Physical Sciences and Mathematics Commons^™

The Structure And Regulatory Mechanism Of The Emrb Rna Motif In Lactobacillus Acidophilus, Isabella J. Mezzenga, Brian M. Lee

Journal of the South Carolina Academy of Science

Major facilitator superfamily (MFS) transporters aid bacteria in expelling toxic compounds such as antibiotics, bile acids, and other substances. Previous bioinformatic studies identified the emrB motif as a potential regulatory RNA element. In Lactobacillus, this RNA motif is generally found in the intergenic region upstream of an MFS transporter gene with homology to the emrB gene from Escherichia coli. Secondary structure predictions of the intergenic region were used to define the structural features of this RNA motif. The emrB motif comprises two hairpins, though inclusion of neighboring regions is predicted to stabilize alternative secondary structures. A potential rho independent terminator …

Exploring The Dynamics Of Tilted, Truncated Accretion Disks, José L. Montés, Chris Fragile, Deepika Bollimpalli, Matthew Liska

Journal of the South Carolina Academy of Science

Tilted accretion disks are theoretically not uncommon in stellar mass black hole systems. The dynamics of tilted disks display interesting physical behaviors that could explain certain observational phenomena such as quasi-periodic oscillations. We present results of recent numerical simulations of tilted, truncated accretion disks around rotating black holes. Our simulations model systems composed of a thick inner torus surrounded by a thin outer disk and were run with the goal of investigating the behaviors of the torus because of the exchange of angular momentum between it and the outer disk. Multiple simulations produced surprising results, such as the potential tearing …

From Classification To Segmentation: Evaluating Machine Learning Defect Localization And Inspector Performance In Manufacturing, Gavin Smithson, Dakota Fulp, William M. Jones, Sharmistha Chakrabarti

Journal of the South Carolina Academy of Science

High-volume manufacturing at Los Alamos National Laboratory requires rigorous quality assurance; however, sustained manual inspection can be inconsistent, costly, and fatiguing. This paper presents the model-evaluation component of a larger human-in-the-loop artificial intelligence project for manufacturing anomaly detection. MicroSentryAI uses pretrained models to identify potential anomaly regions, while AnnoMate provides accessible tools for annotating, validating, and comparing those regions. The study emphasizes the distinction between classification, which determines whether a sample is anomalous, and segmentation, which identifies the location of an anomaly. Using Intersection over Union (IoU), precision, recall, and Euclidean distance between centroids, experiments with simulated mask errors demonstrated …

Waste Streams From Next Generation Molten Salt Reactors: The Challenge Of Creating An Insoluble Ceramic For Chloride Salt Waste, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Molten salt reactors (MSRs) design development is of interest to many research groups and companies. Waste management for MSRs is one of the most important issues that needs to be resolved due to its impact on environmental safety, primarily via the dissolution of radionuclides in water. Furthermore, the waste treatment strategy will have a significant influence on the operating cost of MSRs, which is why a reliable process for the immobilization, transportation, storage and disposal of MSR waste must be addressed. This work presents a new approach for the immobilization of chloride salts from molten salt reactors in stable oxyhalide …

Crystal Structure Of New Polar Rare Earth Borates Na2.62Ln2.12(Bo3)3 (Ln = Pr, Nd, Sm) Containing Isolated Bo3 Groups, Alevtina A. Maksimova, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

Three new rare earth borates, Na2.62Ln2.12(BO3)3 (Ln = Pr, Nd, Sm), were synthesized via a high-temperature solution reaction using a BaCO3–H3BO3–NaF flux and structurally characterized by single-crystal X-ray diffraction analysis. The compounds crystallize in the orthorhombic space group Amm2 with lattice parameters a = 5.0985(10) Å, b = 11.180(2) Å, c = 7.1483(14) Å, and a unit cell volume of 407.48(14) ų (Z = 2) for Na2.62Pr2.12(BO3)3, a = 5.0983(10) Å, b = 11.181(2) Å, c = 7.1491(14) Å, and a unit cell volume of 407.51(14) ų (Z = 2) for Na2.62Nd2.12(BO3)3, and a = 5.08630(10) Å, b …

Single Crystal Growth Of The Orthoborate Nabalu(Bo3)2 And Optical Investigation Of Eu3+ And Tb3+ Doped Nabalu(Bo3)2, Alevtina A. Maksimova, Mark D. Smith, Lakshani W. Masachchi, Hans Conrad Zur Loye

Faculty Publications

Sodium barium lutetium borate NaBaLu(BO₃)₂ crystals were synthesized using a high-temperature solution method. The crystal structure of this layered orthoborate is described and corresponds to that of an extensive orthoborates family, NaBaR(BO₃)₂ (R = Sc, Y, Yb, Tb – Lu). NaBaLu(BO₃)₂ was doped by Eu³⁺ and Tb³⁺ to explore its performance as a host material and to investigate the luminescent properties of the Eu³⁺ and Tb³⁺ doped materials. The emission spectra of the NaBaLu(BO₃)₂:Ln (Ln = Eu, Tb) crystals are presented. The most …

Eeg P300 Ai Classification And Accessibility Keyboard Control Using Openbci’S Ultracortex Mark Iv For Reactive Brain-Computer Interaction, Grant King

Theses and Dissertations

Brain-computer interfaces provide people who cannot feasibly control a keyboard and mouse with an alternative method to type, to move a cursor, or to generally issue commands and make selections. A non-invasive recording modality for brain-computer interfaces is electroencephalography, or EEG. The OpenBCI Ultracortex Mark IV is an EEG headset enabling relatively low-cost EEG acquisition using wet or dry electrodes. P300 is an event-related potential involving a deflection in an EEG channel's voltage typically 300 milliseconds after the onset of an "oddball" stimulus. A person's P300 response can be used to control a selector application. This study investigates classification of …

Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Brian C. Benicewicz, Huina Lin

Faculty Publications

Proton exchange membrane (PEM) fuel cells are promising for clean and efficient energy conversion across diverse applications. High-temperature PEM fuel cells (HT-PEMFCs) using phosphoric acid (PA)-doped polybenzimidazole (PBI) can operate up to 200°C, but at lower temperatures, water-induced PA loss often leads to performance degradation and reduced durability. In this work, we present a new class of main-chain ion-pair PBI membranes by integrating the imidazolium-biphosphate ion-pair units directly into the PBI backbone. This design results in membranes with high acid content, stronger acid-polymer interactions and stabilized acid retention. In single-cell tests, the Im+-PBI15-3 wt.% exhibits peak power densities of 0.79 …

Saag: Structured Agent Assessment And Grounding, Ritvik Garimella, Vedant Khandelwal, Anvi Kohli, Amit Sheth

Publications

Exact-match evaluation of agent-calling obscures qualitatively different failure modes: a model may select the right function yet hallucinate argument values, or satisfy a schema while choosing a agent for the wrong reason. Existing benchmarks collapse these distinctions into a single binary score, leaving practitioners unable to diagnose where agent calls fail. We propose SAAG a cascaded diagnostic framework that decomposes agent-calling evaluation into three sequential stages: registry conformance, structural completeness, and argument grounding, each producing interpretable stage-specific diagnostics. These diagnostics additionally enable iterative self-repair: on prediction failure, the stage-specific signal guides targeted correction without leaking ground-truth values. We evaluate this …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Towards Improving The Performance Of The Adcirc Storm Surge Modeling Software, Nick Weldner, Tim Stitt, Jijun Tang

Caravel Undergraduate Research Journal

Accurately predicting storms and hurricanes is critical to saving lives and reducing economic loss. Therefore, it is necessary to use the most efficient software and hardware technology available in order to improve the performance and fidelity of these predictive mathematical models. For over ten years, the Computational Hydraulics Lab (CHL) at the University of Notre Dame has been involved in developing the high-resolution ADvanced CIRCulation (ADCIRC) storm surge model to predict storm surges in coastal areas. The objective of the work reported here was to port a novel adaption of the parallel ADCIRC code to the state-of-the-art Intel Xeon Phi …

Sustaining The Land Of Ice And Fire, Chandler Green

Caravel Undergraduate Research Journal

No abstract provided.

Proofs Of A Trigonometric Inequality, Cameron Butler, Wei-Kai Lai

Caravel Undergraduate Research Journal

A trigonometric inequality is introduced and proved using Hölder’s inequality, Cauchy-Schwarz inequality, and Chebyshev’s order inequality.

Characterizing The Unique Chemical Imprint Of On-Axis, Lower-Temperature Hydrothermal Flow To The Deep Ocean (Southern East Pacific Rise, 16.5°–18.0°S), Laura E. Moore, Randelle M. Bundy, Joseph A. Resing, Scott M. White, Tamara Baumberger, Peter N. Sedwick, Nathaniel J. Buck, Anson M. Antriasian, Isaac Keohane

Faculty Publications

In addition to high-temperature vents, lower-temperature flow (LTF) (< 300°C) is abundant along mid-ocean ridges and contributes globally-important fluxes of heat and water along with largely-unconstrained geochemical influences on the ocean. We examined the impact of on-axis LTF on the chemical composition of the overlying water column (< 40 m above seafloor) along the 16.5°–18.0°S sector of the ultrafast-spreading southern East Pacific Rise using autonomous underwater vehicle Sentry surveys and conductivity-temperature-depth rosette casts. LTF sites were typically spatially isolated from high-temperature systems and imparted unique chemical signatures to the overlying ocean. Water column samples impacted by LTF exhibited low particulate iron:sulfur ratios and high methane: total-dissolvable manganese ratios, whereas samples influenced by high-temperature venting exhibited opposite trends. We confirmed that LTF imparts a distinct and measurable chemical signature to the water column, independent from high-temperature vents. Isolated, on-axis LTF will be important to consider when assessing hydrothermal circulation impacts upon ocean biogeochemistry.

Understanding The Binding Of Nickel(Ii) Bromide To A Zirconium Metal-Organic Cage For Heterogeneous Catalysis, Luci Green

Caroliniana Undergraduate Research Journal

Heterogeneous catalysts offer inherent advantages in improving the sustainability of industrial chemical processes. Their high ease of separation and recyclability has the potential to reduce the cost, waste, and energy consumption of processes that currently rely on homogeneous catalysts. Metal–organic cages (MOCs) are an attractive material for heterogeneous catalysis due to their discrete and highly tunable structures, which can be functionalized by binding these complexes with catalytically active metals. The specific objective of this study is to provide preliminary insight into the binding of nickel(II) bromide (NiBr₂) to zirconium MOCs, which was done by studying the binding of …

Psychosocial Mediators Of A Physical Activity And Dietary Intervention In Pregnant Women With Overweight Or Obesity, Meghan Baruth, Sarah Wilcox, Jihong Liu, Rebecca Schlaff

Faculty Publications

Background

Mediation analyses provide insight into both ‘pieces’ of the mediation chain; they allow us to look into the ‘black box’ that is behavior change. They allow researchers to better understand the ‘how’ of an intervention’s effects and/or the ‘why’ behind why an intervention worked or did not work. The lack of publications in pregnant populations highlights the need for additional studies to be conducted and published. The purpose of this study is to examine the psychosocial mediators of physical activity and dietary outcomes in a sample of pregnant women with overweight or obesity participating in the Health in Pregnancy …

Bgc-Argo Float Reveals Shifts In Nitrogen-Carbon Cycling In An Oxygen-Deficient Zone, Mariana B. Bif, Colette Kelly, Mark A. Altabet, Annie Bourbonnais, Claire Elbon, Edgart Flores, Alanna Mnich, Josh Plant, Kenneth S. Johnson

Faculty Publications

Oxygen-deficient zones are hotspots of marine fixed nitrogen loss, but the temporal dynamics of their microbial processes remain poorly resolved. Here we present a nearly three-year high-resolution record from a Biogeochemical Argo float in the Eastern Tropical North Pacific that captures a decline in nitrite concentrations, reflecting a shift in nitrogen redox balance. Using a stoichiometric mass-balance model, we quantify nitrogen transformations, including dissimilatory nitrate reduction to nitrite, denitrification, anammox, and nitrite oxidation, and their coupling to carbonate chemistry. The model shows that dissimilatory nitrate reduction to nitrite dominates nitrogen transformations, while denitrification and anammox vary over depth, biogeochemical transition, …

A Guide To Environmentally Sustainable Filmmaking In South Carolina, Christina Vera Dobrowolski

Senior Theses

The entertainment industry has a massive environmental impact. This information is not new in the filmmaking world, as multiple mainstream efforts exist to curb the material-intensive production of live action films and TV. One of these efforts is the use of voluntary sustainable guidelines, which serve as tools that outline sustainable best practices and resources that can help achieve them. However, current guidelines often lack practicality— focusing more on altruism rather than core economic factors that ultimately drive filmmaking. This project aims to address that gap for filmmakers in South Carolina by offering a website featuring attainable, state-specific resources for …

Synthesis Of Copper-Phenanthroline Complexes: A Solvothermal-Compatible Approach For The Exploration Of Metal Complexes, Yunping Zhoujin, Michael Anim Safo, Navindra Keerthisinghe, Mark D. Smith, Sophya Garashchuk, Hans Conrad Zur Loye

Faculty Publications

Inorganic–organic hybrid materials have been widely investigated for their applications in catalysis, optics, magnetism, and biomedicine. Copper halide complexes are of particular interest due to their structural diversity and physicochemical properties. Conventional crystal growth approaches, such as slow evaporation and hydro(solvo)thermal synthesis, typically require extended reaction times and often favor thermodynamically stable phases. In this study, we prepared ten copper-phenanthroline halide (X = Cl, Br, and I) complexes using both traditional hydrothermal reactions and microwave-assisted hydrothermal methods and obtained [CuI(C₁₂H₈N₂)₂][I₃], [C₁₂H₉N₂][CuI₂]·(H_{2 …}

Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex

Senior Theses

Programming DNA-binding proteins is an effective strategy for developing therapeutics that regulate gene expression. These proteins can directly bind to DNA to activate or repress transcription of specific genes. Zinc finger proteins are a class of DNA-binding proteins commonly found in eukaryotic organisms. Their DNA-binding function is derived from unique amino acid sequences within each domain that recognizes specific nucleotides, allowing each finger to selectively recognize three DNA base pairs. Adjoining of multiple domains in tandem allows recognition of a specific DNA sequence. Artificial transcription factors can be made of multiple zinc finger domains arranged in tandem and engineered to …

Designing Surface-Induced Entatic States In Copper Complexes For Tunable Reactivity, Rachel Kiser

Senior Theses

Copper catalysts play an important role in electrocatalytic oxidation reactions due to their redox flexibility and relative abundance compared to noble metal catalysts. In biological systems, copper metalloenzymes often achieve enhanced reactivity through an entatic state. Entasis is described as an active site or metal center being constrained to a geometric and electronic state, minimizing primary sphere reorganization energy and achieving higher rates of electron transfer.  This study investigates whether entasis can be achieved in synthetic molecular catalysts by immobilizing Cu(I) complexes onto metal oxide surfaces. Two Cu(I) complexes bearing carboxylate-functionalized ligands were examined both in homogeneous solution and when …

Searching For Temporal Variations In The Fine-Structure Constant Using Espresso Spectrograph Data, David Hoffman Iv

Senior Theses

The fine-structure constant α is a dimensionless constant, defined as e²/(4πε₀ℏc) ≈ 1/137. On the order of human timescales, its value is very much unchanging, however, in recent years there has been extensive debate over whether or not the value of α has remained constant over cosmological timescales. With the natural corollary to a changing α being that either one or multiple of its constituent physical constants have also changed in value, observing a variation in the fine-structure constant would have vast ramifications for our understanding of the nature of the early universe and how it has evolved. While past …

Factors Associated With Lapses In Care Among People Living With Hiv In South Carolina, Xueying Yang Ph.D., Fanghui Shi, Shujie Chen, Gavi Samuel, Bankole Olatosi Ph.D., Sharon Weissman, Xiaoming Li Ph.D., Jiajia Zhang Ph.D.

Faculty Publications

Utilizing statewide electronic health records (EHR) data, this study aims to assess the factors determining the occurrence of lapses in HIV care among people with HIV (PWH) in South Carolina (SC). All adult (≥ 18 years old) PWH who were diagnosed with HIV between 2006 and 2018 with at least two HIV care encounters and at least 1-year follow-up record were included in the analysis. The outcome, a lapse in care, was defined as a repeated measure of HIV care encounter that occurs over a year following the previous visit. Generalized Estimation Equation models were employed. The study cohort had …

Inferring The Breakdown Scales Of The Chiral Expansions For GA And MN, Andreas Ekström, Daniel R. Phillips, Lucas Platter, Matthias Schindler

Faculty Publications

We apply Bayesian inference to the order-by-order chiral perturbation theory (χPT) expansions for the axial-vector coupling constant g_A and the nucleon mass m_N, and thereby infer the scales at which χPT breaks down for these two observables. Using a pointwise Bayesian analysis, we find that the inferred breakdown scales are notably different for the two observables. For the chiral expansion of g_A, we obtain 251⁺²⁰₋₅₀ MeV and 211⁺²⁰₋₃₀ MeV using two distinct sets of low-energy constants, while for the chiral expansion of m_N we infer a significantly …

Implementation And Costs Of A Food Insecurity Resource Navigation Program For Primary Care Patients With Diabetes And Hypertension In South Carolina, Deeksha Gupta, Darin Thomas, Stella Coker Watson Self Ph.D., Ms, Edward A. Frongillo Jr. Ph.D., Alain H. Litwin, Joseph A. Ewing, Lynnette Ramos-Gonzalez, Lynnette Ramos-Gonzalez

Faculty Publications

Objective

To examine food insecurity resource navigation program costs and how navigation intensity relates to clinical outcomes, healthcare costs, and quality of life (QOL) for diabetes and/or hypertension patients.

Methods

This retrospective study included patients receiving resource navigation (July 12, 2021-December 31, 2022 with twelve-month follow-up) across three primary care practices in South Carolina's largest health system. Participants were 18+ years old (from electronic medical records/Epic), had food insecurity (from Hunger Vital Sign™), and diabetes and/or hypertension (from Epic registries). Matched controls came from food insecurity screening-only practices. Patients in each group (n= 219) had diabetes (9.13%), hypertension …

The Eye: A Science-Fiction Screenplay Examining Space-Time, Meteorology, And Human Connection, Ella K. Lukowiak

Senior Theses

This thesis explores the nature of time, meteorology, and human interconnection to the universe through the lens of a science-fiction screenplay. The creative project spans a three-act, detailed outline, and a screenplay draft of Act I. It is based upon extensive scientific research regarding hurricane development, the inner workings of organizations such as the National Weather Service, Einstein’s Theory of Relativity, and the space-time continuum. I will delve into the various factors that shaped my science-fiction premise, including pivotal films such as Christopher Nolan’s INTERSTELLAR (2014) and Denis Villeneuve’s ARRIVAL (2016). Both of these filmmakers integrated complex science-fiction concepts into …

Data Tracking And Analytics Within Inventory Management: Coffee Shop And Retail Store Optimization, Mateo J. Moyon

Senior Theses

This thesis examines the application of inventory management theory in the small and medium-sized business context, with a specific focus on the food and beverage industry. Drawing on the foundational academic literature spanning from Harris’s EOQ formula in 1913 through stochastic inventory theory, ABC analysis, and just-in-time strategy, this paper establishes the mathematical and operational bases for modern inventory management practice. Although there are proven value to these frameworks, research demonstrates that small to medium sized businesses adopt inventory management systems at lower rates citing cost and implementation as barriers. This thesis argues that the emergence of low-cost inventory and …

The Effects Of Climate Change On Competition And Recovery From Disturbance In An Iconic Marine Community, Lauren Tibbits

Senior Theses

This paper explores how the recovery of populations of Semibalanus balanoides is affected by climate variation. In intertidal marine ecosystems, larval recruitment is important in shaping all ecological processes. S. balanoides is a cold-water barnacle species that is competitively dominant over Chthamalus montagui and C. stellatus, two warm-water species. This competitive interaction is well studied, though it is not understood how that competition influences the recovery of S. balanoides after a disturbance nor how this process varies over a temperature gradient. 19 sites were studied across the United Kingdom, spanning from northern Scotland to southwestern England. At each site, a …

Conservation Communication In Web 2.0: A Mixed Methods Analysis Of Alveus Sanctuary's Strategies On Twitch.Tv, Hope Denison

Senior Theses

This thesis examines how environmental creators can effectively transmit conservation messages in the evolving Web 2.0 media environment. The case of Alveus Sanctuary, a virtual sanctuary and education center on Twitch.TV, is used to explore the strategies currently used to engage audiences and raise ecological awareness online. Thematic analysis of interviews with the sanctuary’s founder revealed that Alveus combines traditional environmental education with an influencer business model to engage online audiences, leveraging parasocial behavior, interactivity, and collaboration to garner support. A quantitative content analysis of social media posts revealed that these strategies effectively induce parasocial engagement in online spaces. These …

Crystallization And Utility Of Brominated Phenylethynylene Bis-Urea Macrocycles, Paras Srivastava

Senior Theses

Macrocycles are large, cyclic molecules with central cavities that can encapsulate other molecules and that have uses in supramolecular chemistry. The Shimizu group has previously synthesized Macrocycle 1, a phenylethynylene bis-urea macrocycle that crystallizes in a columnar form, enabling its utility as a host in host-guest systems. Reactions within these systems can be used to modify stereospecificity, kinetics, and other physical properties. Previously, photodimerization reactions between coumarins and chromones have been studied in systems of Macrocycle 1, resulting in the improved specificity of photodimerization products. Herein, we apply a dynamic covalent chemistry (DCC) strategy to synthesize Macrocycle 1 and its …