Physical Sciences and Mathematics Commons^™

Ai For Life Sciences: From Geometric Protein Modeling To Multimodal Drug Design, Feng Jiang

Computer Science and Engineering Dissertations

Predicting biomolecular interactions, from immune recognition to drug–target binding, is a central problem in the life sciences and computational drug discovery. Deep learning has advanced this area, yet three challenges persist: the topology of large, highly imbalanced interaction networks; structural noise in computationally predicted protein models; and the integration of multimodal information such as functional text and taxonomic annotations. This dissertation develops a coherent set of models spanning immune complex prediction and small-molecule drug design: graph learning that addresses network topology and severe class imbalance; a noise-tolerant method that fuses predicted structures with evolutionary sequence features; and multimodal representation learning …

Fourier Pseudospectral Methods For The Variable-Order Space Fractional Wave Equations, Yanzhi Zhang, Xiaofei Zhao, Shiping Zhou

Mathematics and Statistics Faculty Research & Creative Works

In this paper, we propose Fourier pseudospectral methods to solve the variable-order space fractional wave equation and develop an accelerated matrix-free approach for its effective implementation. In constant-order cases, fast algorithms can be designed via the fast Fourier transforms (FFTs), and the computational cost at each time step is O(Nlog⁡N) with N the total number of spatial points. In variable-order cases, however, the spatial dependence in the power s(x) leads to the failure of inverse FFTs. While the direct matrix-vector multiplication approach becomes impractical due to excessive memory requirements. Hence, we propose an accelerated matrix-free approach for effective implementation in …

Micronutrients (Trace Elements) For High Rainfall Pastures In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

Micronutrient deficiencies can result from removal of agricultural products over many years, changes in soil acidity, or from large increases in plant biomass production and export. This page is specific to high rainfall pastures (more than 600mm average annual rainfall) in the south-west of Western Australia.

The Department of Primary Industries and Regional Development recommends tissue testing to check plant micronutrient nutrient needs.

Potassium For High Rainfall Pastures In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

Potassium (K) deficiency can lead to a decline in clover content and severely limit pasture productivity in high rainfall pastures. Large amounts of potassium can be lost each year through leaching and removal of potassium in hay or silage.

This information is specific to high rainfall pastures receiving more than 600mm average annual rainfall in the south-west of Western Australia.

Soil Sampling High Rainfall Pastures In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

Soil sampling and testing is an essential part of making good fertiliser decisions. Fertilisers are a large cost to farming pastures in high rainfall areas. This page is specific to sampling high rainfall pastures (more than 600mm average annual rainfall) in the south-west of Western Australia.

The Department of Primary Industries and Regional Development recommends soil sampling and testing as part of a plant nutrient management program.

Sulfur For High Rainfall Pastures In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

Sulfur deficiency can substantially reduce pasture yield on sandy soils, particularly in wet years where the sulfate form of sulfur leaches below the root zone of pasture plants, making it unavailable.

This information applies specifically to high rainfall pastures (over 600mm average annual rainfall) in the south-west of Western Australia.

The Department of Primary Industries and Regional Development recommends basing fertiliser decisions on good evidence (soil and tissue test results)

Tissue Sampling And Analysis For High Rainfall Pastures In Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

Tissue testing helps identify nutrient deficiencies that impact plant health. In high rainfall areas ( > 600 mm), pastures are highly productive and have greater demand for both macro- and micronutrients. Micronutrient status is best assessed through plant tissue, as soil levels are difficult to measure accurately.

The Department of Primary Industries and Regional Development recommends tissue testing to assess the effectiveness of fertiliser and soil testing programs, and diagnose emerging macronutrient and micronutrient deficiencies that could cause production losses.

Environmental Impact Of Nitrogen And Phosphorus Fertilisers In High Rainfall Pasture Areas Of Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

The most commonly used nitrogen and phosphorus fertilisers in the high rainfall (>600mm annual average) south-west of Western Australia can be leached into the groundwater and washed into waterways, resulting in serious environmental and economic damage.

The Department of Primary Industries and Regional Development recommends regular soil testing and consultation with FertCare-accredited advisers to reduce leaching losses and increase profit from added nutrients.

Plastic Waste Imports & Coastal Litter: Evidence From Citizen Science Data, Rebecca L.C. Taylor, Hebe Williams, Shan Zhang

Economics Faculty Publications

Plastic waste is an internationally traded commodity, where importing countries recycle plastic waste into usable materials. However, there are concerns that the importation process creates plastic litter - a negative externality - in importing countries. While this concern has received much media and policy attention, quantifying the magnitude of this externality has been hindered by a lack of data on plastic litter across countries and over time. To this end, we use unconventional citizen science data on litter from Ocean Conservancy's International Coastal Cleanup, together with the United Nations Comtrade Database, to estimate the correlation between traded plastic waste and …

Operational Hallucination And Safety Drift In Ai Agents, Shasha Yu, Fiona Carroll, Barry L. Bentley

School of Professional Studies

Large language models (LLMs) serving as planners in tool-using autonomous agents introduce dynamic reliability risks in multi-turn execution. While single-turn safety mechanisms are relatively mature, extended interactions reveal structural vulnerabilities where initial alignment degrades over time. This paper empirically characterizes two observed failure modes across multiple state-of-the-art LLMs: Safety Drift, the gradual erosion of declared safety intent leading to constraint-violating actions (e.g., textual refusal followed by reconnaissance and unsafe execution), and Operational Hallucination, persistent repetitive tool calls indicative of flawed state perception (e.g., livelocks even in legitimate tasks). Through controlled multi-turn evaluation on high-stakes ethical dilemmas, malicious requests, and benign …

When Saying "No" Is Not Enough: Cognitive-Action Decoupling And The Illusion Of Safety In Llm Agents, Shasha Yu, Fiona Carroll, Barry L. Bentley

School of Professional Studies

Current safety evaluations of large language models (LLMs) predominantly rely on textual compliance, implicitly assuming that refusal-style responses correspond to safe behavior. This assumption becomes fragile when LLMs are embedded in agentic systems with the ability to execute state-changing actions. In this paper, we present an empirical critique of text-centric safety evaluation through an action-aware study of LLM agents under controlled conditions. Across multiple state-of-the-art models, we observe a recurring cognitive–action decoupling: agents generate policy-aligned refusal language while still producing unsafe tool-mediated action proposals. This produces an illusion of safety, where conversational audits indicate compliance even as operational risk persists. …

Twisted Electron Collisions Enhance The Production Of Circular Rydberg States, H. S. Parker, S. L. Sims, D. J. Lamphere, Allison L. Harris

Faculty publications – Physics

Circular Rydberg states offer advantages for quantum information and quantum simulation platforms due to their long lifetimes and strong dipole–dipole interactions. Unfortunately, current techniques for the production of these states remain technically challenging. Here we investigate the ability of twisted electron collisions to produce circular Rydberg states. Twisted electrons carry quantized orbital angular momentum (OAM) that can be transferred to the electronic state of the atom, potentially providing an efficient means to generate circular Rydberg states. Using a fully quantum mechanical framework, we compute total excitation cross sections for circular Rydberg states of hydrogen, lithium, rubidium, and cesium targets using …

Big Tech As Transnational Spyware Regulator, Natalie R. Davidson

Fordham Intellectual Property, Media and Entertainment Law Journal

Spyware has emerged as a potent tool for leaders to shrink dem- ocratic contestation. In response to calls for constraints on the trade in spyware, states have updated the principal multilateral agree- ment on export controls, civil society groups have employed strate- gic litigation, and the European Union has altered its regulation, in each case with the aim of limiting exports where there is a risk of human rights violations. Yet, scandals involving the Israeli company NSO, among others, have made clear that even the updated regula- tory landscape is inadequate. Many actors are currently debating the reasons for existing …

Monomeric And Dimeric Metal Complexes Of A New Tridentate Azole-Isoindoline-Urea Ligand, Ben Hudak

Williams Honors College, Honors Research Projects

1,3-Diiminoisoindoline (DII) compounds have been found to be novel materials for both metal binding and chromophore applications. In this work, I am investigating the next synthetic step in developing pyrazole- and indazole-DII compounds. These compounds stem from the reaction of the unsubstituted imine of the pyrazole- or indazole-DII adduct with an isocyanate. These DII compounds, DII-pyrazolePhNCO, DII-pyrazolenapthylNCO, DII-indazolePhNCO, DII-indazolenapthylNCO, DII-pyrazoleptolylNCO, and DII-indazoleptolylNCO were prepared using ethanol as the solvent and heat. Metal acetates were then reacted with the ligands using DMF and heat. The acetate salts included copper (II) and nickel(II). Some distinctive hydrogen bonding interactions were observed in the …

Eigenvalue Bound Preservation: Numerical Experiments On The 2d Q-Tensor Flow, Marcel C. Deguzman

Knowledge and Creativity Expo

We study the evolution of nematic liquid crystals in two dimensions using the Q-tensor model, a continuum framework that describes the orientational order of rod-like molecules via symmetric, traceless matrices. Focusing on the Landau-de Gennes energy and its associated gradient flow, we consider a reduced two-dimensional formulation in which the Q-tensor is fully described by two scalar functions. This reduction simplifies the system to a nonlinear, coupled PDE for the scalars, while preserving essential physical features. A key question is whether the eigenvalues of the Q-tensor remain within the physically admissible range under this flow. Building on a theoretical result …

Ransomware As Organization: A Comparative Analysis Of Corporate And Criminal Structures In Conti, George Urling

Theses, Dissertations and Capstones

Cybercriminal groups continue to pose major threats to global cybersecurity. One of the most common types of cybercriminal groups are, “Ransomware-as-a-Service (RaaS)" groups, who create and sell ransomware. While research is conducted into the development of ransomware, there is limited reporting on the organizational structure and habits of RaaS groups. In 2022, prominent RaaS group Conti had their chat logs leaked, with the logs ranging from 2020 to 2022. This study seeks to provide a deeper understanding of RaaS group structures by utilizing the Conti leaked logs as a case study. The study, entitled “Ransomware as Organization: A Comparative Analysis …

Lifestyle Factors' Effect On Political And Religious Behavior, Madison A. Price

SPARK Symposium Presentations

There is a general understanding of an individuals’ political/religious beliefs when you analyze predictors like support of same sex marriage or views on abortion, but there is not a ton of research on how everyday lifestyle factors might affect how someone aligns themselves politically or religiously. Researchers have begun to expand the horizons of political and religious research by investigating how income, health, and politics affect religion (Francis-Tan & Tian, 2022), but there is a need to expand into more specific lifestyle factors. Which brings reason to question a few things: what lifestyle and demographic factors predict how religious someone …

A Macrocognitive Design Taxonomy For Simulation-Based Training Systems: Bridging Cognitive Theory And Human-Computer Interaction, Jessica M. Johnson

Virginia Digital Maritime Center (VDMC) Faculty Publications

Simulation-based training systems are increasingly deployed to prepare learners for complex, safety-critical, and dynamic work environments. While advances in computing have enabled immersive and data-rich simulations, many systems remain optimized for procedural accuracy and surface-level task performance rather than the macrocognitive processes that underpin adaptive expertise. Macrocognition encompasses higher-order cognitive processes that are essential for performance transfer beyond controlled training conditions. When these processes are insufficiently supported, training systems risk fostering brittle strategies and negative training effects. This paper introduces a macrocognitive design taxonomy for simulation-based training systems derived from a large-scale meta-analysis examining the transfer of macrocognitive skills from …

Hfpo-Da Aquatic Toxicity And Bioaccumulation, Bailey Dawn Rappold

Theses, Dissertations and Capstones

Per- and polyfluoroalkyl substances (PFAS) have been detected globally in environmental media and biota. Legacy compounds PFOA and PFOS have been observed to be toxic and bioaccumulative in low doses and have been removed from production and industrial processes. Replacement PFAS chemicals are less understood and present a gap in current knowledge in their toxicological effects. This research utilized extended chronic toxicity studies to assess the impacts of HFPO-DA, a short chain replacement PFAS, on the standard aquatic toxicology organism Pimephales promelas. Organisms were exposed for 29 to 30 days at environmentally relevant concentrations of the toxicant, 7.8125 ng/L …

Development And Validation Of An Analytical Method For Quantitative Determination Of Small Aldehydes In Plasma, Stephanie T. Clark

Chemistry & Biochemistry Theses - Archive

Small aldehydes such as formaldehyde and acetaldehyde are highly reactive metabolites that play important roles in biological processes related to oxidative stress, metabolism, and DNA damage. Because of their chemical reactivity, volatility, and low endogenous concentrations, accurate measurement of these compounds in biological samples remains analytically challenging. The goal was to develop and evaluate a practical analytical method for detecting small aldehydes in biologically relevant matrices using headspace gas chromatography mass spectrometry (HS-GC-MS). The method combined chemical derivatization with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and headspace sampling to stabilize aldehydes and enable selective detection by mass spectrometry. Method development focused on optimizing derivatization …

A Stable Isotope Comparison Of The Biogenic Carbonate Of Mammalian Tooth Enamel From The Modern Ohio River Valley And Fort Ancient Buffalo Sites, Sara Elizabeth Slack

Theses, Dissertations and Capstones

δ¹⁸O and δ¹³C values change in response to anthropogenic factors (Ghosh & Brand, 2003). Little is known about the effects of anthropogenic climate and land use change on the ecology of the Ohio River Valley. The goal of this research was to quantify the effects of European colonization on the native ecology of the region. The specific questions of this research were: (1) How have mammalian tooth enamel δ¹⁸O and δ¹³C compositions shifted over time within the Ohio River Valley in response to anthropogenic climate change and vegetation? (2) Are there differences …

Towards Multimodal Guideline-Aligned Agentic Systems, Wenliang Zhong

Computer Science and Engineering Dissertations - Archive

I present my work on building multimodal guideline-aligned agentic systems designed to enable AI agents to solve complex real-world tasks. My research addresses two critical perspectives: (1) Instruction-Aware Embedding Models for flexible and universal embedding tasks, and (2) Guideline-Driven LLM Agents that leverage domain-specific guidelines to perform expert-level tasks. These components address embedding and generation tasks, respectively, and lay the foundation for a hybrid agent capable of tackling challenging real-world applications.

From the embedding perspective, I first address the instruction-following capabilities of embedding models. While Large Language Models (LLMs) excel at instruction following, they are primarily designed for generation rather …

Microwave Synthesis And Characterization Of Fe2ptge Nanoparticles, Ally T. Fennell, David Carnevale

Chemistry Theses

Magnetic, semiconductor, and spintronic materials are vital to the functionality of devices from household appliances and sensors to medical and computing systems. This study discusses a novel synthesis and characterization of nanoscale Fe₂PtGe nanoparticles. The material was synthesized using microwave irradiation (175oC, 5 minutes) and characterized using XRD, XRF, TEM, and VSM. XRD of the synthesized particles correlates to a cubic crystal structured, indicating a face-centered cubic (fcc) platinum structure with iron and germanium incorporated in a disordered manner. XRF confirms the presence and relative ratios of iron, platinum, and germanium species. TEM imagery shows spherical nanoparticles with an average …

Characterization Of Heusler Alloys: Co2nisn, Ni2cosn, And Conisn At The Nano And Bulk Level, Paige E. Klos, David Carnevale

Chemistry Theses

This project centered around the synthesis and modification of three materials in the Heusler alloy family CoxNiySn. These compounds consist of the two full Heuslers, Co2NiSn (10.7 nm) and Ni2CoSn (17.4), as well as the half-Heusler counterpart, CoNiSn (14.9 nm). This work also studies the growth of the nanoscale Heusler alloys to the bulk material through annealing at 600°C, which lead to increased crystallinity of Ni2CoSn but phase segregation of the Co2NiSn and CoNiSn. The initial nanoparticles were synthesized utilizing a CEM microwave with temperatures of 175/200°C. Samples were analyzed by X-Ray diffraction (XRD) for their crystallinity, which showed a …

Accelerator Based Fusion Reactor With Magnetic Mirror, Keh-Fei Liu

Physics and Astronomy Faculty Publications

We consider an implementation of the novel accelerator-based fusion reactor scheme using a setup in which ion and electron beams are injected into the end openings of an axisymmetric magnetic mirror. While the magnetic mirror ensures transverse confinement of the plasma, the injected beams contribute to axial confinement, thereby extending the overall plasma lifetime. The ion beam energy is initially set above the resonance region of the fusion reactions, allowing fusion to occur both via resonance and thermal mechanisms as the beam slows down to the plasma temperature. Beam energy loss (stopping power) contributes to plasma heating, offsetting radiative losses …

Dynamical Phases Of Higher Dimensional Floquet Cfts, Diptarka Das, Sumit R. Das, Arnab Kundu, Krishnendu Sengupta

Physics and Astronomy Faculty Publications

This paper investigates the dynamical phases of Floquet Conformal Field Theories (CFTs) in space-time dimensions greater than two. Building upon our previous work which introduced quaternionic representations for studying Floquet dynamics in higher-dimensional CFTs, we now explore more general square pulse drive protocols that go beyond a single SU(1,1) subgroup. We demonstrate that, for multi-step drive protocols, the system exhibits distinct dynamical phases characterized by the nature of the eigenvalues of the quaternionic matrix representing time evolution in a single cycle, leading to different stroboscopic responses. Our analysis establishes a fundamental geometric interpretation where these dynamical phases directly correspond to …

Emission-Line Diagnostics At Z ≳ 2: A Probe Of The Ionizing Spectrum And Α-Enhancement Beyond Cosmic Noon, Leonardo Clarke, Natalie Lam, Alice E. Shapley, Michael W. Topping, Gabriel B. Brammer, Ryan L. Sanders, Naveen Reddy, Shreya Karthikeyan

Physics and Astronomy Faculty Publications

We analyze several key rest-optical emission-line ratios in a sample of 828 galaxies as well as composite spectra from JADES DR3 in the range 1.4 <  z <  7. These emission-line ratios include: [O iii]λ5008/Hβ, [N ii]λ6585/Hα, [S ii]λλ6718, 6733/Hα, [O i]λ6302/Hα, O32, R23, Ne3O2, and RO2Ne3. We find evidence for a harder ionizing spectrum at z ∼ 3.5 compared to z ∼ 2 at fixed gas-phase metallicity, resulting in a pronounced shift in the star-forming galaxy locus on the [N ii]/Hα Baldwin-Phillips-Terlevich (BPT) diagram and the O32 versus R23 diagram. At …

Computational Clinical Judgment: Predicting Risk With Large Language Models, Hannah Laqueur, Ryan W. Copus

Faculty Works

For seventy years, research has shown actuarial methods outperform clinical judgment. Yet actuarial approaches have limitations: they generally rely on structured data; cannot exploit rare case-specific details; have limited accuracy where outcome data are scarce or incomplete; and cannot offer case-level justifications. Large language models (LLMs) offer a different approach. Like actuarial methods, they aggregate information algorithmically, but like clinicians, they bring general knowledge and can provide case-level justifications. We prompted seven LLMs to assess rearrest risk from 113 parole hearing transcripts and compared their predictions to a machine learning model trained on 4,000 cases with 91 administrative variables. GPT-5 …

Part Em: Classical Electrodynamics, Konstantin Likharev

Essential Graduate Physics

Includes: Electric Charge Interaction; Charges and Conductors; Polarization of Dielectrics; DC Currents; Magnetism; Time-Dependent Electromagnetism; Electromagnetic Wave Propagation; Radiation, Scattering, Interference, and Diffraction; Special Relativity; Radiation by Relativistic Charges

Empirical-Based Model Of Spatio-Temporal Errors, Godwin Naaba Ndaa

Masters Theses

This research develops an empirical model to characterize spatial-temporal InSAR errors and improve the accuracy of deformation time-series analysis. Using standardized Sentinel-1 HyP3 products and MintPy, the study quantifies how correlated noise affects velocity precision and validates the results against continuous GNSS velocities.

Residual velocities are near-Gaussian, with σ ~0.92–2.04 cm/yr and ~1 cm/yr on average. Variograms show power-law spatial structure with a non-zero nugget implicating troposphere and decorrelation while errors drop exponentially with more acquisitions; spatial uncertainty is strongly affected by unwrapping errors, coherence, and tropospheric noise, not simply troposphere.

A comparative assessment of on-demand cloud processing with other …