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Articles 1 - 30 of 410

Full-Text Articles in Computational Chemistry

Characterization Of Combined Adsorption Using Fermi Levels, Molecular Dynamics, And Monte Carlo Simulations To Prevent Cu–Zn (111) Alloy Corrosion, Mushtaq Jerri Meften, Ammar Abdul Jabbar Kadhim, Mohammed Shafeeq Abed Sep 2026

Characterization Of Combined Adsorption Using Fermi Levels, Molecular Dynamics, And Monte Carlo Simulations To Prevent Cu–Zn (111) Alloy Corrosion, Mushtaq Jerri Meften, Ammar Abdul Jabbar Kadhim, Mohammed Shafeeq Abed

Makara Journal of Science

Experimentally developing corrosion inhibitors requires a significant amount of money and time. In silico advancement empowers selecting inhibitor molecules based on their properties derived from theoretical studies, thereby reducing costs. Our main approaches include theoretical studies such as Fermi levels, electrostatic potential surface (EPS), Fukui indices, molecular dynamics stimulations, and Monte Carlo as indispensable tools to investigate the adsorption mechanisms of molecules 6-((5-(((3S,5R)-2-oxo-5-((2-(pyrazin-2-yloxy) thiazol-5-yl) thio) tetrahydro-2H-thiopyran-3-yl) oxy)isothia-zol-3-yl)thio) nicotinic acid (PTT), and (S)-2-((5-((6-((3-(2-thioxoethoxy)-1,2,4-thiadiazol-5-yl)thio)-1,6-dihydropyra-zin-2-yl)oxy)-1,3,4-thiadiazol-2-yl) thio) acetaldehyde (TTD) on the Cu/Zn (111) alloy. We electronically characterized PTT and TTD, which were proven effective inhibitors. Notably, all results suggested that the two exhibited high …


An Ion-Neutral Reaction To Form Cyanobenzene And Ethynylbenzene In Titan’S Atmosphere, Rachel M. Huchmala, Vincent J. Esposito Sep 2026

An Ion-Neutral Reaction To Form Cyanobenzene And Ethynylbenzene In Titan’S Atmosphere, Rachel M. Huchmala, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The ion-neutral reaction between cyanoacetylene (HC3N) and phenyl anion (C6H5–) leads to the formation of cyanobenzene (C6H5CN) and the ethynyl anion (C2H–) via a submerged, exothermic pathway. Through a different mechanism, the same two reactants also form ethynylbenzene (C6H5C2H) and CN–. These new reactions can be a foundation for the production of substituted benzenes using molecules currently present on Saturn’s largest moon, Titan. Cyclic aromatic molecules like C6H5CN and C6H5 …


The Role Of External Factors In Shaping Carbohydrate Conformational Landscapes, Murat Yaman Sep 2026

The Role Of External Factors In Shaping Carbohydrate Conformational Landscapes, Murat Yaman

Dissertations, Theses, and Capstone Projects

Carbohydrates (glycans) are among the most structurally diverse biomolecules and participate in a wide range of biological processes, including molecular recognition, cell adhesion, immune response, host-pathogen interactions, and cellular signaling. Their biological functions are governed by a complex interplay between sequence, stereochemistry, conformational flexibility, and environmental factors. However, the structural heterogeneity and dynamic nature of glycans present significant challenges for both experimental characterization and theoretical modeling. In particular, the relationships between glycan structure, conformational dynamics, and the resulting potential energy surfaces remain incomplete.

This dissertation investigates how external factors modulate the potential energy surfaces of carbohydrates through a combination of …


In Situ Electrochemical Characterization Techniques For Active Hydrogen In Electrocatalytic Nitrate Reduction To Ammonia, Hong-Mei Li, Mei Yi, Zhao-Yu Jin, Ming-Hao Xie, Khalid M. Omer, Yong Guo, Pan-Pan Li Aug 2026

In Situ Electrochemical Characterization Techniques For Active Hydrogen In Electrocatalytic Nitrate Reduction To Ammonia, Hong-Mei Li, Mei Yi, Zhao-Yu Jin, Ming-Hao Xie, Khalid M. Omer, Yong Guo, Pan-Pan Li

Journal of Electrochemistry

Electrocatalytic nitrate reduction to ammonia (NitRR) represents a sustainable pathway that integrates environmental remediation with the production of high-value ammonia. However, the activity and selectivity of this process are limited by the generation, consumption, and dynamic equilibrium of the key transient intermediate—active hydrogen (*H). Precise modulation of *H necessitates a comprehensive understanding of its behavior, which relies fundamentally on advanced in situ electrochemical characterization techniques. However, a systematic review dedicated to the rational selection and application of in situ electrochemical techniques for the specific characterization of *H in NitRR, with clear definitions of each technique's "detectable targets, quantitative accuracy, and …


Neural Network Driven By Electrochemical Performance Data For Predicting The Discharge Termination Time Of Seawater Electrolyte-Based Metal-Air Batteries, Peng-Peng Shen, Yi-Chi Pan, Yu-Rong Liu, Lu-Dan Zhang, Ning Niu, Guan-Jun Wang, De-Kun Yang, Xin-Long Tian, Peng Rao Aug 2026

Neural Network Driven By Electrochemical Performance Data For Predicting The Discharge Termination Time Of Seawater Electrolyte-Based Metal-Air Batteries, Peng-Peng Shen, Yi-Chi Pan, Yu-Rong Liu, Lu-Dan Zhang, Ning Niu, Guan-Jun Wang, De-Kun Yang, Xin-Long Tian, Peng Rao

Journal of Electrochemistry

Seawater electrolyte-based metal-air batteries exhibit great promise for marine energy supply systems. However, conventional statistical analysis methods, though applicable to seawater metal-air battery lifetime prediction, have inherent limitations of insufficient prediction accuracy and large error. Herein, a deep time-series regression framework based on InceptionTime and incorporating prior-biased attention pooling is proposed to construct a nonlinear mapping between electrochemical performance sequences and the discharge termination time of catalysts. Specifically, chronoamperometric profiles are employed to extract long-term stability features, while prior knowledge derived from linear sweep voltammetry is introduced to strengthen the attention weighting over critical potential regions. Under a nested leave-one-catalyst-out …


Electronic Structure Discretization And Compression Using Diagonal Basis Sets, Casey Lee Dowdle Aug 2026

Electronic Structure Discretization And Compression Using Diagonal Basis Sets, Casey Lee Dowdle

Dartmouth College Ph.D Dissertations

Numerically solving the electronic structure problem is a fundamentally difficult problem due to the exponential growth in the dimension of the Hilbert space as the system size increases. In order to solve problems at a chemically relevant accuracy, both the choice of basis set and numerical method are important factors that are intrinsically connected.

In this thesis, we study the discretization and resulting compression of electronic Hamiltonians using diagonal basis sets. A diagonal basis set approximately diagonalizes the matrix and tensor representations of the one- and two-body potentials. This can reduce storage, simplify matrix-vector products, and lower the complexity of …


Structure And Dynamics Of Associative Polymers Under Quiescent State And Flow, Rosita Sivaraj Aug 2026

Structure And Dynamics Of Associative Polymers Under Quiescent State And Flow, Rosita Sivaraj

All Dissertations

Associative polymers, including ionizable polymers, are widely used in membranes, coatings, fuel cells, energy storage, and other advanced soft materials. Their properties are governed by ionic aggregation and associative interactions, which influence chain mobility, phase behavior, self-assembly, interdiffusion, and flow response. This dissertation employs large-scale molecular dynamics (MD) simulations to investigate the structure, dynamics, phase behavior, interdiffusion, and extensional flow response of ion-containing and associative polymer systems under quiescent and nonequilibrium conditions.

The influence of molecular architecture is first examined by comparing ring and linear associative polymers using the Kremer–Grest bead-spring model. In linear chains, their closed-loop architecture reduces interchain …


Preparation And Performance Study Of In-Situ Self-Assembled Biphasic Smmn2O5-Nimn2O4 Composite Cathode, Neng-Chu Xia, Yu Zhou, Qin Wang, Jia-You Zhang, Chun Yu, Yang Zhang, Wan-Bing Guan, Jian-Xin Wang Jul 2026

Preparation And Performance Study Of In-Situ Self-Assembled Biphasic Smmn2O5-Nimn2O4 Composite Cathode, Neng-Chu Xia, Yu Zhou, Qin Wang, Jia-You Zhang, Chun Yu, Yang Zhang, Wan-Bing Guan, Jian-Xin Wang

Journal of Electrochemistry

Mullite-structured oxides exhibit excellent oxygen reduction reaction activity, possess a low thermal expansion coefficient due to their unique crystal structure, and can eliminate the need for a barrier layer and simplify the preparation process as they contain no alkaline earth elements. Thus, they hold great promise as novel cathode materials for solid oxide fuel cells. In this work, a mullite-spinel-structured SmMn2O5-NiMn2O4 (SMO-NMO) composite cathode was one-step synthesized via a solid-liquid composite route, and its in-situ self-assembly enabled good compatibility with the electrolyte without any barrier layer. Characterization results showed that the SMO:NMO = …


In-Situ Stm Visualization Of Molecular Structural Evolution During Electrochemical Oxidation Coupling Of Para-Aminothiophenol On Au(111), Zi-Wei Ma, Tai-Rui Wu, An-Ni Zheng, Lai-Ke Chen, Yuan-Hui Xiao, Zhao-Bin Chen, Qing-Na Zheng, Jian-Zhang Zhou, Jia-Wei Yan, De-Yin Wu Jul 2026

In-Situ Stm Visualization Of Molecular Structural Evolution During Electrochemical Oxidation Coupling Of Para-Aminothiophenol On Au(111), Zi-Wei Ma, Tai-Rui Wu, An-Ni Zheng, Lai-Ke Chen, Yuan-Hui Xiao, Zhao-Bin Chen, Qing-Na Zheng, Jian-Zhang Zhou, Jia-Wei Yan, De-Yin Wu

Journal of Electrochemistry

Para-aminothiophenol (PATP) is not only a widely-used probe molecule in the field of surface-enhanced Raman spectroscopy (SERS), but also an important model molecule for interfacial reactions, exhibiting distinct photo- and electro-oxidation pathways, so that PATP is selectively activated under different external fields. The evolution of products and intermediates during electrochemical oxidative coupling remains unknown. In this study, we have investigated the dynamic electrochemical oxidation process of PATP on the Au(111) surface using cyclic voltammetry, electrochemical (EC)-SERS, and in situ electrochemical scanning tunneling microscopy (EC-STM). The results showed that PATP forms an unsaturated adsorption coverage on Au(111) in an acidic solution. …


Distribution And Transport Of Lithium Ions At Interfaces Between Graphite And Carboxymethyl Celluloses, Zi-Jun Huang, Zhen-Ying Zheng, Hua-Wei Cao, Jian Wang, Qing-Feng Zhang, Sheng-Li Chen Jun 2026

Distribution And Transport Of Lithium Ions At Interfaces Between Graphite And Carboxymethyl Celluloses, Zi-Jun Huang, Zhen-Ying Zheng, Hua-Wei Cao, Jian Wang, Qing-Feng Zhang, Sheng-Li Chen

Journal of Electrochemistry

Carboxymethyl cellulose (CMC) is a water-processable binder widely used for graphite anodes. However, a microscopic understanding of why the identity of CMC counterions (Li+/Na+/K+) strongly affects electrode performance remains limited. Here, molecular dynamics (MD) simulations are used to track Li+ transport accessibility across electrolyte/CMC/graphite three-phase interfaces, comparing pure CMC-Li, CMC-Na, CMC-K, and mixed-counterion CMC binders. We find that CMC-Li sustains a continuous Li+ transport pathway from the electrolyte through the binder phase toward graphite. In contrast, in CMC-Na and CMC-K, Na+/K+ ions preferentially enrich at the graphite/binder interface, forming …


Distinct Co2 Electroreduction Behaviors Over Planar And Non-Planar Cobalt Molecular Catalysts, Ru Jia, Cheng-Biao Zhu, Zi-Mo Zhang, Tuo Wang, Kai-Cong Yang, Guang-Zhe Wang, Yang Hu, Ting-Ting Zhang, Zhen-Wei Wei, Li Xiao, Gong-Wei Wang, Lin Zhuang Jun 2026

Distinct Co2 Electroreduction Behaviors Over Planar And Non-Planar Cobalt Molecular Catalysts, Ru Jia, Cheng-Biao Zhu, Zi-Mo Zhang, Tuo Wang, Kai-Cong Yang, Guang-Zhe Wang, Yang Hu, Ting-Ting Zhang, Zhen-Wei Wei, Li Xiao, Gong-Wei Wang, Lin Zhuang

Journal of Electrochemistry

Molecular catalysts serve as ideal platforms for studying electrocatalytic reaction mechanisms. While current research mainly focuses on modulating central metals or surrounding ligands, the influence of molecular spatial configuration remains largely unexplored. Herein, we synthesized two cobalt complexes with similar ligand environments but distinct spatial geometries, a planar cobalt hexaazamacrocyclic complex (CoHAM) and a non-planar acyclic Co(phen)2Cl2, and evaluated their performance in CO2 reduction reaction (CO2RR). The planar CoHAM exhibited dramatically superior CO2RR performance compared to the non-planar Co(phen)2Cl2. Through a series of combined analyses using in-situ …


Tuning Ion Mobility And Molecular Confinement In High-Performance Polymer Electrolytes For Energy Storage, Ezzeldien Yousef Muhammed Yousef Jun 2026

Tuning Ion Mobility And Molecular Confinement In High-Performance Polymer Electrolytes For Energy Storage, Ezzeldien Yousef Muhammed Yousef

Theses and Dissertations

This research addresses the critical energy density limitations of aqueous supercapacitors, which are traditionally constrained by the narrow electrochemical stability window (ESW) of water 1.23 V. By employing two distinct molecular engineering strategies, this study developed high-performance electrolyte systems that significantly extend voltage stability and thermal resilience.

The first system, CsBr@PAM/HA, utilizes a polyacrylamide and hyaluronic acid hydrogel matrix. This system exploits the chaotropic nature of Cs+ ions to disrupt the aqueous hydrogen-bonding network, enhancing ionic conductivity to 104 mS cm-1. Through systematic salt screening, CsBr was identified as the optimal electrolyte, enabling a stable 2.0 V …


Supramolecular Assembly In Short Peptide Systems For Selective Metabolite Recognition And Drug Nanoencapsulation, Maithreyi Ramakrishnan Jun 2026

Supramolecular Assembly In Short Peptide Systems For Selective Metabolite Recognition And Drug Nanoencapsulation, Maithreyi Ramakrishnan

Dissertations, Theses, and Capstone Projects

Short peptides can form adaptive supramolecular assemblies, and understanding how minimal sequences organize around neurometabolites or hydrophobic cancer drugs enables the rational design of functional materials. This thesis combines molecular dynamics with experimental validation to establish design rules linking peptide sequence to emergent structure and function. Chapter 1 outlines the molecular determinants governing peptide assembly. Chapter 2 reviews computational workflows that reveal sequence-dependent conformations and supramolecular organization. Chapter 3 applies these principles to Dynamic Peptide Libraries which identify tetrapeptides that selectively interact with neurometabolites. Chapter 4 extends the same interaction-driven framework to design tryptophan-rich pentapeptides that co-assemble with kinase inhibitors …


Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel Jun 2026

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …


Computer-Aided Development Of Novel Antioxidants, Rita Bernadett Vlocsko May 2026

Computer-Aided Development Of Novel Antioxidants, Rita Bernadett Vlocsko

Graduate Doctoral Dissertations

Physiological redox homeostasis is a fine balance between prooxidants and antioxidants that are integrated elements of several reduction-oxidation mechanisms at molecular, organellar, cellular and tissue levels. When this equilibrium is disrupted and prooxidants become dominant, the body relies on endogenous and exogenous antioxidants to counterbalance the dysregulation and ultimately prevent the progression of oxidative stress. Reactive species (reactive oxygen species, reactive nitrogen species, or reactive sulfur species) are significant contributors to prooxidant activity. Over the years, substantial knowledge has been accumulated regarding their origin and roles in disease development, leading to the discovery and development of antioxidants that effectively target …


Computational-Experimental Synergy As A Predictive And Interpretive Tool Through Metal-Organic Framework Investigations, Cristian Sayers May 2026

Computational-Experimental Synergy As A Predictive And Interpretive Tool Through Metal-Organic Framework Investigations, Cristian Sayers

Graduate Student Theses and Dissertations

In the search for tunable materials platforms capable of addressing both clean energy conversion and viable post-combustion carbon capture, metal-organic frameworks (MOFs) have emerged as a uniquely versatile class of porous solids offering high specific surface area, structural tunability, and chemically addressable metal nodes and organic linkers. Realizing their potential requires understanding behavior that spans atomic-scale electronic structure and bulk-scale property response, a regime in which neither computation nor experiment alone is sufficient. This work attempts to develop a tighter integration between density functional theory (DFT) and laboratory investigation, treating the two modalities as mutually informing probes of the same …


Microtubules In Breast Cancer: Exploring The Α/Β-Tubulin Toggle Switch And Its Implications In Human Breast Cancer, Annemarie Ianos May 2026

Microtubules In Breast Cancer: Exploring The Α/Β-Tubulin Toggle Switch And Its Implications In Human Breast Cancer, Annemarie Ianos

Student Theses and Dissertations

Microtubules, composed of a/b-tubulin heterodimers, play a central role in breast cancer tumor growth by polymerizing, leading to metastasis and depolymerizing, contributing to proliferation. Human enzymes protein kinase Ca (PKC-a) and cyclin-dependent kinase 1 (Cdk-1) mediate phosphorylation at sites a:Ser165 and b:Ser172, respectively, influencing the growth of microtubules. It is possible that alternating phosphorylation at these sites contribute to an a/b-tubulin “toggle switch” that mediates microtubule instability and tumor growth.

The project investigates the influence of the toggle switch model on microtubule stability by determining the impact of mutants (a:S165D, a:S165N, a:S165SP, b:S172SP and a:S165SP/b:S172S …


Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix May 2026

Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix

Chemistry and Chemical Biology ETDs

Advancements in machine learning have emerged as a pivotal tool in computational biochemistry, offering new advancements to address challenges in protein structure and function. However, current machine-learning approaches offer limited insight in understanding protein dynamics. The purpose of this work is to combine traditional physics-based computational tools, such as molecular dynamics and coarse-grained simulations, with recently developed AI-driven computational tools to bridge gaps and advance the understanding of proteins in both structural and dynamic aspects. I investigated several approaches such as (i) traditional physics-based methods to study protein conformation and ensembles; (ii) identifying a peptide inhibitor for the PICK1 PDZ …


Energetic Eutectics: An Experimental And Computational Investigation On Explosive Deep Eutectic Solvents, Connor J. Parker May 2026

Energetic Eutectics: An Experimental And Computational Investigation On Explosive Deep Eutectic Solvents, Connor J. Parker

All Theses

This study reports on the incorporation an extreme gradient boosting (XGBoost) machine learning strategy tailored to identifying potential high-energy, insensitive explosive deep eutectic solvents. 1,1-diamino-2,2-dinitroethylene (FOX-7) was investigated as the explosive of interest in our eutectic modeling. The resulting predictions highlighted a wide range of binary compositions demonstrating significant depression from the FOX-7 melting temperature with >70% probabilities of formation. Subsequent computational investigation into select mixtures provided underlying stabilization energies and optimized mixture geometries, which were then assessed experimentally with near simulant compounds oxalyldihydrazide and 1-methyl-3- nitroguanidine replacing FOX-7.

Experimental results with these chosen simulants did not demonstrate classical eutectic …


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 …


Exploring The Effects Of Polymer-Graphene Interactions On Bulk Composite Properties Using Finite Element Analysis, Bryant Grove May 2026

Exploring The Effects Of Polymer-Graphene Interactions On Bulk Composite Properties Using Finite Element Analysis, Bryant Grove

Dissertations

As a filler in high performance materials, graphene significantly enhances the mechanical properties of polymer composites. Experimental characterization of graphene composite enhancements is limited by labor-intensive processes in both synthesizing composites for different purposes and in characterizing the interactions between graphene and polymer composites that lead to these enhancements. Computational approaches such as finite element analysis (FEA) are suitable alternatives that go beyond experimental analysis. This dissertation demonstrates the utility of FEA in analyzing polymer graphene composites with an emphasis on modeling the interaction between graphene fillers and the matrix within the interphase formed between them. The accessible design framework …


Computational Studies Of Alpha-Lactalbumin Binding To Perfluorodecanoic Acid, Randhal Smith Ramirez Orozco May 2026

Computational Studies Of Alpha-Lactalbumin Binding To Perfluorodecanoic Acid, Randhal Smith Ramirez Orozco

Open Access Theses & Dissertations

This thesis investigates the structural and thermodynamic interactions between Perfluorodecanoic acid (PFDA) and bovine alpha-lactalbumin (ALAC), a critical milk protein essential for infant nutrition. The primary objectives were to computationally determine the most probable binding sites of PFDA to ALAC and to quantify the strength of these interactions alongside the structural changes they induce. This study addresses a critical gap in understanding how persistent environmental contaminants like PFDA are recruited and transported by nutritional proteins within the milk matrix. The methodology integrated high-throughput molecular docking with long-range, molecular dynamics (MD) simulations to provide a dynamic characterization of the ALAC-PFDA complex. …


Evaluating The Applicability Of Gamess For Determining Bond Lengths And Bond Dissociation Energies Through Constructing Potential Energy Curves For H2, N2, F2, Cl2, And Br2, Iaroslavna Kovalenko, Jillian Pabalan Apr 2026

Evaluating The Applicability Of Gamess For Determining Bond Lengths And Bond Dissociation Energies Through Constructing Potential Energy Curves For H2, N2, F2, Cl2, And Br2, Iaroslavna Kovalenko, Jillian Pabalan

Research and Creativity Symposium

The applicability and limitations of the GAMESS dihydrogen potential energy curve computational tool were evaluated for the following diatomic molecules: H2, N2, F2, Cl2, and Br2. The aug-cc-pVDZ basis set and the B3LYP density functional theory (DFT) functional were employed to ensure more accurate electronic energy results for each calculation. Potential energy curves were generated for each molecule by plotting the electronic energy as a function of interatomic distance, and the bond dissociation energies (BDEs) and radii of diatomic molecules were determined. The radii were determined to be 76 pm …


Robust Thermodynamic Analysis Of Flexible Protein-Ligand Binding Using Statistical Mechanics, Mitchell Dulaney Apr 2026

Robust Thermodynamic Analysis Of Flexible Protein-Ligand Binding Using Statistical Mechanics, Mitchell Dulaney

Create@State

Understanding how proteins bind small molecules is essential for accurate computational modeling of biological systems. However, calculating binding free energy (delta G), enthalpy (delta H), and entropy (delta S) becomes unreliable when proteins are flexible, and ligands are between multiple binding positions. This motion causes traditional computational methods to produce inconsistent thermodynamic values.

A computational workflow was implemented that included docking to predict likely binding positions, molecular dynamics simulations to sample how the protein and ligand move over time, and statistical mechanics analysis to calculate thermodynamic quantities. A new theoretical framework was developed and implemented in a custom program to …


Exploring Ancestral Enzymes Through Sequence Reconstruction And Stability Prediction, Jeyun Park, Masakatsu Watanabe Apr 2026

Exploring Ancestral Enzymes Through Sequence Reconstruction And Stability Prediction, Jeyun Park, Masakatsu Watanabe

SACAD: Scholarly Activities

Proteins evolve through sequence changes that shape structure, stability,

and function. Ancestral sequence reconstruction (ASR) infers ancestral

proteins from modern homologs, but many studies focus on sequence

inference without evaluating structural or energetic feasibility.

β-lactamases provide an ideal model due to their evolutionary diversity and

clinical relevance in antibiotic resistance.

Here, we present an integrated ASR workflow combining phylogenetic

inference (IQ-TREE), ancestral reconstruction, and structural and stability

validation using AlphaFold and FoldX. By reanalyzing a curated β-

lactamase dataset and comparing with a recent study (Risso et al., 2013),

we provide a controlled comparison of ancestral sequences, predicted

structures, and …


Calculating Potential Energy Curves Of Molecular Hydrogen And Its Ion Using Psi4 For Blinc Fusion Applications*, Angelina Castillo, Oscar Coral, Canaan Hercules, Blake Laing, Vola Andrianarijaona Apr 2026

Calculating Potential Energy Curves Of Molecular Hydrogen And Its Ion Using Psi4 For Blinc Fusion Applications*, Angelina Castillo, Oscar Coral, Canaan Hercules, Blake Laing, Vola Andrianarijaona

Campus Research Month

Southern Adventist University’s Beamline for Ionic and Neutral Collisions (BLINC) is investigating the interactions between hydrogen molecules and fusion particles. To perform in-house theoretical calculations, the BLINC Theory and Analysis Group is testing Psi4 as a viable computational method for BLINC fusion research. Successful calculations of the potential energy curves and dissociation energies of H2 and H2+ have been completed and compared to known values. Preliminary results align with known values, demonstrating Psi4’s potential for BLINC research. Future work will focus on the vibrational energies, wavefunctions, and transition probabilities of H2 and H2+.


The Hartree-Fock Method: Quantum Theory To Python Code, Joshua Lohr Apr 2026

The Hartree-Fock Method: Quantum Theory To Python Code, Joshua Lohr

Campus Research Month

This poster presents a Restricted Hartree-Fock (RHF) program that solves the Roothaan-Hall equations within a finite basis set. Starting from an initial guess density, the Fock matrix is constructed via Coulomb and Exchange contributions. The resulting pseudo-eigenvalue problem is solved iteratively until self consistency. The electronic energy of water was calculated using the STO-3G basis set and validated against PySCF as a reference.


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 …


Entropy Of Metal/Solution Interfaces: Thermodynamic Framework, Theoretical Models, And Roles Of Interfacial Water, Zeng-Ming Zhang, Zi-Xi Liang, Jun Huang Mar 2026

Entropy Of Metal/Solution Interfaces: Thermodynamic Framework, Theoretical Models, And Roles Of Interfacial Water, Zeng-Ming Zhang, Zi-Xi Liang, Jun Huang

Journal of Electrochemistry

Entropy is a basic thermodynamic property of the electrical double layer (EDL) at metal/solution interfaces, yet, its definition, measurement, and theoretical treatment are dispersed in the literature, and, in some cases, ambiguous. In this paper, we revisit the thermodynamic theory of EDL, from which two variants of entropy, excess entropy and formation entropy, are obtained and compared. In terms of the formation entropy, two calculation routes are validated in the context of a primitive EDL model, namely, the Gouy-Chapman (GC) model. After clarifying the concepts and calculation routes, we investigate interfacial water effects on the EDL entropy, using a refined …


Deciphering The Role Of Binder Reaction Exothermicity In Thermal Runaway Of Lithium-Ion Cells, Wen Wen, Jing-Hong Zhou, Hao-Tian Lu, Xing-Gui Zhou Mar 2026

Deciphering The Role Of Binder Reaction Exothermicity In Thermal Runaway Of Lithium-Ion Cells, Wen Wen, Jing-Hong Zhou, Hao-Tian Lu, Xing-Gui Zhou

Journal of Electrochemistry

Thermal safety associated with lithium-ion cells as power sources remains a critical industry concern. A comprehensive understanding of how internal exothermic side reactions contribute to temperature rise is fundamental for accurately analyzing thermal runaway processes and predicting the thermal safety of lithium-ion cells. While various side-reactions, such as decomposition of solid electrolyte interphase layer, reaction between anode materials and electrolyte, reaction between cathode materials and electrolyte, and electrolyte decomposition, have been identified as heat generation sources in previous studies, the quantification of these reactions remains insufficiently standardized. Particularly, the impact of heat generation from binder decomposition (most commonly polyvinylidene difluoride) …