leakage errors in neutral atom systems can be converted to atom loss errors and detected using two entangling gates with an auxiliary atom, where a SWAP-based leakage detection unit outperforms the standard design. Next, we …

Understanding The Long-Run Effect Of Historical Redlining Practices, Yujian Lu

Geography ETDs

Historical redlining practices initiated by Home Owners’ Loan Corporation (HOLC) in the 1930s have produced enduring persistent socioeconomic and environmental disparities in U.S. cities. This dissertation examines their long-term impacts on social vulnerability, urban flood risk, along with public discourse about redlining practices. Results indicate that neighborhoods with HOLC grade A (greenlined) exhibit the lowest overall social vulnerability, while those graded D (redlined) face the highest across U.S. cities. In Chicago, associations between redlining practices and flood risk disparities are stronger than in Los Angeles, reflecting place-specific characteristics among environmental, socioeconomic, and demographic factors shaping flood risk disparities in long …

How Forest Structure And Climate Influence Snowpack For Water Resources In The Southwestern United States, Lindsey L. Rotche

Geography ETDs

Climate change, declining snowpack, and increasing wildfire risk have profound impacts on water availability in the southwestern United States. Because the southwestern United States is a global hotspot for freshwater vulnerability, and snowpack provides much of the region’s freshwater, understanding how climate and forest structure influence snowpack dynamics is increasingly important. In this dissertation I aim to better understand and communicate these dynamics through empirical data collection and the development of a simple vegetation driven temperature-index snow model: SNOW-17(VEG). I then implement the model at a watershed scale using remotely sensed imagery to create vegetation zones and climate simulations to …

Reading The Martian Surface: Impact Crater Distributions And Geochemical Signatures In Gale Crater As Recorded By The Curiosity Rover, Megan E. Hoffman

Earth and Planetary Sciences ETDs

The Curiosity rover has been exploring Gale crater, a large impact basin near the Mars equator since 2012. This mission has greatly improved our ability to explore the surface of Mars with a suite of geologic tools and cameras and has revealed that Mars likely once resembled present-day Earth. In this dissertation, I utilize measurements and data taken by Curiosity to analyze the distribution and preservation of small impact craters at meter scales, I quantify the formation characteristics of a small impact crater cluster, and I examine the presence of barium in a geologic unit with high-Si to constrain sediment …

Pebble Accretion: Compositions And Water Origins Of Terrestrial Planets, Susmita Garai

Earth and Planetary Sciences ETDs

Two leading models of planet formation invoke either stochastic collisions among km-sized planetesimals, or pebble accretion of sub-mm-cm solids regulated by gas drag. While collision based models typically require tens to hundreds of millions of years to assemble terrestrial planets, pebble accretion can produce Mars to Jupiter-mass bodies within the lifetime of the protoplanetary disk. Although widely accepted for the rapid growth of giant planet cores, the role of pebble accretion in forming terrestrial planets, including Earth, remains debated. Here, we investigate the consequences of pebble accretion for Earth’s origin. Here, I combine numerical models and laboratory experiments to find …

Algorithmic Sculpting Of Complex Fused Silica Surfaces For Nondestructive, Mode-Matched Cavity Quantum Electrodynamics: Adaptive Co2 Milling And Simulation-Guided Ultrafast Inscription, From Fiber Fabry-Perot Cavities To Monolithic Architectures, Meagan E. Parker

Optical Science and Engineering ETDs

Quantum sensors achieve exceptional measurement sensitivity through coherent, well-isolated quantum systems, but practical deployment is hindered by destructive readouts that require repeated state preparation and create long system dead times. Optical cavities enable continuous, nondestructive measurements with minimal back-action, yet integrating high-finesse cavities into scalable quantum devices remains limited by existing fabrication methods. To overcome these constraints, an adaptive CO₂ laser-milling platform was developed. Guided by glass thermodynamics and melt dynamics, this closed-loop system uses in-situ phase-shifting interferometry to sculpt complex fused-silica surfaces with sub-nanometer root-mean-square roughness. The platform was validated by fabricating extended-length fiber Fabry–Pérot cavities and monolithic micro-cavity …