Digital Commons Network^™

Domain Rearrangement And Denaturation In Ebola Virus Protein Vp40, Rudramani Pokhrel, Pornthep Sompornpisut, Prem Chapagain, Brian Olson, Bernard Gertsman, Ras B. Pandey

Faculty Publications

The VP40 protein plays a critical role in coordinating the virion assembly, budding, and replication of the Ebola virus. Efforts have been made in recent years to understand various aspects of VP40 structure, dynamics, and function such as assembly of the protein and its roles in virus replication and penetration of the protein into the plasma membrane. A major conformational transformation is necessary for VP40 to form some of its oligomeric structures and to perform various functions. This conformational change from a compact structure with the N-terminal domain (NTD) and C-terminal domain (CTD) closely associated involves a dissociation or springing-out …

Insights Into The Association Of Proteins And Small Molecules With The Minor Groove Of Dna, Emma Kathleen Carter

Chemistry Dissertations

The recognition of specific DNA sequences is fundamental to the central dogma of molecular biology wherein DNA is transcribed to RNA and RNA is translated to protein. Without the ability to recognize specific target sties errors in transcription occur that can result in detrimental mutations and disease. Through the use of molecular dynamics and biophysical computational methods, it is possible to investigate the interactions between nucleic acids other biomolecules at the atomistic level. This leads to a physical interpretation of the underlying mechanics of these crucial interactions. In this dissertation two biomolecules that interact specifically with the minor groove of …

Optimization And Validation Of Efficient Models For Predicting Polythiophene Self-Assembly, Evan D. Miller, Matthew L. Jones, Michael M. Henry, Paul Chery, Kyle Miller, Eric Jankowski

Materials Science and Engineering Faculty Publications and Presentations

We develop an optimized force-field for poly(3-hexylthiophene) (P3HT) and demonstrate its utility for predicting thermodynamic self-assembly. In particular, we consider short oligomer chains, model electrostatics and solvent implicitly, and coarsely model solvent evaporation. We quantify the performance of our model to determine what the optimal system sizes are for exploring self-assembly at combinations of state variables. We perform molecular dynamics simulations to predict the self-assembly of P3HT at ~350 combinations of temperature and solvent quality. Our structural calculations predict that the highest degrees of order are obtained with good solvents just below the melting temperature. We find our model produces …

Metal Segregation During The Solidification Of Titanium-Aluminum Alloys For 3d Printing Applications, Jwala Parajuli

Master's Theses

Titanium-Aluminum alloys are one of the widely used alloys in multiple engineering applications. They are highly preferred in Selective Laser Melting (SLM) processes due to their low density, high melting temperature, and good strength. Segregation occurs during the solidification of most alloys and produces a non-uniform distribution of atoms. In SLM, segregation may depict the type of adhesion between the two deposited interfacial layers and the strength between the interphase between an already solidified layer and a new one, and overall, the quality of the printed part. In order to avoid segregation, the understanding of the segregation behavior at atomistic …

Real-Time Observation Of Molecular Spinning With Angular High-Harmonic Spectroscopy, Lixin He, Pengfei Lan, Anh-Thu Le, Baoning Wang, Bincheng Wang, Xiaosong Zhu, Peixiang Lu, C. D. Lin

Physics Faculty Research & Creative Works

We demonstrate an angular high-harmonic spectroscopy method to probe the spinning dynamics of a molecular rotation wave packet in real time. With the excitation of two time-delayed, polarization-skewed pump pulses, the molecular ensemble is impulsively kicked to rotate unidirectionally, which is subsequently irradiated by another delayed probe pulse for high-order harmonic generation (HHG). The spatiotemporal evolution of the molecular rotation wave packet is visualized from the time-dependent angular distributions of the HHG yields and frequency shift measured at various polarization directions and time delays of the probe pulse. The observed frequency shift in HHG is demonstrated to arise from the …

Phylogeny, Heat-Stress And Enzymatic Heat-Sensitivity In The Antarctic Psychrophile, Chlamydomonas Sp. Uwo 241, Marc Possmayer

Electronic Thesis and Dissertation Repository

Psychrophilic species, micro-organisms which are unable to grow at temperatures of or above 20°C, are abundant in perennially cold ecosystems across the globe. Intensifying scientific investigation of these organisms from ecological to molecular scales has underscored the ability of life on Earth to adapt to environments which seem inhospitable due to high or low temperatures, high salinity, pressure and light, and ultra-low nutrient availability. Psychrophilic organisms that are also photosynthetic represent a much more limited group than psychrophiles generally, as their habitats must be well buffered against the warming influence of the infra-red energy accompanying sunlight. Photosynthetic psychrophiles face the …

Lowest Matric Potential In Quartz: Metadynamics Evidence, Chao Zhang, Yi Dong, Zhen Liu

Zhen Liu

The lowest matric potential is an important soil property characterizing the strength of retaining water molecules and a key parameter in defining a complete soil water retention curve. However, the exact value of the lowest matric potential is still unclear and cannot be measured due to the limitation of current experimental technology. In this study, a general theoretical framework based on metadynamics was proposed to determine the lowest matric potential in quartz minerals. The matric potential was derived from partial volume free energy and can be further calculated by the difference between the adsorption free energy and self‐hydration free energy. …

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This …

Modeling And Performance Analysis Of A Sloshing Ferrofluid Based Electromagnetic Energy Harvester, Qi Liu

All Dissertations

Computational modeling and performance analysis are carried out for a ferrofluid based electromagnetic energy harvester which converts ambient vibratory energy into electromotive force through sloshing motion of a ferrofluid. The system consists of a tank partially filled with ferrofluid, magnets placed on the opposite sides of the tank and a copper coil wound around the tank. In the presence of an external magnetic field, magnetic dipoles in the ferrofluid rotate and produce a net magnetic moment aligned in the direction of the field. When the device is subjected to an external excitation, the ferrofluid in the tank undergoes a sloshing …

Structure-Function Relationships In Hexacoordinate Heme Proteins: Mechanism Of Cytoglobin Interactions With Exogenous Ligands, Antonija Tangar

FIU Electronic Theses and Dissertations

Cytoglobin (Cygb) and neuroglobin (Ngb) are among the newest members of vertebrate globin family characterized by a classical 3-over-3 α-helical fold and a heme prosthetic group capable of reversibly binding small ligands such as O₂, CO and NO. The physiological functions of Cygb and Ngb remain to be determined; however, current data suggest that both proteins have a significant role in cytoprotection in hypoxic and genotoxic conditions. Cytoglobin and Ngb are distinct from their better-known counterparts, hemoglobin (Hb) and myoglobin (Mb), in several structural features. First, in the absence of an external ligand, the sixth coordination site of …

Nearly Defect-Free Dynamical Models Of Disordered Solids: The Case Of Amorphous Silicon, Raymond Atta-Fynn, Parthapratim Biswas

Faculty Publications

It is widely accepted in the materials modeling community that defect-free realistic networks of amorphous silicon cannot be prepared by quenching from a molten state of silicon using classical or ab initio molecular-dynamics (MD) simulations. In this work, we address this long-standing problem by producing nearly defect-free ultra-large models of amorphous silicon, consisting of up to half a million atoms, using classical MD simulations. The structural, topological, electronic, and vibrational properties of the models are presented and compared with experimental data. A comparison of the models with those obtained from using the modified Wooten-Winer-Weaire bond-switching algorithm shows that the models …

Discovering Key Unknowns For Tungsten-Hydrogen-Helium Plasma Material Interactions Using Molecular Dynamics, Mary Alice Cusentino

Doctoral Dissertations

Molecular dynamics simulations have been used to study plasma material interactions to better understand the performance of a tungsten divertor. A tendril-like geometry was modeled to study the diffusion of helium in nanotendrils and its relation to fuzz growth. The tendrils remain stable throughout the simulation and a modified helium release mechanism is found that allows the helium retention to reach a steady state within the tendril. The helium retention within the tendril inversely depends on the surface to volume ratio. There is limited diffusion deep into the tendril and extrapolating the flux calculated to experimentally relevant time scales indicates …

Mass Transport Of Metallic Nanostructures During Sintering Process: A Molecular Dynamics Perspective, Jiaqi Wang

Masters Theses

Sintering of nanomaterials has been broadly utilized as a joining technique in various applications for achieving excellent mechanical, thermal, and electronic properties. However, the joining of the nanomaterial will facilitate the growth of the nanograin, which deteriorate the performance of the mechanical properties. Also, different defects developed during the sintering process deteriorate the thermal and electronic properties. Therefore, how to prevent the growth of the nanograin and the development of the defects during sintering have become an extremely important issue for improving the properties of sintered joints. This research employs molecular dynamics approach to reveal the atomic-scale sintering dynamics and …

Computational Analysis Of Poliovirus Structural Dynamics Using A Coarse-Grained Model, Maneesh Koneru

University Scholar Projects

Though eradicated in most of the world, poliovirus remains a common model virus for a family of mammalian viruses known as Picornaviruses. Despite the development of a vaccination, little is understood about the infection process, particularly the mechanism of cell entry. Experimental studies have attempted to elucidate the dynamics of this process and have proposed pathways focused on VP4, the smallest of the four peptides which makes up the viral capsid, and its interaction with the pentameric interfaces of the five fold axes. This study utilizes coarse-grained molecular dynamics to supplement these proposed mechanisms with simplified simulations which reduce the …

Molecular Dynamics Simulations Of Apo And Holo Forms Of Fatty Acid Binding Protein 5 And Cellular Retinoic Acid Binding Protein Ii Reveal Highly Mobile Protein, Retinoic Acid Ligand, And Water Molecules, Nathanael H. Hunter, Blair C. Bakula, Chrystal D. Bruce

2018 Faculty Bibliography

Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences …

Structure Based Drug Design Of High Affinity Kras Inhibitors, Michael Mccarthy

Dissertations & Theses (Open Access)

RAS, one of the most well characterized membrane-associated small GTPases, is a notorious oncogene with >15% of all tumors harboring RAS mutations. When RAS is mutated it becomes constitutively active sending cell growth, survival and proliferation into overdrive, which subsequently leads to cancer. Although, RAS has been aggressively targeted with drug design efforts for more than 30 years an FDA approved direct inhibitor has not yet been developed. There are three isoforms of RAS in cells; HRAS, NRAS and KRAS. We focused on KRAS since it is the most frequently mutated isoform in cancer. To identify novel non-covalent small molecules …

Enhancing Performance Of Ionic Liquid Property Prediction With Molecular Dynamics., Trisha H. Patel

Electronic Theses and Dissertations

Molecular dynamics have been used to predict thermodynamic and transport properties of eight room-temperature ionic liquids. Simulation parameters including box size and van der Waals cutoffs were varied. The density, heat capacity, and self-diffusion coefficients of the ionic liquids were computed and compared to experimental data and to previously published simulations. Predicted properties were generally close to their experimentally observed values. It was determined that the prediction of ionic liquid properties via molecular dynamics simulations could be accelerated several-fold by using less stringent integration parameters and smaller simulation sizes. The properties of density and heat capacity did not change significantly …

Singlet Oxygen Oxidation Of Guanine, 9-Methylguanine And Guanine-Cytosine Base Pair: Dynamics And Kinetics Revealed By Parallel Gas- And Solution-Phase Experiments And Computations, Wenchao Lu

Dissertations, Theses, and Capstone Projects

Singlet oxygen (¹O₂) oxidatively generated damage of DNA gives rise to mutagenesis, carcinogenesis, and cellular death. Guanine is the most susceptible DNA target of ¹O₂. The related process has been studied over three decades but the mechanism has remained elusive. My thesis research has focused on reaction mechanism, dynamics and kinetics of ¹O₂ oxidation of guanine, 9-methylguanine and guanine-cytosine base pair, from the gas-phase bare ions, through hydrated clusters, to aqueous solution. Various techniques have been adapted in the work, including ¹O₂ generation and detection, guided-ion beam tandem mass …

Computational And Analytical Modelling Of Droplet-Macroion Interactions, Myong In Oh

Electronic Thesis and Dissertation Repository

Charged droplets involving macromolecules undergo distinct disintegration mechanisms and shape deformations as a consequence of droplet-macroion interactions. Three general classes of droplet-macroion interactions that have been identified in the Consta group are: contiguous extrusion of a linear macroion from a droplet, "pearl-necklace" droplet conformations, and "star"-shaped droplets. This dissertation probes in a systematic manner the onset and various outcomes of macroion-droplet interactions, using atomistic molecular dynamics and realistic examples of solvent and macromolecules.

When the charge-squared-to-volume ratio of a droplet is below but near a threshold value, certain flexible macromolecules, such as poly(ethylene glycol), extrude from a droplet, induced by …

Sum Frequency Generation Spectroscopy Of Simulated Protein Secondary Structures., Andrew J. Adams

Electronic Theses and Dissertations

Sum frequency generation (SFG) spectroscopy is an experimental technique for differentiating between various conformations and orientations of interfacial proteins. Combining a theoretical framework for SFG with molecular dynamics (MD) simulations provides a powerful tool for studying systems containing interfacial proteins with applications in cell transport, biofilms, and fermentation processes. Roeters’ method was used to calculate theoretical SFG responses for a variety of individual α-helix and β-sheet peptide secondary structures simulated using MD. Results show how the shape and locations of SFG amide I responses change with differences in hydrogen bonding patterns, peptide orientations, and SFG polarization combinations. The data presented …

Stress Modulated Grain Boundary Mobility, Derek Michael Lontine

Theses and Dissertations

This thesis consists of a thermodynamically based kinetic model that more accurately predicts grain boundary mobility (GBM) over a large range of thermodynamic states including changes in temperature, pressure and shear stress. The form of the model was validated against calculated GBM values for Al bicrystals via molecular dynamics (MD) simulations. A total of 98,786 simulations were performed (164 different GBs, each with a minimum of 250 different thermodynamic states, and 2 different driving forces). Methodology for the computation of the GBM via MD simulations is provided. The model parameters are directly linked to extensive thermodynamic quantities and suggest potential …

Understanding Homogeneous Nucleation In Solidification Of Aluminum By Molecular Dynamics Simulations, A. Mahata, Mohsen Asle Zaeem, M. I. Baskes

Materials Science and Engineering Faculty Research & Creative Works

Homogeneous nucleation from aluminum (Al) melt was investigated by million-atom molecular dynamics simulations utilizing the second nearest neighbor modified embedded atom method potentials. The natural spontaneous homogenous nucleation from the Al melt was produced without any influence of pressure, free surface effects and impurities. Initially isothermal crystal nucleation from undercooled melt was studied at different constant temperatures, and later superheated Al melt was quenched with different cooling rates. The crystal structure of nuclei, critical nucleus size, critical temperature for homogenous nucleation, induction time, and nucleation rate were determined. The quenching simulations clearly revealed three temperature regimes: sub-critical nucleation, super-critical nucleation, …

Hard-Sphere-Like Dynamics In Highly Concentrated Alpha-Crystallin Suspensions, Preeti Vodnala, Laurence Lurio, Michael C. Vega, Elizabeth Gaillard

Faculty Peer-Reviewed Publications

The dynamics of concentrated suspensions of the eye-lens protein alpha crystallin have been measured using x-ray photon correlation spectroscopy. Measurements were made at wave vectors corresponding to the first peak in the hard-sphere structure factor and volume fractions close to the critical volume fraction for the glass transition. Langevin dynamics simulations were also performed in parallel to the experiments. The intermediate scattering function f(q,τ) could be fit using a stretched exponential decay for both experiments and numerical simulations. The measured relaxation times show good agreement with simulations for polydisperse hard-sphere colloids.

3d Momentum Imaging Spectroscopy Probing Of Strong-Field Molecular And Surface Dynamics, Lin Fan

Wayne State University Dissertations

Electron-ion coincidence measurements in combination with 3-dimensional (3D) momentum imaging can provide comprehensive 3D-momentum information to unravel multichannel photoionization/dissociation processes, and thus is an effective tool to investigate atomic/molecular dynamics. A camera-based 3D coincidence momentum imaging system and the velocity mapping imaging (VMI) based machine were introduced in Chapter 2. Studies of strong field dissociative single and double ionization of relatively large molecules camphor and 2-phenylethyl-N, N-dimethylamine (PENNA) were carried out and illustrated in Chapter 3. We demonstrated the main products of double ionization of PENNA were singlet diradicals. In Chapter 4, a novel angle resolved-photoemission spectroscopy based on VMI …

Improved Embedded Atom Method Potentials For Metal Hydride Systems, Robert Fuller

Theses, Dissertations and Capstones

Metal hydride systems are an important research topic in materials science because of their many practical, industrial, and scientific applications. Therefore, the development of reliable and efficient interatomic potentials for metal hydrides systems, to be utilized in molecular simulations, can be of great value in accelerating the research in this field. In this research, fully analytical interatomic Embedded Atom Method (EAM) potentials are developed for the PdAgH system. Ab initio simulations were performed to obtain the properties of selected PdAgH structures for fitting. The potentials are fit utilizing the central atom method without employing time-consuming molecular dynamics simulations in the …

Size- And Composition-Dependent Structure Of Ternary Cd-Te-Se Nanoparticles, Mustafa Kurban

Turkish Journal of Physics

In this study, the geometrical, thermal, and energetic properties of zinc-blende CdTe1-xSex (x = 0.25, 0.50, and 0.75) nanoparticles were investigated using the bond order potential based on the modern classical molecular dynamics (MD) method. All MD simulations were performed using LAMMPS. Some physical properties were investigated, such as compositional variations of Cd, Te, and Se atoms; order parameter; radial distribution function; coordination number; potential energy; and heat capacity (Cv). The simulation results were compared with the available experimental results. The obtained results revealed that an increase in the composition of Se atoms can provide contributions to stability, which is …

Anti-Correlation Between The Dynamics Of The Active Site Loop And C-Terminal Tail In Relation To The Homodimer Asymmetry Of The Mouse Erythroid 5-Aminolevulinate Synthase, Insung Na, Dominique Catena, Min J. Kong, Gloria C. Ferreira, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Biosynthesis of heme represents a complex process that involves multiple stages controlled by different enzymes. The first of these proteins is a pyridoxal 5′-phosphate (PLP)-dependent homodimeric enzyme, 5-aminolevulinate synthase (ALAS), that catalyzes the rate-limiting step in heme biosynthesis, the condensation of glycine with succinyl-CoA. Genetic mutations in human erythroid-specific ALAS (ALAS2) are associated with two inherited blood disorders, X-linked sideroblastic anemia (XLSA) and X-linked protoporphyria (XLPP). XLSA is caused by diminished ALAS2 activity leading to decreased ALA and heme syntheses and ultimately ineffective erythropoiesis, whereas XLPP results from “gain-of-function” ALAS2 mutations and consequent overproduction of protoporphyrin IX and increase in …

Understanding Carbohydrate Recognition Mechanisms In Non-Catalytic Proteins Through Molecular Simulations, Abhishek A. Kognole

Theses and Dissertations--Chemical and Materials Engineering

Non-catalytic protein-carbohydrate interactions are an essential element of various biological events. This dissertation presents the work on understanding carbohydrate recognition mechanisms and their physical significance in two groups of non-catalytic proteins, also called lectins, which play key roles in major applications such as cellulosic biofuel production and drug delivery pathways. A computational approach using molecular modeling, molecular dynamic simulations and free energy calculations was used to study molecular-level protein-carbohydrate and protein-protein interactions. Various microorganisms like bacteria and fungi secret multi-modular enzymes to deconstruct cellulosic biomass into fermentable sugars. The carbohydrate binding modules (CBM) are non-catalytic domains of such enzymes that …

Atomistic Insights Into Photoprotein Formation: Computational Prediction Of The Properties Of Coelenterazine And Oxygen Binding In Obelin, Thomas M. Griffiths

University of Wollongong Thesis Collection 2017+

Bioluminescence in marine systems is dominated by the use of one ligand for light production, coelenterazine. The bioluminescent reaction of coelenterazine is an enzyme catalysed, oxidative decarboxylation. During the reaction coelenterazine reacts with molecular oxygen to form carbon dioxide, coelenteramide and light. One such class of bioluminescent systems is the Ca[sup]2+-regulated photoproteins. These proteins, rather than continuously processing substrate, bind 2-hydroperoxycoelenterazine as an intermediate along the reaction pathway. The reaction is halted here until an external stimulus triggers the continuation of the bioluminescent reaction. There are currently no reported experimental, atomistic descriptions of the states that lead to this ternary …

Mathematical Modelling For Graphitic Nanostructures, Thomas Dyer

University of Wollongong Thesis Collection 2017+

Graphitic nanomaterials have been some of the most widely studied materials of the last decade. The isolation of monolayer graphene in 2004 sparked attention from numerous researchers due to the sheer breadth of its exceptional properties. Thus, it is important that theoretical models keep up with the pace of experimental discovery.

Remarkably, macroscale modelling techniques translate well to nanoscale application. Treating graphitic structures as continuous surfaces allows the application of continuum mechanics and variational calculus amongst others. This thesis involves the formulation and subsequent analysis of three mathematical models relating to the conformation of graphitic structures.

Firstly, we study the …