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University of Arkansas, Fayetteville

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Full-Text Articles in Chemistry

Isolation, Purification, And Characterization Of Α-Galactosidase From Watermelon (Citrullus Lanatus), Christopher Henley Jr. May 2026

Isolation, Purification, And Characterization Of Α-Galactosidase From Watermelon (Citrullus Lanatus), Christopher Henley Jr.

Chemistry & Biochemistry Undergraduate Honors Theses

The enzyme α-galactosidase is a type of glycosidase that removes galactose sugar units from larger molecules in cells. Compounds that inhibit glycosidases have been useful for understanding the structure and function of the enzymes they inhibit, and some have been used to treat certain diseases. Using inhibitors of α-galactosidase to study its characteristics and mechanisms may provide insights into its role in disease and its general utility. Advances in fields such as agriculture, sustainable fuels, and biomedicine may be facilitated by inhibition studies of α-galactosidase, but the current library of known inhibitors is relatively lacking. Obtaining α-galactosidase enzymes from chemical …

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Tunable Physical Color In Nanostructured Materials: Exploring Reversible Mechanisms For Active Optical Control, Matt Hughes May 2026

Tunable Physical Color In Nanostructured Materials: Exploring Reversible Mechanisms For Active Optical Control, Matt Hughes

Chemistry & Biochemistry Undergraduate Honors Theses

Vanadium Dioxide (VO2) thin films have been grown on silicon wafers using atomic layer deposition of TDMAV (tetrakis(dimethylamino)vanadium(IV)) and H2O as precursors. A quartz crystal microbalance (QCM) measurement was used during deposition to confirm growth and resulted in a growth rate of approximately 0.6 Angstroms/cycle. X-Ray Reflectivity (XRR) was performed to confirm growth thickness and reported an approximately 30 nm thin film after 500 cycles of TDMAV precursor deposition. X-Ray photoelectron spectroscopy was utilized to determine the phase of the vanadium samples and confirmed the presence of vanadium dioxide as prepared and after annealing under nitrogen …

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Hollow Nickel-Iron Nanoshells As Electrocatalysts For The Oxygen Evolution Reaction, Jonathan Batey May 2026

Hollow Nickel-Iron Nanoshells As Electrocatalysts For The Oxygen Evolution Reaction, Jonathan Batey

Chemistry & Biochemistry Undergraduate Honors Theses

The development of highly active and affordable catalysts for the oxygen evolution reaction is crucial to achieve a future where hydrogen is generated cleanly using renewable methods. Ni-Fe nanocatalysts show great promise in this area, as they are affordable and highly active. However, to overcome the industrial dominance of steam methane reforming, their activity needs improvement. This work aims to increase the activity of Ni-Fe nanocatalysts by making hollow nanostructures. Hollow Ni-Fe nanostructures were synthesized by coating a Cu template with Ni and Fe, followed by the etching of the Cu template. This left hollow Ni-Fe nanoshells, which were used …

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Advancement In Electrochemical Generation-Collection: Snapshot Redox Cycling Voltammetry For Rapid Analysis At Chip-Based, Individually Addressable Microband Electrode Arrays, Blake Aleck Sterling May 2026

Advancement In Electrochemical Generation-Collection: Snapshot Redox Cycling Voltammetry For Rapid Analysis At Chip-Based, Individually Addressable Microband Electrode Arrays, Blake Aleck Sterling

Graduate Theses and Dissertations

Snapshot redox cycling voltammetry (Snapshot RCV) is introduced as a rapid electrochemical technique that reconstructs the current-potential profile of a redox active species using a microband electrode array. By simultaneously biasing individual generator electrodes alternating in the array to different voltages across the analyte’s potential range while individually holding collector electrodes at a reversing potential, “spatial” voltammetry is achieved in as little as 1 s with the temporal speed of chronoamperometry, rapidly capturing the steady-state redox cycling (RC) profiles. During RC (a mode of generation-collection), the analyte is oxidized (or reduced) at generator electrodes and converted back at neighboring collector …

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Deciphering Chemomechanical Couplings In Proteins Using Molecular Dynamics And Enhanced Sampling Techniques, Matthew Brownd May 2026

Deciphering Chemomechanical Couplings In Proteins Using Molecular Dynamics And Enhanced Sampling Techniques, Matthew Brownd

Graduate Theses and Dissertations

Proteins function through a complex interplay between chemical interactions and mechanical motions across multiple spatial and temporal scales. Understanding how ligand binding, conformational dynamics, and structural flexibility collectively regulate protein function remains one of the central challenges in molecular biophysics. This dissertation presents a computational investigation into chemomechanical coupling in three distinct classes of biomolecular systems using all-atom molecular dynamics (MD) simulations and enhanced sampling methods, with particular emphasis on free-energy calculations and long-timescale conformational analysis. The first part of this work focuses on ligand binding in hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which regulate rhythmic electrical activity in the heart …

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Nanoscale Electrochemical Measurements: Theory, Instrumentation, And Operation, Kamsy Lerae Anderson May 2026

Nanoscale Electrochemical Measurements: Theory, Instrumentation, And Operation, Kamsy Lerae Anderson

Graduate Theses and Dissertations

Electrochemical processes underpin many modern technologies (e.g., batteries, fuel cells, and corrosion protection systems), and because these processes are often controlled by interactions that occur at the nanoscale, gaining insight into nanoscale electrochemical behavior is essential to advancing these technologies. Nanoscale electrochemical imaging probes measure electrochemical activity with nanoscale spatial resolution and have enabled researchers to gain new insights into diverse experimental systems. However, limitations remain, including a lack of methods for direct quantitative interpretation, the influence of atmospheric conditions on experimental reproducibility and stability, and a knowledge barrier resulting from limited accessible resources, all of which continue to restrict …

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Fret Studies On The Binding Of Fibroblast Growth Factor (Fgf) Proteins To The Hard Corona Of Cuins2-Based Quantum Dots, Colette Robinson May 2026

Fret Studies On The Binding Of Fibroblast Growth Factor (Fgf) Proteins To The Hard Corona Of Cuins2-Based Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

Fibroblast Growth Factor (FGF) has been shown to be an important protein in angiogenesis, which is critical in developmental biology and wound healing but has also been implicated in cancer metastasis. FGF interacts with an FGF Receptor (FGFR) to signal the onset of angiogenesis but the detailed mechanism of angiogenesis, and particularly its regulation, is still largely unknown. Imaging the interaction of FGF with FGFR in biologically-relevant environments, such as directly in cells, is key towards furthering this understanding and may eventually aid in the development of better cancer treatments. CuInS2/ZnS quantum dots (QDs) are an attractive fluorescent probe to …

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Fast Hyperspectral And Super-Resolved Mapping Of Lipid Membrane Polarity With Single-Molecule Sensitivity, Elric Dion Pott, Meek Yang, James Ethan Batey, Jole Embree, Bin Dong Apr 2026

Fast Hyperspectral And Super-Resolved Mapping Of Lipid Membrane Polarity With Single-Molecule Sensitivity, Elric Dion Pott, Meek Yang, James Ethan Batey, Jole Embree, Bin Dong

Chemistry & Biochemistry Faculty Publications and Presentations

Cell membranes display nanoscale heterogeneity in lipid composition and organization that regulates vital biological processes yet remain challenging to resolve with conventional imaging. We introduce spectral phasor single-molecule localization microscopy (SP-SMLM), a hyperspectral and super-resolution method that combines wavefront-like optical filtering with single-molecule imaging for simultaneous spatial and spectral analysis. A lab-built three-channel imager with sine/cosine filters encodes emission spectra of single molecules into the phasor space, enabling high-throughput, high-SNR mapping of membrane polarity at sub-50 nm spatial and 15 s temporal resolutions. Through simulation, we validate that the phasor angle correlates with the spectral mean for single dye molecules. …

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Effects Of Varying Ph, Temperature, And Sucrose Concentration On The Activity Of Invertase Enzyme, B. Rainwater, S. Pratihar Feb 2026

Effects Of Varying Ph, Temperature, And Sucrose Concentration On The Activity Of Invertase Enzyme, B. Rainwater, S. Pratihar

Journal of the Arkansas Academy of Science

The purpose of this research is to study the factors that affect the enzymatic activity of invertase, extracted from baker’s yeast, on hydrolysis of sucrose in aqueous medium. Invertase, a glycoprotein, is an enzyme in the glycoside hydrolase family. It catalyzes the hydrolysis of sucrose producing equimolar mixture of a-D-glucose and b-D-fructose. Invertase shows high affinity for the substrate, and is capable of both cleaving the glycosidic linkage in sucrose and transferring ab-D-O-fructofuranoside residue to an acceptor substrate. (Toledo et al. 2019). A detailed mechanism of the action of invertase was postulated by Shall et al. (Shall et al. 1971). …

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One-Step Purification Of A Bioactive Pak1-Derived Peptide, Djamali Muhoza, Emily P. Esquivel, Stacy R. Hunter, Pateince S. Okoto, Thallapuranam K.S. Kumar, Paul D. Adams Feb 2026

One-Step Purification Of A Bioactive Pak1-Derived Peptide, Djamali Muhoza, Emily P. Esquivel, Stacy R. Hunter, Pateince S. Okoto, Thallapuranam K.S. Kumar, Paul D. Adams

Chemistry & Biochemistry Faculty Publications and Presentations

The serine/threonine kinase PAK1 serves as a mediator of cytoskeletal reorganization and cancer-related signaling downstream of the small GTPases. Due to the challenges in purifying PAK1 complexes, a 46-residue peptide from PAK1, is widely used to study PAK1-Cdc42 signaling. Traditionally, this purification involved multi-step chromatography of recombinant GST-PBD46 complexes, yielding approximately 1 mg per 1.5 L culture. In this study, a 30 min heat treatment step after thrombin cleavage was used to precipitate GST while leaving pure PBD46 in solution. This step eliminated the need for further affinity and size-exclusion chromatography steps. This improved protocol produces proteins with a 6.5-fold …

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Crispr-Cas9 Unleashed: Gene-Slicing Adventures In The Cancer Battlefield, Shivakuma Sonnaila, Shilpi Agrawal Jan 2026

Crispr-Cas9 Unleashed: Gene-Slicing Adventures In The Cancer Battlefield, Shivakuma Sonnaila, Shilpi Agrawal

Chemistry & Biochemistry Faculty Publications and Presentations

Cancer, a global health menace, continues to pose significant challenges in terms of incidence and mortality, necessitating innovative therapeutic strategies. Despite existing treatments, the limitations persist, prompting a quest for novel approaches. The emergence of immunotherapy marked a transformative era in solid tumor treatments, yet its efficacy is constrained by adverse effects. Concurrently, the integration of advanced technologies into cancer treatment explores the vast potential residing at the molecular level through gene analysis and manipulation. This review articulates the role of state-of-the-art genome editing technology, notably clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), in overcoming the constraints of immunotherapy for …

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Sustainable Polyaddition Path To Polyesters Via Catalytic Homocoupling Of Renewable Dicrotonate Monomers, Shabbir Asif, Mahsa Saeidi, Braden D. Pickle, Nicholas J. Tabbah, Michael L. Mcgraw Dec 2025

Sustainable Polyaddition Path To Polyesters Via Catalytic Homocoupling Of Renewable Dicrotonate Monomers, Shabbir Asif, Mahsa Saeidi, Braden D. Pickle, Nicholas J. Tabbah, Michael L. Mcgraw

Chemistry & Biochemistry Faculty Publications and Presentations

The development of biorenewable polyhydroxyalkanoate (PHA) chemistry has generated interest in crotonate-based monomers as versatile building blocks. Crotonates can be obtained through the pyrolysis of PHAs, offering both a sustainable end-of-life pathway for PHAs and a renewable route to crotonate monomers. This study presents a new polyaddition-type step-growth polymerization of dicrotonates in which alkene-functionalized polyesters are synthesized using potassium tert-butoxide as a simple base catalyst. The reaction proceeds rapidly at room temperature, achieving >99% conversion within seconds and requiring no byproduct removal. The properties of the resulting polyesters can be tuned via the choice of bridging diol, and the materials …

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Synthesis And Characterization Of Copper Nanoparticles: A Laboratory Experiment For Undergraduate Physical Chemistry, Jonathan Batey, Deborah Okyere, Sarah York, Feng Wang, Jingy Chen Dec 2025

Synthesis And Characterization Of Copper Nanoparticles: A Laboratory Experiment For Undergraduate Physical Chemistry, Jonathan Batey, Deborah Okyere, Sarah York, Feng Wang, Jingy Chen

Chemistry & Biochemistry Faculty Publications and Presentations

Nonprecious metal nanoparticles have been the subject of intensive research, due to their potential applications in promoting sustainability. This integrated laboratory experiment is designed to provide undergraduate students with hands-on experience in synthesizing and characterizing nonprecious metal nanoparticles, specifically copper nanoparticles. The experiment consists of three sections, each tailored to teach a unique aspect of nanochemistry. Section 1 focuses on the air-free synthesis of copper nanoparticles using a solution-based method with an emphasis on understanding their plasmonic properties and how oxidation impacts them. Section 2 explores the quantitative analysis of copper, where students apply crystal field theory to understand the …

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Novel Radical Chemistry Of Electron-Rich Double Bonds, Claire Allyson Beard Dec 2025

Novel Radical Chemistry Of Electron-Rich Double Bonds, Claire Allyson Beard

Graduate Theses and Dissertations

This work delves into the reactivity of nucleophilic N-heterocyclic carbenes (NHCs) and their ability to form electron-rich alkene intermediates, which can undergo various chemical transformations depending on the nature of the electrophile. Initial reports by Hahn disclosed the NHC promoted radical nature of electron-rich N,N’-benzyltetraazafulvalenes, which led to 2,2’- biimidazoles. We found that N-aryl substituted pyridinium salts also underwent rapid a similar NHC promoted dimerization when exposed to a base, producing 2,2’-bipyridyls. This is likely due to the adept radical nature of the bipyridinylidene intermediate for C-Naryl bond scission. We have also uncovered an unprecedented C-N bond scission of Breslow-like …

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Free Radical Reactions Of Electron Rich Alkenes, David A. May Jr Dec 2025

Free Radical Reactions Of Electron Rich Alkenes, David A. May Jr

Graduate Theses and Dissertations

Radical reactions have known for over a century but have only been thought of as useful synthetic strategies for the last 70 years. During this period, much work has been done to develop theoretical explanations for their reactivity and modes of termination, resulting in them becoming a fundamental type of organic reaction in academia and industry. Previous studies by the McIntosh group have shown that a radical [1,3]-Rearrangement occurs when N-substituted pyridines are heated. Here, the scope of this new reaction is expanded to include polycyclic pyridines including neocuproine (2,9-dimethylphenanthroline) and 2-methylquinoline while also expanding the range of reactions available …

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Automation And Upgrading Of Custom Cold Wall Uhv-Cvd Reactor For Group Iv Material Development, Alexander Golden Dec 2025

Automation And Upgrading Of Custom Cold Wall Uhv-Cvd Reactor For Group Iv Material Development, Alexander Golden

Graduate Theses and Dissertations

Group IV alloys have shown promising results for infrared optoelectronic applications where III-V materials are currently dominant. The III-V material system has vacancies that Group IV materials can fill, most importantly complementary metal oxide semiconductor (CMOS) process compatibility making quality devices much cheaper and widely available compared to the current state of the art. Silicon, being an indirect band gap Group IV material, has poor performance in optoelectronic applications but is the dominant material for most of the electronic industry. However, when silicon is alloyed or substituted with other group IV materials, these optoelectronic properties can be enhanced and, in …

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Studies Of Trispyrazolylborate Molybdenum-Oxo Compounds And Related Reactions, Miranda Sanders Dec 2025

Studies Of Trispyrazolylborate Molybdenum-Oxo Compounds And Related Reactions, Miranda Sanders

Graduate Theses and Dissertations

This dissertation details the design, development, and synthesis of a molybdenum-dioxo complex bearing a trispyrazolylborate ligand. The system was tested for its efficiency as a catalyst for deoxydehydration with a small substrate scope. Deoxydehydration reactions with 1-phenyl-1,2-ethanediol, diethytartrate, and 1,2-octanediol show low yields with catalytic turnover only found for diethyltartrate. Electrochemical studies show well behaved PCET behavior with two distinct electron transfer events in the presence of a proton donor. Studies of two molybdenum-dioxo complexes bearing dianionic pincer ligands were conducted to expand further on systems that have been extensively studied in our lab. Deoxydehydration of glycerol by a molybdenum-dioxo …

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Ring-Opening And Monofunctionalization Study On Spiro Cyclic Aminals And N, O-Acetals System Via Nitrogen-Centered Radical Intermediates, Chujun Zhou Dec 2025

Ring-Opening And Monofunctionalization Study On Spiro Cyclic Aminals And N, O-Acetals System Via Nitrogen-Centered Radical Intermediates, Chujun Zhou

Graduate Theses and Dissertations

The nitrogen-centered radical has been drawing increasing attention among researchers. Radical polarity is one of the key factors in studying nitrogen-centered radicals’ reactivity, and the functional groups attached to the nitrogen atom are of vital importance. Among different types of nitrogen-centered radicals, aminium radical and metal aminium radical are electrophilic due to the positive charge on the intermediate. The sulfonamide radical, amidyl radical, and cyanide amine radical are also electrophilic since the nitrogen is adjacent to electron electron-withdrawing group. The neutral amino radical, iminyl radical, masked nitrogen radical are nucleophilic because of the electron-donating groups. After classifying the nitrogen-centered radical, …

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Multiplexed Integrin Detection And Cancer Cell Classification Using Multicolor Gap-Enhanced Gold Nanorods And Machine Learning Algorithm, Suprava Shah, Reed Youngerman, Alberto Luis Rodriguez-Nieves, Mitchell Lee Taylor, William Rodney Bantom, David Thompson, Jingyi Chen, Yongmei Wang, Xiaohua Huang Nov 2025

Multiplexed Integrin Detection And Cancer Cell Classification Using Multicolor Gap-Enhanced Gold Nanorods And Machine Learning Algorithm, Suprava Shah, Reed Youngerman, Alberto Luis Rodriguez-Nieves, Mitchell Lee Taylor, William Rodney Bantom, David Thompson, Jingyi Chen, Yongmei Wang, Xiaohua Huang

Chemistry & Biochemistry Faculty Publications and Presentations

Integrins, cell-surface adhesion receptors involved in tumor progression, invasion, and metastasis, serve as crucial biomarkers for cancer diagnosis and therapeutic targeting. Multiplexed detection of integrins and cancer cell classification at the single-cell level allows for comprehensive profiling, facilitating precise identification and categorization of tumor cells that are heterogeneous in integrin expression and cell subtype. In this study, we developed a five-plex detection platform and demonstrated integrin profile for cancer cell classification leveraging surface-enhanced Raman scattering (SERS) with gap-enhanced gold nanorods (GENRs) in conjunction with advanced computational analysis. Specifically, we synthesized GENRs bearing five distinct Raman nanotags, each producing a unique …

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Chemistry And Biochemistry Affiliated Publications: Snapshot Of The Research Publications 2019-2024., Jeremy J. Smith, Lutishoor Salisbury Oct 2025

Chemistry And Biochemistry Affiliated Publications: Snapshot Of The Research Publications 2019-2024., Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report highlights the chemistry and biochemistry faculty publications for the period 2019-2024. It includes tables identifying the types of publications, the characteristics of the authors, inter-departmental and external cooperation, summary of the citations of the publications, and the JCR ranking of the journals in which they published.

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An Adaptive Force Matching Potential For Alanine Developed With Møller-Plesset Perturbation Theory And Smooth Fourier Transform Correction Map, Ying Yuan, Feng Wang Sep 2025

An Adaptive Force Matching Potential For Alanine Developed With Møller-Plesset Perturbation Theory And Smooth Fourier Transform Correction Map, Ying Yuan, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Developing accurate force fields for biomolecules remains a significant challenge due to the subtle energetic differences between various conformational states. We present a novel force field model for polyalanine, ALAMP2_25, developed using adaptive force matching (AFM) with M & oslash;ller-Plesset perturbation theory at the second order (MP2) as the reference method. By fitting smaller model compounds and transferring parameters to larger peptides, we overcome the limitations of traditional AFM approaches and enable the use of more accurate electronic structure methods. The ALAMP2_25 model incorporates a new correction scheme, Smooth Fourier Transform-based phi, psi correction map (SFT-CMAP), which efficiently describes phi, …

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Molecular Dynamics Simulations Of Liposomes: Structure, Dynamics, And Applications, Ehsan Khodadadi, Ehsaneh Khodadadi, Parth Chaturvedi, Mahmoud Moradi Aug 2025

Molecular Dynamics Simulations Of Liposomes: Structure, Dynamics, And Applications, Ehsan Khodadadi, Ehsaneh Khodadadi, Parth Chaturvedi, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Liposomes are nanoscale, spherical vesicles composed of phospholipid bilayers, typically ranging from 50 to 200 nm in diameter. Their unique ability to encapsulate both hydrophilic and hydrophobic molecules makes them powerful nanocarriers for drug delivery, diagnostics, and vaccine formulations. Several FDA-approved formulations such as Doxil (R) (Baxter Healthcare Corporation, Deerfield, IL, USA), AmBisome (R) (Gilead Sciences, Inc., Foster City, CA, USA), and Onivyde (R) (Ipsen Biopharmaceuticals, Inc., Basking Ridge, NJ, USA) highlight their clinical significance. This review provides a comprehensive synthesis of how molecular dynamics (MD) simulations, particularly coarse-grained (CG) and atomistic approaches, advance our understanding of liposomal membranes. We …

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Harnessing Emergent Multiple Scattering Resonances In A Photonic Glass Structure For Photoelectrochemical Energy Conversion, Ashlyn G. Descarpentrie, Robert H. Coridan Aug 2025

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 …

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Yizhi Sun: Profile Of The Newest Chbc Faculty Member., Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury Aug 2025

Yizhi Sun: Profile Of The Newest Chbc Faculty Member., Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Yizhi Sun, Assistant Professor, Chemistry and Biochemistry department. It highlights his research interests, education, and impact of his research.

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Crystal Structures Of Escherichia Coli Glucokinase And Insights Into Phosphate Binding, Joseph Andrews, Joshua Sakon, Chenguang Fan Aug 2025

Crystal Structures Of Escherichia Coli Glucokinase And Insights Into Phosphate Binding, Joseph Andrews, Joshua Sakon, Chenguang Fan

Chemistry & Biochemistry Faculty Publications and Presentations

Here, we report the crystal structure of Escherichia coli glucokinase (GLK), which has phosphate bound in the cleft between the alpha and beta domains adjacent to the active site. A ternary complex consisting of GLK, glucose and phosphate is also reported in this work. Diffraction data were collected at 2.63 angstrom resolution for the phospate-bound form (R-work/R-free = 0.191/0.230) and at 2.54 angstrom resolution for the ternary complex (R-work/R-free = 0.202/0.258), both at 297 K. A B-factor analysis of the phosphate-bound GLK structure revealed consistently lower values for phosphate-interacting basic residues in the alpha 4, alpha 5 and alpha 9 …

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Exploring The Promise And Limitations Of Point-Charge-Free Potentials For Hydrocarbon Modeling, Raymond Weldon, Feng Wang Jul 2025

Exploring The Promise And Limitations Of Point-Charge-Free Potentials For Hydrocarbon Modeling, Raymond Weldon, Feng Wang

Chemistry & Biochemistry Faculty Publications and Presentations

Models for hydrated and neat hydrocarbons are developed with the adaptive force matching method using either B3LYP-D3(BJ) or MP2 as reference. Hydrocarbons, being non-polar, present an opportunity to explore the possibility of creating force fields without modeling electrostatics. For liquid methane, ethane, cyclopentane, and cyclohexene, models without partial charges achieved excellent agreement with experiments when fitted against MP2 reference with SAPT dispersion. In aqueous solutions, models without solute partial charges maintain high quality for saturated hydrocarbons but exhibit reduced accuracy for cyclohexene. Notably, liquid methane's weak intermolecular interactions make it particularly sensitive to the choice of reference method. Our findings …

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Comprehensive Insights Into The Cholesterol-Mediated Modulation Of Membrane Function Through Molecular Dynamics Simulations, Ehsaneh Khodadadi, Ehsan Khodadadi, Parth Chaturvedi, Mahmoud Moradi Jun 2025

Comprehensive Insights Into The Cholesterol-Mediated Modulation Of Membrane Function Through Molecular Dynamics Simulations, Ehsaneh Khodadadi, Ehsan Khodadadi, Parth Chaturvedi, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Cholesterol plays an essential role in biological membranes and is crucial for maintaining their stability and functionality. In addition to biological membranes, cholesterol is also used in various synthetic lipid-based structures such as liposomes, proteoliposomes, and nanodiscs. Cholesterol regulates membrane properties by influencing the density of lipids, phase separation into liquid-ordered (Lo) and liquid-disordered (Ld) areas, and stability of protein-membrane interactions. For planar bilayers, cholesterol thickens the membrane, decreases permeability, and brings lipids into well-ordered domains, thereby increasing membrane rigidity by condensing lipid packing, while maintaining lateral lipid mobility in disordered regions to preserve overall membrane fluidity. It modulates membrane …

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Molecular Insights: Advances In Single Molecule And Single Particle Detection For Analysis Of Chemical, Physical, And Biological Phenomena, James Ethan Batey May 2025

Molecular Insights: Advances In Single Molecule And Single Particle Detection For Analysis Of Chemical, Physical, And Biological Phenomena, James Ethan Batey

Chemistry & Biochemistry Undergraduate Honors Theses

This thesis is focused on recent advancements made in the field of chemical imaging, optical microscopy, and recent developments that have improved spatial, temporal, or spectral resolution or have made certain techniques more accessible and cost effective for their wider adoption. This thesis is organized based on the systems of interest we studied with each new technique. Although, it is important to note that many of the methods here can be used with a multitude of systems even if not explicitly mentioned. The first chapter of this thesis will discuss the current state of chemical imaging, common terminology, and important …

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Using Gaussian Process Regression To Learn Thermodynamic Equations Of State With Uncertainty Quantification, Austen T. Lee May 2025

Using Gaussian Process Regression To Learn Thermodynamic Equations Of State With Uncertainty Quantification, Austen T. Lee

Chemical Engineering Undergraduate Honors Theses

This study investigates the use of derivative-informed Gaussian Process (GP) models to estimate thermodynamic behavior across temperature and density by building a Helmholtz-based equation of state. Argon, a stable monatomic gas, was chosen as a case study within the vapor region. The GP model was trained using values of experimentally measurable properties found by taking first and second derivatives of the original potential function. Results show that while the GP model offered uncertainty quantification and informed thermodynamic behavior, it predicted values that deviated from the ground truth depending on the property. The model exhibited high confidence in regions with substantial …

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Protein Structural Changes Of Envelope Glycoprotein In Human Immunodeficiency Virus Type 1, Abigail S. Bridges May 2025

Protein Structural Changes Of Envelope Glycoprotein In Human Immunodeficiency Virus Type 1, Abigail S. Bridges

Chemistry & Biochemistry Undergraduate Honors Theses

The envelope glycoprotein (Env), present on the viral surface of human immunodeficiency virus type 1 (HIV-1) facilitates host cell infection, making it a critical target for immune responses and vaccine development. Env is able to transition through three prevalent prefusion conformational states, state-1 (pre-triggered), state-2 (closed), and state-3 (open). By transitioning through these conformation states, Env can successfully evade immune responses and initiate viral entry into the host cell. This study uses molecular dynamics (MD) simulations to analyze the conformational dynamics of the mature, cleaved Env glycoprotein in the state-2 conformation (PDB ID: 4ZMJ). Simulations were conducted with five replicates, …

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