Physical Sciences and Mathematics Commons^™

Mycelial Modeling: Teaching Biology Students Statistical Modeling With Mushrooms, Colette Wolf

University Honors Theses

This paper summarizes and describes the development of a set of learning materials that were created to educate students and professionals from other fields in statistical modeling techniques. These materials are primarily aimed at biology students, but are still intended to be useful for anyone who is interested in incorporating decision trees and random forest models into their personal research in the future. By directing the reader towards the JMP software, these materials navigate around the statistical knowledge base and coding implementation practices that otherwise would serve as a barrier to learning statistical modeling techniques, and instead focus on the …

Assessing Spatial Distribution Of Plausible Earthquake-Triggered Landslides Relative To Ca. 1000 Ybp Earthquake On The Gales Creek Fault, Jacqueline Rheingans

University Honors Theses

Modern coseismic landslides cluster near the surface trace of the fault that ruptured, suggesting that clustering of paleolandslides may record information about paleoearthquakes. This study documents the pattern of prehistoric landslides near the Gales Creek Fault (GCF), northwest Oregon, to assess whether it reflects an independently known paleoearthquake. The GCF is located northwest of Portland through the Cascadia fore-arc basin where landslides are often triggered by intense rainfall during the wet season or potentially by seismic shaking on the megathrust or on crustal faults. In order to understand how a seismic event on the GCF will impact landslide distribution I …

Pitching Fwar Vs Bwar As Predictors Of Team Success In The Mlb Regular Season, Jason Lee

University Honors Theses

Pitching Wins Above Replacement (WAR) is an area of sabermetrics capable of being used to predict regular season success in Major League Baseball. Fangraphs WAR (fWAR) and Baseball Reference WAR (bWAR) were used to construct regression models to predict regular season winning percentage, to build logistic models to establish a relationship between pitching WAR and the probability to win an individual regular season game, and to overlay density plots to consider WAR accumulation by pitching role and observe the difference of impact between starter and relief pitchers. This research finds that while pitching fWAR and pitching bWAR are both statistically …

The Role Of Urban Forests In Mitigating Flooding Effects: A Case Study In Savannah, Georgia, Gillian Bush

Undergraduate Theses, Capstones, and Recitals

Flooding in coastal communities is shaped by the interaction between natural systems and urban development. Chatham County, a low-elevation region in the Savannah, Georgia metropolitan area along the eastern coast of the United States, is prone to coastal storms and frequently affected by flooding. It serves as a useful case study to better understand the factors behind flooding and the areas that are most at risk. This study uses GIS-based analysis to examine the overlap between flood risk, urban forest cover, and impervious surfaces. The results indicate elevated vulnerability along major transportation corridors and barrier islands, where high-risk flood zones …

Digital Bodily Autonomy: Consent Issues, Labor Displacement, And Legal Understandings Of Ai Generated Deepfake Pornography, Mariah Barrett

Undergraduate Theses, Capstones, and Recitals

In the United States, nonconsensual pornographic deepfakes are becoming an increasingly prevalent problem as AI deepfake creation software improves and becomes widely available. Despite this, patchwork legislation across the country is inconsistent and conflicting regarding this issue. In this paper, I explore the background of pornography and obscenity laws and demonstrate how these frameworks are not properly constructed to apply to the digital sphere. Then, I address major themes within deepfake literature such as consent issues, bodily autonomy, labor displacement, and verifiable identity as a commodity through the case study of OnlyFans. I explore current and proposed legislation within the …

Rapid-Prototyping Nanofabrication: Lcd-Based Projection Lithography And Physical Vapor Deposition, Sabeel Saleem Mohammmed

University Honors Theses

The semiconductor industry's continued growth, driven in large part by demand for artificial intelligence hardware, has highlighted the need for greater workforce development in regions adjacent to major fabrication centers like Oregon's Silicon Forest. This capstone project lays the groundwork for a small scale and student led semiconductor fabrication lab at Portland State University by demonstrating two of the core steps in chip manufacturing: photolithography and thin film deposition. Rather than relying on conventional fixed reticles, this work explores a unique, low cost approach to patterning that uses an ultraviolet-compatible liquid crystal display (LCD) as a programmable reticle, allowing arbitrary …

A Novel, Embedding-Based Approach To Longitudinal Survey Data Imputation, Julia Rezvani

University Honors Theses

Longitudinal surveys are ubiquitous in the social sciences as a means of tracking changes in behavior and opinions with time and identifying potential causal mechanisms. These surveys are frequently plagued by missing data and semantic drift, both of which limit their effectiveness and scientific utility. Imputation algorithms allow researchers to fill gaps in collected survey datasets, imperfectly reconstructing lost data. Although deep learning algorithms have been used in imputation to great success, approaches which simultaneously leverage the semantic and temporal structure of longitudinal surveys have not yet been developed. We propose a novel imputation architecture which is capable of leveraging …

Bias, Structure, And Inference In Applied Network Analysis, Anna Vasenina

Dartmouth College Ph.D Dissertations

This dissertation develops mathematical and statistical methods for extracting reliable information from network data across biological applications, with an emphasis on understanding what observed network structure can and cannot resolve. The first study leverages protein–protein interaction network topology in the c-di-GMP signaling system of Pseudomonas fluorescens, showing that node centrality measures accurately classify protein domain types and that physical interaction structure contributes statistically significant predictive power for biofilm formation phenotypes across nearly 200 environments, while gene expression does not. The second study examines sampling bias in lemur-plant trophic interaction networks in Madagascar, demonstrating that differential detection of diurnal versus …

Phase-Resolved Measurement And Arbitrary Mode Conversion Of Structured Light, Somayeh Ghazanfarpour

Electronic Theses and Dissertations

This dissertation presents a single-shot phase and amplitude retrieval technique based on spatial light modulator (SLM)-based digital holography. The proposed method enables accurate reconstruction of complex optical fields from a single interferogram, reducing sensitivity to environmental fluctuations and improving experimental stability compared to conventional multi-shot approaches. In addition, a programmable arbitrary mode converter is developed using SLM-based wavefront shaping. By introducing controlled astigmatism and engineering the differential Gouy phase between orthogonal components, the system enables flexible transformation between structured light modes, including Hermite–Gaussian and Laguerre–Gaussian beams. Numerical results demonstrate reliable phase recovery and efficient mode conversion, validating the performance of …

Quantifying Terrain Controls On Satellite-Based Snow Water Equivalent Estimation: A Spatially Explicit Machine Learning Approach, Brant Giovannetti

Geography and the Environment: Graduate Student Capstones

Terrain variables are widely incorporated into machine learning Snow Water Equivalent (SWE) models but are rarely evaluated for their independent contribution relative to spectral predictors. Using a four-tier stepwise Random Forest framework with Harmonized Landsat Sentinel-2 imagery and Airborne Snow Observatory LiDAR ground truth, this study isolates the contribution of elevation, slope, northness, and eastness across Peak and Ablation snowpack regimes in the East Taylor River Watershed, Colorado. During peak snowpack, adding terrain improved R² by 0.214, with elevation alone accounting for 42.8% of model importance. During ablation, full-dataset terrain gains were modest, increasing R² by only 0.036. However, when …

Geospatial Governance Failures In The Department Of Defense: Contractor Noncompliance, Ai Adoption, And The Parallel Treatment Of Gis And Cybersecurity, Lyndsey Olmstead

Geography and the Environment: Graduate Student Capstones

The Department of Defense's treatment of geographic information systems and cybersecurity as parallel rather than integrated policy domains produces geographically predictable vulnerability patterns across its global military installation footprint. This capstone investigates that conclusion through original spatial analysis, constructing a five-variable composite geospatial vulnerability index across the six U.S. Combatant Command regions using publicly available unclassified data. EUCOM ranked highest overall, driven by GPS/PNT spoofing density, commercial satellite coverage, and cyber incident frequency; CENTCOM ranked second, driven by OSINT exposure incidents and governance risk. The null hypothesis of random geographic distribution is rejected. Findings confirm the structural governance gap documented …

Data Governance Maturity, Ai Integration, And Equity In Colorado K-12 Public Schools, John R. Curtin

Electronic Theses and Dissertations

Colorado's 179 K-12 public school districts operate as autonomous governance units, each responsible for securing and managing student data assets that span health, financial, residential, and academic records. The accelerating integration of artificial intelligence (AI) and machine learning (ML) tools into administrative workflows, productivity software, and instructional platforms has fundamentally altered the risk landscape for student data, yet governance frameworks at the state, district, and school levels have not kept pace. This dissertation investigates whether Colorado's decentralized educational governance structure is institutionally capable of producing equitable, secure, and sustainable data governance outcomes in the AI era.

Drawing on Institutional Theory …

Some Results In Maximal Pattern Complexity, Casey Schlortt

Electronic Theses and Dissertations

For a finite alphabet 𝒜 and a sequence 𝑥 ∈ 𝒜^ℕ_⊬ , Kamae and Zamboni combined the ideas of block complexity and topological sequence entropy to define the maximal pattern complexity, 𝑝^∗_𝑛 (𝑥). They defined an aperiodic sequence 𝑥 over two letters as pattern Sturmian if it had the lowest possible maximal pattern complexity, 2𝑛. Later, Kamae and Rao extended their definition of pattern Sturmian sequences to be sequences over ℓ ≥ 2 letters which are not periodic by projection and have maximal pattern complexity ℓ𝑛.

This dissertation answers a question posed by Kamae and Zamboni …

Ka Here Tāngata:1 Mātauranga And Te Ao Māori In Biocultural Kākāpō (Strigops Habroptilus) Conservation Approaches, Sophie Perfetto

Electronic Theses and Dissertations

This master's thesis examines conservation as a form of living cultural heritage practice through the co-management of kākāpō (Strigops habroptilus), a critically endangered parrot and taonga species in Aotearoa New Zealand. Situated within ongoing histories of colonial dispossession and Western frameworks of land and species management, contemporary kākāpō conservation is shaped through the partnership between the Department of Conservation’s Kākāpō Recovery Programme and Ngāi Tahu. Drawing on semi-structured interviews collected during fieldwork from July to August 2025, this study examines how institutional partnerships structure decision-making, authority, and responsibility in contemporary conservation governance. Findings demonstrate that Māori knowledge systems …

Evaluation And Distillation Of Source Code Generation Tasks By Large Language Models, Danny Brahman

Electronic Theses and Dissertations

Large Language Models (LLMs) are predominantly assessed based on their common sense reasoning, language comprehension, and logical reasoning abilities. While models trained in specialized domains like mathematics or coding have demonstrated remarkable advancements in logical reasoning, there remains a significant gap in evaluating their code generation capabilities. Existing benchmark datasets fall short in pinpointing specific strengths and weaknesses, impeding targeted enhancements in models’ reasoning abilities to synthesize code.

To bridge this gap, this thesis introduces two novel contributions: CodeEval and CodeQual. CodeEval is an innovative, pedagogical benchmarking method that mirrors the evaluation processes encountered in academic programming courses. It comprises …

Design Principle For Staple-Mediated Stabilization Of Peptides And Proteins, Samantha C. Hatfield

Theses and Dissertations

Macrocyclization, or stapling, has emerged as a powerful strategy to enhance the stability and function of peptides and proteins by constraining their conformational ensembles. Stapling can improve thermodynamic stability, increase resistance to proteolytic degradation, and enhance biomolecular recognition, making it particularly valuable for the development of peptide-based therapeutics. Despite these advantages, staple design remains largely empirical, relying on iterative screening of linker chemistries, lengths, and attachment sites. This trial-and-error approach limits scalability and hinders the rational design of stabilized peptide systems. In this work, we address this challenge by integrating large-scale experimental datasets with molecular dynamic simulations to develop predictive …

Projected Climate Change Impacts On Soil Greenhouse Gas Emissions From A Restored Freshwater Marsh, Annika Hendrickson

University Honors Theses

Wetlands provide valuable ecosystem services, one of which is a wetlands ability to sequester carbon. Climate change and human land use threaten a wetlands ability to do so. Globally, 21% of wetlands have been lost since the 1700s. As a result, restoration of wetlands has been increasing. However, wetlands in the process of restoration emit more methane than degraded ones, and as the climate continues to change, these fluxes could respond. Projected sea level rise is expected to cause salt water to infiltrate coastal freshwater systems, increasing the salinity. Past research has found that increased salinity has led to suppressed …

Beyond Emergency: Charting Pathways To Sustainable Development In Fragile And Conflict-Affected Settings: A Case Study Of Yemen, Sharif Abdurabu Salem Farid Alsahbool

Theses and Dissertations

For nearly a decade, Yemen's eastern governorates of Hadramawt, Shabwah, and Al‑Mahrah have been relatively stable, yet the international aid system has kept delivering short‑term humanitarian relief like food baskets and water trucking instead of shifting to sustainable development that could rebuild people's lives, create jobs, fix infrastructure, and strengthen local government. This thesis investigates why this transition has taken so long. Based on 21 interviews with government officials, international NGO staff, and local NGO managers in these three governorates, the study develops a new way of understanding the problem. It introduces three ideas: the 'emergency mentality', which is a …

Uniform Stability Of Katyusha In Strongly-Convex Settings, Don Li

University Honors Theses

Acceleration of convergence and reduction of variance constitute a trade-off in the design of stochastic optimization machine learning algorithms. Katyusha was introduced to address this trade-off, synthesizing Nesterov Accelerated Gradient (NAG) and Stochastic Variance-Reduced Gradient (SVRG) into a single first-order optimizer with promising empirical performance. However, the generalization properties of Katyusha remain largely unexplored. We conjecture that, in the smooth quadratic regime (i.e., under assumptions of strong convexity and smoothness of the loss function, and boundedness of gradients), Katyusha is uniformly stable in the sense of Bousquet and Elisseeff. Instantiating our framework for NAG, we extend the use of Lyapunov …

Hot Jupiter Atmospheres Through Time, Annabelle E. Niblett

Physics and Astronomy Undergraduate Senior Theses

Transmission spectroscopy of hot Jupiters enables mass and atmospheric composition measurements, providing insight into population dynamics and evolution when other methods are hindered by stellar activity. To effectively plan observations and interpret transmission spectra, we must have a robust understanding of how atmospheres evolve over time. To that end, we present a suite of hot Jupiter transmission spectra models with ages ranging from 3 Myr to 11 Gyr. We incorporate the cooling and contraction of the planet, which impacts the atmospheric profile, and the evolution of the stellar UV spectrum, which moderates photodissociation and photoionization. Using PICASO,  VULCAN, and FastChem …

Unraveling The Nanoscopic Characteristics Of The Heterogeneous Deep Eutectic Solvent Formed By Lauric Acid And N-Methylacetamide: An Experimental And Computational Approach, Laura X. Sepulveda

LSU Doctoral Dissertations

Deep eutectic solvents (DESs) are attractive systems for extraction and separation of compounds. One example of this is the DES formed by the combination of lauric acid (LA) and N-methylacetamide (NMA), system that has been shown to efficiently separate oil/water mixtures through gel formation between LA and oil molecules. Structural characterization of this system using small-angle X-ray scattering (SAXS) and vibrational spectroscopy revealed the existence of nanometer-scale LA domains embedded in a continuous polar NMA phase, where LA and NMA interact through hydrogen bonding. These LA domains are responsible for the separation efficiency of linear organic molecules. However, this DES …

Integrating Reflection Data With Stratigraphic Analysis In Little Lake Sunapee, New Hampshire, Caleb S. Saks

Earth Sciences Undergraduate Senior Theses

Reflection events within ground penetrating radar (GPR) and CHIRP seismic data are commonly used to infer changes in stratigraphy in lake basins. My thesis provides ground truth for these data by correlating reflection events to measured changes in sediment characteristics including composition and density. My focus is Little Lake Sunapee (LLS), located in central New Hampshire, which contains sediments deposited during and after the retreat of the Laurentide Ice Sheet (LIS), during late Pleistocene and Holocene time. These sediments provide a record of post-glacial climate and environmental change.

I present detailed coverage of the LLS sub-bottom sediment stratigraphy based on …

Context-Sensitive Control-Flow Analysis For Non-Standard Language Semantics, Tim Whiting

Theses and Dissertations

Control-Flow Analysis (CFA) is a static technique for understanding the execution of higher-order programs without running the code. CFA aids in identifying bugs, assisting program comprehension, and exposing optimization opportunities. Constructing a CFA typically begins with an idealized evaluator--such as an abstract machine or interpreter--and proceeds by approximating components of evaluation to ensure that: (a) the analysis is sound (representing all possible behaviors), and (b) the analysis is guaranteed to terminate (finitely representable). These constraints necessitate a loss of precision, providing an approximation of the values that flow to program locations rather than exact execution traces. This imprecision causes the …

How Quickly Do Eastern Floodplains Store Carbon? Quantifying Reference Carbon Flux On The Dead Diamond River, Jacob Schnell

Earth Sciences Undergraduate Senior Theses

Terrestrial Earth systems sequester an estimated 30% of annual anthropogenic CO2 emissions. The largest share is stored in global soils which collectively store more than 3 times the amount of carbon as the atmosphere. Floodplains and river systems, while covering only 5–8% of land area, store 20–30% of the global soil organic carbon (SOC), yet, the rate at which floodplains sequester carbon remains highly uncertain. Here I constrain floodplain carbon sequestration rates for a model northeastern river that has not been impacted by development or significant human activity. I calculate carbon stock using total organic carbon and derive carbon flux …

Investigating Broadband Plasma Waves As A Driver Of Radiation Belt Energetic Electron Loss To Earth's Atmosphere, Lauren Zanarini

Physics and Astronomy Undergraduate Senior Theses

Wave-particle interactions play a central role in transferring energy between different particle populations in space plasmas. In the radiation belts, these interactions govern the acceleration, scattering, and loss of energetic particles to Earth’s atmosphere. Understanding the drivers of these energetic particle losses is essential, as these particles can collide with satellites and contribute to ozone depletion as they enter the atmosphere. Developing a clearer picture of these processes will improve our ability to predict radiation belt variability and quantify the impacts, ultimately allowing us to mitigate the adverse effects.

Previous research has identified wave modes important for scattering electrons into …

Pedersen By Proxy: Neutral Wind Drivers Of The Magnetosphere, Shreya Gandhi

Physics and Astronomy Undergraduate Senior Theses

Measurements of Saturn’s radio and magnetic periodicities suggest that atmospheric forcing influences the magnetosphere-coupled current systems on the planet (Gurnett et al., 2007). A proposed mechanism for this phenomenon is that thermospheric heating drives strong neutral winds which drag ionospheric plasma and generate currents that close along magnetic field lines (Smith, 2011). However, the local current-closure physics of these processes is di!cult to isolate in global Saturn models even if they suggest neutral wind forcing is a plausible driver for these changes (Jia et al., 2012). This thesis uses the Earth-based auroral GEMINI (Geospace Environment Model of Ion-Neutral Interactions) model …

Tracing The Seam: Machine Learning Models Of The Open–Closed Boundary From Upstream Solar Wind Drivers, Arnav Singh

Physics and Astronomy Undergraduate Senior Theses

The open–closed magnetic field line boundary (OCB) demarcates closed terrestrial field lines from those threaded into the interplanetary medium, and its latitude encodes the instantaneous balance between dayside and nightside reconnection that governs much of the high-latitude space-weather hazard. No single instrument resolves it globally in real time. In this thesis I close that gap empirically. Pairing nearly three decades (1983–2012) of Defense Meteorological Satellite Program particle-precipitation boundaries with the 5-minute OMNI solar-wind and geomagnetic-index record yields ∼9.1×10⁵ causally matched crossings, partitioned into six hemispheric/MLT sectors after a |MLat| ≥ 40° physics cut.

On this corpus I train three …

The Method Of Periodic Averaging Applied To Reduced Coupled Mode Theory Models For Fiber Laser Amplifiers, Rebecca Nicole Bryant

Dissertations and Theses

Fiber laser amplifier (FLA) models are often implemented without rigorous mathematical justification or thorough numerical validation. Without a proper theoretical basis for assumptions and approximations, or a technical analysis of model performance, there is significant uncertainty about the limitations of any given reduced model and its suitability for an application. This research aims to address the lack of comprehensive assessment of FLA models by directly comparing distinct models and recommending a mathematical alternative to replace heuristic model-reduction techniques. The work in this dissertation is divided into two projects: a comparative study that uses existing FLA models to assess the validity …

Late Pleistocene-Holocene Environmental Change From May Pond Sediment Cores And Upland 10be Ages, Adrianna Drindak

Earth Sciences Undergraduate Senior Theses

The goal of this project is to reconstruct the deglaciation and post-glacial environmental conditions of northern Vermont that occurred during the transition from the Pleistocene to the Holocene, ~15,000 to 11,000 years ago. This transition marks a major climatic shift, from a glacial period to an interglacial period, and regionally involved the retreat of the Laurentide Ice Sheet (LIS). The retreat of the LIS influenced the surficial geology of North America, exposing the Earth’s surface, leaving glacial deposits, and carving out proglacial lakes. The timing of ice retreat in the region provides information about past climate conditions, which may inform …

Constraints On Crystallization Conditions From Pseudosection Thermobarometry Of The New World Mining District Porphyries Near Cooke City, Montana, Jacob Jared Gordon

Earth Sciences Undergraduate Senior Theses

The New World Mining District (NWMD), located two miles northeast of Cooke City, Montana, is host to a series of epithermal sills, dikes, and plutons, the intrusion of which is responsible for significant Au-Ag-Cu mineralization. These intrusive bodies were emplaced in the Eocene, potentially contemporaneously with the Heart Mountain Detachment - Earth’s largest subaerial landslide, and have been proposed as a potential trigger for the event. The pre-emplacement crys- tallization conditions for the porphyritic dikes in the region, however, remain unknown and have previously been limited to surface observations. Constraining the magmatic conditions of the in- trusives in the region …