Physical Sciences and Mathematics Commons^™

Balancing Functional Tradeoffs Between Protein Stability And Ace2 Binding In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic And Energetic Changes, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and …

Optimizing Photosystem I And Plastocyanin Isolation To Develop A Photosystem I-Catalyst System For Photochemical Hydrogen Production, Angelina Vuong

Honors Program Theses and Projects

Over the course of many years, greenhouse gases such as carbon dioxide (CO2) and methane (CH4) have formed in large amounts in the atmosphere, which has contributed to global warming. Global warming can lead to extreme weather conditions or have an impact on living organisms, for example, wildfires, droughts, limited amount of food sources, and respiratory issues from pollution. This is mainly due to the use of burning fossil fuel as an energy source, which emits greenhouse gases into the air and traps heat into the atmosphere. Thus, the aim of this study is to assemble and characterize a system …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

An Investigation Into The Use Of Ionic Liquid Solvents As Potential Therapeutic Agents To Help Alleviate Disease Caused By The Formation Of Insoluble Plaque Or Depositions, Sundus Alchaar

Honors Program Theses and Projects

Many diseases are caused or worsened by the formation of insoluble aggregates inside the human body, most of which are currently treated by maintenance medication or surgery. Biocompatible Ionic Liquids (ILs) have been explored for use as therapeutic agents, and are also excellent solvents, due to their versatile physical and chemical properties. The aim of this project was to conduct a preliminary exploration of the use of ILs to dissolve different types of depositions, such as kidney stones and crystal-induced arthropathies, and plaques. An imidazolium-based IL and four biocompatible choline amino acid-based ILs ([Ch][AA]-ILs) were synthesized, which are 1-methyl-3-butyl-methylimidazolium iodide …

Halide Exchange And Transport In Halide Perovskite Lattices, Temban Acha Billy

Department of Chemistry: Dissertations, Theses, and Student Research

In recent years, metal-halide perovskites (MHPs) have risen quickly to prominence as promising materials across a variety of fields, from photovoltaics to optoelectronics in general. We show here a facile solution growth for creating a variety of mixed halide MAPbBr_3-xI_x crystals, which we will use to study halide exchange and transport in halide perovskites. We generated a calibration curve between the optical response and chemical composition in mixed Br/I MHPs at room temperature. All mixed Br/I MHP crystals were subjected to measurements of photoluminescence (PL) and Raman spectroscopy. A subset of mixed-halide MHP crystals exhibited multiple emission …

Partial Coalescence Of Cdse/Cds Core/Shell Nanocrystals, Jordyn Wray

Honors Program Theses and Research Projects

Quantum dots are semiconductor nanocrystals that are a few nanometers in size that have different optical and electrical properties depending on size and shape. Some applications that quantum dots are used for, include, lasers, quantum computing, and solar cells. The goal of the research was to fuse cadmium selenide, cadmium sulfide (CdSe/CdS) core shells into dimers to increase the communication between particles in these applications. The CdSe were synthesized to 3 nm cores. Various procedures were used for CdSe/CdS synthesis, but the best performing sample contained 5 nm particles in diameter and a promising size for fusion. A metal salt …

Small Community Water Systems Have The Highest Prevalence Of Mn In Drinking Water In California, Usa, Miranda Aiken, Samantha C. Ying

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Manganese (Mn) is currently regulated as a secondary contaminant in California, USA; however, recent revisions of the World Health Organization drinking water guidelines have increased regulatory attention of Mn in drinking water due to increasing reports of neurotoxic effects in infants and children. In this study, Mn concentrations reported to California’s Safe Drinking Water Information System were used to estimate the potentially exposed population within California based on system size. We estimate that between 2011 and 2021, over 525,000 users in areas with reported Mn data are potentially exposed to Mn concentrations exceeding the WHO health-based guideline (80 μg L …

Structure-Guided Mutagenesis Reveals The Catalytic Residue That Controls The Regiospecificity Of C6-Indole Prenyltransferases, Ahmed R. Aoun, Nagaraju Mupparapu, Diem N. Nguyen, Tae Ho Kim, Christopher M. Nguyen, Zhengfeiyue Pan, Sherif I. Elshahawi

Pharmacy Faculty Articles and Research

Indole is a significant structural moiety and functionalization of the C−H bond in indole-containing molecules expands their chemical space, and modifies their properties and/or activities. Indole prenyltransferases (IPTs) catalyze the direct regiospecific installation of prenyl moieties on indole-derived compounds. IPTs have shown relaxed substrate flexibility enabling them to be used as tools for indole functionalization. However, the mechanism by which certain IPTs target a specific carbon position is not fully understood. Herein, we use structure-guided site-directed mutagenesis, in vitro enzymatic reactions, kinetics and structural-elucidation of analogs to verify the key catalytic residues that control the regiospecificity of all characterized regiospecific …

Microwave Regeneration And Thermal And Oxidative Stability Of Imidazolium Cyanopyrrolide Ionic Liquid For Direct Air Capture Of Carbon Dioxide, Yun-Yang Lee, Eda Cagli, Aidan Klemm, Ruth Dikki

Faculty Scholarship

Understanding the oxidative and thermal degradation of CO2 sorbents is essential for assessing long-term sorbent stability in direct air capture (DAC). The potential degradation pathway of imidazolium cyanopyrrolide, an ionic liquid (IL) functionalized for superior CO2 capacity and selectivity, is evaluated under accelerated degradation conditions to elucidate the secondary reactions that can occur during repetitive absorption-desorption thermal-swing cycles. The combined analysis from various spectroscopic, chromatographic, and thermal gravimetric measurements indicated that radical and SN2 mechanisms in degradation are encouraged by the nucleophilicity of the anion. Thickening of the liquid and gas evolution are accompanied by 50 % reduction in CO2 …

Synthesis Of A Pharmaceutical Precursor From Bioderived Glucose, Justin O. P. Waters

Electronic Theses and Dissertations

Medication costs in the U.S. are high, and manufacturing and production comprise the largest share of those costs. As the world continues to shift to more sustainable methods of production, there are opportunities to reduce these costs through green synthesis. A large number of pharmaceuticals are derived from a precursor (S-3-hydroxy-gamma-butyrolactone ‘HBL’). Drugs that treat cancer, antivirals, antibacterial drugs, and some cholesterol medications all can be derived from HBL. Currently, HBL is almost exclusively derived from petroleum through an expensive and resource intensive process. Until recently, ‘green’ efforts to derive HBL from biomass have been plagued with many of the …

Isolating The Electronic Effects Of Systematic Twist In Highly Substituted Aromatic Hydrocarbons Using Density Functional Theory, Grace Tully, Emily A. Jarvis

Honors Thesis

Density functional theory (DFT) was employed to investigate dodecaphenyltetracene as well as similar molecules containing differing backbone lengths and electron withdrawing groups with interest in manipulating the twist to lower the LUMO level for increased electron mobility. Optimization and frequency time-independent calculations followed by time-dependent (TD-DFT) energy calculations were performed at the B3LYP/G-311G level of theory to analyze electronic trends as a result of increased backbone length and consequently distorted end-to-end molecular twist. These calculations demonstrate a linear relationship with negative slope between the estimated HOMO-LUMO, fundamental, and optical gaps as a function of the number of fused rings along …

Effects Of Fibril Morphology And Interfacial Interactions On The Behavior Of Polymer-Grafted Cellulose Nanofibril Reinforced Thermoplastic Composites, Peter V. Kelly

Electronic Theses and Dissertations

Mechanically refined cellulose nanofibrils (CNFs) promise to be a high-volume, sustainable, nanoscale reinforcement for thermoplastic composites. They are currently held back by poor interfacial interactions with composite matrices, energy intensive drying, and drying induced fibril aggregation. In this dissertation, we explored how a grafting-through polymerization scheme modified the surface of CNFs with a wide variety of commodity polymers and overcame many of these technical challenges.

The first phase of the research was concerned with characterizing the unique morphology of these CNFs as a function of refinement energy. This characterization was employed to understand how the materials’ morphologies affected their interfacial …

Quantum Mechanical Studies Of Water Splitting Reaction With (Zno)3 Nanoclusters As Catalysts, Duwage C. Perera

Electronic Theses and Dissertations

With the current energy crisis, H₂ production through the water-splitting reaction has drawn attention recently. In this thesis, I studied the structural (geometry) and electronic properties (vertical detachment energy and electron affinity) of ZnO monomers and dimers using density functional theory. ZnO is a metal oxide with a 3.37 eV band gap and can be a commercially cheaper photocatalyst in hydrogen (H₂) production. The B3LYP/DGDZVP2 pair was selected after investigating different pairs of exchange functionals and basis sets to study the hydration, hydrolysis, and water-splitting reaction. The singlet-triplet energy gaps of small (ZnO)_n clusters (n=1-6) of …

Influence Of Platinum Nanoparticles On Ionic Transport And Hydrogen Reactivity Of Yttria-Stabilized Zirconia Thin Films, Firas Mahyob

Electronic Theses and Dissertations

Yttria-stabilized zirconia (YSZ) is a widely used ceramic material in solid oxide fuel cells, oxygen sensors, and sensing applications due to its high ionic conductivity, chemical inertness, and thermal stability. YSZ is promising active coating for use in miniaturized harsh environment wireless surface acoustic sensors to monitor gases such as H₂. Adding catalytic Pt nanoparticles can enhance gas reactivity and lead to associated film conductivity changes.

In this work, thin films with an (8% Y₂O₃ - 92% ZrO₂) composition were deposited onto piezoelectric langasite substrates using RF magnetron sputtering in Ar:O₂ - …

Improvements To Isru For Rocket Fuel Generation, Justin Sharp

James Madison Undergraduate Research Journal (JMURJ)

The development of efficient in-situ resource utilization (ISRU) technologies is crucial for the establishment of an extraterrestrial, self-sustaining colony. The generation of rocket fuel at potential colony locations is necessary to provide the transportation of people and cargo to and from these locations.Three processes are discussed for the improvement of ISRU methods to generate rocket fuel: electrolysis and electrochemical improvements to the process of crude fuel production, physical and chemical methods for separation of gaseous H2 and O2, and materials and cryogenics engineering for storage and transportation of liquid hydrogen (LH2) and liquid oxygen (LOX). Storage and transportation of cryogenics …

Biosynthesis Of Copper Nanoparticles Using Hylocereus Costaricensis Peel Extract And Their Photocatalytic Properties, Suriati Eka Putri, Netti Herawati, Ahmad Fudhail, Diana Eka Pratiwi, Sumiati Side, Abd Rahman, Susilo Sudarman Desa, Nur Ahmad, Subaer Junaedi, A. Surleva

Karbala International Journal of Modern Science

A green chemistry method was used for the first time to synthesize copper nanoparticles (Cu-NPs) using CuSO4 as a precursor and red dragon fruit (Hylocereus costaricensis) peel wasted extract as a bio-reductor. Cu-NPs produced were then used as a photocatalysts for acid orange 7 (AO7) dyes degradation. The results showed that the smallest average crystallite size of the products ranged from 8.84 - 8.86 nm, and the FCC crystal structure had a surface area of 244.38-278.85 m2g-1. Furthermore, the optimum degradation of AO7 dye occurred at a ratio of 1:3 with a percentage of 81.07% for four cycles. These findings …

Assessing The Possibility And Properties Of Types I And Ii Chalcogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Type I and II halogen bonds are well-recognized motifs that commonly occur within crystals. Quantum calculations are applied to examine whether such geometries might occur in their closely related chalcogen bond cousins. Homodimers are constructed of the R1R2C=Y and R1R2Y monomers, wherein Y represents a chalcogen atom, S, Se, or Te; R1 and R2 refer to either H or F. A Type II (T2) geometry wherein the lone pair of one Y is closely aligned with a σ-hole of its partner represents a stable arrangement for all except YH2, although not all such structures are true minima. The symmetric T1 …

Photodynamic Therapy Agents: The Power Of Mjöllnir To Eradicate Cancer, Sidney M. Hopper

Honors College Theses

After its discovery back in the 1900s, photosensitizers became a critical study for potential treatments and cures for medical issues, including cancer. It was discovered that porphyrins appeared to target and accumulate in proliferating cells, and to reach the cells, a certain wavelength of light with maximum absorbance associated with the porphyrin was necessary to achieve cell death. Photodynamic therapy involves making use of porphyrins or metalloporphyrins as activators when exposed to such light. When activated, these compounds generate reactive oxygen species (ROS), such as HO- or O2-, which can react with nucleic acids found in DNA and RNA. In …

Studying Competing Reaction Pathways In Methanol Decomposition On Platinum Catalysts Under Ultra-High Vacuum (Uhv) Conditions Using Tpd And Sfg Spectroscopy, Quy Loi, Kevin Alvorado Jimenez, Sarah Lelea, Lauren Villegas, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Catalysts are important in manufacturing processes, as they make them more efficient and useful. To develop better catalysts, we need to know how they work by studying how methanol breaks down on platinum. TPD and TD-SFG spectroscopy are used to study by providing the vibrational spectra of methanol on the platinum surface as temperature changes.

Hollow Mn3o4 Nanoparticles For Catalytic Oxidation Of Alkenes In Air, Nathan R. Loutsch

Honors Thesis

Oxidized hydrocarbons (epoxides, alcohols, carboxylic acids, ketones, and aldehydes) have many uses including fuel production, pollution treatment, and chemical synthesis. These compounds can be formed by oxidizing alkenes and alkanes with the assistance of a catalyst. Heterogeneous catalysts have greater recyclability, but traditionally have lower activity and selectivity. Due to the increased relative surface area, nanomaterials can overcome some of the physical limitations. The Hoefelmeyer lab developed a new nanomaterial: hollow Mn3O4 nanoparticles. Sensitive synthetic conditions have been optimized. Due to the increased relative number of edge and corner atoms, the reactive properties of most small nanomaterials increase. Because of …

Crystal Chemistry, Optic And Magnetic Characterizations Of A New Copper Based Material Templated By Hexahydrodiazepine, Mansoura Bourwina, Rawia Msalmi, Sandra Walha, Mark M. Turnbull, Thierry Roisnel, Ahlem Guesmi, Ammar Houas, Naoufel Ben Hamadi, Houcine Naïli

Chemistry

Crystals of the new organic-inorganic material (DAP-H2)[CuBr₄] (1); (DAP = hexahydrodiazepine (C₅H₁₄N₂)) were successfully synthesized by slow evaporation and characterized by single-crystal X-ray diffraction, infrared spectroscopy, thermal analysis, UV-Vis-NIR diffuse reflectance spectroscopy, and magnetic measurements. X-ray investigation demonstrates that 1 crystallizes in the monoclinic space group C2/c. The supramolecular crystal structure of 1 is guided by several types of hydrogen bonding which connect anions and cations together into a three-dimensional network. The optical band gap was determined by diffuse reflectance spectroscopy to be 1.78 eV for a direct allowed transition, implying that …

Utilization Of Cellulose Symbiotic Culture Of Bacteria And Yeast (Scoby) With Sweet Tea Media As Methylene Blue And Brilliant Green Biosorbent Material, Leonard Mateus Sigiro, Ahmad Maksum, Donanta Dhaneswara

Journal of Materials Exploration and Findings

The cellulose from Symbiotic Culture of Bacteria and Yeast (SCOBY) can be used as a biosorbent for dye adsorption, such as Methylene Blue and Brilliant Green. This study used sweet tea with a 6% of sugar concentration and 14 days of fermentation time to synthesize biosorbent material from SCOBY. The results from this synthesis are then characterized using FTIR, SEM, and BET. From the result of characterization, it was found that SCOBY has pores formed from cellulose. The results of the average pore size are 1.5976nm with a pore volume of 0.229cc/g, while the specific surface area is 143.244m2/g. The …

Enhancing Compatibility And Mechanical Properties Of Natural Rubber Composites, Krisma Yessi Sianturi, Adam Febriyanto Nugraha, Belle Kristaura, Mochamad Chalid

Journal of Materials Exploration and Findings

Pure natural rubber (NR) exhibits low mechanical properties, necessitating the incorporation of additives like vulcanizing agents and fillers. Carbon black and silica, conventional fillers, are relatively expensive and not environmentally friendly. This study explores using Oil Palm Empty Fruit Bunch (OPEFB) fiber as an affordable, abundant, and biodegradable alternative filler for NR. However, compatibility issues arise between the nonpolar NR and the polar OPEFB fiber. A latex-starch hybrid coupling agent (CA (NR-St)) was added to the composite formulation to address this. NR, OPEFB fiber, and the coupling agent were mixed using an open roll mill with a 10 phr OPEFB …

Synthesizing, Purifying, And Characterizing Molten Chloride Salts, Phillip W. Halstenberg

Doctoral Dissertations

Molten chloride salts have vast potential as heat transfer fluids with both nuclear and concentrated solar power applications. For application in energy systems, the characteristics that govern these systems must be well understood. This work focuses on inorganic molten chloride salts with a special emphasis on the experimental aspect of chemical research. Chapter 2 covers the synthetic approaches for the formation of molten chloride mixtures. Many salts can be purchased from industrial suppliers, but most must be purified therefore, Chapter 3 evaluates various methodology developed for removal of impurities in salt mixtures. Once the salt of proper content and purity …

Mechanochemical Synthesis Of Task-Specific Conjugated Porous Networks Towards Enhanced Energy Storage, Juntian Fan

Doctoral Dissertations

Conjugated scaffolds with high electronic conductivity, high surface area, etc. are promising materials for diverse technological applications, especially in the electrochemical field. However, the current synthesis methods are still limited to the traditional solution-based method or the ionothermal method, which always require an inert atmosphere shield, large amounts of organic solvents, noble catalysts, long reaction time up to days, and high temperatures, etc. Therefore, there is a common goal of developing conjugated scaffolds through facile, green, straightforward pathways. Mechanochemistry, which is an efficient, sustainable, solvent-free methodology, could provide a unique reaction environment to synthesize this kind of functionalized materials, resulting …

Utilizing Ultra-Performance Chromatography High-Resolution Mass Spectrometry To Investigate Fatty Acid Mediated Antibiotic Tolerance, Brittni Woodall

Doctoral Dissertations

The lipid membrane is the first component necessary to sustain life. To maintain homeostasis, segregate cellular machinery, provide protection from the environment, and reproduce, an organism must establish a boundary in which the processes can occur. Throughout the last two decades, research has propelled our knowledge of lipid membranes much beyond original hypotheses. Once thought of to be static and uniform, the understanding of the lipid membrane has evolved to encompass a structure that is responsive, unique, and intricately constructed by the organism itself. By chance or by choice, organisms adapt the lipid membrane according to the environment for which …

Different Approaches To Overcome Antibiotic Resistance, Samantha Biaesch

Chemistry

In the recent years, there has been a growing demand for the development of antibiotic treatments as bacterial infections have acquired defense mechanisms to commonly used antibiotics, such as penicillin. During the growth of bacterial cells, resistant mutants are able to survive antibiotic treatment and continue proliferation. Thus, creating a resistant bacterial cell population that can no longer be targeted through antibiotic treatment. Due to the recent need of new approaches, there has been an explosion of research in developing techniques that combat bacterial resistance. Both bacteriophage-RNA aptamer binding and modifications in bacterial tRNA show potential to be exploited for …

College Of Natural Sciences Newsletter, March - May 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 2

Page 1 Dean's Message
Page 2-7 Awards and Recognition
Page 8 March 3rd Corothers Seminar
Page 9 54th Geography Convention
Page 10 Spring 2023 Day of Scholars
Page 11 2023 URSCAD Snaps
Page 12-14 Media Coverage of CNS
Page 15 Open PRAIRIE Data

Developing And Applying Computational Methods On Biomolecules, Shengjie Sun

Open Access Theses & Dissertations

Computational biophysics is an interdisciplinary subject that uses numerical algorithms to study the physical principles underlying biological phenomena and processes. Electrostatic interactions play an important role in computational molecular biophysics and their potential impact on disease mechanisms. At distances larger than several Angstroms, electrostatic interactions dominate all other forces, while the alteration of short-range electrostatic pairwise interactions can also have significant effects. The dual nature of electrostatic interactions, being dominant at long-range and specific at short-range, underscores their profound implications for wild-type structure and function. Any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could …

Structure Study Of Small Heat Shock Protein 27, Zhaobo Li

Open Access Theses & Dissertations

Molecular chaperones are a class of oligomeric proteins that play a critical role inpreventing the aggregation of non-native protein so that these proteins can later be refolded. Chaperones are ubiquitously expressed in all the kingdoms of life where their function is to counteract cellular stress and to maintain protein homeostasis. One subgroup of molecular chaperones is characterized by low molecular weight and are termed small heat shock proteins. The focus of the proposed research is the small heat shock protein 27 (Hsp27). Hsp27 is an ATP independent chaperone that is overexpressed in response to heat shock, radiation damage, oxidative damage, …