Digital Commons Network^™

Probing The Regulatory Role Of Allostery Via Protein Dynamics Of Biological Systems, Michael G. Souffrant

Chemistry Dissertations

Allostery is a universal process in cellular interaction and function. Allosteric regulation occurs when local changes from a distant site of the biomolecular structure alter the changes at the binding site. Allosteric regulation is an intrinsic property, which is assumed to be a propagation of conformational or dynamical changes through a network of interactions from the regulatory site to the binding site cavity. Despite many approaches, the concept of allostery is vaguely understood, as this phenomenon occurs at different cellular levels for regulation. In this dissertation, we provide more insight on allosteric regulation, using three different protein systems as models …

Classification Of Nuclear Pastas Through Alpha Shapes Model, Daniela Ramirez Chavez

Open Access Theses & Dissertations

The nuclear pasta is important because is an astromaterial with incredible strength that may be a source for gravitational waves, which observe from the rotation of neutron stars. The characterization of the pasta is vital because the nuclear phases have transport properties - compressibility, neutrino opacity, thermal conductivity, and electrical conductivity - associated with their shape for which neutron stars may be sensitive. These properties could interpret observations of supernova neutrinos, magnetic field decay, and crust cooling of accreting neutron stars. Here, we study the nuclear pasta using alpha shapes to achieve a phase characterization with the Minkowski functionals (area, …

Comparative Analysis Of Conformational Transition Pathways In Homologous Proteins, Dylan Sebastien Ogden

Graduate Theses and Dissertations

Molecular dynamics (MD) simulations are routinely used to study the dynamics of proteins. However, conventional MD limited to the sampling of local conformational changes as the functionally important conformational transitions of proteins often extend beyond the timescales of the simulations employed, for example, membrane transport proteins. We have determined the combination of multiple MD based techniques that allows for a rigorous characterization of energetics and kinetics of large-scale conformational changes in membrane proteins. The methodology is based on biased, nonequilibrium collective variable based simulations including nonequilibrium pulling, string method with swarms of trajectories, bias-exchange umbrella sampling, and rate estimation techniques. …

Multiscale Investigation Of Freeze Cast Process And Ion Transport For Graphene Aerogel Electrodes, Yu-Kai Weng

Doctoral Dissertations

Effective use of renewable energy resources has been regarded as the most promising solution to climate emergency and energy crisis. However, the fluctuating and intermittent nature of renewable resources causes stability issues in the electric grid. High-capacity electrical energy storage is essential to stabilize the electric power supply using renewable resources. Among various types of energy storage systems, organic redox flow battery (ORFB) has attracted attentions due to their high stability, flexibility, low cost, and environmental compatibility, but the performance of the ORFB still needs a significant improvement due to their low energy or current density. Specifically, even though the …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

A Numerical Simulation Of The Powder Bed Additive Manufacturing Process With Molecular Dynamics Simulation, Yeasir Mohammad Akib

Theses and Dissertations

Many manufacturing industries utilize powder bed fusion (PBF) since it can produce microscale precision 3D parts. During PBF, powder particles are selectively fused layer by layer using thermal energy. The build quality in the PBF process relies heavily on powder bed properties and thermal energy deposition. Powder flowability, spreadability, and packing fraction are some of the insightful factors that determine the quality of the powder bed. In this study, a two-dimensional powder bed is developed using the LAMMPS package. A cloud-based pouring of powders with varying volumes and initialization is adopted for the work. A blade-type and circular recoater is …

Molecular Dynamics Simulations Of The Adenylate Kinase Enzyme And Its Mutant States, Beata Izabella Dulko Smith

Chemistry & Biochemistry Dissertations

Adenylate kinase (AK) is a small, monomeric enzyme present across all domains of life. It is responsible for maintaining homeostasis of an intracellular adenylate pool and catalyzes a reversible transfer of the phosphoryl group from NTP (nucleoside triphosphate) to NMP producing two NDP molecules. While most known isoforms take ATP as phosphate donor, AK3 present in mitochondrial matrix employs GTP. Crystallographic investigations revealed that the basis for its selectivity for GTP over ATP came from an additional hydrogen bond between guanosine’s O6 and backbone nitrogen of threonine is responsible for recognition of GTP. Molecular dynamics (MD) simulations have demonstrated that …

Understanding Effect Of Ionic Liquid On Metalloproteins: Laccase And Azurin, Aashka Y. Patel

Theses and Dissertations

Interactions between ionic liquids and biomolecules have been of great interest due to the intrinsic properties of ionic liquids and the flexibility to mix and match cations and anions to create unique ionic liquids. A number of ionic liquid-biomolecule studies have focused on the interactions with proteins, including industrially relevant enzymes. One of these, laccase from Trametes versicolor, is a naturally derived enzyme used in the breakdown of phenolic compounds in a wide variety of industries, especially useful in breakdown of lignocellulosic materials. Here, a combination of experiments and molecular dynamics (MD) simulations were used to investigate the interactions …

Phytochemical Investigation Of Egyptian Spinach Leaves, A Potential Source For Antileukemic Metabolites: In Vitro And In Silico Study, Shimaa M. Abdelgawad, Mona H. Hetta, Mohamed A. Ibrahim, Premalatha Balachandran

Faculty and Student Publications

Spinacia oleracea L., Amaranthaceae, leaves cultivated in Egypt demonstrated a potential antileukemic activity against the chronic myeloid leukemia, K562 cell line. Thus, the aim of this study is to carry out a phytochemical investigation of S. oleracea leaves as well as the isolation of its antileukemic phytoconstituents. Phytochemical investigation of S. oleracea leaves resulted in the isolation of seventeen known compounds. The biological study revealed that compounds hexaprenol, phytol, and 18-[(1-oxohexadecyl) oxy]-9-octadecenoic acid exhibited a remarkable antiproliferative activity against K562 cells in vitro. A mechanistic in silico study showed that hexaprenol, phytol, and 18-[(1-oxohexadecyl) oxy]-9-octadecenoic acid exhibited a strong binding …

Shear Localization In The Metallic Nanolayered Composites, Shujing Dong

Theses and Dissertations

In this dissertation, the influences of layer thickness (h), interface orientation relationship (OR) and dislocation slip activities on shear band (SB) formation mechanisms was investigated by means of molecular dynamics (MD) simulations.

The effect of h and dislocation slip systems on the shear localization in Cu-FCC/Nb-BCC MNCs was studied. The strain softening observed in those samples was triggered by the SB formation. The microstructure evolutions and dislocation slips revealed that the unsymmetrical dislocation transmission across the interface induces the shear localization and promotes the SB formation. The quantitative analysis of the change in the separation distance of initially …

Probing Mechanisms Of Binding And Allostery In The Sars-Cov-2 Spike Omicron Variant Complexes With The Host Receptor: Revealing Functional Roles Of The Binding Hotspots In Mediating Epistatic Effects And Communication With Allosteric Pockets, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we performed all-atom MD simulations of RBD–ACE2 complexes for BA.1, BA.1.1, BA.2, and BA.3 Omicron subvariants, conducted a systematic mutational scanning of the RBD–ACE2 binding interfaces and analysis of electrostatic effects. The binding free energy computations of the Omicron RBD–ACE2 complexes and comprehensive examination of the electrostatic interactions quantify the driving forces of binding and provide new insights into energetic mechanisms underlying evolutionary differences between Omicron variants. A systematic mutational scanning of the RBD residues determines the protein stability centers and binding energy hotpots in the Omicron RBD–ACE2 complexes. By employing the ensemble-based global network analysis, we …

Ligand-Based Virtual Screening And Molecular Docking Of Benzimidazoles As Potential Inhibitors Of Triosephosphate Isomerase Identified New Trypanocidal Agents, Lenci K. Vazquez-Jimenez, Alfredo Juarez-Saldivar, Rogelio Gomez-Escobedo, Timoteo Delgado-Maldonado, Domingo Mendez-Alvarez, Isidro Palos, Debasish Bandyopadhyay, Carlos Gaona-Lopez, Eyra Ortiz-Perez, Benjamin Nogueda-Torres, Esther Ramirez-Moreno, Gildardo Rivera

Chemistry Faculty Publications and Presentations

Trypanosoma cruzi (T. cruzi) is a parasite that affects humans and other mammals. T. cruzi depends on glycolysis as a source of adenosine triphosphate (ATP) supply, and triosephosphate isomerase (TIM) plays a key role in this metabolic pathway. This enzyme is an attractive target for the design of new trypanocidal drugs. In this study, a ligand-based virtual screening (LBVS) from the ZINC15 database using benzimidazole as a scaffold was accomplished. Later, a molecular docking on the interface of T. cruzi TIM (TcTIM) was performed and the compounds were grouped by interaction profiles. Subsequently, a selection of compounds was made based …

Elucidating The Interfacial Bonding Behavior Of Over-Molded Hybrid Fiber Reinforced Polymer Composites: Experiment And Multiscale Numerical Simulation, Gideon A. Lyngdoh, Sumanta Das

Faculty Publications - Biomedical, Mechanical, and Civil Engineering

This paper implements molecular dynamics (MD) simulation using reactive force field (ReaxFF) to evaluate the

atomistic origin of the interfacial behavior in the overmolded hybrid unidirectional continuous carbon fiber low-melt PAEK (CFR- LMPAEK)-short carbon fiber reinforced PEEK (SFR-PEEK) polymer composites. From the MD simulation, it was observed that the

interfacial properties improve with increasing maximum processing temperature and injection pressure although such an improving trajectory gets saturated beyond specific limits. The interfacial strength and fracture response of the hybrid polymer system at the interface are also evaluated. The mechanical responses obtained from MD simulation are used as adhesive properties in …

Investigation Of Adhesion Performance Of Wax Based Warm Mix Asphalt With Molecular Dynamics Simulation, Chao Peng, Hanneng Yang, Zhanping You, Hongchao Ma, Fang Xu, Lingyun You, Aboelkasim Diab, Li Lu, Yudong Hu, Yafeng Liu, Jing Dai, Zhibo Li

Michigan Tech Publications

Compared with traditional hot mix asphalt (HMA), wax based warm mix asphalt (WWMA) can be mixed with the aggregate at a lower temperature and achieve the desired compaction. However, the adhesion performance of WWMA on aggregate is uncertain. To evaluate the adhesion performance of asphalt and aggregate, researchers used contact angle test, pull-off test, and ultrasonic washing experiments. However, these tests cannot adequately explain the microscopic mechanism of the interface between asphalt and aggregate. Molecular dynamics (MD) can better explain the adhesion mechanism of asphalt aggregates because they can be simulated at the molecular scale. So, the purpose of this …

Computational Methods, Investigations, And Codes To Support Corrosion Experiments In Molten Lead And Transfer To Reactor Conditions, Khaled A. Talaat

Nuclear Engineering ETDs

Lead cooled fast reactors have many potential economic advantages over other Generation IV reactor designs due to the high boiling point of lead (~1750 °C) at atmospheric pressure and excellent neutronic properties which have made them attractive to the commercial energy sector in the recent years. They, however, remain hampered by challenges in cladding material compatibility with the heavy liquid metal coolant. A forced circulation loop was established at the University of New Mexico (“Lobo Lead Loop”) to prequalify materials for Versatile Test Reactor (VTR) testing and to improve the understanding of flow accelerated corrosion in molten lead environment. Corrosion …

Probing The Link Between Pancratistatin And Mitochondrial Apoptosis Through Changes In The Membrane Dynamics On The Nanoscale, Stuart R. Castillo, Brett W. Rickeard, Mitchell Dipasquale, Michael H.L. Nguyen, Aislyn Lewis-Laurent, Milka Doktorova, Batuhan Kav, Markus S. Miettinen, Michihiro Nagao, Elizabeth G. Kelley, Drew Marquardt

Chemistry and Biochemistry Publications

Pancratistatin (PST) is a natural antiviral alkaloid that has demonstrated specificity toward cancerous cells and explicitly targets the mitochondria. PST initiates apoptosis while leaving healthy, noncancerous cells unscathed. However, the manner by which PST induces apoptosis remains elusive and impedes the advancement of PST as a natural anticancer therapeutic agent. Herein, we use neutron spin-echo (NSE) spectroscopy, molecular dynamics (MD) simulations, and supporting small angle scattering techniques to study PST's effect on membrane dynamics using biologically representative model membranes. Our data suggests that PST stiffens the inner mitochondrial membrane (IMM) by being preferentially associated with cardiolipin, which would lead to …

Enhancement Of Cement Paste With Carboxylated Carbon Nanotubes And Poly(Vinyl Alcohol), Yuyang Zhao, Jinrui Zhang, Gang Qiao, Dongshuai Hou, Biqin Dong, Hongyan Ma

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Cement has been a major consumable material for construction in the world since its invention, but its low flexural strength is the main defect affecting the service life of structures. To adapt cement-based materials to a more stringent environment, carboxylated carbon nanotubes (CNTs-COOH) and poly(vinyl alcohol) (PVA) are proposed to enhance the mechanical properties of cement paste. This study systematically verifies the synergistic effect of CNTs-COOH/PVA on the performance of cement paste. First, UV-Vis spectroscopy and FTIR spectroscopy prove that CNTs-COOH can provide attachment sites for PVA and PVA can improve the dispersion and stability of CNTs-COOH in water, which …

The Importance Of Fitting In: Investigating The Role Of Protein Dynamics In Dna Sequence Specificity, Kenneth Huang

Chemistry Dissertations

Specificity for protein/DNA complexes is well-studied in context of DNA sequence requirements, but the precise mechanisms for how segregation of affinity in consensus-bearing DNA has not been well characterized. Nonspecific sites are dictated by the lack of a consensus site, but high/low affinity binding rise from discrepancies in flanking sequences. Low-affinity DNA has been recently implicated as a general mechanism used by cells to regulate gene expression. Ets-1, the progenitor member of the ETS transcription family, offers a useful model to understand how cognate site discrimination occurs. We then performed molecular dynamics simulations of Ets-1 unbound and bound to nonspecific, …

Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie

Open Access Theses & Dissertations

Computational biology is an interdisciplinary area that applies computational approaches in biological big data, including protein amino acid sequences, genetic sequences, etc., which is widely used to analyze protein-protein interactions, make predictions in drug discovery, develop vaccines, etc. Popular methods include mathematical modeling, molecular dynamics simulations, data science mythology, etc. With the help of computational algorithms and applications, drug development is much faster than traditional processes, as it reduces risks early on in a drug discovery process and helps researchers select target candidates that have the highest potential for success. In my doctoral research, I applied multi-scale computational approaches to …

Spike Protein Structural Dynamics Of Sars-Cov-2 Coronaviruses Studied Using Molecular Dynamics, William Strickland

Biological Sciences Undergraduate Honors Theses

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has overwhelmingly impacted the global population, accounting for millions of confirmed infections and deaths over the last year. The virus’s influence on the health and safety of individuals, the economy, and daily life has been disruptive and devastating. While SARS-CoV-2 and SARS-CoV-1, two closely related members of the SARS coronaviruses, have shown the ability to cross the species barrier and infect humans, SARS-CoV-2 has predominantly been the virus responsible for the number of infections presently known. SARS-CoV-2 has also proven to be volatile, as many variants have …

Computational Studies On Polyunsaturated Fatty Acid Uptake And Its Effects On Antimicrobial Resistance, Andrew Turgeson

Masters Theses and Doctoral Dissertations

The topic of this research was initiated by the discovery, in part by Dr. David Giles, that Vibrio cholerae, the enteric bacteria responsible for the disease cholera, has the ability to uptake and utilize long chain polyunsaturated fatty acids up to 22 carbon atoms long. Before this discovery was made, conventional belief was that fatty acids of greater than 18 carbons long were toxic to bacteria. Further investigations have revealed that this uptake is not unique to Vibrio cholerae, and a range of bacteria such as Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and even Escherichia coli have been found to …

Defining Interactions Between Deformable Dna Origami And Lipid Bilayers Through Molecular Dynamics Simulation, Zachary A. Loyd

Chancellor’s Honors Program Projects

No abstract provided.

Implications Of Metal Coordination In Damage And Recognition Of Nucleic Acids And Lipid Bilayers, Ana Dreab

Chemistry & Biochemistry Theses & Dissertations

Metal ions have a myriad of biological functions from structural stability to enzymatic (de)activation and metabolic electron transfer. Redox-active metals also mediate the formation of reactive oxygen species which may either cause oxidative damage or protect cellular components. Computational modeling is used here to investigate the role of (1) metal-ion binding to antimicrobial peptides, (2) metal-ion removal and disulfide formation on zinc finger (ZF) proteins, and (3) coordination of thiones/selones for the prevention of metal-mediated redox damage.

Piscidins, natural-occurring antimicrobial peptides, efficiently kill bacteria by targeting their membranes. Their efficacy is enhanced in vitro by metal-binding and the presence of …

Computational Investigations Into Binding Dynamics Of Tau Protein Antibodies: Using Machine Learning And Biophysical Models To Build A Better Reality, Katherine Lee

University Scholar Projects

Misregulation of post-translational modifications of microtubule-associated protein tau is implicated in several neurodegenerative diseases including Alzheimer’s disease. Hyperphosphorylation of tau promotes aggregation of tau monomers into filaments which are common in tau-associated pathologies. Therefore, tau is a promising target for therapeutics and diagnostics. Recently, high-affinity, high-specificity single-chain variable fragment (scFv) antibodies against pThr-231 tau were generated and the most promising variant (scFv 3.24) displayed 20-fold increased binding affinity to pThr-231 tau compared to the wild-type. The scFv 3.24 variant contained five point mutations, and intriguingly none were in the tau binding site. The increased affinity was hypothesized to occur due …

A Molecular Dynamics Study Of The Laser Sintering Process And Subsequent Mechanical Properties Of Γ-Tial Nanoparticles, Eleanor Dickens

Honors Theses

Using molecular dynamics (MD) simulations, the laser sintering additive manufacturing process is investigated through the observation of γ-TiAl nanoparticles. This process is conducted using both uni-directional chain and stacking configurations. By mimicking the heating process and varying laser sintering parameters such as heating rater, sintering temperature, and particle orientation, the fusion behavior and resulting products are analyzed for both chain and stacking NP patterns. In of single chain cases, it is noticed that slower heating rates and higher melting temperatures yield larger neck growth between each individual particle and thus produce a more stable product. This leads to stronger mechanical …

Computer Simulations And Network-Based Profiling Of Binding And Allosteric Interactions Of Sars-Cov-2 Spike Variant Complexes And The Host Receptor: Dissecting The Mechanistic Effects Of The Delta And Omicron Mutations, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we combine all-atom MD simulations and comprehensive mutational scanning of S-RBD complexes with the angiotensin-converting enzyme 2 (ACE2) host receptor in the native form as well as the S-RBD Delta and Omicron variants to (a) examine the differences in the dynamic signatures of the S-RBD complexes and (b) identify the critical binding hotspots and sensitivity of the mutational positions. We also examined the differences in allosteric interactions and communications in the S-RBD complexes for the Delta and Omicron variants. Through the perturbation-based scanning of the allosteric propensities of the SARS-CoV-2 S-RBD residues and dynamics-based network centrality and …

A Molecular Dynamics Study Of Monomer Melt Properties Of Cyanate Ester Monomer Melt Properties, Rebecca T. Haber, Andrea R. Browning, Bayleigh R. Graves, William P. Davis, Jeffrey S. Wiggins

Faculty Publications

The objective of this work was to computationally predict the melting temperature and melt properties of thermosetting monomers used in aerospace applications. In this study, we applied an existing voids method by Solca. to examine four cyanate ester monomers with a wide range of melting temperatures. Voids were introduced into some simulations by removal of molecules from lattice positions to lower the free-energy barrier to melting to directly simulate the transition from a stable crystal to amorphous solid and capture the melting temperature. We validated model predictions by comparing melting temperature against previously reported literature values. Additionally, the torsion and …

Repurposing Lansoprazole And Posaconazole To Treat Leishmaniasis: Integration Of In Vitro Testing, Pharmacological Corroboration, And Mechanisms Of Action, Yash Gupta, Steven Goicoechea, Jesus G. Romero, Raman Mathur, Thomas R. Caulfield, Daniel P. Becker, Ravi Durvasula, Prakasha Kempaiah

Journal of Food and Drug Analysis

Leishmaniasis remains a serious public health problem in many tropical regions of the world. Among neglected tropical diseases, the mortality rate of leishmaniasis is second only to malaria. All currently approved therapeutics have toxic side effects and face rapidly increasing resistance. To identify existing drugs with antileishmanial activity and predict the mechanism of action, we designed a drug-discovery pipeline utilizing both in-silico and in-vitro methods. First, we screened compounds from the Selleckchem Bio-Active Compound Library containing ~1,622 FDA-approved drugs and narrowed these down to 96 candidates based on data mining for possible anti-parasitic properties. Next, we completed preliminary in-vitro testing …

Repurposing Lansoprazole And Posaconazole To Treat Leishmaniasis: Integration Of In Vitro Testing, Pharmacological Corroboration, And Mechanisms Of Action, Yash Gupta, Steven Goicoechea, Jesus G. Romero, Raman Mathur, Thomas R. Caulfield, Daniel P. Becker, Ravi Durvasula, Prakasha Kempaiah

Chemistry: Faculty Publications and Other Works

Leishmaniasis remains a serious public health problem in many tropical regions of the world. Among neglected tropical diseases, the mortality rate of leishmaniasis is second only to malaria. All currently approved therapeutics have toxic side effects and face rapidly increasing resistance. To identify existing drugs with antileishmanial activity and predict the mechanism of action, we designed a drug-discovery pipeline utilizing both in-silico and in-vitro methods. First, we screened compounds from the Selleckchem Bio-Active Compound Library containing ~1622 FDA-approved drugs and narrowed these down to 96 candidates based on data mining for possible anti-parasitic properties. Next, we completed preliminary in-vitro testing …

Morphology Of Mos2 Nanosheets And Its Influence On Water/Oil Interfacial Tension: A Molecular Dynamics Study, Yang Feng, Jirui Hou, Yulong Yang, Shuting Wang, Dongsen Wang, Tingting Cheng, Zhenjiang You

Research outputs 2022 to 2026

Plate-shaped nanoparticles exhibit huge potential for a broad range of cutting-edge applications in interfacial-based science and technology, such as enhanced oil recovery in hydrocarbon reservoirs, owing to their remarkable features in superior affinity toward interfaces. Understanding the adsorption behavior of nanosheets (NSs) self-assembled at the water/oil interface (W/O interface) is crucial to elucidate the variation of interfacial tension (IFT) and establish special design criteria for efficient industrial use of NSs. Here we present a molecular dynamics study to reveal the morphology of carbon-chain modified molybdenum disulfide (MoS₂) nanosheets. The stress exerted on a nanosheet is analyzed. The simulation …