Physical Sciences and Mathematics Commons^™

Towards Practical And Real-Time Decoding Of Quantum Hypergraph Codes, Binghong (Leo) Li

Computer Science Theses

Quantum error correction (QEC) enables scalable quantum computation by detecting and correcting physical errors. However, decoding remains a key bottleneck—particularly for quantum low-density parity-check (qLDPC) codes, whose hypergraph structures demand complex reasoning. Most existing decoders are either too slow for real-time use or lack formal guarantees, and often struggle to generalize across diverse quantum hardware.

This thesis introduces the Minimum-Weight Parity Factor (MWPF) algorithm, a unified and certifiable decoding formulation that extends minimum-weight perfect matching to general hypergraph-based stabilizer codes. We focus on making MWPF practical and performant through a two-phase decoding architecture, consisting of a fast search phase and …

B-Spline Representations For Hyperspectral Inverse Rendering, Rachel Liang

Computer Science Theses

This work explores the use of a B-spline-based approach for hyperspectral inverse rendering from RGB images, experimenting on both spectral and geometric reconstruction. While the B-spline method is less accurate than brute-force optimization, it offers significant improvements in computational efficiency- reducing both runtime and memory usage.

Our experiments show that the B-spline representation can approximate smooth spectral data effectively but struggles with sharper spectral features unless more knots are introduced. Notably, wavelengths near the edges of the visible spectrum (around 400 nm and 700 nm) were less stable during optimization, reflecting lower convergence reliability. Despite these challenges, the final RGB …

Sequence Conservation Of Suppressor Of Ikk Epsilon Phosphorylation Sites, Kaydence M. Isaacs

Undergraduate Honors Theses

Suppressor of IKK epsilon (SIKE) is a protein that is implicated in immune response signaling pathways. SIKE interaction networks suggest roles in cell motility and macromolecular complexes mediating kinase/phosphatase activity. In this project, we aim to better understand the function of SIKE by analyzing amino acid sequences across different species. In human SIKE, viral infection leads to phosphorylation of SIKE at defined serine residues. Comparing SIKE sequences, and specifically these phosphorylation sites, allows us to discover its ancestral connections to innate immune function. This has particular applications in bridging the evolutionary gap between fungi and metazoa SIKE sequences. Multiple sequence …

Decarbonized Shipping: Is It The Best Sustainable Shipping Solution?, Olivia Akers

Sustainable Supply Chain Management

In the era of globalization and the fourth industrial revolution, the maritime shipping industry has grown exponentially in the twenty-first century. In fact, 90% of today’s goods travel across the ocean before reaching the end consumer, meaning that ocean transportation of goods contributes significantly to overall environmental impacts on the ocean. Awareness of this impact has increased as humans strive to eliminate unsustainable practices in an effort to protect the long term health of our planet. Decarbonized shipping has been proposed as a possible solution for unsustainable shipping practices, and the goal of this chapter is to evaluate this solution …

Human Endogenous Retroviruses (Hervs) Associated With Glioblastoma Risk And Prognosis, Harun Mazumder, Hui Yi Lin, Melody Baddoo, Wojciech Gałan, Diana Polania-Villanueva, Chindo Hicks, David Otohinoyi, Francesca Peruzzi, Zbigniew Madeja, Victoria P. Belancio, Erik K. Flemington, Krzysztof Reiss, Monika Rak

School of Medicine Faculty Publications

Emerging evidence suggests expression from human endogenous retrovirus (HERV) loci likely contributes to, or is a biomarker of, glioblastoma multiforme (GBM) disease progression. However, the relationship between HERV expression and GBM malignant phenotype is unclear. Applying several in silico analyses based on data from The Cancer Genome Atlas (TCGA), we derived a locus-specific HERV transcriptome for glioma that revealed 211 HERVs significantly dysregulated in the comparisons of GBM vs. normal brain (NB), GBM vs. low-grade glioma (LGG), and LGG vs. NB. Our analysis supported development of a unique HERV scoring algorithm that segregated GBM, LGG, and NB. Interestingly, lower HERV …

Programming A More Efficient Onboarding Process For New Employees, Long H. Pham

Undergraduate Honors Theses

The current onboarding process for new hires in the University of San Diego’s Shiley-Marcos School of Engineering is inefficient. There is no central location where new hires and administrators can track onboarding progress. Both parties have to manage multiple email chains and write their own reminders to keep track of everything. This leads to delays, missing deadlines, and confusion for both parties. A web-based onboarding application has been developed recently to address these issues and streamline the onboarding process for new hires. However, this application contains several accessibility issues and does not follow all of the standards for effective employee …

Setting Up Students For Success: Analysis Of Effectiveness Of Mathematics Placement, Jeff Carvell, Jason Ho, David Klanderman, Sarah Klanderman

University Faculty Publications and Creative Works

How do we e!ectively and equitably place students into math classes in a way that provides them the best chance of success? As many higher education institutions veer away from placement based on standardized testing, many departments are seeking placement alternatives that will properly support students. Additionally, math placement determines not only a student’s mathematics courses but also influences their progress in related fields, including physics, chemistry, engineering, and more. This paper will describe three di!erent existing placement systems at each of our liberal arts institutions as well as the a!ordances and constraints of each approach. Further, we analyze data …

Estimating The Future Frequency Of Bonnet Carré Spillway Openings, Kayla Thomas

LSU Master's Theses

In the 2010s, the Bonnet Carré Spillway (BCS) in southeastern Louisiana, U.S.A., experienced an unprecedented uptick in openings to mitigate the possibility of flooding, including a record double-opening in 2019. Both the environmental consequences of BCS openings associated with nutrients that run from the Mississippi River into Lake Pontchartrain and the synoptic-scale meteorological conditions that necessitate these openings are poorly understood. With the unexpectedly frequent openings in recent years and the ever-present threat of climate change, it is vital to consider the future shift of synoptic-scale climate patterns and how it can relate to BCS openings. Understanding the potential for …

Re: Comment Letter For The Butte Priority Soils Operable Unit (Bpsou) Insufficiently Reclaimed Sites Bres No. 158 – Waste Rock Dump Remedial Action Work Plan (Rawp) (Dated March 28, 2025), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Re: Approval Letter For The Butte Priority Soils Operable Unit (Bpsou) Revised Draft Final Insufficiently Reclaimed Sites Bres No. 158 Site Evaluation Summary Report (Dated February 24, 2025), Molly Roby

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Asymmetric, Carboxy And Ester Functionalized Fluorophthalocyanines: Synthesis, Adsorption, And Reactivity, Sean J. Scally

Seton Hall University Dissertations and Theses (ETDs)

Strong electron-deficient compounds, fluorinated metal phthalocyanines (F_xPcM), exhibit enhanced photosensitizing properties, making them optimal candidates for photocatalytic studies. Perfluoroalkyl-substituted phthalocyanines are notably thermally robust materials that are chemically inert and resistant to electrophilic, nucleophilic, and radical, including reactive oxygen species (ROS) attacks. These properties can be attributed to their ‘Teflon-like’ inert organic shield that surrounds a reactive metal center, as well as their complete (x = 16, 40, 64), or almost complete (x = 48) lack of C-H bonds. Third-generation, functionalized, asymmetric phthalocyanines are of interest due to their ability to bind to oxidic supports via a carboxyl …

A Novel Approach To Model The Pion Structure Using Advanced Polynomial Functions, Lucas Kotz

Physics Theses and Dissertations

In the coming years, new experiments at the Electron-Ion Collider (EIC) and the Large Hadron Collider (LHC) will provide unprecedented insight into the building blocks of matter. To make the most of these opportunities, scientists must reduce uncertainties in the theoretical models that connect what we observe in experiments to what is happening inside particles like protons and pions. A critical part of these models involves describing how a particles momentum is shared among its internal components – quarks and gluons.

This work focuses on improving how we model the internal structure of the pion. We propose a new approach …

Simulating 3d Humanoid Ragdoll Physics Using Velocity Verlet Integration, Pin Constraints, And Rigid Body Collision Systems, Son D. Nguyen

Programming Theses and Dissertations

Ragdoll physics simulates realistic character collapse with physical realism by responding to environmental forces rather than using predefined animations.

Complementary Design Of Optical And Photochemical Systems, Joshua Plank

Chemistry Theses and Dissertations

The ability to manipulate chemical systems has been prized through history as the bridge between the macroscopic and microscopic worlds. As an example, the camera obscura has arguably existed since the earliest days of humanity; however, it was the discovery of early silver halide chemistry that lead to the ability to fix these images into the earliest photographs. In modern photolithography employed in electronics manufacturing, the primary resolution limits arise not from the chemistry of the molecules involved, but from the limits of the systems used to project light. Thus, as much as photochemistry advances, optical imaging and projection techniques …

Quantum Chemical Methods And Multiscale Modeling In Computer-Aided Drug Design, Hunter W. La Force

Chemistry Theses and Dissertations

Computer-Aided Drug Design (CADD) leverages a diverse toolkit of computational methods to accelerate the discovery and development of novel therapeutics. Among these, quantum chemical calculations provide unparalleled accuracy in understanding molecular interactions, albeit at a higher computational cost. This accuracy is crucial for identifying and quantifying fundamental interactions that dictate drug efficacy and selectivity, as exemplified by our investigation of ruthenium polypyridyl complexes. These metal-based compounds are model systems for studying covalent coordination bonds between ruthenium and its ligands and noncovalent interactions with DNA and protein targets. Local Mode Vibrational Theory emerges as a powerful lens within this framework, enabling …

The State Of Municipal Scale Highest Use Urban Wood Reclamation Projects, Bradley C. Almond

Graduate Liberal Studies Theses and Dissertations

Millions of urban trees are downed annually for various reasons, such as storms, disease, or development. We are all witnesses to the loss of trees as we see the piles of woody waste assembled on the curbside, ready for public works pickup. Today, most urban wood waste ends up in landfills, mulching/chipping facilities, or firewood production. Each of these alternatives results in the release of sequestered carbon back into the atmosphere.

The initial research led to successful diversion from landfills to mulch and firewood operations. Then, the research shifted to converting urban wood waste for its best use, which outlined …

Nonlinear Phenomena Of Discrete Wave Systems With Nonlocal Coupling, Austin E. Marstaller

Mathematics Theses and Dissertations

There is a long and rich story of nonlinear dynamics in discrete lattices. A particular well studied model is the discrete Nonlinear Schr\"odinger Equation, with many applications, most notably in nonlinear optics.

Recent studies have explored dynamics in scenarios where coupling amongst the array elements is nonlocal. The interest in particular is that in the longwave approximation, it leads to fractional diffraction. In this contribution, we consider two long range interaction lattice wave models, the fractional discrete nonlinear Schr\"odinger equation and the Long Range Ablowitz-Ladik system. By use of perturbation methods, asymptotics and numerical simulations, we present results on modulational …

Data Encoding, Compilation, And Algorithms For Quantum Machine Learning, Aviraj Sinha

Computer Science and Engineering Theses and Dissertations

Quantum computing enables new approaches to data processing, especially in quantum machine learning. Unlike classical systems, quantum data must be synthesized through operations and can exist in superposition. Encoding choices affect efficiency, noise resilience, and trainability—key factors in quantum machine learning models. This dissertation enhances quantum data encodings by extending quantum read-only memory (QROM) beyond binary representations, improving efficiency and parallelism. It introduces new compilation methods for quantum random number generators (QRNGs), supporting non-parametric distributions for post-quantum cryptography. Additionally, it explores Cayley graph-based encodings to extract spectral features for quantum machine learning.

Hybrid Graph-Recurrent Architecture For Citation Recommendation Via Future Embedding Forecasting, Mohammad Ausaf Ali Haqqani

Computer Science and Engineering Theses and Dissertations

The rapid expansion of scientific literature has intensified the challenge of identifying relevant citations, particularly for newly published or under-cited papers. Traditional citation recommendation systems typically model static relationships or respond to past citation activity, offering limited predictive power for emerging works. In response, this thesis presents a temporal modeling framework for citation recommendation that anticipates future scholarly relevance by forecasting the latent representations of academic papers.

Building on prior work that utilized Temporal Graph Networks (TGNs) to model dynamic citation flows, we propose Graph-Time, a hybrid architecture that integrates a Graph Transformer with a GRU-based time series predictor. The …

A Computational Method For Detecting Compound Promiscuity In Early-Stage Pharmaceutical Discovery, John Allen Ringer

Computer Science ETDs

Modern drug discovery and chemical biology research relies heavily on analyzing bioassay data. One of the many challenges in bioassay data analysis is identifying false trails, i.e., chemical compounds which initially appear to have desirable activity but are found to be problematic upon further investigation. Badapple (the BioAssay-Data Associative Promiscuity Pattern Learning Engine) was created over ten years ago to help researchers identify promiscuous compounds and thus avoid a common source of these false trails. Through an effort involving software engineering, cheminformatics, and biomedical data science we have developed Badapple 2.0, which incorporates updated assay records and expanded data semantics. …

Noise-Embedded Image Processing Based On Quantum Data Encodings, Yayu Mo

Multidisciplinary Studies Theses and Dissertations

Advancements in quantum information have significantly impacted the field of image processing, although challenges remain. Especially in the edge detection and image encoding area, distorted feature and noises would affect the further classification or super resolution tasks. In our work, we conduct researches on two stages to both evaluate the potential of Quantum-based Convolutional Structure in extracting distorted feature and further explore the effects of quantum noise channels on quantum image encodings.

In the first stage, we propose a method to extract distorted edge features by applying shallow layers in quantum convolutional neural networks (QCNN). By combining the advantages of …

Challenging $\Lambda$Cdm: Unraveling Cosmic Distances, Dark Sector Phenomenology, And Alternative Primordial B-Mode Sources, Kylar L. Greene

Physics & Astronomy ETDs

The dominant Lambda Cold Dark Matter (LCDM) cosmological model, while remarkably successful, increasingly shows signs that it may not fully describe our Universe, as persistent tensions in expansion rates and structure formation remain unresolved. In this thesis, I challenge the LCDM paradigm using novel theoretical frameworks combined with rigorous numerical analyses. I demonstrate that the expansion-rate tension fundamentally reflects underlying distance disagreements, and that the Thomson scattering rate strongly restricts higher pre-recombination expansion rates without additional physics. Further, I present a novel cosmological model using a mirror dark sector and varying fundamental constants, revealing an observational degeneracy allowing significantly higher …

Evaluating San Francisco Urban Green Spaces And Policy To Inform Future Decision-Making: How Climate Change Adaptation Strategies Can Be Prioritized And Incorporated In Urban Park Design And Planning Through A Decision-Making Tool, Holley Anne Maassen

Master's Projects and Capstones

Amid the current climate crisis, enhancing urban green spaces (UGS), parks, and open spaces with climate change adaptation (CCA) as a strategic pillar in San Francisco’s urban planning is an essential strategic pillar to develop more resilient cities. However, in complex bureaucratic landscapes, integrating CCA strategies that meet project goals while ensuring inclusive stakeholder engagement presents a challenge. This project presents the identification, development, and application of a holistic decision-making tool (DMT) in the form of a Pugh matrix/decision matrix and with a focus on urban planning in San Francisco, California. Key decision-making criteria are identified and weighted through a …

Floating Pv In Bulawayo: Evaluating Evaporation Mitigation, Energy Yields And Economic Viability., Fidelis Hazvineyi Dambudzo Gorogodo

Master's Projects and Capstones

Water scarcity and energy shortages are critical challenges in Zimbabwe, particularly in the semi-arid regions reliant on reservoir-based water supply systems. Evaporation losses from water reservoirs amplified by rising global temperatures has become a concern, particularly for Zimbabwe which has a relatively low water per-capita (776 liters). Electricity blackouts extending to 12-20 hours per day further worsens the situation by failing to pump available water, calling for solutions to enhance water and energy security. This study evaluates the feasibility of integrating Floating Photovoltaics (FPV) on the Umzingwane catchment dams (Umzingwane, Upper and lower Ncema, Insiza, Mtsabezi and Inyankun) to mitigate …

Who Owns The Wind: The Absence Of Community Wind Farms In California, Sky Berry-Weiss

Master's Projects and Capstones

Community ownership structures for wind farms have been around for decades, particularly in European countries, due to high socioeconomic benefits. Given these significant benefits, one might expect community wind to thrive in the United States—especially in a state like California, which prides itself on progressive climate policy and renewable energy leadership. Yet utility-scale community wind remains largely absent from research on California’s energy system, raising questions about its existence in the state. To pinpoint how many utility-scale community owned wind farms are in California, this study surveys every operational wind turbine in the state. After classifying each wind farm by …

The Nanograv 15 Yr Data Set: Harmonic Analysis Of The Pulsar Angular Correlations, Gabriella Agazie, Akash Anumarlapudi, Anne M. Archibald, Zaven Arzoumanian, Jeremy G. Baier, Paul T. Baker, Bence Bécsy, Laura Blecha, Kimberly K. Boddy, Adam Brazier, Paul R. Brook, Sarah Burke-Spolaor, Rand Burnette, J. Andrew Casey-Clyde, Maria Charisi, Shami Chatterjee, Tyler Cohen, James M. Cordes, Neil J. Cornish, Fronefield Crawford, H. Thankful Cromartie

Pacific Faculty Work

Pulsar timing array observations have found evidence for an isotropic gravitational-wave background with the Hellings-Downs angular correlations between pulsar pairs. This interpretation hinges on the measured shape of the angular correlations, which is predominantly quadrupolar under general relativity. Here we explore a more flexible parameterization: we expand the angular correlations into a sum of Legendre polynomials and use a Bayesian analysis to constrain their coefficients with the 15 yr pulsar timing data set collected by the North American Nanohertz Observatory for Gravitational Waves (NANOGrav). When including Legendre polynomials with multipoles ℓ ≥ 2, we only find a significant signal in …

Effectiveness Of Urban Composting And Waste Management In The San Francisco Bay Area, Elijah Ashiagbor

Master's Projects and Capstones

The increasing food waste epidemic contributes to environmental degradation through amplified GHG emissions, notably CH4, from MSW landfills. Addressing this challenge is essential for public health and environmental sustainability. This research reviews municipal composting initiatives within the San Francisco Bay Area, evaluating effectiveness, efficiency, and sustainability. Utilizing data from CalRecycle and local municipalities, this study analyzes different composting processes, regulatory compliance with California’s Senate Bill 1383, and factors affecting waste diversion rates. Key discoveries indicate that in-vessel composting shows better efficiency and compost quality compared to windrow methods, particularly suitable for urban counties with space limitations. However, participation rates in …

Analyzing Ballast Water Treatments, Invasive Species, And Pathogens, And A Decade-Long Analysis On The San Francisco And Baltimore Ports, Jasmin Ibarra-Cortes

Master's Projects and Capstones

Installation of advanced technologies to treat ballast water on ships is necessary to meet current ballast water management standards and reduce the secondary spread of invasive species during intracoastal voyages. This research includes a literature review on non-native aquatic species, particularly diapausing eggs, and available treatment methods for installation. A comparative analysis from 2014 - 2024 on bulker, tanker, and container vessels arriving coastwise to the ports of San Francisco and Baltimore was performed to evaluate treatment installation trends, traffic patterns, and the effectiveness of treatment(s) on targeting diapausing eggs. Use of ultraviolet (UV) radiation combined with filtration has increased …

Fe/Co/Ni-Doped Mos2 An Electrocatalyst For Overall Water Splitting, Himanshi Lnu

Electronic Theses & Dissertations

Electrochemical water splitting is a promising method for sustainable hydrogen production, addressing global energy challenges. However, its practical application is limited by the need for efficient and durable electrocatalysts for both the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). In this study, MoS₂ was doped with Co, Ni, and Fe at varying concentrations (5:0.5, 5:1, and 5:1.5) using a hydrothermal synthesis method to evaluate their potential as electrocatalysts for water splitting. Characterization revealed that metal doping significantly altered the electronic and morphological properties of MoS₂, enhancing its catalytic performance. Electrochemical evaluations in alkaline media demonstrated that Co-doped MoS₂ …

Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel

Electronic Theses & Dissertations

The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …