Physical Sciences and Mathematics Commons^™

Evaluating Acridones As Novel Therapeutics For Human Babesiosis, Pratap Vydyam, Elizabeth Zhang, Papireddy Kancharla, Rozalia A. Dodean, Jane X. Kelly

Chemistry Faculty Publications and Presentations

Human babesiosis is an emerging tick-borne disease caused by Babesia parasites, most notably Babesia microti and Babesia duncani in North America and Babesia divergens in Europe. Infections can be severe or persistent or relapse despite treatment, and current therapeutic options remain limited, underscoring the urgent need for new and effective treatment options. Acridone derivatives originally developed as potent antimalarial agents against multiple life cycle stages of the malaria parasites were evaluated for their antibabesial activity using continuous in vitro culture systems of B. duncani and B. divergens. Lead candidates were assessed for selectivity against human cell lines to establish preliminary …

Detecting Eigenvectors Of An Operator That Are Near A Specified Subspace, David Darrow, Jeffrey S. Ovall

Mathematics and Statistics Faculty Publications and Presentations

In modeling quantum systems or wave phenomena, one is often interested in identifying eigenstates that approximately carry a specified property; scattering states approximately align with incoming and outgoing traveling waves, for instance, and electron states in molecules often approximately align with superpositions of simple atomic orbitals. These examples—and many others—can be formulated as the following eigenproblem: given a selfadjoint operator L on a Hilbert space H and a closed subspace W ⊂ H, can we identify all eigenvectors of L that lie approximately in W? We develop an approach to answer this question efficiently, with a userdefined tolerance and range …

Accelerated Coupled Mode Model For Fiber Laser Amplifiers As An Averaged Dynamical System, Rebecca Bryant, Jacob Grosek, Jay Gopalakrishnan

Mathematics and Statistics Faculty Publications and Presentations

We apply a known theorem for simplifying dynamical systems with bounded error to a specific optical fiber waveguide problem, thereby supplementing the physical intuition and heuristics used in the optics community with proper mathematical justification. Using techniques from the averaging theory of dynamical systems, a reliable accelerated model based on the coupled mode theory (CMT) approach for a common fiber laser amplifier application is derived. Computational testing reveals that this accelerated model achieves a ∼4000x increase in computational speed compared to the CMT model while preserving high accuracy in key figures of merit such as output power and amplification efficiency. …

Multiple-Valued Quantum Automata For Robotics, Yuchen Huang

Dissertations and Theses

This dissertation introduces a new type of quantum automata, their encoding and circuit realization. I concentrate on possible applications in robotics. Several methods and application of quantum automata and quantum circuit-based controllers for elementary robotic systems, with a focus on humanoid robot motion, emotion, and behavior generation are illustrated in detail. The research introduces several novel methodologies that bridge quantum computing principles with robotic control, aiming to overcome the limitations of classical deterministic and probabilistic approaches.

The dissertation first presents a quantum-circuit-based framework for generating non-repetitive and expressive (e)motions in a humanoid robot actor, using superposition and entanglement to produce …

A Comprehensive Calibration Framework For The Northwest River Forecast Center, Geoffrey Walters, Cameron Bracken, Brad Gillies, Leah Pope, Henry Pai, Sonali Chokshi, Victor Stegemiller, Stephen King, Julie Bracken, Taylor Dixon, Multiple Additional Authors

Mathematics and Statistics Faculty Publications and Presentations

We present a comprehensive framework developed by the Northwest River Forecast Center for calibrating hydrologically diverse basins. The framework includes models for snow, soil moisture, routing, channel loss, and consumptive use. Data inputs include a wide range of open-access datasets for meteorology, land use, topography, and land cover. The framework uses conceptual hydrologic models to handle basins with various hydrologic regimes including rain-driven and snowmelt-dominated basins. We also develop a flexible automatic calibration system that can handle numerous unobservable model parameters in a computationally efficient manner. A single-basin automatic calibration run can typically be completed on a modern laptop in …

Forest Fires Increase Vulnerability To Midwinter Rain-On-Snow Snowmelt In The Western Oregon Cascades, Sage C. Ebel, Kelly Gleason

Environmental Science and Management Faculty Publications and Presentations

Forest fires and rain-on-snow events in the seasonal snow zone of the Pacific Northwest are increasing in frequency and magnitude, yet the combined impacts of these events on snowpack and water resources remain poorly understood. We show that forest fires doubled midwinter snowmelt proportions in 2023 and 2024 compared to unburned reference sites in the western Oregon Cascades. Data from snow monitoring and micrometeorological stations installed across an elevational gradient revealed increased snowpack vulnerability during midwinter rain-on-snow events, where we observed more snowmelt per rain-on-snow event in the burned forest, indicating higher vulnerability of these snowpacks to rapid melt, increasing …

Toxicity, Chemistry, And Public Health Relevance Of Emerging Nicotine Analog Vapes, Pods, And Pouches., Rhea Raghu, Mohana Sengupta, Karen Lin, Felix Effah, Robert M. Strongin, Irfan Rahman

Chemistry Faculty Publications and Presentations

Electronic nicotine delivery system manufacturers, such as Charlie's Holdings Inc., ECBlend, Outlaw, and NicRiver, have recently introduced nicotine analogs, such as 6-methyl nicotine, 6-MN ("Metatine"), and nicotinamide, NA ("Nixamide," "Nixodine," or "Nixotin-free base and salt") in products to circumvent the U.S. FDA's premarket tobacco product application (PMTA) requirements. Marketed as "tobacco-free," "PMTA-exempt," or "FDA-approved," these compounds now appear in oral nicotine pouches and disposable bars/vapes from brands such as Outlaw Dip, Kumi-Six, SBX, Katchmi, and Spree Bar under proprietary labels including "NoNic6," "Metatine," or "NIC-SAFE." These products often mimic the appeal of conventional nicotine delivery systems, with extensive use of …

Properties Of The Graph Modularity Matrix And Its Applications, Benjamin Quiring, Panayot S. Vassilevski

Mathematics and Statistics Faculty Publications and Presentations

We study the popular modularity matrix and respective functional ([20]) used in connection with graph clustering and derive some properties useful when performing vertex aggregation of the associated graph. These properties are employed in the derivation of a multilevel parallel pairwise aggregation algorithm. Comparative performance results of the studied algorithm applied to graph clustering tested against the popular Louvain algorithm [4], [3] are presented. Some illustrative examples show that the resulting aggregates if used in an adaptive algebraic multigrid (AMG) are able to follow strong direction of anisotropy in finite element problems. 1.

Analysis Of Novel Cannabis Products Labeled As Containing Thc-Jd, Kaelas R. Munger, Carlton C. B. Bone, Killian M. Anreise, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Objective:

THC-JD (tetrahydrocannabioctyl) is a semi-synthetic cannabinoid with an eight-carbon C3 side chain, present in only trace amounts in hemp, requiring synthesis for commercial use. It has been promoted as potentially 19 times more potent than delta-9-THC, consistent with enhanced CB1 receptor affinities for cannabinoids with 7-8 carbon C3 side chains. While one peer-reviewed report identified THC-JD (tetrahydrocannabioctyl) in Japanese online products, an anecdotal report from the U.S. suggests mislabeling. Method: To inform regulatory efforts and consumer awareness and to address these discrepancies, this study chemically analyzed five U.S. commercial cannabis vape products marketed as containing THC-JD. Results: Utilizing GC-MS …

Toward A Didactical Phenomenology For The Completeness Axiom, Sean Larsen, Tenchita Alzaga Elizondo, Kristen Vroom, Stephen Strand Ii

Mathematics and Statistics Faculty Publications and Presentations

The study is part of an instructional design project focused on introductory real analysis. The goal of the project is to develop a theoretically grounded and empirically supported instructional approach that builds on students’ experiences in the calculus sequence to engage them in the reinvention of the rigorous foundations of the calculus. An essential aspect of this foundation is the completeness of the real numbers. Drawing on the didactical phenomenology heuristic from the theory of Realistic Mathematics Education (RME), we conducted an iterative instructional design study focused on the completeness axiom. The work proceeded in two phases. First, we conducted …

Agnostic Tomography Of Stabilizer Product States, Sabee Grewal, Vishnu Iyer, William Kretschmer, Daniel Liang

Computer Science Faculty Publications and Presentations

We define a quantum learning task called agnostic tomography, where given copies of an arbitrary state ρ and a class of quantum states C, the goal is to output a succinct description of a state that approximates ρ at least as well as any state in C (up to some small error ε). This task generalizes ordinary quantum tomography of states in C and is more challenging because the learning algorithm must be robust to perturbations of ρ. We give an efficient agnostic tomography algorithm for the class C of n-qubit stabilizer product states. Assuming ρ has fidelity at least …

Reasoning In Large Language Models Across Multilingual, Long-Context, And Symbolic Settings, Sina Bagheri Nezhad

Dissertations and Theses

Large Language Models (LLMs) are increasingly deployed as general-purpose reasoners, yet their reliability degrades in three settings that frequently arise in practice: multilingual inputs, long contexts, and symbolic or formally constrained domains. In multilingual settings, uneven training coverage produces substantial performance disparities and uncertain generalization to languages with little or negligible pretraining exposure. In long-context settings, relevant evidence may be sparsely distributed, and models exhibit the "lost-in-the-middle" phenomenon, undermining retrieval and multi-step synthesis. In symbolic settings such as mathematics, small arithmetic or logical slips invalidate solutions, and prose rationales are difficult to verify automatically.

This dissertation first characterizes these failure …

Nonstationary Flood Frequency Analysis For Urban Watersheds Using Open-Source Bayesian Software: Contrasting Case Studies From Texas, C. Haden Smith, Brian Skahill, David A. Margo

Mathematics and Statistics Faculty Publications and Presentations

Urban flood frequency analysis faces unique challenges as land development alters watershed hydrology, producing nonstationary flood records. This study demonstrates nonstationary flood frequency analysis (NSFFA) using RMC-BestFit, an open-source Bayesian software, through two Texas case studies. Brays Bayou at Houston (96 years of record) exemplifies an urbanized watershed with increasing flood trends; a step-logistic model captures both the abrupt increase in mean flood magnitude around 1968 and the progressive decrease in log-space variance as urbanization homogenized runoff response. O.C. Fisher Reservoir (169 years of record) exhibits decreasing trends attributed to brush encroachment and groundwater extraction; despite a sinusoidal model achieving …

Designing Novel Bisquinoline Antimalarials From Historical 4-Aminoquinolines To Combat Drug-Resistant Malaria, Mason J. Handford, Yuexin Li, Terry Riscoe, Xiaowei Zhang, Jane X. Kelly, Michael K. Riscoe

Chemistry Faculty Publications and Presentations

Plasmodium falciparum, the deadliest causative agent of malaria, continues to evade eradication efforts through widespread drug resistance. The recent development of ADC-028, a 4-aminoquinoline antimalarial with excellent activity and pharmacokinetic properties, prompted the investigation of bisquinoline analogs featuring similar structural motifs. Here, we describe a structure-activity relationship study that guided the optimization of compounds with key features, including the 4-anilinoquinoline core and diverse bridging linkers. Several analogs exhibited potent in vitro activity (IC50 < 20 nM) against both drug-sensitive and multidrug-resistant P. falciparum strains, while maintaining favorable cytotoxicity profiles. Among them, 25 demonstrated improved intrinsic metabolic stability (t1/2 = 121 min) and potent in vivo efficacy (ED50 = 0.32 mg/kg/day), achieving complete curative protection at a reduced dose compared to ADC-028. While 25 showed moderately reduced oral bioavailability (F = 43%) and a shorter half-life (T1/2 = 27.2 h) relative to ADC-028, its enhanced in vivo efficacy underscores its therapeutic potential. This work highlights a promising path forward in developing antimalarials that retain the efficacy of legacy compounds while overcoming modern resistance mechanisms.

A Cryptographic Perspective On The Verifiability Of Quantum Advantage, Nai-Hui Chia, Honghao Fu, Fang Song, Penghui Yao

Computer Science Faculty Publications and Presentations

In recent years, achieving verifiable quantum advantage on a NISQ device has emerged as an important open problem in quantum information. The sampling-based quantum advantages are not known to have efficient verification methods. This article investigates the verification of quantum advantage from a cryptographic perspective. We establish a strong connection between the verifiability of quantum advantage and cryptographic and complexity primitives, including efficiently samplable, statistically far but computationally indistinguishable pairs of (mixed) quantum states (EFI), pseudorandom states (PRS), and variants of minimum circuit size problems (MCSP). Specifically, we prove that a) a sampling-based quantum advantage is either verifiable or can …

How Agile Became The Design Philosophy Of Ai Fishbowl Under Real-World Constraints, Jad Saad

University Honors Theses

This capstone review examines the development of AI Fishbowl, a public-facing, interactive artificial intelligence system, as a case study in how Agile methods evolve from a project management tool into a design philosophy under real-world constraints. Although the project adopted an Agile workflow early on through a Kanban-style task management approach, the initial system design and architecture were still shaped by a largely plan-first mindset. This created a mismatch between flexible process and rigid design assumptions, which became increasingly apparent as the team moved from high-level architecture into implementation.

A critical turning point occurred when early architectural plans proved difficult …

Bl(U)E Crab: Bluetooth Low Energy Connection Risk Assessment Benchmarking, Dylan Christopher Conklin

Dissertations and Theses

The usage of Bluetooth Low Energy (BLE)-based tracker devices for stalking has become a salient privacy concern. Detecting unwanted or suspicious trackers is challenging due to their cross-platform compatibility issues, inconsistent detection methods, and lack of an industry-wide standard for detecting malicious devices. BL(u)E CRAB, Bluetooth Low Energy Connection Risk Assessment Benchmarking, scans data and generates risk factors about nearby devices to classify them as suspicious or not. These risk factors include the number of encounters the user had with a device, the duration of time a device has been near the user, the distance a device has traveled …

Reliable Eigenspace Error Estimation Using Source Error Estimators, Jay Gopalakrishnan, Gabriel Pinochet-Soto

Mathematics and Statistics Faculty Publications and Presentations

We introduce a framework for repurposing error estimators for source problems to compute an estimator for the gap between eigenspaces and their discretizations. Of interest are eigenspaces of finite clusters of eigenvalues of unbounded nonselfadjoint linear operators with compact resolvent. Eigenspaces and eigenvalues of rational functions of such operators are studied as a first step. Under an assumption of convergence of resolvent approximations in the operator norm and an assumption on global reliability of source problem error estimators, we show that the gap in eigenspace approximations can be bounded by a globally reliable and computable error estimator. Also included are …

Nonenzymatic Glucose Biosensor Based On Selective Reduction Of Silver Ions, Maryam Sarlak, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

A nonenzymatic conductivity-based glucose biosensor, reported here, designed for potential noninvasive measurement in accessible biofluids such as saliva, sweat, and tears. The sensor exploits a classic Tollens’ silvering process that deposits metallic silver on a sensitized surface via a quantitative, selective reduction of silver ions by glucose. Of the two surface sensitization methods used, the self-assembled bifunctional thiol/silane surfactant yields a more stable and sensitive sensor than tin(II) chloride. The conductometric sensor consists of two spiral interdigitated silver electrodes fabricated by lithography and wet etching. The sensor impedance changes after selective metallic silver deposition between the electrodes. The sensor exhibits …

Chemical Control Strategies For Poa Annua In Managed Turfgrass Systems, James D. Mccurdy, Rebecca G. Bowling, Aaron J. Patton, Edicarlos B. De Castro, James T. Brosnan, David E. Ervin, Shawn D. Askew, Clebson G. Goncalves, Matthew T. Elmore, J. Scott Mcelroy, Multiple Additional Authors

Environmental Science and Management Faculty Publications and Presentations

Poa annua L. is a widespread and persistent weed in managed turfgrass systems, exhibiting both annual and short-lived perennial growth habits. Effective management requires an integrated approach, with chemical herbicides remaining a primary tool. This review outlines the current landscape of chemical control strategies, including pre-emergence and post-emergence herbicide options, plant growth regulators, and emerging chemistries. Herbicide resistance in Poa annua continues to pose a significant challenge, with confirmed cases spanning multiple modes of action. Consequently, sustainable management depends on rotating herbicide classes, using mixtures and sequences of treatments, and integrating nonchemical tactics.

Selective Reversal Of Cu-Amyloid Aggregation Monitored In Real Time By Fluorescence Anisotropy: Ni-Bme-Dach Vs Edta Benchmarks, Alyssa N. Schroeder, Eleanor K. Adams, Dane C. Frost, Erica Lopez, Jennie R. Giacomini, Marilyn R. Mackiewicz

Chemistry Faculty Publications and Presentations

Metal dyshomeostasis, particularly involving Cu2+, is increasingly recognized as a key contributor to amyloid-β (Aβ) aggregation and neurotoxicity in Alzheimer’s disease, motivating the development of chelators capable of selectively disrupting pathogenic metal-Aβ interactions without perturbing essential biological metals. Here, we employ steady-state fluorescence anisotropy as a real-time probe of TAMRA-Aβ1–42 rotational mobility to quantify metal-induced aggregation and its reversibility by two chelators with distinct selectivities: EDTA, a broad-spectrum benchmark, and Ni-bme-dach, a sulfur-rich metallodithiolate with high Cu affinity. Cu2+ induces the most significant increases in anisotropy, consistent with rapid formation of large nanoscale aggregates, while Fe3+ produces moderate aggregation and …

Clustering Of Temporal And Visual Data: Recent Advancements, Priyanka Mudgal

Computer Science Faculty Publications and Presentations

Clustering plays a central role in uncovering latent structure within both temporal and visual data. It enables critical insights in various domains including healthcare, finance, surveillance, autonomous systems, and many more. With the growing volume and complexity of time-series and image-based datasets, there is an increasing demand for robust, flexible, and scalable clustering algorithms. Although these modalities differ—time-series being inherently sequential and vision data being spatial—they exhibit common challenges such as high dimensionality, noise, variability in alignment and scale, and the need for interpretable groupings. This survey presents a comprehensive review of recent advancements in clustering methods that are adaptable …

The Gut Microbiota Shapes The Human And Murine Breath Volatilome, Ariel J. Hernandez-Leyva, Amalia Z. Berna, Maggie H. Bui, Yang Liu, Anne L. Rosen, Michael A. Lint, Samantha A. Whiteside, Natalia Jaeger, Nikhilesh Joardar, Wentai Luo, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The gut microbiota is crucial to health, yet implementation of microbiota-based therapeutics is limited by the lack of rapid diagnostics. We hypothesize that breath contains gut microbe-derived volatile organic compounds (VOCs) reflecting microbiota composition and metabolism. In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function. By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome. VOCs from cultured gut microbes were identified in vivo in monocolonized gnotobiotic colonized mice. …

Ureilite Meteorite Petrofabrics: Evolution And Formation Deformational Conditions, Benjamin Botwe Agyemang

Dissertations and Theses

This thesis examines the origin and development of crystallographic fabrics in ureilites, which are primitive achondritic meteorites interpreted as residues of partial melting from a differentiated parent body. In this study, we evaluate three fabric-forming mechanisms: gravitational cumulate crystallization, shock-induced deformation, and flow alignment associated with melt extraction and convective stirring. A quantitative Electron Backscatter Diffraction (EBSD) analysis was conducted on six ureilitic meteorites to assess olivine Lattice Preferred Orientation (LPO), Shape Preferred Orientation (SPO), the connection between SPO and LPO, and other deformation metrics, including Grain Orientation Spread (GOS), and Crystal Rotation Axis (CRA). Our results suggest that most …

Microbial Communities And Biogeochemistry Of A Melting Rocky Mountain Glacier, Pacifica Sommers, Elizabeth Traver, Alison Orthel, Andrew G. Fountain, Jacki Klancher, Steven K. Schmidt

Geology Faculty Publications and Presentations

Mountain glaciers are disappearing rapidly, and with their disappearance, we may be losing unstudied biodiversity and genetic resources. A variety of habitats for microorganisms exist on glaciers, especially within pockets of supraglacial sediments (cryoconite) that support high levels of biological activity and diversity. We used biogeochemical approaches, high-throughput DNA sequencing, and microscopy to describe the biogeochemistry and microbial communities of supraglacial sediments on the Dinwoody Glacier in the Wind River Range, Wyoming. Carbon (C) and nitrogen (N) concentrations were high, and C:N ratios were close to the Redfield ratio indicating active nutrient cycling. We found unique microbial communities in sediments …

Wild@Fire2025: Overview Of Word-Level Code-Mixed Language Identification In Dravidian Languages, Ameeta Agrawal, Asha Hegde, Sharal Coelho, Sabur Butt, Fazlourrahman Balouchzahi, Sudha V, Shashirekha Hosahalli Lakshmaiah

Computer Science Faculty Publications and Presentations

Code-mixing is considered as a linguistic phenomenon that combines several languages into one text. It has now become very common in multilingual societies, especially in digital communication. Word-Level Identification of Languages in Dravidian Languages (WILD) - a Code-mixed Language Identification (CoLI) in Dravidian languages shared task, organized as a part of Forum for Information Retrieval and Evaluation (FIRE) 2025, put forward these challenges to the researchers by asking them to develop models capable of classifying words in code-mixed texts involving Dravidian languages - Tamil, Telugu, Malayalam, Kannada, and Tulu, which are interwoven with English. It poses significant challenges due to …

The Distribution Of A-Numbers Of Hyperelliptic Curves In Characteristic Three, Derek Garton, Jeffrey Lin Thunder, Colin Weir

Mathematics and Statistics Faculty Publications and Presentations

In this paper we present a new approach to counting the proportion of hyperelliptic curves of genus g defined over a finite field Fq with a given a-number. In characteristic three this method gives exact probabilities for curves of the form Y 2 = f(X) with f(X) ∈ Fq[X] monic and cubefree, probabilities that match the data presented by Cais et al. in previous work. These results are sufficient to derive precise estimates (in terms of q) for these probabilities when restricting to squarefree f. As a consequence, for positive integers a and g we show that the nonempty strata …

Key To Spartina Of The West Coast Based On Vegetative Characteristics, Mary Pfauth, Mark D. Sytsma, Mitchell Kloer, Jennifer Riddle, Jacob Rose, Gabriel E. Campbell

Center for Lakes and Reservoirs Publications and Presentations

In their natural condition, Pacific Coast estuaries have extensive open mudflats in the intertidal area that are important shorebird feeding habitat and are used for oystering and recreational fishing. Several non-native cordgrass species are invading Pacific estuaries and damaging these functions and uses. Early detection is critical to effective management of cordgrass infestation. This key is intended to provide an easy-to-use reference for quick identification of Spartina (synonym: Sporobolus) species on the Pacific coast. We choose to focus on vegetative characteristics here, since flowers are not always visible when it can be advantageous to survey.

This publication is intended to …

An Introduction To Field Excursions For The 2026 Geological Society Of America Cordilleran Section Meeting In Loreto, Baja California Sur, México, Scott E.K. Bennett, Michael H. Darin, Genaro Martínez Gutiérrez

Geology Faculty Publications and Presentations

The 122nd annual meeting of the Geological Society of America (GSA) Cordilleran Section will be held in Loreto, Baja California Sur, México, an idyllic and historic Sonoran Desert city nestled on the eastern shore of the Baja California peninsula. The 2026 Loreto meeting marks a milestone for GSA as it is the first time in the Section’s century-plus history that the meeting has been held on the Baja California peninsula and only the third time that the meeting has been held in México. Thus, the 2026 Loreto meeting and related field trips represent a meaningful expansion of the Section’s engagement …

Aquatic Invasive Species Survey And Treatment On Lake Umatilla And Lake Celilo 2024-2025 Report, Jacob Rose, Gabriel E. Campbell

Center for Lakes and Reservoirs Publications and Presentations

Flowering Rush (Butomus umbellatus) is an invasive aquatic plant in the Pacific Northwest that threatens salmon habitat. The Center for Lakes and Reservoirs staff surveyed for this and other aquatic species from 2024 and 2025 in the Columbia River in Lake Umatilla and Lake Celilo. This document summarizes their survey efforts including their protocols, data, and small-scale removal efforts.