Physical Sciences and Mathematics Commons^™

Improving The Scalability Of Neural Network Surface Code Decoders, Kevin Wu

Undergraduate Honors Theses

Quantum computers have recently gained significant recognition due to their ability to solve problems intractable to classical computers. However, due to difficulties in building actual quantum computers, they have large error rates. Thus, advancements in quantum error correction are urgently needed to improve both their reliability and scalability. Here, we first present a type of topological quantum error correction code called the surface code, and we discuss recent developments and challenges of creating neural network decoders for surface codes. In particular, the amount of training data needed to reach the performance of algorithmic decoders grows exponentially with the size of …

Code Syntax Understanding In Large Language Models, Cole Granger

Undergraduate Honors Theses

In recent years, tasks for automated software engineering have been achieved using Large Language Models trained on source code, such as Seq2Seq, LSTM, GPT, T5, BART and BERT. The inherent textual nature of source code allows it to be represented as a sequence of sub-words (or tokens), drawing parallels to prior work in NLP. Although these models have shown promising results according to established metrics (e.g., BLEU, CODEBLEU), there remains a deeper question about the extent of syntax knowledge they truly grasp when trained and fine-tuned for specific tasks.

To address this question, this thesis introduces a taxonomy of syntax …

Evaluating Large Language Model Performance On Haskell, Andrew Chen

Undergraduate Honors Theses

I introduce HaskellEval, a Haskell evaluation benchmark for Large Language Models. HaskellEval’s curation leverages a novel synthetic generation framework, streamlining the process of dataset curation by minimizing manual intervention. The core of this research is an extensive analysis of the trustworthiness of synthetic generations, ensuring accuracy, realism, and diversity. Additional, I provide a comprehensive evaluation of existing open-source models on HaskellEval.

Security And Interpretability In Large Language Models, Lydia Danas

Undergraduate Honors Theses

Large Language Models (LLMs) have the capability to model long-term dependencies in sequences of tokens, and are consequently often utilized to generate text through language modeling. These capabilities are increasingly being used for code generation tasks; however, LLM-powered code generation tools such as GitHub's Copilot have been generating insecure code and thus pose a cybersecurity risk. To generate secure code we must first understand why LLMs are generating insecure code. This non-trivial task can be realized through interpretability methods, which investigate the hidden state of a neural network to explain model outputs. A new interpretability method is rationales, which obtains …

Modeling The Neutral Densities Of Sparc Using A Python Version Of Kn1d, Gwendolyn R. Galleher

Undergraduate Honors Theses

Currently, neutral recycling is a crucial contributor to fueling the plasma within tokamaks. However, Commonwealth Fusion System’s SPARC Tokamak is expected to be more opaque to neutrals. Thus, we anticipate that the role of neutral recycling in fueling will decrease. Since SPARC is predicted to have a groundbreaking fusion power gain ratio of Q ≈ 10, we must have a concrete understanding of the opacity
and whether or not alternative fueling practices must be included. To develop said understanding, we produced neutral density profiles via KN1DPy, a 1D kinetic neutral transport code for atomic and molecular hydrogen in an ionizing …

Dimensionlessly Comparing Hydrogen And Helium Plasmas At Lapd, Lela Creamer

Undergraduate Honors Theses

This project compares the hydrogen and helium gas puff plasmas created at the Large Plasma Device (LAPD) using dimensionless numbers to determine the extent to which the turbulence pattern can be explained by plasma physics. Since turbu- lence tends to dissipate energy and particles in a plasma, it can cause problems for fusion reactors by reducing their efficiency. With a better understanding of turbu- lence’s causes and behavior, some of this energy loss could potentially be avoided. In recent experiments at LAPD, an unexpectedly high amount of turbulence was de- tected when helium was used to create the plasma, which …

Identifying Transitions In Plasma With Topological Data Analysis Of Noisy Turbulence, Julius Kiewel

Undergraduate Honors Theses

Cross-field transport and heat loss in a magnetically confined plasma is determined by turbulence driven by perpendicular (to the magnetic field) pressure gradients. The heat losses from turbulence can make it difficult to maintain the energy density required to reach and maintain the conditions necessary for fusion. Self-organization of turbulence into intermediate scale so-called zonal flows can reduce the radial heat losses, however identifying when the transition occurs and any precursors to the transition is still a challenge. Topological Data Analysis (TDA) is a mathematical method which is used to extract topological features from point cloud and digital data to …

Mathematical Modeling And Examination Into Existing And Emerging Parkinson’S Disease Treatments: Levodopa And Ketamine, Gabrielle Riddlemoser

Undergraduate Honors Theses

Parkinson’s disease (PD) is the second most common neurodegenerative disease across the world, affecting over 6 million people worldwide. This disorder is characterized by the progressive loss of dopaminergic neurons within the substantia nigra pars compacta (SNpc) due to the aggregation of α-synuclein within the brain. Patients with PD develop motor symptoms such as tremors, bradykinesia, and postural instability, as well as a host of non-motor symptoms such as behavioral changes, sleep difficulties, and fatigue. The reduction of dopamine within the brain is the primary cause of these symptoms. The main form of treatment for PD is levodopa, a precursor …

Process Modeling The Neuroprotective Effects Of A Plant-Based Diet On Parkinson's Disease, Julia Mitchell

Undergraduate Honors Theses

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor symptoms such as tremors, bradykinesia, rigidity, and postural instability. Recent research suggests an avenue for potential neuroprotection through dietary intervention, specifically the adoption of a plant-based diet. A plant-based diet predominantly comprises foods derived from plants, emphasizing fruits, vegetables, grains, legumes, and nuts while minimizing or excluding animal products. This thesis aims to explore the biochemical pathways implicated in PD progression and the potential impact of dietary choices on these pathways. The investigation focuses on several key pathways: alpha-synuclein aggregation, the blood-brain barrier crossing of levodopa, oxidative stress, ferroptosis, …

Use Of Molecular Logic Gates For The Tuning Of Chemosensor Dynamic Range, Orhan Acikgoz

Undergraduate Honors Theses

The first molecular logic gates were created in the 1990s; integrating such logic gates into fluorescent chemosensors allowed for the detection of different types of ions in solution. In this study, we have developed a new use of molecular logic gates by having two of the same type of binding site. The two binding sites on a fluorophore that both detect Na⁺ ions led to an increase in the detection limit compared with the chemosensor with a single binding site. Since the two sodium binding sites create an AND logic gate, two sodium ions are needed to generate a …

Modeling Group 3 Medulloblastoma: Describing The Interconnected Pathway Of The Most Common Pediatric Brain Cancer, Amber Cantú

Undergraduate Honors Theses

Group 3 medulloblastoma is one of the most common pediatric brain cancers. Affecting infants and children, this cancer has the worst prognosis of the medulloblastoma group. Current treatments use surgical resection, radiation, and chemotherapy to afflict the cancer, however no cure has been found. This project aims to model one of the many pathways being investigated in Group 3 medulloblastoma which may be used to synthesize future treatments. Specifically, showing the interconnections between various precursors of BCL-xL, an antiapoptotic protein, and how these factors influence the progression of the disease. Scientific databases were used to find previous research articles which …

Harnessing The Power Of Virtual Reality For Organic Chemistry Education, Jungmin Shin

Undergraduate Honors Theses

Understanding organic chemistry concepts heavily relies on visualization of the geometry of molecules and spatial arrangement of molecules during mechanisms. 2D textbook depictions have their limitations in visualizing the three-dimensionality of organic chemistry. Student learning outcomes could be greatly improved from 3D visualizations of these topics. This project explores the potential of an emerging technology, Virtual Reality (VR), being incorporated as a teaching resource for organic chemistry.

This paper discusses two trials for evaluating the potential of VR as a teaching resource for organic chemistry in select topics of the Diels-Alder reaction and R/S configurations and stereoisomers. The Diels-Alder reaction …

Roads And Corresponding Travel Time To Markets: Assessing Climate Vulnerability In Nepal, Kaitlyn Crowley

Undergraduate Honors Theses

Roads exist as a physical and theoretical connection between people and places around the globe. In addition to providing a route from one point to another, roads are also an indicator of access to markets and of poverty. However, current road datasets, particularly the Global Roads Open Access Data Set, are out of date or incomplete, necessitating new sources of data for analyses involving road networks. This study explores the relationship between climate change and access to markets in Nepal. We seek to identify isolated communities that are likely to experience detrimental outcomes associated with environmental threats, such as increasing …

Transcriptional Dynamics During Rhodococcus Erythropolis Infection With Phage Wc1, Dana Willner, Sudip Paudel, Andrew D. Halleran, Grace E. Solini, Veronica Gray, Margaret Saha

Arts & Sciences Articles

Background

Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process.

Results

By five …

Ecological Monitoring Program At Vims Esl: Annual Report 2023, Paige G. Ross, Richard A. Snyder

Reports

An Ecological Monitoring Program (EMP) has been established at the Virginia Institute of Marine Science Eastern Shore Laboratory (VIMS ESL) for the coastal environment near the Wachapreague lab. The goals of the initiative are to 1) provide status and trends information to scientists who study and regulators who manage Virginia’s marine resources, 2) provide a scientific context for short-term research and grant proposals 3) provide pedagogical enrichment for educators to use in their classes, and 4) build capacity in staff expertise and training of interns and students at VIMS ESL.

The program formalizes and standardizes data collection for a long-term …

Ecology And Conservation Of Diamondback Terrapins In Virginia, Cypress Ambrose

Undergraduate Honors Theses

The diamondback terrapin (Malaclemys terrapin) is the only turtle species native to North America with specific morphological and physiological adaptations to estuarine environments. Along with many other pressures contributing to population declines, terrapins frequently become trapped and drown as bycatch in crab pots used in the commercial and recreational blue crab (Callinectes sapidus) fishery. A wealth of evidence supports the use of inexpensive bycatch reduction devices (BRDs) that can be attached to the entrances of these traps, which leads to a marked decrease in terrapin bycatch while not reducing crab catch dramatically. Virginia is the only …

Artificial Intelligence For The Electron Ion Collider (Ai4eic), C. Allaire, ..., Cristiano Fanelli, James Giroux, Joey Niestroy, Justin R. Stevens, Patrick Stone, L. Suarez, K. Suresh, Eric Walter, Et Al.

Arts & Sciences Articles

The Electron-Ion Collider (EIC), a state-of-the-art facility for studying the strong force, is expected to begin commissioning its first experiments in 2028. This is an opportune time for artificial intelligence (AI) to be included from the start at this facility and in all phases that lead up to the experiments. The second annual workshop organized by the AI4EIC working group, which recently took place, centered on exploring all current and prospective application areas of AI for the EIC. This workshop is not only beneficial for the EIC, but also provides valuable insights for the newly established ePIC collaboration at EIC. …

Monitoring The Abundance Of American Shad And River Herring In Virginia's Rivers: 2023 Annual Report, Eric J. Hilton, Patrick E. Mcgrath, Ashleigh Magee, Timothy Hoyt

Reports

This report describes the results of the twenty-sixth year of a continuing study to estimate the relative abundance and assess the status of American shad (Alosa sapidissima) stocks in Virginia by monitoring the spawning runs in the James, York and Rappahannock rivers in spring 2023, evaluating hatchery programs, and contributing to coast-wide assessments (ASMFC 2007, ASMFC 2020). We also report on two fisheryindependent monitoring programs using anchor gillnets in the Rappahannock River (year 6) and a major tributary of the James River, the Chickahominy River (year 9), to determine relative abundance and stock structure for the adult spawning run of …

Eluquant: Event-Level Uncertainty Quantification In Deep Inelastic Scattering, Cristiano Fanelli, James Giroux

Arts & Sciences Articles

We introduce a physics-informed Bayesian neural network with flow-approximated posteriors using multiplicative normalizing flows for detailed uncertainty quantification (UQ) at the physics event-level. Our method is capable of identifying both heteroskedastic aleatoric and epistemic uncertainties, providing granular physical insights. Applied to deep inelastic scattering (DIS) events, our model effectively extracts the kinematic variables x, Q2, and y, matching the performance of recent deep learning regression techniques but with the critical enhancement of event-level UQ. This detailed description of the underlying uncertainty proves invaluable for decision-making, especially in tasks like event filtering. It also allows for the reduction of true inaccuracies …

Policy Recommendations For Tire Additive 6ppd And Its Derivative 6ppd-Q, Ashley E. King

Dissertations, Theses, and Masters Projects

Around 3.1 billion tires are produced around the world annually1. The antioxidant additive, 6PPD (i.e., N-(1,3-dimethylbutyl)-N’-phenyl-p-phenylenediamine) is widely employed in passenger and commercial vehicle tires at 0.4-2% by mass to impede tire degradation2. Antioxidants are intended to migrate to tire surfaces and form protective films to prevent rubber oxidation. 6PPD is designed to react with oxidant species like ozone, intentionally forming chemical transformation products that can then escape from the tire and into the environment. 6PPD-Q (i.e., 2-anilino-5-[(4-methylpentan-2-yl)amino]cyclohexa-2,5-diene-1,4-dione) is one such transformation product.

After release and disbursement in the environment, 6PPD-Q is bioavailable to aquatic animals and mammals and acute …

Aquaculture Governance: Five Engagement Arenas For Sustainability Transformation, Darien D. Mizuta, Stefan Partelow

VIMS Articles

A greater focus on governance is needed to facilitate effective and substantive progress toward sustainability transformations in the aquaculture sector. Concerted governance efforts can help move the sector beyond fragmented technical questions associated with intensification and expansion, social and environmental impacts, and toward system-based approaches that address interconnected sustainability issues. Through a review and expert-elicitation process, we identify five engagement arenas to advance a governance agenda for aquaculture sustainability transformation: (1) setting sustainability transformation goals, (2) cross-sectoral linkages, (3) land–water–sea connectivity, (4) knowledge and innovation, and (5) value chains. We then outline the roles different actors and modes of …

Northern Neck Regional Shallow Draft Channel Dredging Plan: Feasibility Phase, Donna A. Milligan, Cameron W. Green, C. Scott Hardaway Jr., Christine A. Wilcox, Claire M. Rae, Scott Lerberg, Alex Demeo, George Brooks, Mark Mansfield

Reports

The Initial Phase of the project (Phase 1), used remote sensing and other data collection to develop a method for determining which waterbodies on the Northern Neck of Virginia need dredging. The analysis included most of the waterbodies in the counties of Lancaster, Northumberland, Richmond, and Westmoreland. From this analysis, 19 waterbodies emerged as potentially needing dredged based on physical parameters and residential and economic usage (Milligan et al., 2023).

In this Feasibility Phase (Phase 2), more detailed site data were collected to provide data to the localities for consideration. These tasks were included in the analysis:

1. Historic shore …

Northern Neck Regional Shallow Draft Channel Dredging Plan: Initial Phase, Donna A. Milligan, Grace M. Massey, C. Scott Hardaway Jr., Christine A. Wilcox, Cameron W. Green, Mark Mansfield

Reports

The purpose of this project is to develop a regional dredging program for the localities of the Northern Neck. This report encompasses Phase 1 of the project, which included creating a database of waterbodies in Lancaster, Northumberland, Richmond, and Westmoreland Counties and the Town of Colonial Beach along the Potomac and Rappahannock Rivers and Chesapeake Bay. Generally, these waterbodies can be categorized into three basic types of shallow draft channels: federally-authorized to include aids to navigation (ATONS), non-federal with ATONS, and non-federal without ATONs. Along the Northern Neck, presently identified, are 13 federal channels, 37 non-federal channels in creeks with …

Parameter Estimation For Patient Enrollment In Clinical Trials, Junyan Liu

Undergraduate Honors Theses

In this paper, we study the Poisson-gamma model for recruitment time in clinical trials. We proved several properties of this model that match our intuitions from a reliability perspective, did simulations on this model, and used different optimization methods to estimate the parameters. Although the behaviors of the optimization methods were unfavorable and unstable, we identified certain conditions and provided potential explanations for this phenomenon and further insights into the Poisson-gamma model.

Results For The 2023 Vims Industry Cooperative Surveys Of The Mid-Atlantic Bight And Georges Bank Scallop Resource Areas, Sally Roman, David Rudders, Carter Lin, Edwin D. Sánchez

Reports

The Virginia Institute of Marine Science (VIMS) conducted high resolution sea scallop dredge surveys of the Mid-Atlantic Bight (MAB) and Georges Bank (GB) scallop resource areas during May–July 2023.

Crystal Structure And Hirshfeld Surface Analysis Of Cyclo-Tetrabromido-1k2br,3k2br-Tetrakis(Pi2-2-{[(Pyridin-2-Yl)Methyl]Amino}Ethane-1-Thiolato-Krystal Structure And Hirshfeld Surface Analysis Ofcyclo-Tetrabromido-1j2br,3j2br-Tetrakis(L2-2-{[(Pyridin-2-Yl)Methyl]Amino}Ethane-1-Thiolato-K3n,S:S)Tetramercury(Ii), I. D. Thomas, K. R. Kocher, J. A. Viehweg, Robert Pike, Deborah Bebout

Arts & Sciences Articles

The macrometallacyclic title compound, [Hg4Br4(C8H11N2S)4] or [((HgL2)(HgBr2))2] (1) where HL = 2-{[(pyridin-2-yl)meth­yl]amino}­ethane-1-thiol, was prepared and structurally characterized. The Hg2+ complex crystallizes in the P21/c space group. The centrosymmetric Hg4S4 metallacycle is constructed from metal ions with alternating distorted tetra­hedral Br2S2 and distorted seesaw N2S2 primary coordination environments with pendant pyridyl groups. The backfolded extended chair metallacycle conformation suggests inter­actions between each of the bis-chelated mercury atoms and Br atoms lying above and below the central Hg2S4 plane. Supra­molecular inter­actions in 1 include a fourfold aryl embrace and potential hydrogen bonds with bromine as the acceptor. Hirshfeld surface analysis indicates that …

Dataset: Marsh Migration Methodology Development For Wetland Restoration Targeting, Molly Mitchell, Karinna Nunez, Christine Tombleson, Julie Herman

Data

Coastal marsh loss is a significant issue globally, due in part to rising sea levels and high levels of coastal human activity. Marshes have natural mechanisms to allow them to adapt to rising sea levels, however, migration across the landscape is one of those mechanisms and is frequently in conflict with human use of the shoreline. Ensuring the persistence of marshes into the future requires an understanding of where marshes are likely to migrate under sea level rise and targeting those areas for conservation and preservation activities. The goal of this project was to 1) compile existing datasets and information …

Synthesis Of Shoreline, Sea Level Rise, And Marsh Migration Data For Wetland Restoration Targeting Final Report, Molly Mitchell, Karinna Nunez, Christine Tombleson, Julie Herman

Data

Coastal marsh loss is a significant issue globally, due in part to rising sea levels and high levels of coastal human activity. Marshes have natural mechanisms to allow them to adapt to rising sea levels, however, migration across the landscape is one of those mechanisms and is frequently in conflict with human use of the shoreline. Ensuring the persistence of marshes into the future requires an understanding of where marshes are likely to migrate under sea level rise and targeting those areas for conservation and preservation activities. The goal of this project was to 1) compile existing datasets and information …

Assessment Of Changes Of Complex Shoreline From Medium‑Resolution Satellite Imagery, Nikolay P. Nezlin, Julie Herman, Jonathan Hodge, Stephen Sagar, Robbi Bishop-Taylor, Guangming Zheng, John M. Digiacomo

VIMS Articles

The imagery collected by medium-resolution earth-observing satellites is a powerful and cost-effective tool for the quantitative assessment of shoreline dynamics for water bodies of different spatial scales. In this study, we utilize imagery collected in 1984–2021 on the Middle Peninsula, Virginia, bordering the Chesapeake Bay, USA, by medium-resolution (10–30 m) satellites Landsat-5/7/8 and Sentinel-2A/B. The data was managed in the Earth Analytics Interoperability Lab (EAIL) Data Cube built and configured by the Commonwealth Scientific and Industrial Research Organization (CSIRO, Australia and Chile). The assessments of shoreline change demonstrate adequate agreement with assessments based on aerial photography collected during 1937–2009 by …

A Language Framework For Modeling Social Media Account Behavior, Alexander C. Nwala, Alessandro Flammini, Filippo Menczer

Arts & Sciences Articles

Malicious actors exploit social media to inflate stock prices, sway elections, spread misinformation, and sow discord. To these ends, they employ tactics that include the use of inauthentic accounts and campaigns. Methods to detect these abuses currently rely on features specifically designed to target suspicious behaviors. However, the effectiveness of these methods decays as malicious behaviors evolve. To address this challenge, we propose a language framework for modeling social media account behaviors. Words in this framework, called BLOC, consist of symbols drawn from distinct alphabets representing user actions and content. Languages from the framework are highly flexible and can be …