Physical Sciences and Mathematics Commons^™

An Algorithm For Identifying Eigenvectors Exhibiting Strong Spatial Localization, Jeffrey S. Ovall, Robyn Reid

Mathematics and Statistics Faculty Publications and Presentations

We introduce an approach for exploring eigenvector localization phenomena for a class of (unbounded) selfadjoint operators. More specifically, given a target region and a tolerance, the algorithm identifies candidate eigenpairs for which the eigenvector is expected to be localized in the target region to within that tolerance. Theoretical results, together with detailed numerical illustrations of them, are provided that support our algorithm. A partial realization of the algorithm is described and tested, providing a proof of concept for the approach.

Classifying Dead Code In Software Development, Arman Alavizadeh

University Honors Theses

Dead code pervades as an issue in the world of software development as a source of many famous software disasters such as the ARIANE 5 rocket failure and chemical bank withdrawal error. Defining dead code on narrow levels of granularity has not been fully explored, yet is crucial to better our understanding of dead code. Here we will be starting a discussion on how to approach classifying dead code via comparing dead code research specific to an industry segment. Research will be compared primarily by methodology and limitations. Dead code subtype classifications are gleaned from research comparisons and can serve …

Continuum Dynamics And Statistical Correction Of Compositional Heterogeneity In Multivalent Idp Oligomers Resolved By Single-Particle Em, Barmak Mostofian, Russell Mcfarland, Aiden Estelle, Jesse Howe, Elisar J. Barbar, Steve L. Reichow, Daniel M. Zuckerman

Chemistry Faculty Publications and Presentations

Multivalent intrinsically disordered protein (IDP) complexes are prevalent in biology and act in regulation of diverse processes, including transcription, signaling events, and the assembly and disassembly of complex macromolecular architectures. These systems pose significant challenges to structural investigation, due to continuum dynamics imparted by the IDP and compositional heterogeneity resulting from characteristic low-affinity interactions. Here, we developed a modular pipeline for automated single-particle electron microscopy (EM) distribution analysis of common but relatively understudied semi-ordered systems: 'beads-on-a-string' assemblies, composed of IDPs bound at multivalent sites to the ubiquitous ∼20kDacross-linking hub protein LC8. This approach quantifies conformational geometries and compositional heterogeneity on …

An Introduction To Number Theory, J. J. P. Veerman

PDXOpen: Open Educational Resources

These notes are a preliminary text intended for a graduate course in Number Theory. A thoroughly improved, revised, and expanded version of this book will be published in 2026 through Springer under the title Numbers from All Angles.

Chapters 1-14 of this preliminary text represent almost 3 trimesters of the course. No prior familiarity with number theory is assumed. The current content represents courses the author taught in the academic years 2020-2021 and 2021-2022.

Does Restoration Of Urban Riparian Zones Impact Stream Water Quality In Portland, Oregon, Ash Ivanov

University Honors Theses

Riparian zones influence urban stream quality through factors such as shading the stream, adding nutrients through leaf litter, stabilizing the stream banks to reduce turbidity, and filtering toxins out of the water. Riparian restoration often involves changing plant assemblage to be more diverse and include primarily native species instead of non-native, improving connection to the stream through changing stream morphology, improving species habitat, and reducing pollution. The goal of this study was to determine if urban riparian restoration projects in the region were successful, and if not, why that may be the case. The study was performed in the Portland, …

Minimality Of Integer Bar Visibility Graphs, Emily Dehoff

University Honors Theses

A visibility representation is an association between the set of vertices in a graph and a set of objects in the plane such that two objects have an unobstructed, positive-width line of sight between them if and only if their two associated vertices are adjacent. In this paper, we focus on integer bar visibility graphs (IBVGs), which use horizontal line segments with integer endpoints to represent the vertices of a given graph. We present results on the exact widths of IBVGs of paths, cycles, and stars, and lower bounds on trees and general graphs. In our main results, we find …

Efficient Capture Of Co2 And Its Selective Reduction To Formic Acid Using Tin-Based Nanomaterials, Emmanuel Oluwaseun Abdul

Dissertations and Theses

CO₂ emissions from the combustion of fossil fuels and other anthropogenic sources have become the main contributing factors to global warming. Chemical methods of absorbing/capturing CO₂ from combustion flue gases have made it a sought-after approach in engineering emission solutions because of its simplistic and convenient operation and high absorption efficiency. The conversion of CO₂ into renewable fuels and high energy density chemicals by clean and economic processes has drawn scientists' attention over the decades. The electrocatalytic conversion of CO₂ using Sn-based materials has been demonstrated to be a promising method for producing formate, an important …

Stratigraphic And Geochemical Evaluation Of Distal Flows Of The Columbia River Flood Basalts In The Greater Vale Area, Southeastern Oregon, Lena Marie Fox

Dissertations and Theses

Exposures of Columbia River Basalt Group (CRBG) in southeastern Oregon are dominated by the four main phase CRBG units: Steens Basalt, Imnaha Basalt, Grande Ronde Basalt (GRB), and Picture Gorge Basalt (PGB). These units are best seen in stratigraphic sequence along the Malheur Gorge corridor of southeastern Oregon, between the towns of Vale and Juntura, with flows of Steens Basalt from the south overlain by flows of Imnaha and GRB from the north. Recently, PGB flows were found to be part of the eastern Malheur Gorge stratigraphy as well.

In Malheur Gorge, local units of Birch and Hunter Creek Basalt …

Visualizing Connectivity For Wildlife In A World Without Roads, Catherine De Rivera, Leslie Bliss-Ketchum, Martin Lafrenz, A. V. Hanson, L. E. Mckinney-Wise, A. H. Rodriguez, J. Schultz, Alana Simmons, D. Taylor Rodriguez, Multiple Additional Authors

Environmental Science and Management Faculty Publications and Presentations

Roads are not the only determining factor for wildlife movement across the landscape, but due to the extensive distribution of the road network their impact can be dramatic. Although it has been well documented that roads decrease habitat connectivity for wildlife due to animal-vehicle collisions, habitat fragmentation, and avoidance behavior, approaches for identifying connectivity across the landscape often do not fully examine the barrier effect of roads. Here, we explored the extent of the impact of roadways on wildlife connectivity by using Omniscape to model connectivity including and without the barrier effect of roads, then evaluating the difference between these …

Speciation Of Diaryliodonium Salts In Solution And Their Reactivity Towards N-Nucleophiles (Phthalimide And Amines) And O-Nucleophiles (Phenols And Phenoxide), Souradeep Basu

Dissertations and Theses

Benzenoid rings are prevalent in pharmaceutical drug molecules, agrochemical molecules and even in some polymers used in electronic device. Aryl rings are often installed using metal catalysis, however, metal free arylations are known but limited. Diaryliodonium salts are novel electrophilic arylating agents. Herein, metal free N-arylation of phthalimide and diarylether formation using aryl(TMP)iodonium salts is described.

The structure of diaryliodonium salts has been primarily studied in either the solid state or in-silico. The structure and speciation of diaryliodonium salts in solution is not well explored. In this work evidence of dimer formation of aryl(Mes)iodonium salts in chloroform using …

Variability Of Potential Soil Nitrogen Cycling Rates In Stormwater Bioretention Facilities, Erin N. Rivers, Jennifer L. Morse

Environmental Science and Management Faculty Publications and Presentations

Low-impact development (LID) is a common management practice used to infiltrate and filter stormwater through vegetated soil systems. The pollutant reduction potential of these systems is often characterized by a single pollutant removal rate; however, the biophysical properties of soils that regulate the removal of pollutants can be highly variable depending on environmental conditions. The goal of this study was to characterize the variability of soil properties and nitrogen (N) cycling rates in bioretention facilities (BRFs). Soil properties and potential N cycling processes were measured in nine curbside bioretention facilities (BRFs) in Portland, OR during summer and winter seasons, and …

Maximum Entropy And Constraints In Composite Systems, John D. Ramshaw

Physics Faculty Publications and Presentations

The principle of maximum entropy (PME), as expounded by Jaynes, is based on the maximization of the Boltzmann-Gibbs-Shannon (BGS) entropy subject to linear constraints. The resulting probability distributions are of canonical (exponential) form. However, the rationale for linear constraints is nebulous, and probability distributions are not always canonical. Here we show that the correct noncanonical distribution for a system in equilibrium with a finite heat bath is implied by the unconstrained maximization of the total BGS entropy of the system and bath together. This procedure is shown to be equivalent to maximizing the BGS entropy of the system alone subject …

The Castle Rock And Ironside Mountain Calderas, Eastern Oregon, Usa: Adjacent Venting Sites Of Two Dinner Creek Tuff Units—The Most Widespread Tuffs Associated With Columbia River Flood Basalt Volcanism, Matthew Cruz, Martin J. Streck

Geology Faculty Publications and Presentations

The Dinner Creek Tuff is an important unit of mid-Miocene rhyolite volcanism contemporaneous to flood basalts of the Columbia River magmatic province. Field mapping along with analytical data of tuff samples identify two calderas, the Castle Rock and Ironside Mountain calderas, as the venting sites of two widespread ignimbrites of the Dinner Creek Tuff. Both calderas lie within the area of the proposed general storage sites of main-phase Columbia River Basalt magmas. The Castle Rock caldera formed during the eruption of the 16.16 Ma Dinner Creek Tuff unit 1. The northwestern boundary of the caldera is roughly defined by the …

Exploring Student Perceptions Of Behavioral, Cognitive, And Emotional Engagement At The Activity Level In General Chemistry, Nicole Naibert, Elizabeth Vaughan, Kylee M. Brevick, Jack Barbera

Chemistry Faculty Publications and Presentations

Although active learning strategies are being incorporated into many higher-education STEM courses, not all students benefit from these activities to the same extent. As these types of activities are designed to engage students in their learning, differences in student engagement may explain some of the differences in learning outcomes. However, before student engagement in active learning activities can be meaningfully measured using a self-report survey, it is important to evaluate if students perceive engagement similarly to the literature definitions on which these measures are based. Therefore, this study sought to explore students’ perceptions of the behavioral, cognitive, and emotional dimensions …

Development And Evaluation Of A Survey To Measure Student Engagement At The Activity Level In General Chemistry, Nicole Naibert, Jack Barbera

Chemistry Faculty Publications and Presentations

Student engagement is an important consideration when incorporating active learning activities into a classroom. To facilitate the large-scale assessment of students’ engagement in activities, a survey measure must first be developed and evaluated. Therefore, the goal of this study was to create a self-report measure of student engagement for use with active learning activities in general chemistry classes. The Activity Engagement Survey (AcES) was modified from an existing survey of engagement of middle and high school science students that contained behavioral, cognitive, emotional, and social engagement items. Multiple rounds of response process interviews and factor analyses were used to modify …

A New Agent-Based Model Offers Insight Into Population-Wide Adoption Of Prosocial Common-Pool Behavior, Garry Sotnik, Thaddeus Shannon, Wayne Wakeland

Complex Systems Faculty Publications and Presentations

New theoretical agent-based model of population-wide adoption of prosocial common-pool behavior with four parameters (initial percent of adopters, pressure to change behavior, synergy from behavior, and population density); dynamics in behavior, movement, freeriding, and group composition and size; and emergence of multilevel group selection. Theoretical analysis of model’s dynamics identified six regions in model’s parameter space, in which pressure-synergy combinations lead to different outcomes: extinction, persistence, and full adoption. Simulation results verified the theoretical analysis and demonstrated that increases in density reduce number of pressure-synergy combinations leading to population-wide adoption; initial percent of contributors affects underlying behavior and final outcomes, …

New Opportunities And Untapped Scientific Potential In The Abyssal Ocean, Jeffrey J. Marlowe, Rika E. Anderson, Anna-Louise Reysenbach, Jeffrey S. Seewald, Timothy M. Shank, Andreas P. Teske, V. Dorsey Wanless, S. Adam Soule

Biology Faculty Publications and Presentations

The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as …

Linear Nearest Neighbor Flocks With All Distinct Agents, Robert G. Lyons

Dissertations and Theses

This dissertation analyzes the global dynamics of 1-dimensional agent arrays with nearest neighbor linear couplings. The equations of motion are second order linear ODE's with constant coefficients. The novel part of this research is that the couplings are different for each agent. We allow the forces to depend on the relative position and relative velocity (damping terms) of the agents, and the coupling magnitudes differ for each agent. Further, we do not assume that the forces are "Newtonian'" (i.e., the force due to A on B equals minus the force of B on A) as this assumption does not apply …

An Automated Zoom Class Session Analysis Tool To Improve Education, Jack Arlo Cannon Ii

Dissertations and Theses

The recent shift towards remote education has presented new challenges for instructors with respect to teaching evaluation. Students in traditional classrooms send signals to instructors which provide feedback for the effectiveness of a given lecture. Virtual learning environments lack some of these communication channels and require new ways of collecting feedback. This work presents a suite of analysis tools for the virtual instructor. Given the transcript and video files for a Zoom meeting, this tool summarizes student sentiment and speaking characteristics. Sentiment scores are derived using state of the art Natural Language Processing (NLP) models. The video file is used …

A Biomimetic Model For Oxidative Metabolism Of Thiopurine Drugs, Oluyemi Oludare Alo

Dissertations and Theses

Type B hepatotoxicity has been reported for thiopurines, and this has limited their clinical uses. Although a lot of research has been done on thiopurines, the precise mechanism of their hepatotoxicity is still unclear. The results of the in vitro and in vivo experiments aimed at assessing the products of their CYP450-mediated bioactivation have been contradictory. Although it has been theorized that the hepatic toxicity of this class of drug is caused by their bioactivation to electrophilic reactive metabolite (RM) and concomitant protein binding to form immunogenic adducts, resulting in direct cellular dysfunction or an immune response via the formation …

Rate Maximization In A Uav Based Full-Duplex Multi-User Communication Network Using Multi-Objective Optimization, Syed Muhammad Hashir, Sabyasachi Gupta, Gavin Megson, Ehsan Aryafar, Joseph Camp

Computer Science Faculty Publications and Presentations

In this paper, we study an unmanned-aerial-vehicle (UAV) based full-duplex (FD) multi-user communication network, where a UAV is deployed as a multiple-input–multiple-output (MIMO) FD base station (BS) to serve multiple FD users on the ground. We propose a multi-objective optimization framework which considers two desirable objective functions, namely sum uplink (UL) rate maximization and sum downlink (DL) rate maximization while providing quality-of-service to all the users in the communication network. A novel resource allocation multi-objective-optimization-problem (MOOP) is designed which optimizes the downlink beamformer, the beamwidth angle, and the 3D position of the UAV, and also the UL power of the …

Adverse Reactions In A Phase 1 Trial Of The Anti-Malarial Dm1157: An Example Of Pharmacokinetic Modeling And Simulation Guiding Clinical Trial Decisions, Stephen J. Balevic, Shruti M. Raja, Rachel Randall, Gregory A. Deye, Thomas Conrad, Aya Nakamura, David H. Peyton, Sandra Shotwell, Katherine May Liebman, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

Introduction: There is an urgent need to develop new drugs to treat malaria due to increasing resistance to first-line therapeutics targeting the causative organism, Plasmodium falciparum (P. falciparum). One drug candidate is DM1157, a small molecule that inhibits the formation of hemozoin, which protects P. falciparum from heme toxicity. We describe a first-in-human, phase 1 trial of DM1157 in healthy adult volunteers that was halted early because of significant toxicity.

Methods: Adverse events were summarized using descriptive statistics. We used pharmacokinetic modeling to quantitatively assess whether the DM1157 exposure needed for P. falciparum inhibition was achievable at safe doses.

Results: …

Phosphorylation Of The Aggregate-Forming Protein Alpha-Synuclein On Serine-129 Inhibits Its Dna-Bending Properties, Sydney E. Dent, Dennisha P. King, Valerie R. Osterberg, Eleanor K. Adams, Marilyn R. Mackiewicz, Tamily A. Weissman, Vivek K. Unni

Chemistry Faculty Publications and Presentations

Alpha-synuclein (aSyn) is a vertebrate protein, normally found within the presynaptic nerve terminal and nucleus, which is known to form somatic and neuritic aggregates in certain neurodegenerative diseases. Disease-associated aggregates of aSyn are heavily phosphorylated at serine-129 (pSyn), while normal aSyn protein is not. Within the nucleus, aSyn can directly bind DNA, but the mechanism of binding and the potential modulatory roles of phosphorylation are poorly understood. Here we demonstrate using a combination of electrophoretic mobility shift assay and atomic force microscopy approaches that both aSyn and pSyn can bind DNA within the major groove, in a DNA length-dependent manner …

Quadrature For Implicitly-Defined Finite Element Functions On Curvilinear Polygons, Jeffrey S. Ovall, Samuel E. Reynolds

Mathematics and Statistics Faculty Publications and Presentations

Abstract

H¹" role="presentation" style="box-sizing: border-box; margin: 0px; padding: 0px; display: inline-block; line-height: normal; font-size: 16.2px; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; position: relative;">H1-conforming Galerkin methods on polygonal meshes such as VEM, BEM-FEM and Trefftz-FEM employ local finite element functions that are implicitly defined as solutions of Poisson problems having polynomial source and boundary data. Recently, such methods have been extended to allow for mesh cells that are curvilinear polygons. Such extensions present new challenges for determining suitable quadratures. We describe an approach …

Temperature And Predator Effects On Green Crabs (Carcinus Maenas) And Their Distribution In South Slough National Estuarine Research Reserve, Elissa Connolly-Randazzo

Dissertations and Theses

The invasive green crab (Carcinus maenas) has increased in abundance and distribution among Oregon's estuaries. Its global success in establishing in new environments and tolerance for abiotic stressors, such as temperature, raises concern for C. maenas to negatively influence native crab species, especially given global climate change. To improve in predicting invasion impacts, this work analyzed the results from a controlled tank experiment at Portland State University and the field data on a population of C. maenas in South Slough National Estuarine Research Reserve (SSNERR). The aquarium experiment documented predation pressure on C. maenas across a range of …

Effects Of Green Crab (Carcinus Maenas) Across Variable Densities Of Eelgrass (Zostera Marina), Kimberly Alexis Brown

Dissertations and Theses

Eelgrass (Zostera marina) plays a critical role in estuarine ecosystem function by sustaining a variety of marine and freshwater species, but it's increasingly threatened by the aggressive non-native green crab (Carcinus maenas). The abundance of C. maenas is on the rise within the coastal environment of Oregon and it is imperative to know how these populations will affect the long-term health of Z. marina. C. maenas have been linked to declines in Z. marina coverage and shellfish abundance, but there has been no research on to what extent the density of Z. marina affects its …

Spatial And Seasonal Variations Of Microplastic Concentrations In Portland's Freshwater Ecosystems, Rebecca Talbot

Dissertations and Theses

Microplastics are a pollutant of growing concern and are ubiquitous in a variety of environmental compartments. The majority of microplastics research to date has been conducted in marine waters, and less is known regarding the sources and delivery pathways of microplastics in urban rivers. The first chapter is comprised of a review of the scientific literature regarding the spatial and temporal factors affecting global freshwater microplastic distributions and abundances. Microplastic spatial distributions are heavily influenced by anthropogenic factors, with higher concentrations reported in regions characterized by urban land cover, high population density, and wastewater treatment plant effluent. Temporal variables of …

The New Shiny Penny? Regenerative Agriculture Beliefs And Practices Among Portland's Urban Agriculturalists, Melia Ann Chase

Dissertations and Theses

Regenerative agriculture (RA) is a set of farming and land management practices intended to support or enhance soil health and carbon sequestration potential of soils while producing food, fiber, or other agricultural products. It has received broad acclaim from scholars, corporations, and governmental bodies as a potential means of sequestering carbon and mitigating climate change impacts. It has also received critique and pushback for its vague definition, shifting metrics, and lack of acknowledgement of the Indigenous practices underlying the modern suite of regenerative practices. The purpose of this research is to investigate the beliefs Portland, Oregon urban agricultural practitioners hold …

Materials And Methodologies For Spectroscopic And Optical Analytical Applications In Cultural Heritage Conservation Science, Lyndsay Nichole Kissell

Dissertations and Theses

The field of conservation science falls in the intersection of science and art. The work of conservation scientists may include any single subdiscipline of chemistry, though it is most commonly a highly interdisciplinary field taking skills from analytical, organic, and inorganic chemistry, as well as surface and materials science. The aims of conservation scientists are to answer questions about the production and aging of material cultural heritage. Knowing the materials used by an artist can lead to insight about the intentions of the object and knowing how those materials degrade will enable the use of preventative measures to ensure the …

Inverse Modeling Of Atmospheric Ch4 And Δ13C-Ch4 Measurements From Surface Observation Sites To Understand Trends In Global Methane Emissions Over More Than Three Decades, Sayantani Karmakar

Dissertations and Theses

Methane (CH₄) is the second most important greenhouse gas with a radiative forcing of 0.97 W/m² including both direct and indirect effects and a global warming potential of 28 over a 100-year time horizon. Unlike CO₂ whose rate of growth in the atmosphere has remained positive and increased in recent decades, the behavior of atmospheric methane is considerably more complex and is much less understood on account of the spatiotemporal variability of its emissions which include biogenic (e.g., wetlands, ruminants, rice agriculture), thermogenic (fossil fuels), and pyrogenic (i.e., biomass burning) sources. After sustained growth during most …