Physical Sciences and Mathematics Commons^™

Topnet R1: A Multi-Stage Ai Framework For Topic Discovery In Scientific Abstracts, Md Elias Hossain

Theses and Dissertations

Scientific abstracts are rich sources of knowledge, yet extracting meaningful topics remains challenging due to limitations in existing topic modeling techniques. Traditional methods often struggle with interpretability, scalability, and contextual understanding. To overcome these issues, we introduce TopNet R1, a multi-stage ensemble framework that integrates traditional topic models with contextual embeddings from Bidirectional Encoder Representations from Transformers (BERT) and Generative Pre-trained Transformer 4 (GPT-4) large language models (LLMs). Top- Net R1 operates in three phases: (1) topic generation using Latent Dirichlet Allocation (LDA), Non-Negative Matrix Factorization (NMF), Latent Semantic Analysis (LSA), and Hierarchical Dirichlet Process (HDP); (2) LLM-assisted pattern recognition …

Exploring The Use Of A Random Forest In Correcting Gfs Tropical Cyclone Landfall Errors, Victoria Grace Maxwell

Theses and Dissertations

While Tropical Cyclone (TC) track forecasting has improved over the years it has been slow. These improvements can be attributed to increased computer capability and better model inputs. Machine learning has been used for forecasting different TC track and intensity. The study here looks to use a Random Forest to predict the TC latitude/longitude “landfall” at 72-hr and quantify improvements to the GFS forecast. Principal Component Analysis was used to reduce the dimensionality of the meteorological variables. Stepwise regression was used to determine the principal components that were important for forecasting landfall. These variables were then tested with a multivariate …

Unboxing The Black Box: Graph-Based Interpretability In Transformer Models, Ramak Nassiri

Theses and Dissertations

This thesis introduces a novel interpretability framework for transformer encoder models by hypothesizing that their internal embedding updates define a state transition system. We propose that transformers implicitly learn token-to-token influence dynamics, which can be analyzed using graph-theoretic methods. To validate this, we construct transition graphs from embedding changes and rank token importance using the PageRank algorithm. We develop two transformer models from scratch: a self-supervised model that incorporates serotype tokens to learn contextualized embeddings, and a supervised model initialized with these embeddings. Cosine similarity analysis of their token influence patterns reveals strong structural alignment, with values exceeding 93%. This …

Soil Ethics In Practice: Harvesting Conservation Choices Among Puerto Rican Coffee Farmers, Patricia Marie Cordero-Irizarry

Theses and Dissertations

Coffee farming in Puerto Rico has declined over recent decades, partly due to deteriorating soil quality. However, the decision-making process behind farmers’ adoption of soil conservation practices remains unclear, particularly the overlooked role of soil ethics, which emphasizes the moral principles guiding human relationships with the soil. This mixed-methods study examined coffee farmers’ adoption of soil conservation practices by integrating the Values-Beliefs-Norms (VBN) theory and a newly developed Soil Ethics Survey (SES) instrument for the quantitative component, while using Decision-Making Theory and Social Cognitive Theory to qualitatively explore how farmers’ experiences and reflections shape their soil ethics. Quantitative findings revealed …

Understanding How Nws Meteorologists Tailor Hazardous Weather Messaging To Core Partners And Identify Local Vulnerabilities, Allison Camille Harvey

Theses and Dissertations

Over the past few decades, the National Weather Service (NWS) has continued to improve impact-based decision support services (IDSS) efforts to strengthen communication with core partners. This study addressed how a new spatially hazard-specific vulnerability tool called the Brief Vulnerability Overview Tool (BVOT) may impact how NWS meteorologists tailor messaging to their core partners. It was found that relationship building between NWS meteorologists and core partners is key to enhancing trust, especially during blue sky days. This was done by learning core partners’ needs, thresholds, and communication styles when presenting weather information. Core partners also noticed cues from NWS meteorologists …

Augmenting Healthcare Communication: Context-Aware Ai Frameworks For Clinical Decision Support And Automated Summarization, Subash Neupane

Theses and Dissertations

Healthcare communication is plagued by fragmented medical knowledge, patient misunderstanding of care plans, and clinician burnout from documentation burdens. These inefficiencies cost the U.S. healthcare system over $300 billion annually due to preventable nonadherence and administrative waste [47, 19]. While Artificial Intelligence (AI) technology like Large Language Models (LLMs) offer potential solutions, existing systems fail to deliver personalized, context-aware guidance or automate documentation without sacrificing accuracy. This dissertation addresses these gaps through three novel context-aware AI frameworks such as MedInsight, ClinicSum, and ClinicDuo. MedInsight leverages a multi-source context augmentation approach to synthesize patient centric medical responses by integrating Electronic Health …

Estimating Reliability Of Electric Vehicle Charging Ecosystem Using Principle Of Maximum Entropy, Himanshu Tripathi

Theses and Dissertations

This thesis addresses the challenge of estimating electric vehicle (EV) charging system reliability against unpredictable threats like cyberattacks and extreme weather, where traditional methods fail. We utilize the Principle of Maximum Entropy (PME), a statistical tool that provides unbiased risk estimates using limited information. Applied to the EV charging ecosystem, our case study shows how PME models stress factors to predict failures and optimize maintenance. This approach extends beyond EVs to other complex systems with scarce data, such as smart grids or healthcare devices. By linking uncertainty directly to reliability, PME offers a universal method to improve decision-making under unpredictable …

Determining The Toxic Threshold And Other Use Characteristics For Industrial Hemp Seed Oil Used For Wood Product Protection, Daylan M. Barnes

Theses and Dissertations

Plant-based wood treatments have been utilized for many years, with varying success. Oils such as those extracted from linseed (flax), tung, and hemp plants have been used for thousands of years as finishes on wood. These are all drying oils, which dry to a film when exposed to air. Hemp seed oil has a high fatty acid content and can take a long time to dry on wood products but is valued in woodworking for being easy to use, food-safe, and having little to no odor. In this study, cold-pressed hemp seed oil, blended with a soybean carrier oil, is …

Autonomous Generation Of Ids Rules From Threat Intelligence, Azim Bazarov

Theses and Dissertations

Signature-based Intrusion Detection Systems (IDS) detect malicious activities by matching network or host activity against predefined rules. These rules are derived from Cyber Threat Intelligence (CTI), which includes attack signatures and behavioral patterns obtained through automated tools and manual threat analysis, such as sandboxing. The CTI is then transformed into actionable rules for the IDS engine, enabling real-time detection and prevention of threats. The constant evolution of cyber threats necessitates frequent rule updates, which delay deployment time and weaken overall security readiness. Recent advancements in autonomous agentic systems powered by Large Language Models (LLMs) offer the potential for automatic IDS …

A Mathematical Theory Of Epitaxial Growth, Brock C. Price

Theses and Dissertations

In this dissertation we investigate several PDE models of Epitaxial growth. These models are fourth-order PDE’s featuring exponential nonlinearities as well the p-Laplacian and 1-Laplacian. The presence of the exponential nonlinearity is what provides the main mathematical difficulty. Theexponent in particular does not have enough estimates to guarantee any compactness. Because of this, one has to allow the inclusion of a singular portion to the exponent in the sense of the Lebesgue decomposition theorem. In thefirst chapter weinvestigate a related epitaxial growth, with transition rates of the Metropo lis variety and a linear exponent. The metropolis rates induce an extra …

Unraveling Quantum Properties Of Novel Two-Dimensional Systems Using A First-Principles Approach, Binod Regmi

Theses and Dissertations

We used first-principles density functional theory (DFT) to investigate the structural, electronic, and magnetic properties of an oxygen crystal in a copper slab, a ferrimagnetic electride with highly tunable magnetic anisotropy energy (MAE), and the Fermi surface analysis of different kagome metal phases. The Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional was used in the Vienna ab initio simulation package (VASP) for all these calculations. Because of dimensionality reduction, the electronic properties of copper change significantly at the two-dimensional (2D) scale due to whichwe observe more reconstruction in the geometry of the Fermi surface. Dimensionality reduction also influences charge transport. Moreover, we present …

Development Of A Health Knowledge And Skill-Based Framework For The Digital Age, Evelyn Hovenga, Osama El-Hassan, Manal Almalki, Jawad Ahmed, Paul Barach, Mowafa Househ, Amr Jamal

College of Population Health Faculty Papers

The Gulf Cooperation Council (GCC) region is tackling a significant digital healthcare workforce skills gap by creating a computable unified digital health competency framework and repository. Digital technologies and global competency standards are leveraged to professionalize the digital health knowledge domain and facilitate the development of clear career pathways in digital health. A mixed-methods approach was employed to develop the framework. A standardized categorial structure and information model has been developed to support the creation of this computable framework for workforce evaluation and competency-based career development.

Capers-Lrd-Z9: A Gas-Enshrouded Little Red Dot Hosting A Broad-Line Active Galactic Nucleus At Z = 9.288, Anthony J. Taylor, Vasily Kokorev, Dale D. Kocevski, Hollis B. Akins, Fergus Cullen, Mark Dickinson, Steven L. Finkelstein, Pablo Arrabal Haro, Volker Bromm, Mauro Giavalisco, Kohei Inayoshi, Stéphanie Juneau, Gene C.K. Leung, Pablo G. Pérez-González, Rachel S. Somerville, Jonathan R. Trump, Ricardo O. Amorín, Guillermo Barro, Denis Burgarella, Madisyn Brooks, Adam C. Carnall

Pacific Faculty Work

We present CAPERS-LRD-z9, a little red dot (LRD) that we confirm to be a z = 9.288 broad-line active galactic nucleus (BLAGN). First identified as a high-redshift LRD candidate from PRIMER NIRCam photometry, follow-up NIRSpec/PRISM spectroscopy of CAPERS-LRD-z9 from the CANDELS-Area Prism Epoch of Reionization Survey (CAPERS) has revealed a broad 3500 km s⁻¹ full width at half-maximum Hβ emission line and narrow [O iii] λλ4959, 5007 lines, indicative of a BLAGN. Based on the broad Hβ line, we compute a canonical black hole mass of log ( M BH / M ⊙ ) = 7.58 ± 0.15 , …

Activation Or Deactivation? Rethinking Ferrate(Vi) Reactivity Within A Broader Modulation Framework, Zepei Tang, Yang Deng

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

No abstract provided.

A 12,800-Year-Old Layer With Cometary Dust, Microspherules, And Platinum Anomaly Recorded In Multiple Cores From Baffin Bay, Christopher R. Moore, Vladimir A. Tselmovich, Malcolm A. Lecompte, Allen West, Stephen J. Culver, David J. Mallinson, Mohammed Baalousha M.Sc, Ph.D., James P. Kennett, William M. Napier, Michael Bizimis, Victor Adedeji, Seth R. Sutton, Gunther Kleteschka, Kurt A. Langworthy, Jesus P. Perez, Timothy Witwer, Marc D. Young, Jordan Jeffreys, Richard C. Greenwood, James A. Malley

Faculty Publications

The Younger Dryas Impact Hypothesis (YDIH) posits that ~12,800 years ago Earth encountered the debris stream of a disintegrating comet, triggering hemisphere-wide airbursts, atmospheric dust loading, and the deposition of a distinctive suite of extraterrestrial (ET) impact proxies at the Younger Dryas Boundary (YDB). Until now, evidence supporting this hypothesis has come only from terrestrial sediment and ice-core records. Here we report the first discovery of similar impact-related proxies in ocean sediments from four marine cores in Baffin Bay that span the YDB layer at water depths of 0.5–2.4 km, minimizing the potential for modern contamination. Using scanning electron microscopy …

Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ongoing evolution of SARS-CoV-2 variants has underscored the need to understand not only the structural basis of antibody recognition but also the dynamic and allosteric mechanisms that could underlie complexity of broad and escape-resistant neutralization. In this study, we employed a multi-scale approach integrating structural analysis, hierarchical molecular simulations, mutational scanning and network-based allosteric modeling to dissect how Class 4 antibodies (represented by S2X35, 25F9, and SA55) and Class 5 antibodies (represented by S2H97, WRAIR-2063 and WRAIR-2134) can modulate conformational behavior, binding energetics, allosteric interactions and immune escape patterns of the SARS-CoV-2 spike protein. Using hierarchical simulations of the …

Extracting Magnetic Exchange Interactions From Magnetic Pair Distribution Function Data Via Monte Carlo Simulations, Emma Zappala

Theses and Dissertations

The magnetic pair distribution function (mPDF) is a powerful tool used to analyze diffuse magnetic scattering data in real-space. Presently, mPDF is usually used to model real-space spin configurations of materials, offering important insights into the local magnetic structure, but not to directly probe the magnetic interactions giving rise to the magnetic structure in the first place. Using Monte Carlo simulations, a robust algorithm to simulate the magnetic structure of materials, we can connect the underlying magnetic exchange parameters to the spin configurations from experimental mPDF data. We prove this concept using a simple two-dimensional Ising model and then demonstrate …

Bring Back The Blue-Book Exam: In An Age Of Ai, We Need To Return To Handwritten Assignments., Katie Day Good

University Faculty Publications and Creative Works

When ChatGPT was released three years ago, its ability to mimic human writing unsettled me. I’m a professor of communication; what did it mean that my students now had access to a machine that could communicate for them? My initial unease led to a half-joke with my colleagues. Universities could survive this threat, I ventured, but only if we reverted back to 19th-century teaching methods like Socratic dialogue, oral defenses, and lengthy essay exams. This once-laughable scenario is now a serious consideration for many faculty, including me.

Like many professors, I’ve recently abandoned take-home essays in favor of blue-book exams. …

Harnessing Emergent Multiple Scattering Resonances In A Photonic Glass Structure For Photoelectrochemical Energy Conversion, Ashlyn G. Descarpentrie, Robert H. Coridan

Chemistry & Biochemistry Faculty Publications and Presentations

Light trapping nanostructures are often necessary to improve carrier collection yields in semiconductor photoelectrodes with intrinsically poor electron transport. Photonic crystal templates can generate tailorable light trapping via periodic and precise nanostructure, though this is not a scalable strategy for photoelectrochemical (PEC) applications. It is therefore critical to identify alternative mechanisms for light trapping that tolerate disorder. Light trapping in disordered media is generated by the diffusive transport caused by multiple scattering. In some cases, multiple scattering can generate resonances that resemble those observed in photonic crystals. While resonant multiple scattering is a disorder tolerant light trapping mechanism, it is …

Monte Carlo Stellar Evolution Models And Their Application On Globular Clusters, Jiaqi Ying

Dartmouth College Ph.D Dissertations

Stellar evolution models serve as fundamental tools in astronomy, essential for interpreting the interiors and evolutionary stages of stars, and have wide applications in astronomy, from searching for exoplanets to estimating the age of the universe. This thesis explores the inherent uncertainties arising from the complex physics used in stellar evolution models. By adopting a Monte Carlo approach to vary over 20 key stellar evolution parameters, we quantify their impact on model predictions, highlighting substantial influences on age, luminosity, and temperature. Through a detailed analysis of Milky Way globular clusters (GCs), this work rigorously investigates the uncertainties inherent in stellar …

Developing Microelectrode Arrays As Multiplex Point-Of-Care Diagnostics, Yu-Chia Chang

Arts & Sciences Graduate Student Theses and Dissertations

Antibiotic resistance poses a significant global health challenge, particularly in urinary tract infections (UTIs), where 92% of cases exhibit resistance to at least one antibiotic, causing over 260,000 deaths annually. The emergence of antibiotic-resistant bacteria and growing awareness of the adverse effects of unnecessary antibiotic use highlight the urgent need for better UTI diagnostics. Current state-of-the-art methods are either expensive and time-consuming, or they lack specific details about the nature of the antibiotic and only determine inflammation. This hinders timely and effective treatment decisions regarding whether an antibiotic is actually necessary. Given this backdrop, there is a demand for a …

An Enzyme-Coupled Isotope Dilution Mass Spectrometry Assay For Non-Adjacent Dna Photoproducts As Intrinsic Probes For G-Quadruplexes In Vitro, Savannah Sharee Scruggs

Arts & Sciences Graduate Student Theses and Dissertations

G-quadruplexes are noncanonical secondary structures that form in guanine-rich nucleic acid sequences and are thought to be involved in the control of gene expression.1 Unfortunately, it has been difficult to prove that these structures exist in vivo because of their dynamic nature. Rather than try to develop G-quadruplex specific binders as others have done,2 our idea is to photochemically trap certain types of G-quadruplexes by irreversible photoproduct formation3–5 and then detect the stable G-quadruplex-specific photoproducts by Isotopic Dilution Mass Spectrometry (IDMS).6 This IDMS method could then be used to unambiguously confirm the presence of specific types of G-quadruplexes in vivo …

Differentiation And Certain Operators On Scaled Sectional Hypercomplex Numbers, Daniel Alpay, Ilwoo Choo

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this paper, we study certain sectional structures of the t-scaled hypercomplex numbers H_t for a scale t ∈ R, including the quaternions H_-1, and the split quaternions H₁. For a fixed scale t ∈ R, by defining the collection S_t of certain pureimaginary t-scaled hypercomplex number in H_t , we sectionize H_t from the imaginaries of S_t. We concentrate on a section SH_It for an arbitrarily fixed imaginary I_t ∈ S_t , called the t-scaled section for I_t. Differentiation theory on the …

A Groundwater Flow System Investigation In The Upper Rowena Creek Drainage, Oregon, Catelee Yamei Kambur

Dissertations and Theses

Groundwater level declines are a growing concern within the upper Rowena Creek drainage, Oregon. This area is home to a small community located on the upper limb of the Columbia Hills anticline, where local residents rely on aquifers within the Columbia River Basalt Group (CRBG) for domestic water supplies. Groundwater level declines in CRBG aquifers have been studied more extensively in the Mosier area, which lies approximately 5 miles to the northwest of Rowena, but there has been little research conducted specifically on the upper Rowena Creek drainage area. Rowena is located higher up the dip of the Columbia Hills …

Antifungal Peptides From Casein Milk Of Etawa Crossbreed (Capra Hircus) As Biopreservation Agent For Bread And Molecular Docking Studies, Dian Riana Ningsih, Winarto Haryadi, Rachma Wikandari, Tri Joko Raharjo

Karbala International Journal of Modern Science

Bread without peptide fraction treatment started to grow mold on the fourth day with a total of 24x10⁷ fungi colonies/ml. Meanwhile, the addition of peptide fractions GMC5, GMC6, GMC7, and GMC8 effectively preserved bread for up to 4 days, indicated by no mold growth. The best treatment was the GMC6 peptide fraction on day 8 which grew the least amount of fungus at 7x10⁷ spores/ml. Peptide interaction with the CaATPase receptor Aspergillus sp. was carried out using HADDOCK 2.4. The 3D CaATPase structure prediction resulted in a model with good structural quality. This was supported by residues in …

Skolem Number Of Kagome Lattice Graphs, Braxton Carrigan, Max Martone

Theory & Applications of Graphs

A proper Skolem labelling of a graph $G$ is a function assigning a positive integer to each vertex of $G$ such that any two vertices assigned the same integer are that distance apart in the graph. The Skolem number of a graph is smallest number $n$ such that there exists a proper Skolem labelling only using the positive integers less than or equal to $n$. In this paper, we will begin by proving the Skolem number for another family of subgraphs of the hexagonal lattice and then prove the Skolem number for two families of subgraphs of the Kagome Lattice.

A Deep Learning Framework With Explainable Ai For Atmospheric Blocking Detection And Interpretation, Devansh Khandelwal

Discovery Undergraduate Interdisciplinary Research Internship

Atmospheric blocking is a large-scale quasi-stationary phenomenon in mid-latitude circulation, characterized by persistent high-pressure systems that disrupt the typical west-to-east flow of the jet stream. These systems can cause extreme weather events—such as heatwaves, cold spells, or droughts—that persist for days or even weeks. This study proposes a deep learning framework to predict and interpret the occurrence of atmospheric blocking by integrating geophysical precursors such as geopotential height (Z500), stream function (SF200), and potential vorticity. These features, which are dynamically linked to blocking onset and persistence, serve as inputs to a Convolutional Neural Network model trained on the CESM Large …

Transcendental Formulas For The Coefficients Of Ramanujan's Mock Theta Functions, Gradin Anderson

Theses and Dissertations

Ramanujan's 1920 last letter to Hardy contains seventeen examples of mock theta functions, including the famous third order function f(q), which resemble modular forms of weight 1/2. This list has since been expanded by individuals such as Gordon and McIntosh and the McKay--Thompson series arising in moonshine theory. In 1964, Andrews---improving on a result of Dragonette---gave an asymptotic formula for the coefficients of f(q) and conjectured an exact formula: a conditionally convergent series that closely resembles the Hardy--Ramanujan--Rademacher formula for the partition function. A key breakthrough came in 2001, when Zwegers wrote f(q) as the holomorphic component of a vector-valued …

Search For Higgs Boson Pair Production In The Two Light Leptons And One Tau Final State Using Proton-Proton Collision Data With $\Sqrt{S} = 13$ Tev At The Lhc From The Atlas Detector, Susan Bataju

Physics Theses and Dissertations

In this thesis, a search is presented for the pair production of Higgs bosons in a final state containing two same-charge light leptons (e/$\mu$) and one opposite-charge hadronically decaying tau lepton ($\tau_{h}$). The search is based on a data sample of proton-proton (pp) collisions at a center-of-mass energy $\sqrt{s}$ = 13 TeV, collected by the ATLAS detector during Run 2 (2015-2018) of the Large Hadron Collider (LHC), corresponding to an integrated luminosity of 140 fb$^{-1}$. The Standard Model predicts that the Higgs potential has a non-zero expectation value leading to the spontaneous breaking of electroweak symmetry and when some fundamental …

Assembly Of Non-Close-Packed Poly(N-Isopropylacrylamide) Microgels On Metal Halide Perovskite Films, Amal Alruwaili, Osama M. Alkhudhari, Ran Wang, Zhenyu Jia, Jennifer M. Saunders, Eugenio Picheo, Daniel T.W. Toolan, L. Andrew Lyon, Brian R. Saunders

Engineering Faculty Articles and Research

Hypothesis

Experiments