Physical Sciences and Mathematics Commons^™

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.

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 …

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 …

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 …

Numerics: A .Net Library For Numerical Computing, Statistical Analysis, And Risk Assessment, C. Haden Smith, Woodrow L. Fields, Julian Gonzalez, Sadie Niblett, Brennan Beam, Brian Skahill

Mathematics and Statistics Faculty Publications and Presentations

Numerics is a free and open-source numerical computing library for .NET, developed by the U.S. Army Corps of Engineers Risk Management Center (USACE-RMC). The library provides 43 univariate probability distributions with L-moment and maximum likelihood parameter estimation, eight Markov Chain Monte Carlo (MCMC) samplers for Bayesian inference, bootstrap uncertainty quantification, bivariate copulas, optimization algorithms, and numerical methods for integration, differentiation, root finding, and linear algebra. Numerics targets engineers, scientists, and analysts working in infrastructure risk assessment, flood frequency analysis, and Monte Carlo simulation within .NET-based enterprise systems. The library supports .NET 8.0 through 10.0 and .NET Framework 4.8.1 and is …

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 …

Machine Learning For Economists, John Luke Gallup

Economics Faculty Publications and Presentations

Explication of machine learning algorithms and their usefulness for economic research. The prediction algorithms of Random Forest, Gradient Boost Machines, Neural Networks and Support Vector Machines are built from simple steps applied at large scale to generate surprisingly precise nonlinear estimates. Although useful for processing and interpreting new forms of data, their application to economics research is limited because they do not provide readily interpretable evidence of the causes of outcomes.

Data And Code For: Combined Effects Of Forest Fire And Climate Warming On Seasonal Snow In The Western Oregon Cascades, Joseph D. Vigil

Environmental Science and Management Datasets

This dataset supports a study examining the combined effects of forest fire and climate warming on seasonal snow in the Breitenbush watershed of the western Oregon Cascades. The archive includes daily SnowModel snow water equivalent outputs for forested, current post-fire, mid-century, and end-century climate scenarios; field meteorological and manual snow observations; station metadata; modified SnowModel code used to represent post-fire snow-albedo decay; and R code used to calculate snow metrics and statistical comparisons reported in the associated manuscript. Derived results and documentation are included to support reproduction of the primary analyses.

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.

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 …

Congruences For Hecke Eigenvalues Via Period Polynomials, Liobomir Chiriac

Mathematics and Statistics Faculty Publications and Presentations

We study a conjecture motivated by Coleman and Stein’s work on approximating eigenforms of infinite slope by those of finite slopes, which was recast by Rustom [‘Congruences modulo prime powers of Hecke eigenvalues in level 1’, Res. Number Theory 5(1) (2019), Article no. 10, 27 pages] as a congruence for the second Fourier coefficient. We establish the weight condition required for this coefficient to be divisible by nine and obtain the full conjecture under a natural ramification hypothesis. The proof uses period polynomials, especially Zagier’s description of the Hecke action on them.

Becoming A Shape, Becoming Yourself: Geometry, Identity, And Belonging In An Early Childhood Classroom, Eva Thanheiser, Molly Robinson, Simon Byeonguk Han, Amanda T. Sugimoto, Courtney Koestler, Mathew D. Felton-Koestler

Mathematics and Statistics Faculty Publications and Presentations

This paper examines how a first-grade geometry lesson became a site for exploring shape, selfhood, and belonging in an early childhood classroom. Drawing on interaction analysis of a lesson built around the picture book The Greedy Triangle , we show how children named personal strengths, identified shapes, followed a triangle through changing categories, reflected on why they liked being themselves, and used their bodies to form polygons. We ask what counts as mathematical activity in this lesson and argue that mathematics is not limited to naming shapes. It also involves noticing attributes, negotiating criteria, tracking transformation, coordinating bodies, and reasoning …

The Johnson-Křížek-Mercier Elasticity Element In Higher Dimensions, Jay Gopalakrishnan, Johnny Guzman, Jeonghun J. Lee

Mathematics and Statistics Faculty Publications and Presentations

Mixed methods for linear elasticity with strongly symmetric stresses of lowest order are studied in this paper. On each simplex, the stress space has piecewise linear components with respect to its Alfeld split (which connects the vertices to barycenter), generalizing the Johnson–Mercier two-dimensional element to higher dimensions. Further reductions in the stress space in the three-dimensional case (to 24 degrees of freedom per tetrahedron) are possible when the displacement space is reduced to local rigid displacements. Proofs of optimal error estimates of numerical solutions and improved error estimates via postprocessing and the duality argument are presented.

Microbial Communities Of Selected Regions Of The Deep Springs Lake Aquifer System, Rania Zaki, Emma Bourne, Andrew Storino, Jay Nadeau

Physics Faculty Publications and Presentations

Deep Springs Lake is a small, isolated, highly alkaline soda lake in Inyo County of Eastern California, USA. It is a seasonally filled salt lake or playa, and is part of a closed aquifer system. Such closed systems are globally rare, occurring only in arid zones where annual evaporation is greater than annual rainfall. Deep Springs Lake’s hydrology and geology have been well studied, and it is home to a unique toad species, but its microbiome remains unexplored. Here we perform 16S, 18S, and ITS amplicon sequencing of the lake water, dried salt crust at the edges the lake, and …

Oregon State Rank Assessment For Plumed Clover (Trifolium Plumosum Var. Plumosum), Nora Dunkirk

Institute for Natural Resources Publications

Oregon state conservation status assessment for Plumed Clover (Trifolium plumosum var. plumosum) using NatureServe methodology, 2025.

Online Decision Mamba, Trenton W. Ruf

Dissertations and Theses

Online in-context reinforcement learning enhances offline-trained policies through online fine-tuning. We introduce Online Decision Mamba (ODM), an architecture that replaces the attention mechanism in Online Decision Transformers (ODT) with the Mamba module to improve long-context sequence modeling and overall RL performance. We performed in-depth evaluations on MuJoCo (OpenAI Gym) and Atari benchmarks, comparing ODM against state-of-the-art offline and online baselines—including Decision Mamba (DM) and ODT. Our results show that ODM achieves competitive or superior performance, with particularly robust gains when initial datasets lack expert demonstrations. In the Qbert Atari environment, ODM shows context-length sensitivity similar to offline DM; however, we …