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Full-Text Articles in Chemistry

Probing The Dynamic Behavior Of The Androgen Receptor In The Presence Of Heptyl And Methyl Parabens, Edgardo De Leon May 2026

Probing The Dynamic Behavior Of The Androgen Receptor In The Presence Of Heptyl And Methyl Parabens, Edgardo De Leon

Theses and Dissertations

The androgen receptor (AR) mediates physiological signaling from endogenous androgens, a function that can be disrupted by endocrine disruptors with serious reproductive and developmental consequences. Parabens, widely used preservatives, inhibit AR signaling in cell-based assays, with inhibitory potency correlating with alkyl chain length: heptylparaben exhibits stronger antagonism than methylparaben, which shows no effect. We hypothesize this differential potency arises from allosteric modulation at the AR Binding Function 3 (BF-3) site, altering dihydrotestosterone (DHT) binding dynamics. Docking calculations using antagonist-bound AR crystal structures, followed by molecular dynamics simulations, show that methylparaben fails to remain bound at BF-3, whereas heptylparaben maintains stable …

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Design And In Silico Modeling Of Heterocyclic-Based Xanthone Derivatives As Potential Anticancer Agents Through Tyrosine Kinase Inhibition, Yehezkiel Steven Kurniawan, Ervan Yudha, Nela Fatmasari, Radite Yogaswara, Harno Dwi Pranowo, Eti Nurwening Sholikhah, Jumina Jumina Mar 2026

Design And In Silico Modeling Of Heterocyclic-Based Xanthone Derivatives As Potential Anticancer Agents Through Tyrosine Kinase Inhibition, Yehezkiel Steven Kurniawan, Ervan Yudha, Nela Fatmasari, Radite Yogaswara, Harno Dwi Pranowo, Eti Nurwening Sholikhah, Jumina Jumina

Makara Journal of Science

Cancer is one of the deadliest diseases nowadays, and tyrosine kinase receptors play crucial roles in cancer cell survival, differentiation, proliferation, and migration. This study designed and developed a new inhibitor from heterocyclic-based xanthone derivatives to target two tyrosine kinase receptors, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), through in silico screening. Eighteen heterocyclic-based xanthones were evaluated through molecular docking for both receptors. All heterocyclic-based xanthones gave the root mean square deviation (RMSD) value lower than 2.00 Å. Xanthone with isobenzothiazole substituent (iBzThio) was found as the most potent inhibitor with binding energies of -10.60 and …

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Investigating The In Vitro Antimicrobial Potential And Comprehensive Computational Studies Of New Schiff Base Derivatives, Abrar Hussain, Shahzaib Akhter, Hammad Nasir, Khurram Shahzad, Muhammad Arfan, Sand Hyun Park Jan 2026

Investigating The In Vitro Antimicrobial Potential And Comprehensive Computational Studies Of New Schiff Base Derivatives, Abrar Hussain, Shahzaib Akhter, Hammad Nasir, Khurram Shahzad, Muhammad Arfan, Sand Hyun Park

Chemistry & Biochemistry Faculty Publications

Antimicrobial resistance (AMR) is a growing global health threat driven by multidrug-resistant bacteria (Staphylococcus aureus, Pseudomonas aeruginosa), and fungi (Candida albicans, and C. parapsilosis). This study evaluated six novel Schiff base derivatives (HSB-1 to HSB-6) through integrated in vitro antimicrobial activity and comprehensive computational studies. In vitro disk diffusion assay demonstrated the largest zones of inhibition against S. aureus for HSB-6 and HSB-1 (15–17 mm), activity against P. aeruginosa for HSB-5 and HSB-6 (12 mm), and moderate antifungal activity for HSB-4 (8–11 mm). Molecular docking results correlated with the in vitro findings with the binding energy ΔG = −12.3 kcal/mol …

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Deciphering Ultrafast Photoinduced And Photocatalytic Reaction Dynamics On Oxide Surfaces: Direct Detection Of Radical Intermediates, Fragment Trapping, And Carbon–Carbon, Carbon–Oxygen, And Carbon–Hydrogen Bond Formation Pathways, Aakash Gupta Jan 2026

Deciphering Ultrafast Photoinduced And Photocatalytic Reaction Dynamics On Oxide Surfaces: Direct Detection Of Radical Intermediates, Fragment Trapping, And Carbon–Carbon, Carbon–Oxygen, And Carbon–Hydrogen Bond Formation Pathways, Aakash Gupta

Graduate Studies Theses and Dissertations 2026

Understanding photoinduced reactions at solid interfaces is essential for advancing heterogeneous photocatalysis, surface photochemistry, and energy conversion technologies. This dissertation investigates the ultrafast dynamics of reactive intermediates, fragment trapping, and radical-mediated bond formation on oxide surfaces using time-of-flight mass spectrometry in conjunction with femtosecond pump-probe spectroscopy. Various experimental findings are validated through collaborations via density functional theory (DFT). By combining temporal, mass, and energy-resolved measurements, this work provides molecular-level insight into the elementary processes governing light-driven surface reactions. The photodissociation dynamics of CH3I adsorbed on TiO2(110), TiO2(100), and amorphous silicon oxide surfaces are examined …

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Data-Driven Analysis And Atomistic Simulations Of Next-Generation Materials For Energy Conversion And Storage, Yuliang Shi Dec 2025

Data-Driven Analysis And Atomistic Simulations Of Next-Generation Materials For Energy Conversion And Storage, Yuliang Shi

Dissertations

Metal-organic frameworks (MOFs), with their modular architectures and tunable properties, represent an especially rich domain for accelerated material design and discovery for a range of diverse applications. Within this class of multifunctional materials, two-dimensional (2D) electrically conductive MOFs (EC MOFs) are of particular interest, as their 7r-stacked layered structures combine permanent porosity with electronic conductivity, enabling potential breakthroughs in energy storage, energy conversion, and quantum sensing. But the discovery and design of new EC MOFs based on expensive experimental screening is increasingly impractical due to the infinite chemical space. Furthermore, the practical implementation of EC MOFs for specific tasks depends …

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New Bis-Piperazine Derivatives: Synthesis, Characterization (Ir, Nmr), Gamma-Ray Absorption, Antimicrobial Activity, Molecular Docking And Dynamics Study, Yasemi̇n Ünver, Arzu Coşkun, Fati̇h Çeli̇k, Hali̇l İbrahi̇m Güler, Kadri̇ye İnan Bektaş Dec 2025

New Bis-Piperazine Derivatives: Synthesis, Characterization (Ir, Nmr), Gamma-Ray Absorption, Antimicrobial Activity, Molecular Docking And Dynamics Study, Yasemi̇n Ünver, Arzu Coşkun, Fati̇h Çeli̇k, Hali̇l İbrahi̇m Güler, Kadri̇ye İnan Bektaş

Turkish Journal of Chemistry

A series of novel bis-piperazine derivatives (2a–2f) were synthesized and structurally characterized via Fourier transform-infrared and nuclear magnetic resonance spectroscopic techniques. Their gamma-ray shielding efficiencies were investigated through simulations on the Monte Carlo-based Geant4-GATE platform, and the results were benchmarked against data obtained from the XCOM and Phy-X software. A simulation model incorporating an NaI scintillation detector and a point gamma source was developed. Key shielding parameters, including mass attenuation coefficient, linear attenuation coefficient, half-value layer, and mean free path (MFP), were evaluated at gamma energies of 80, 120, 662, 1173, and 1332 keV. Additionally, the energy absorption buildup factor …

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Defect-Driven Degradation Of Mxenes In Aqueous Environments And Mitigation Strategies: Insights From First-Principles, Ana Maria Stratulat, Valentina Nesterova, Vladislav Korostelev, Majid Beidaghi, Vadym Mochalin, Konstantin Klyukin Oct 2025

Defect-Driven Degradation Of Mxenes In Aqueous Environments And Mitigation Strategies: Insights From First-Principles, Ana Maria Stratulat, Valentina Nesterova, Vladislav Korostelev, Majid Beidaghi, Vadym Mochalin, Konstantin Klyukin

Chemistry Faculty Research & Creative Works

MXenes have attracted considerable attention due to their tunable surface chemistry, high electrical conductivity, and ease of solution processing, making them promising candidates for a wide array of applications. The inherent tendency of MXenes to degrade under environmental conditions constrains their compositional diversity and limits certain practical applications. Our computational study shows that degradation of defect-free Ti3C2Txis kinetically limited, whereas common defects markedly lower the activation barriers for water attack. Using ab initio molecular dynamics simulations (AIMD) combined with thermodynamic analysis, we show that titanium vacancies VTiact as active sites for the protonation of subsurface carbon …

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First Principles Molecular Dynamics Simulations Of Infrared And Raman Vibrational Spectra Of H5o2 +, D5o2 +, Dh4o2 +, And D4ho2 + From 50 To 300 K, Oluwaseun Omodemi, Martina Kaledin Oct 2025

First Principles Molecular Dynamics Simulations Of Infrared And Raman Vibrational Spectra Of H5o2 +, D5o2 +, Dh4o2 +, And D4ho2 + From 50 To 300 K, Oluwaseun Omodemi, Martina Kaledin

Faculty Articles

We report molecular dynamics simulations of infrared (IR) and Raman spectra of H5O2+ and its deuterium-substituted analogs. We use the well-tested HBB potential and dipole surfaces along with a recently fitted polarizability surface of CCSD(T)/aug-cc-pVTZ quality. The focus of the present work is to provide new insights into the O···O stretch region, located in the [500–700] cm–1 spectral range, by means of analyzing the spectra over a broad range of temperatures: from 50 to 300 K. Also, rovibrational thermal averaging was performed to untangle the unusually complex spectra of partially deuterated isotopologues DH4O2+ and D4HO2+ with H and D minority …

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Allosteric Control Overcomes Steric Limitations For Neutralizing Antibodies Targeting Conserved Binding Epitopes Of The Sars-Cov-2 Spike Protein: Exploring The Intersection Of Binding, Allostery, And Immune Escape With A Multimodal Computational Approach, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Sep 2025

Allosteric Control Overcomes Steric Limitations For Neutralizing Antibodies Targeting Conserved Binding Epitopes Of The Sars-Cov-2 Spike Protein: Exploring The Intersection Of Binding, Allostery, And Immune Escape With A Multimodal Computational Approach, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Understanding the atomistic basis of multi-layer mechanisms employed by broadly reactive neutralizing antibodies of the SARS-CoV-2 spike protein without directly blocking receptor engagement remains an important challenge in coronavirus immunology. Class 4 antibodies represent an intriguing case: they target a deeply conserved, cryptic epitope on the receptor-binding domain yet exhibit variable neutralization potency across subgroups F1 (CR3022, EY6A, COVA1-16), F2 (DH1047), and F3 (S2X259). The molecular basis for this variability is not fully understood. Here, we employed a multi-modal computational approach integrating atomistic and coarse-grained molecular dynamics simulations, binding free energy calculations, mutational scanning, and dynamic network analysis to elucidate …

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Unveiling The Interplay Of Electronic And Phononic Excitations In Laser-Induced Oxygen Activation On Ru(0001), Xiangrui Wang, Jiamin Wang, Paul Spiering, Liping Liu, Jörg Meyer, Jerry L. Larue, Hongliang Xin Sep 2025

Unveiling The Interplay Of Electronic And Phononic Excitations In Laser-Induced Oxygen Activation On Ru(0001), Xiangrui Wang, Jiamin Wang, Paul Spiering, Liping Liu, Jörg Meyer, Jerry L. Larue, Hongliang Xin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding laser-induced dynamics on metal surfaces poses significant challenges due to the intricate interplay between electronic and phononic degrees of freedom, which evolve on distinct timescales. In this study, we introduce a machine learning-accelerated approach to molecular dynamics simulations that incorporates anisotropic electronic friction, providing deeper insights into these complex processes. Our framework extends the accessible time and length scales for nonadiabatic dynamics simulations, enabling a detailed investigation of the laser-induced activation of oxygen on the Ru(0001) surface. Statistical analysis reveals that strong electronic excitation dominates the first 800 fs after laser exposure. Beyond this timescale, energy deposited by electronic …

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Revealing The Catalytic Mechanism Of The Fe(Ii)/2-Oxoglutarate-Dependent Human Epigenetic Modifying Enzyme Alkbh5, Fathima Hameed Cherilakkudy, Midhun George Thomas, Ann Varghese, Sodiq Waheed, Anandhu Krishnan, Vincenzo Venditti, Christopher J. Schofield, Deyu Li, Christo Christov, Tatyana Karabencheva-Christova Aug 2025

Revealing The Catalytic Mechanism Of The Fe(Ii)/2-Oxoglutarate-Dependent Human Epigenetic Modifying Enzyme Alkbh5, Fathima Hameed Cherilakkudy, Midhun George Thomas, Ann Varghese, Sodiq Waheed, Anandhu Krishnan, Vincenzo Venditti, Christopher J. Schofield, Deyu Li, Christo Christov, Tatyana Karabencheva-Christova

Michigan Tech Publications

ALKBH5 is one of only two known human non-heme Fe(II)/2-oxoglutarate-dependent oxygenases that catalyze the demethylation of N6-methyladenine (m6A) in single-stranded mRNA, underscoring its role in diverse cancers. Unlike its homolog, the fat mass and obesity-associated protein (FTO), which oxidizes m6A to a stable N6-hydroxymethyladenine (hm6A) intermediate, ALKBH5 demethylates m6A, yielding adenine and formaldehyde as products. Here, we integrate molecular dynamics simulations and quantum mechanics/molecular mechanics methods to elucidate ALKBH5’s complete catalytic mechanism. Two post-hydroxylation pathways were evaluated: a proton transfer pathway and a Schiff base formation pathway, with …

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Ensemble-Based Binding Free Energy Profiling And Network Analysis Of The Kras Interactions With Darpin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants And Universal Architecture Of Regulatory Hotspots And Allosteric Binding, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Jun 2025

Ensemble-Based Binding Free Energy Profiling And Network Analysis Of The Kras Interactions With Darpin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants And Universal Architecture Of Regulatory Hotspots And Allosteric Binding, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conformational restriction and allosteric modulation. Mutational scanning across all four DARPin systems identifies a core set of evolutionarily constrained residues …

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Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker May 2025

Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dynamics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving the broad neutralization effect of these antibodies. We show that S309 targets conserved residues near the ACE2 interface, leveraging synergistic van der Waals and electrostatic interactions, while S304 focuses on …

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Modeling Molten Lithium Carbonate As Pollutant Absorbing Agent, Lucian G. Forestieri May 2025

Modeling Molten Lithium Carbonate As Pollutant Absorbing Agent, Lucian G. Forestieri

Student Summer Scholars Manuscripts

Coal burning generates gaseous pollutants that are toxic to local environments and human health, namely hydrochloric acid and sulfur dioxide ( HCl and SO2). Current methods for capturing these pollutants are flue gas desulfurization, which utilize solid or water- dissolved carbonates. This method, however, is inefficient mainly due to the product salts blocking further reactions. Molten carbonates may be a more efficient alternative. Experimental work cannot observe these reaction mechanisms, and the small number of current computational models do not match experimental properties. This work aims to develop a computational model of gaseous HCl scattering off the surface …

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Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker Feb 2025

Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The rapid evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural and energetic analysis of SARS-CoV-2 spike receptor-binding domain (RBD) complexes with neutralizing antibodies from four distinct groups (A–D), including group A LY-CoV016, group B AZD8895 and REGN10933, group C LY-CoV555, and group D antibodies AZD1061, REGN10987, and LY-CoV1404. Using coarse-grained simplified simulation models, rapid energy-based mutational scanning, and rigorous MM-GBSA binding free energy calculations, we elucidated the molecular mechanisms of antibody binding and escape mechanisms, identified key …

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Quantitative Characterization And Prediction Of The Binding Determinants And Immune Escape Hotspots For Groups Of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling Of The Sars-Cov-2 Spike Complexes With Antibodies, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker Feb 2025

Quantitative Characterization And Prediction Of The Binding Determinants And Immune Escape Hotspots For Groups Of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling Of The Sars-Cov-2 Spike Complexes With Antibodies, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by the balance and tradeoff between multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with epitope residues, remain largely uncharacterized. In this study, we performed molecular dynamics simulations, an ensemble-based deep mutational scanning of SARS-CoV-2 spike residues, and binding free energy computations for two distinct groups …

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Interaction Of Cardiac Leiomodin With The Native Cardiac Thin Filament, Madison Little, Cristina M. Risi, Tania M. Larrinaga, Mason D. Summers, Tyler Nguyen, Garry E. Smith Jr., Jennifer Atherton, Carol C. Gregorio, Alla S. Kostyukova, Vitold E. Galkin Jan 2025

Interaction Of Cardiac Leiomodin With The Native Cardiac Thin Filament, Madison Little, Cristina M. Risi, Tania M. Larrinaga, Mason D. Summers, Tyler Nguyen, Garry E. Smith Jr., Jennifer Atherton, Carol C. Gregorio, Alla S. Kostyukova, Vitold E. Galkin

Department of Biomedical and Translational Sciences Faculty Publications

Every heartbeat depends on cyclical contraction-relaxation produced by the interactions between myosin-containing thick and actin-based thin filaments (TFs) arranged into a crystalline-like lattice in the cardiac sarcomere. Therefore, the maintenance of thin filament length is crucial for myocardium function. The thin filament is comprised of an actin backbone, the regulatory troponin complex and tropomyosin that controls interactions between thick and thin filaments. Thin filament length is controlled by the tropomodulin family of proteins; tropomodulin caps pointed ends of thin filaments, and leiomodin (Lmod) promotes elongation of thin filaments by a “leaky-cap” mechanism. The broader distribution of Lmod on the thin …

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Rational Design Of Small Molecules Targeting Mitochondrial Redox Proteins, Matheus Barbosa Belchior Jan 2025

Rational Design Of Small Molecules Targeting Mitochondrial Redox Proteins, Matheus Barbosa Belchior

Graduate Theses, Dissertations, and Problem Reports (ETD)

Reactive oxygen species play a crucial role in many cellular processes. Despite being a natural byproduct of cellular metabolism, overexpression of these species causes damage to the cell, leading to cell dysfunction. Central to the regulation of these highly reactive molecule is the mitochondria. Impairment in its function has been associated with oxidative stress within the cell. Herein, a ligand-based and structure-based approach to design new small molecules to inhibit mitochondrial redox proteins associated with oxidative stress and reactive oxygen species. In the first project two molecules were synthesized and characterized as potential monoamine oxidase B inhibitors. Results showed two …

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Alphafold2-Based Characterization Of Apo And Holo Protein Structures And Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics And Ligand-Induced Conformational Changes, Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Dec 2024

Alphafold2-Based Characterization Of Apo And Holo Protein Structures And Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics And Ligand-Induced Conformational Changes, Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2, which combines randomized alanine sequence masking with shallow multiple sequence alignment subsampling to expand the conformational diversity of the predicted structural ensembles and capture conformational changes between apo and holo protein forms. Using several well-established datasets of structurally diverse apo-holo protein pairs, the proposed approach enables robust predictions of apo and holo structures and conformational ensembles, …

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Preliminary Molecular Study Of Chloramphenicol Anchoring On Laccase Enzyme From Trametes Hirsuta, Hanzhola Gusman Riyanto, Afiten Rahmin Sanjaya Sep 2024

Preliminary Molecular Study Of Chloramphenicol Anchoring On Laccase Enzyme From Trametes Hirsuta, Hanzhola Gusman Riyanto, Afiten Rahmin Sanjaya

Makara Journal of Science

Antibiotics are one of emerging pollutants generally emitted from livestock production and the food industry to the environment. The presence of this pollutant could initiate the development of resistant bacteria that can be fatal to human health. The degradation of antibiotics using enzymes or microbe could be an alternative because the residue or intermediate product is less harmful than of the conventional method. This research aims to support a preliminary study of the degradation of antibiotics using enzyme through molecular docking via Molecular Operating Environment software and molecular dynamics (MD) study via CABSFLEX 2.0 and WebGro macromolecular simulations. The molecular …

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Alphafold2 Modeling And Molecular Dynamics Simulations Of The Conformational Ensembles For The Sars-Cov-2 Spike Omicron Jn.1, Kp.2 And Kp.3 Variants: Mutational Profiling Of Binding Energetics Reveals Epistatic Drivers Of The Ace2 Affinity And Escape Hotspots Of Antibody Resistance, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker Sep 2024

Alphafold2 Modeling And Molecular Dynamics Simulations Of The Conformational Ensembles For The Sars-Cov-2 Spike Omicron Jn.1, Kp.2 And Kp.3 Variants: Mutational Profiling Of Binding Energetics Reveals Epistatic Drivers Of The Ace2 Affinity And Escape Hotspots Of Antibody Resistance, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

AlphaFold2-based atomistic predictions of structures and conformational ensembles of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the most dominant Omicron variants JN.1, KP.1, KP.2 and KP.3 to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and computations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. The results suggested the existence of epistatic interactions between convergent mutational sites at L455, F456, Q493 positions that protect and restore …

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Structure-Function Relationships In Neurodegenerative And Infectious Diseases: Biophysical Characterization Of Rna Secondary Structures By Computational Techniques, Kendy Guarinoni Aug 2024

Structure-Function Relationships In Neurodegenerative And Infectious Diseases: Biophysical Characterization Of Rna Secondary Structures By Computational Techniques, Kendy Guarinoni

Electronic Theses and Dissertations

The research described in this dissertation focuses on the investigation of the structure and dynamics of regions of RNA implicated in two diseases: COVID-19 and amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Both studies sought to create experimentally corroborated models that were used to characterize the structure and dynamics of the C9orf72 repeat expansion and the s2m region in coronaviruses, respectively and provided the foundation for future work. In our work involving the s2m region of SARS-CoV-2, the virus responsible for COVID-19, we determined that the homology modeling approach commonly used to derive atomistic structures when no coordinates are available yields a …

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A Molecular Dynamics Study On The Destruction Mechanism Of Per And Polyfluoroalkyl Substances Due To Ultrasound Technology, Bruno Bezerra De Souza May 2024

A Molecular Dynamics Study On The Destruction Mechanism Of Per And Polyfluoroalkyl Substances Due To Ultrasound Technology, Bruno Bezerra De Souza

Dissertations

Per- and polyfluoroalkyl substances (PFAS) are a group of stable synthetic chemicals that are highly persistent and harmful pollutants to the environment and human health. PFAS have caused a strong public and regulatory response due to their ubiquitous presence in the environment and toxicity to humans. The application of ultrasound is one of the most effective treatment technologies for the mineralization of PFAS in contaminated water. However, this technology is treated as a black box causing the inability to be optimized. Therefore, there is a pressing need to investigate the intricate dynamics of PFAS degradation under ultrasound to unlock its …

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Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens Mar 2024

Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens

Chemistry and Chemical Biology ETDs

Protein Interacting with C Kinase-1 (PICK1) is a scaffolding protein that offers a promising solution to support individuals suffering from substance use disorders. While many efforts have been put towards identifying small-molecule drugs with the potential to target PICK1 and ultimately support individuals suffering from the effects of substance use disorders, all efforts have so far fallen short. The purpose of this work is to use computational tools to assist the design of a small-molecule inhibitor of PICK1 while also advancing the knowledge of its biological functions. This work provides information that is currently missing the field by (1) revealing …

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Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust Jan 2024

Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust

Graduate Theses/Dissertations

The world today relies on hydrocarbon combustion for many reasons, including its high energy density that provides ease of transportation. However, hydrocarbons sourced from fossil fuels are not expected to last forever. Biodiesel, a renewable alternative, has many attractive benefits but comes with other downsides. Biodiesel can gel in cold environments and may leave residue in an engine. Pyrolysis of biodiesel has shown promise in addressing these common detriments. Inducing pyrolysis on biodiesel feedstock (commonly soybean oil in the USA) would be an attractive option presuming it continues to produce fossil fuel analogs similar to biodiesel pyrolysis. Herein, Langevin molecular …

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Computational Investigations Of Polymer Electrolytes In Aqueous Solutions, Hishara Keshani Gallage Dona Oct 2023

Computational Investigations Of Polymer Electrolytes In Aqueous Solutions, Hishara Keshani Gallage Dona

LSU Doctoral Dissertations

Polymer electrolyte membranes, an intriguing category of soft materials, are characterized by polymer backbones tethered with negatively or positively charged functional groups, finding applications from biological macromolecules to electrochemical separations in fuel cells. This dissertation focuses on computational investigations of polymer electrolytes in aqueous solutions using polypeptoids and ion exchange membranes. Polypeptoids, highly tailorable peptidomimetic polymers lacking backbone hydrogen bonding or chirality, were used as model systems. Micelles formed from these polypeptoid polymers exhibited electrostatic repulsion, which competes with charge-sodium interactions, adding complexity to predicting micelle shapes. This research refined the design strategy, enhancing micelle shape and structure through precise …

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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 May 2023

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 …

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Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel May 2023

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

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Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta Apr 2023

Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable …

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Renewable Fuels: Molecular Dynamics Investigations Into Pyrolysis Of Methyl Linoleate, Elson Osakpolor Eguaosa Jan 2023

Renewable Fuels: Molecular Dynamics Investigations Into Pyrolysis Of Methyl Linoleate, Elson Osakpolor Eguaosa

Graduate Theses/Dissertations

With the rapid depletion of the world’s supply of fossil fuels, especially petroleum products, petroleum prices have risen by approximately 800% between the 1970s and now and are projected to continue rising. It is also expected that the world’s consumption of energy will increase commensurate with its growing population. Although biodiesel is a good renewable alternative, it has its limitations including high production costs and poor low-temperature performance. We seek to improve conventional biodiesel with pyrolysis to produce low molecular-weight compounds with high energy densities. Understanding the pyrolysis path on the atomic scale is key as it will allow us …

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