Physical Sciences and Mathematics Commons^™

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Conello Vendor Marketplace Capstone: A Review On The Capstone Process And Computer Science Degree, Levi Hauck

University Honors Theses

This Capstone Review Thesis discusses the current structure of the Computer Science Degree path and Computer Science Capstone at PSU. This thesis reviews the Conello Vendor Marketplace Capstone, a project designed to help address the issue of teambuilding in the workplace. It points out ways in which teamwork and organization is an underdeveloped skill in Computer Science. During the Capstone project, the project management method of Agile development was recommended and used. However, it became clear that the team, leader included, had a gap in knowledge and skills to be successful, as well as a lack of experience in team …

Shallow-Marine Crinoid Genera May Have Been More Resilient Across Permian Extinction Events In Terms Of Richness Than Deep-Marine Crinoid Genera, Amelia C. Kolstad

University Honors Theses

Throughout the Phanerozoic, one of the most successful phyla of marine invertebrates has been Echinodermata. Echinodermata was particularly successful throughout the Paleozoic, with class Crinoidea making up a majority of occurrences. The proportion of echinoderm occurrences that are crinoids declined massively at the end of the Permian and continued to decrease into modern day, never fully recovering. One of the factors thought to have been so important for crinoid success in the Paleozoic and their decreasing success throughout geologic time has been their propensity for success in shallow-marine environments, though crinoids also exist within deep-marine environments. This study seeks to …

Agile In The Age Of Ai: Considerations And Improvements For Streamlining Developer Workflows, Stephen Feng

University Honors Theses

This paper examines the integration of AI language models into Agile developer workflows during a six-month software development project. Using the development of SagacityWall, a mindfulness-based social media application built by a team of eight undergraduates, it identifies three key areas in Agile processes where AI provided meaningful leverage: translating business requirements into actionable developer work tickets, accelerating framework research and technology stack decisions, and reducing onboarding friction through AI-assisted code scaffolding and Behavior-Driven Development story formatting. The study finds that AI meaningfully boosted productivity across these stages – not by replacing developer judgment, but by reducing overhead at each …

Modeling Turbulent Accretion Flows Around Black Holes: Azimuthal Flux Derivative Density Curves In 3d Mhd Simulations, Sasmitha Purushothaman, Matthew D. Duez, Pavan Chawhan

University Honors Theses

When modeling two-dimensional axisymmetric accretion disks around Kerr black holes, setting the azimuthal terms of the MHD equations to zero causes the loss of turbulence and dynamo effects. In this paper, we use three-dimensional models to identify the turbulence that arises from azimuthal flux derivatives (AFDs) and create probability density functions to characterize them. We establish a pipeline for calculating the AFDs, creating a distribution, and normalizing it. Then, we plot the dependence of the conditional probability of the AFDs on density, magnetic field strength, and velocity for the continuity and magnetic induction equations. Future research can take this information …

Comparing The Sensitivity And Degree Of Boolean Functions Via The Hypercube, Anne-Caroline Rupp

University Honors Theses

This thesis studies three complexity measures of total Boolean functions f:{0,1}ⁿ → {0,1}: maximum sensitivity s(f), polynomial degree deg(f), and spectral sensitivity λ(f), where λ(f) is defined as the spectral norm of the adjacency matrix of the sensitivity graph. Building on the results of Aaronson et al., we examine the inequality chain √s(f) ≤ λ(f) ≤ deg(f) and investigate whether all three quantities can be simultaneously equal.

The first part of the thesis reverse engineers the equality cases of the two known inequalities to isolate necessary extremal conditions on both the Fourier structure of f and the local geometry …

Not Everyone Gets A Tree: Housing Values, Street Trees, And Equity In Portland, Matthew Moller

University Honors Theses

Street trees are positively associated with Portland home sale prices, but exposure and capitalization are uneven by race/ethnic neighborhood context. Urban trees are ecological assets, but their economic and equity implications remain uneven. This thesis examines street-tree exposure and 2023 residential sale prices in Portland, Oregon (n = 6,414) using a mixed-methodology hedonic design. Ordinary least squares models measure inventoried street-tree counts within 20m, 50m, and 100m buffers together with structural controls and census-block racial and ethnic context. Trees are positively and significantly associated with logged prices at all radii, with scale-sensitive magnitudes and modestly better fit as wider buffers. …

Applications Of Prior And Novel Computational Tools In Mental Health Treatment, And Their Potential To Uncover The Explanatory Gap, Ambika Vyas

University Honors Theses

The explanatory gap is a widely discussed concept in scientific and philosophical literature. In neuroscience, the solution to the explanatory gap is highly sought out, but the general consensus is that it is unsolvable. Numerous articles discuss the explanatory gap alongside computational tools and how these tools could aid neuroscientists in uncovering the mental health explanatory gap. However, significant developments in machine learning have been made since 2020, coinciding with the rise in Large Language Models (LLMs). This thesis is a literature review on computational methods, tools, and devices developed and utilized by researchers to improve how mental health disorders …

Hillslope Aspect And Other Potential Controlling Factors On The Spacing Of Periglacial Stone Stripes In Se Oregon, Blue Hansen

University Honors Theses

Stone stripes are a type of patterned landscape that can be polygenetic in origin, but in the High Lava Plains province are interpreted to be relict periglacial features based on similarities to active stone stripe formation in current periglacial settings. Periglacial stone stripes are hypothesized to form via frost process, including ice-driven cracking and soil heave which is dependent on temperature, long-term differences in temperature may contribute to differences in stone stripe patterns or density. Stone stripes in Oregon and Idaho have previously been studied using field techniques, but there is room for reexamination of temperature controls on hillslope density …

Bayesian Optimization Of Laser Wakefield Acceleration Via Spectral Pulse Shaping, B. Z. Djordjević, C. Benedetti, Asa D. Mcnaughton, R. Lehe, H.-E. Tsai, S. C. Wilks, B. A. Reagan, G. J. Williams, J. Van Tilborg, C. B. Schroeder

Physics Faculty Publications and Presentations

In this paper, we investigate the effect of spectral pulse shaping of the laser driver on the performance of channel-guided, laser–plasma accelerators. The study was carried out with the assistance of Bayesian optimization using particle-in-cell simulations. We used a realistic plasma profile based on a novel optical-field-ionized channel technique with ionization injection and low, on-axis plasma densities to maximize the energy gain of the electron bunch trailing the laser. Spectral shaping allows us to modify the temporal profile of the laser driver while keeping the laser energy constant, affecting the acceleration and injection processes. In addition, we consider how modifying …

Oregon State Rank Assessment For Straggling Gilia (Allophyllum Gilioides), Lindsey K. Wise

Institute for Natural Resources Publications

Oregon state conservation status assessment for Straggling gilia (Allophyllum gilioides) using NatureServe methodology, 2026.

Arylation Of Nitrogen, Oxygen And Carbon Nucleophiles By Aryl(Tmp)Iodonium Salts, Joseph Jordan Hatton

Dissertations and Theses

Substituted aromatic rings are present in industry in a plethora of organic molecules such as pharmaceuticals, agrochemicals, materials and beyond. Therefore, methods for broadly installing aryl rings into other compounds to create substituted aromatic rings are valuable to many organic chemists. Historically these transformations are achieved through methods such as nucleophilic aromatic substitution and metal catalyzed cross-coupling. Nucleophilic aromatic substitution is a user-friendly method in this space but is limited by reliance on specific electronics. Metal catalyzed cross-coupling reduced the dependence on electronics in this space, but metals are generally unattractive reagents due to high costs, toxicity and challenges with …

An Integrated Framework For Memory-Centric Analysis: From Trace Collection To Co-Design, Dhruv Gajaria, Prajwal Challa, Yasodha Suriyakumar, Joseph Manzano, Nathan Tallent, Andrés Márquez

Computer Science Faculty Publications and Presentations

IntroductionThe memory wall phenomenon—where advances in processor performance significantly outpace those in memory subsystems-poses a fundamental challenge for contemporary computing systems. In memory-bound applications, memory subsystem behavior dominates performance, yet existing analysis approaches present significant limitations: detailed microarchitectural simulators require days to weeks to simulate modest workloads; hardware performance counters provide only aggregate statistics that obscure temporal and spatial access patterns; and scaled simulation approaches face challenges in capturing contention effects, bandwidth saturation, and interference patterns that emerge at larger scales. These limitations reflect a processor-centric design philosophy—in both performance analysis tools and system co-design methodologies—that is increasingly misaligned with …

Design And Implementation Of Error Estimators For Finite Element Eigenvalue Problems, Gabriel Esteban Pinochet Soto

Dissertations and Theses

We present three publications, all encompassed under the umbrella of a posteriori error estimation theory for eigenvalue problems for finite element discretizations. The central objective of the research is the development of a general framework for the study of reliable estimation of eigenvalues and eigenspaces. We introduce applications to problems of theoretical interest as well as problems arising in real-life scenarios, such as optical fibers. The first paper focuses on the implementation of a dual-weighted residual error estimator for a nonselfadjoint eigenvalue problems arising from the study of leaky modes in optical fibers---Maxwell's equations, Perfectly Matched Layers, and a conforming …

Improving Explainability And Interpretability Of Neural Networks Via Hyperparameter-Extended Influence Functions, William Breslin

Dissertations and Theses

Understanding how model predictions and training outcomes vary with changes in data, features, and modeling choices is central to explainable artificial intelligence. This dissertation introduces a unified framework for explainability by generalizing classical influence functions to encompass user-defined hyperparameters embedded in the training loss, model architecture, or data representation. By extending influence functions in this way, the framework broadens their applicability and integrates multiple explainability techniques into a single, coherent approach. It provides a common mathematical foundation linking data impact, feature importance, and model design analysis, and supports a broad class of additional explainability analyses beyond these settings. The demonstrated …

Local And Indigenous Knowledge, Innovation, And Sustainable Development: Creating Sustainable Futures Amidst Crisis Conditions At The Community Level, Carlos Andrés Arias

Dissertations and Theses

In 1987, the Brundtland Commission's Our Common Future (1987) made clear the need to reject longstanding development processes and focus on sustainable development. The Commission stressed that actual sustainable development integrates three elements: social development, economic development, and environmental protection. Though developed nations have achieved economic growth through conventional and extractive development practices, these practices have intensified natural disasters driven by climate change, increased food insecurity, and deepened poverty. This has acutely impacted Indigenous and local communities, many of whom face crisis conditions, such as war, terrorism, civil disorder, and their aftermath. Even so, many of these communities successfully implement …

Oregon State Rank Assessment For Wiens' Dwarf Mistletoe (Arceuthobium Abietinum Ssp. Wiensii), Lindsey K. Wise

Institute for Natural Resources Publications

Oregon state conservation status assessment for Wiens' dwarf mistletoe (Arceuthobium abietinum ssp. wiensii) using NatureServe methodology, 2026.

Oregon State Rank Assessment For Bedstraw Broomrape (Aphyllon Epigalium Ssp. Epigalium), Lindsey K. Wise

Institute for Natural Resources Publications

Oregon state conservation status assessment for Bedstraw broomrape (Aphyllon epigalium ssp. epigalium) using NatureServe methodology, 2026.

Crossing Boundaries: Brachinites And Their Diverse Asteroidal Origins, B. G. Rider-Stokes, F. A. Davies, T. H. Burbine, E. Maclennan, R. C. Greenwood, S. L. Jackson, M. Anand, Daniel Sheikh, M. M. Grady

Geology Faculty Publications and Presentations

Brachinite meteorites are typically linked to the olivine-rich A-type asteroids. In this study, however, they appear to exhibit unexpected spectral diversity. Spectroscopic analysis of seven meteorites from the brachinite clan reveals two distinct populations in band parameters, overlapping with both the A-type and S-complex asteroids. This dual association shows that a single meteorite group can originate from multiple asteroid taxonomies. Notably, one S-complex-like specimen, Northwest Africa (NWA) 14,635, displays band parameters similar to those of asteroid (65803) Didymos, the target of the European Space Agency's (ESA) ongoing Hera mission. These results underscore the value of spectroscopic characterization of poorly understood …

Rosenzweig's Elements And Universal History, Martin Zwick

Complex Systems Faculty Publications and Presentations

This paper uses Rosenzweig’s conception of the three elements of God, World, and Human from The Star of Redemption in a model of universal history. The model also has some relation to Rosenzweig’s geopolitical essay, Globus, which is very different from the meta-historical Star. Based on a systems-theoretic schema of events and processes, the model views human history in terms of three linked processes: a primary process labeled “World” – the origin and development of human society embedded in nature, a secondary process labeled “God” – the origin and development of the Axial religions and philosophies, and a …

An Infinite Set Of One-Range Addition Theorems Without An Infinite Second Series, For Slater Orbitals And Their Derivatives, Applicable To Multiple Coordinate Systems, Jack C. Straton

Physics Faculty Publications and Presentations

Addition theorems have been indispensable tools for the reduction of quantum transition amplitudes. They are normally utilized at the start of the process to move the angular dependence within plane waves, Coulomb potentials, and the like, into a sum over spherical harmonics that allows the angular integration to be carried out. These have historically been “two-range” addition theorems, characterized by the two-fold notation r>=Max[r1,r2] and r< =Min[r1,r2] and comprising a single infinite series. More recently, “one-range” addition theorems have been created that have no such piecewise notation, but at the cost of the introduction of another infinite series. We use a very different approach to derive an infinite set of addition theorems for Slater orbitals, hydrogenic and Hylleraas wave functions, and so on, that retain the one-range variable dependence but have, at worst, a finite second series rather than an infinite one. In addition, unlike previous addition theorems, they are applicable to more than one coordinate system. One of these addition theorems may also be used for Yukawa-like functions that may appear late in the reduction of amplitude integrals, and we show its utility for an integral that has stubbornly defied reduction to analytic form for nearly sixty years. Finally, we craft indefinite integrals of 15 half-integer Macdonald functions multiplied by (inverse) powers and negative exponentials containing squares of the integration variable.

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 …

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 …

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 …

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 …