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Amyloid Proteins And Fibrils Stability, Farbod Mahmoudinobar

Dissertations

Compared to globular proteins that have a stable native structure, intrinsically disordered peptides (IDP) sample an ensemble of structures without folding into a native conformation.One example of IDP is the amyloid-beta(Abeta) protein which is the main constituent of senile plaques in the brain of Alzheimer's patients.Understanding the process by which IDPs undergo structural changes to form oligomers that eventually aggregate into senile plaques/amyloid fibrils may significantly advance the development of novel therapeutic methods to treat neurodegenerative diseases, for which there is no cure to date. This dissertation has two main objectives. The first one is to investigate and identify structural …

Deciphering The Underlying Physical Processes Responsible For Synergistic Interactions Between Hydrogen And Noble Gases In Materials Under Fusion Relevant Conditions, Zachary Bergstrom Bergstrom

Doctoral Dissertations

The objective of this research is to understand the underlying physical processes responsible for the synergistic interactions between hydrogen and noble gases in materials under fusion relevant conditions. The formation of He bubbles within plasma-facing components is a common phenomena that is expected to occur in the structural materials and first-wall, as well as the divertor, and is has been shown to strongly modify the retention properties for hydrogen of these materials. Molecular dynamics simulations were performed to assess the behavior of H around high pressure helium bubbles. The simulations revealed that hydrogen is strongly trapped to the periphery of …

Study Of Amorphous Boron Carbide And Hydrogenated Boron Carbide Materials Using Molecular Dynamics And Hybrid Reverse Monte Carlo, Rajan Khadka

MSU Graduate Theses

We present a computational study of amorphous boron carbide (a-B_xC) models using Molecular Dynamics (MD) studied with Stillinger-Weber (SW) and ReaxFF potential. The atomic structure factor (S(Q)), radial distribution function (RDF) and bond lengths comparison with other experimental and ab initio models shows that a random arrangement of icosahedra (B₁₂, B₁₁C) interconnected by chains (CCC, CBC) are present in a-B_xC. Afterward, Hybrid Reverse Monte Carlo (HRMC) technique is used to recreate a-B_xC structures. The existing SW potential parameters of Boron are optimized for the α-rhombohedral (Icosahedral B_{12 …}

Molecular Dynamics Simulations Of Interaction Of Dna Nucleotides And Lignin Oligomers With Small Molecules And Interfaces, Xinjie Tong

LSU Doctoral Dissertations

Molecular dynamics (MD) simulations of interaction of DNA nucleotides with self-assembled monolayers (SAMs) provide valuable information that is critical to the development of a new DNA sequencing technique. We investigated the interactions and transport characteristics of mononucleotides moving through nanoslits with SAMs-covered surfaces. Our simulations focused on nanoslits in which the walls were composed of three different types of SAMs: methylformyl terminated, methyl terminated, and phenoxy terminated. The results demonstrated that the phenoxy terminated surfaces have the shortest required nanoslits length for nucleotides separation.

Using MD simulations, we also investigated the interaction of mono-lignin and oligo-lignols with lipid bilayers and …

Combined Molecular Dynamics And Phase Field Simulation Of Crystal Melt Interfacial Properties And Microstructure Evolution During Rapid Solidification Of Ti-Ni Alloys, Sepideh Kavousi

LSU Doctoral Dissertations

Phase field method has become a popular tool to investigate the microstructure evolution during the solidification. Quantitative predictions using this method is still limited, and in this dissertation, we try to study this problem from different perspectives.

Most of the phase field models consider the solid-liquid interface to be in local equilibrium. Solidification during some manufacturing processes like selective laser melting, and electron beam additive manufacturing is rapid and far from equilibrium which can result in supersaturated solid solutions, segregation-free crystals, or metastable phases. Before obtaining any conclusions from the phase field simulations, we must know the answer for “which …

Mechanical Properties Of Hydrogenated Amorphous Silicon (A-Si:H) Particles, Taizhi Jiang, Fardin Khabaz, Aniket Marne, Chenglin Wu, Raluca Gearba, Revanth Bodepudi, Roger T. Bonnecaze, Kenneth M. Liechti, Brian A. Korgel

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

A nanoindenter was used to compress individual particles of hydrogenated amorphous silicon (a-Si:H) ranging in diameter from 290 nm to 780 nm. The colloidal synthesis used to produce the particles enables the hydrogen content to be manipulated over a wide range, from about 5 at. % to 50 at. %, making these a-Si:H particles promising for applications in lithium ion batteries, hydrogen storage, and optical metamaterials. Force-displacement curves generated using a tungsten probe flattened with focused ion beam exhibited elastic and then plastic deformations, followed by fracture and crushing of the particles. For particles with 5% and 50% H, Young's …

Computer Modeling Of Sorption On Composite Sorbents-Photocatalists Based On Bi2wo6 And Reduced Graphene Oxide, Zuhra Chingizovna Kadirova, Mirabbos Ikramovich Hojamberdiev, Zikrilla Bobomuratovich Alimov

CHEMISTRY AND CHEMICAL ENGINEERING

The composite sorbent-photocatalysts based on Bi2WO6 and reduced graphene oxide have been studied by molecular dynamics methods. The sorption and photocatalytic effect of acetaldehyde in the gaseous phase and the chloramphenicol in the aqueous solution are enhanced in the presence of the reduced graphene oxide in the Bi2WO6 composite. The surfaces of the reduced graphene oxide and Bi2WO6 effectively interact with each other with a similar affinity to adsorbate molecules.

Molecular Simulation Study Of Protein Conformation Change, Binding Mechanisms, And Allosteric Communication, Jason Pattis

Doctoral Dissertations

Many processes in biology involve conformational changes or binding events which can be described by a pathway or ensemble of pathways. These processes are challenging to study experimentally as obtaining the temporal and spatial resolution sufficient to understand the underlying physical mechanisms can be challenging. Molecular dynamics (MD) simulations is a powerful tool that can provide atomic resolution on these processes and aid in the design and interpretation of experiments. In this thesis, I will describe MD simulations using enhanced sampling methods to investigate several biomolecular systems, including the Lassa virus nucleoprotein, phosphodiesterase enzymes and a peptide from the Flock …

Fate Of Hydrous Fe-Rich Silicate Melt In Earth's Deep Mantle, Zhixue Du, Jie Deng, Yoshinori Miyazaki, Ho Kwang Mao, Bijaya B. Karki, Kanani K.M. Lee

Faculty Publications

Density of silicate melt dictates melt migration and establishes the gross structure of Earth's interior. However, due to technical challenges, the melt density of relevant compositions is poorly known at deep mantle conditions. Particularly, water may be dissolved in such melts in large amounts and can potentially affect their density at extreme pressure and temperature conditions. Here we perform first-principles molecular dynamics simulations to evaluate the density of Fe-rich, eutectic-like silicate melt (E melt) with varying water content up to about 12 wt %. Our results show that water mixes nearly ideally with the nonvolatile component in silicate melt and …

Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman

Arts & Sciences Electronic Theses and Dissertations

Molecular dynamics simulations are a powerful tool to explore conformational landscapes, though limitations in computational hardware commonly thwart observation of biologically relevant events. Since highly specialized or massively parallelized distributed supercomputers are not available to most scientists, there is a strong need for methods that can access long timescale phenomena using commodity hardware. In this thesis, I present the goal-oriented sampling method, Fluctuation Amplification of Specific Traits (FAST), that takes advantage of Markov state models (MSMs) to adaptively explore conformational space using equilibrium-based simulations. This method follows gradients in conformational space to quickly explore relevant conformational transitions with orders of …

A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers

Arts & Sciences Electronic Theses and Dissertations

The grand challenge of biophysics is to use the fundamental laws of physics to predict how biological molecules will move and interact. The atomistic HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field is meant to address this challenge. It does so by breaking down the intermolecular potential energy function of biomolecular interactions into physically meaningful components (electrostatics, polarization, dispersion, and exchangerepulsion) and using this function to drive molecular dynamics simulations. This force field is able to achieve accuracy within 1 kcal/mol for each component when compared with ab initio Symmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy because …

Algorithmic Improvements And Applications Of Molecular Dynamics Simulations To Probe Condensed Phase Systems, Shanmuga S. Venkatesan

Theses and Dissertations

Molecular dynamics (MD) simulation studies were considered in this study in the fields of phosphonium based ionic liquids (PBILs) and heterogeneous (solid/liquid) zeolite systems. A new generation of ionic liquids (ILs) called phase-separable ionic liquids (PSILs) are able to dissolve cellulose and lignin, a necessary step, for conversion of biomass to fuels and chemicals with co-solvents and are immiscible with water or saline solutions. Molecular simulations on these systems will provide insights of phase behavior and dissolution phenomenon. The knowledge of interfacial phase behavior of ionic liquids/solvent systems is critical for materials discovery for designing efficient dissolution processes. Transition zone …

Analysis Of Individual Molecular Dynamics Snapshots Simulating Wetting Of Surfaces Using Spheroidal Geometric Constructions, Aleksandr Abramov, Stefan Iglauer

Research outputs 2014 to 2021

Accurate characterization of wettability of minerals is important for efficient oil recovery and carbon geosequestration. In studies where molecular dynamics simulations are used to compute the contact angle, emphasis is often placed on results or theoretical details of the simulations themselves, overlooking potentially applicable methodologies for determination of the contact angle. In this manuscript, a concept of a method utilizing spheroidal geometric constructions to estimate the contact angle of a water droplet on a silica surface in carbon dioxide atmosphere is outlined and applied to the final snapshots of two molecular dynamics simulation runs. Two carbon dioxide pressures and two …

Computational Studies Of Thermal Properties And Desalination Performance Of Low-Dimensional Materials, Yang Hong

Department of Chemistry: Dissertations, Theses, and Student Research

During the last 30 years, microelectronic devices have been continuously designed and developed with smaller size and yet more functionalities. Today, hundreds of millions of transistors and complementary metal-oxide-semiconductor cells can be designed and integrated on a single microchip through 3D packaging and chip stacking technology. A large amount of heat will be generated in a limited space during the operation of microchips. Moreover, there is a high possibility of hot spots due to non-uniform integrated circuit design patterns as some core parts of a microchip work harder than other memory parts. This issue becomes acute as stacked microchips get …

An Atomistic Approach For The Survey Of Dislocation-Grain Boundary Interactions In Fcc Nickel, Devin William Adams

Theses and Dissertations

It is well known that grain boundaries (GBs) have a strong influence on mechanical properties of polycrystalline materials. Not as well-known is how different GBs interact with dislocations to influence dislocation movement. This work presents a molecular dynamics study of 33 different FCC Ni bicrystals subjected to mechanical loading to induce incident dislocation-GB interactions. The resulting simulations are analyzed to determine properties of the interaction that affect the likelihood of transmission of the dislocation through the GB in an effort to better inform mesoscale models of dislocation movement within polycrystals. It is found that the ability to predict the slip …

Computational Investigation Of The Interactions Between Bioactive Compounds And Biological Assemblies, Tye D. Martin

Biomedical Engineering ETDs

Small, biologically active molecules with unique properties and applications are potential solutions to a wide range of threats to global health including infectious agents and neurodegenerative disease. Experimental studies on a class of oligomeric p-phenylene ethynylenes (OPEs) have shown potential both as bioactive antimicrobials and fluorescent sensing agents for tracking amyloid-β (Aβ) aggregates found in Alzheimer’s Disease (AD). A second type of small molecule with potential applications in AD therapy, curcumin, has been found to interfere with Aβ fibril growth. Curcumin also attenuates Aβ-membrane interactions and Aβ toxicity. Our goal has been to use computational techniques to better understand the …

Simulation And Software Development To Understand Interactions Of Guest Molecules Inporous Materials, Douglas M. Franz

USF Tampa Graduate Theses and Dissertations

The effect of inclusion of explicit polarization is investigated through several theoret- ical studies of crystalline porous materials herein. In addition to the use of Monte Carlo simulation for such studies, a robust molecular dynamics software is presented which is suitable for analyzing time dependent properties of gases or other molecules in porous materials and other condensed phase systems. Metal-organic frameworks (MOFs) are the main focus of the work included here, a relatively young class of materials originally in- troduced in the early 1990s. These are usually three dimensional crystalline nanoporous materials that exhibit unique properties such as gas separation, …

Multiscale Simulations Of Intrinsically Disordered Proteins, Xiaorong Liu

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) lack stable secondary and/or tertiary structures under physiological conditions. The have now been recognized to play important roles in numerous biological processes, particularly cellular signaling and regulation. Mutation of IDPs are frequently associated with human diseases, such as cancers and neuron degenerative diseases. Therefore, it is important to understand the structure, dynamics, and interactions of IDPs, so as to establish the mechanistic basis of how intrinsic disorder mediates versatile functions and how such mechanisms may fail in human diseases. However, the heterogeneous structural ensembles of IDPs are not amenable to high resolution characterization solely through experimental …

In Silico Identification Of Genetic Mutations Conferring Resistance To Acetohydroxyacid Synthase Inhibitors: A Case Study Of Kochia Scoparia, Yan Li, Michael D. Netherland, Chaoyang Zhang, Huixiao Hong, Ping Gong

Faculty Publications

Mutations that confer herbicide resistance are a primary concern for herbicide-based chemical control of invasive plants and are often under-characterized structurally and functionally. As the outcome of selection pressure, resistance mutations usually result from repeated long-term applications of herbicides with the same mode of action and are discovered through extensive field trials. Here we used acetohydroxyacid synthase (AHAS) of Kochia scoparia (KsAHAS) as an example to demonstrate that, given the sequence of a target protein, the impact of genetic mutations on ligand binding could be evaluated and resistance mutations could be identified using a biophysics-based computational approach. Briefly, …

Conformational Dynamics Of Single Pre-Mrna Molecules During In Vitro Splicing, J. Abelson, M. Blanco, M. A. Ditzler, F. Fuller, P. Aravamudhan, M. Wood, T. Villa, D. E. Ryan, J. A. Pleiss, Corina Maeder, C. Guthrie

Corina Maeder

The spliceosome is a complex small nuclear RNA (snRNA)-protein machine that removes introns from pre-mRNAs via two successive phosphoryl transfer reactions. The chemical steps are isoenergetic, yet splicing requires at least eight RNA-dependent ATPases responsible for substantial conformational rearrangements. To comprehensively monitor pre-mRNA conformational dynamics, we developed a strategy for single-molecule FRET (smFRET) that uses a small, efficiently spliced yeast pre-mRNA, Ubc4, in which donor and acceptor fluorophores are placed in the exons adjacent to the 5′ and 3′ splice sites. During splicing in vitro, we observed a multitude of generally reversible time-and ATP-dependent conformational transitions of individual pre-mRNAs. The …

Predicting The Mechanical Properties Of Nanocomposites Reinforced With 1-D, 2-D And 3-D Nanomaterials, Scott Edward Muller

Graduate Theses and Dissertations

Materials with features at the nanoscale can provide unique mechanical properties and increased functionality when included as part of a nanocomposite. This dissertation utilizes computational methods at multiple scales, including molecular dynamics (MD) and density functional theory (DFT), and the coupled atomistic and discrete dislocation multiscale method (CADD), to predict the mechanical properties of nanocomposites possessing nanomaterials that are either 1-D (carbyne chains), 2-D (graphene sheets), or 3-D (Al/amorphous-Si core-shell nanorod).

The MD method is used to model Ni-graphene nanocomposites. The strength of a Ni-graphene nanocomposite is found to improve by increasing the gap between the graphene sheet and a …

A Combined Molecular Dynamics And Density Functional Theory Approach For Generating Liquid Water Configurations For Aqueous-Phase Heterogeneous Catalysis Studies, Cameron Joseph Bodenschatz

All Dissertations

Aqueous-phase heterogeneous catalysis is an important chemical process in applications such as water remediation, fuel cells, and the production of fuels and chemicals, including from biomass sources. However, designing alternative, improved catalyst materials for these applications is difficult due to fluctuations in the solvation environment surrounding the catalytic species. In order to elucidate the thermodynamics and kinetics of the relevant reactions, it is imperative to gain a better understanding of the roles of liquid water molecules in these reactions. In this work, a method combining both classical and quantum simulations was developed to generate configurations of liquid water molecules over …

Stimulation Of Heat Shock Protein 90 Chaperone Function Through Binding Of A Novobiocin Analog Ku-32, Bhaskar K. Chatterjee, Abhilash Jayaraj, Vinay Kumar, Brian Blagg, Rachel E. Davis, B Jayaram, Shashank Deep, Tapan K. Chaudhuri

Faculty Publications

Heat shock protein 90 (Hsp90) is a eukaryotic chaperone responsible for the folding and functional activation of numerous client proteins, many of which are oncoproteins. Thus, Hsp90 inhibition has been intensely pursued, resulting in the development of many potential Hsp90 inhibitors, not all of which are well-characterized. Hsp90 inhibitors not only abrogate its chaperone functions, but also could help us gain insight into the structure-function relationship of this chaperone. Here, using biochemical and cell-based assays along with isothermal titration calorimetry, we investigate KU-32, a derivative of the Hsp90 inhibitor novobiocin (NB), for its ability to modulate Hsp90 chaperone function. Although …

Shock Compaction Of Graphene Doped Yttria Stabilized Zirconia: An Experimental And Computational Study, Christopher Rueben Johnson

Master's Theses (2009 -)

Yttria stabilized zirconia (YSZ) is a broadly used ceramic due to its impeccable hardness and thermal stability. Limitations of the material, however, subsist within its fracture toughness. Literature indicates that shock consolidation may enable production of composite YSZ and graphene mixtures with improved fracture toughness and other material properties while maintaining the material’s nanostructure dimensionality. Therefore, investigation of the compaction phenomena at non-equilibrium states will provide informative results to be used in the fabrication of bulk graphene-YSZ composites. Computational molecular dynamics (MD) simulations and impact experiments are conducted to explore and characterize the dynamic response of the YSZ variants. Molecular …

Wettability Of Fully Hydroxylated And Alkylated (001) Α-Quartz Surface In Carbon Dioxide Atmosphere, Aleksandr Abramov, Alireza Keshavarz, Stefan Iglauer

Research outputs 2014 to 2021

Wettability of alkylated quartz surfaces is of primary importance in several technological applications, including the development of oil and gas reservoirs and carbon geo-sequestration. It is intuitively understood and experimentally confirmed that hydroxylated quartz surfaces are hydrophilic. By gradually saturating a hydroxylated (001) α-quartz surface with pentyl groups, we show using molecular dynamics simulations that the surface can also exhibit extreme hydrophobicity. Within a range of surface pentyl group density from 0.29 to 3.18/nm², the contact angle of a water droplet under 10 MPa pressure of carbon dioxide at 300 K changes from 10–20 to 180°. This study …

Computational Modelling Of Peptides Containing Non-Standard Amino Acids, David W. Kastner

Undergraduate Honors Theses

Peptides represent a class of abundant and potent pharmaceutic compounds. Despite their appeal, the design, synthesis, and engineering of biologically relevant peptides remain a challenge. Chapter 1 introduces the various computational methods that will be used. Chapter 2 focuses on the incorporation of a special class of amino acids called bulky dehydroamino acids into the turn of β-hairpins to proteolytically stabilize peptides. Our results suggest that dehydroamino acids confer proteolytic stability by favoring a more folded state. Chapter 3 describes the structural calculations of a rare anticancer peptide called Yaku’amide using a combined molecular mechanics/quantum mechanics hybrid method. The …

Interactions Between Dislocations And Three-Dimensional Annealing Twins In Face Centered Cubic Metals, Yanxiang Liang, Xiaofang Yang, Mingyu Gong, Guisen Liu, Qing Liu, Jian Wang

Department of Mechanical and Materials Engineering: Faculty Publications

Annealing twins often form in metals with a face centered cubic structure during thermal and mechanical processing. Here, we conducted molecular dynamic (MD) simulations for copper and aluminum to study the interaction processes between {1 1 1}1/2 <1 1 0> dislocations and a three-dimensional annealing twin. Twin boundaries are characterized with Σ3{1 1 1} coherent twin boundaries (CTBs) and Σ3{1 1 2} incoherent twin boundaries (ITBs). MD results revealed that dislocation-ITB interactions affect slip transmission for a dislocation crossing CTBs, facilitating the nucleation of Lomer dislocation.

Tools For Understanding Static Structure Factors And Their Application To Simulations Of Liquids, Travis Mackoy

Graduate Research Theses & Dissertations

Molecular dynamics (MD) simulations can be used to compute static structure factors (��(��)) and provide an interpretation of the underlying periodic atomic ordering. MD simulations complement experimentally measured ��(��) by allowing qualitative assignment of peaks to various ordering, such as cation-anion ordering in ionic liquids, via decomposition of ��(��) into partial ��(��). Here we present a method for classifying interatomic distances that allows for quantitative peak assignment and visualization of atoms that contribute most to each peak in calculated ��(��) for soft materials. The method is illustrated by investigating ��(��) for the ionic liquid 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl)imide (C4C1pyrrTFSI), which shows two …

Schinus Molle: Anatomy Of Leaves And Stems, Chemical Composition And Insecticidal Activities Of Volatile Oil Against Bed Bug (Cimex Lectularius), Camila D. Machado, Vijayasankar Raman, Junaid U. Rehman, Beatriz H.L.N.S. Maia, Emanuelle K. Meneghetti, Valter P. Almeida, Rosi Z. Silva, Paulo V. Farago, Ikhlas A. Khan, Jane M. Budel

Faculty and Student Publications

© 2019 by the authors The investigation of the constituents that were isolated from Turnera diffusa (damiana) for their inhibitory activities against recombinant human monoamine oxidases (MAO-A and MAO-B) in vitro identified acacetin 7-methyl ether as a potent selective inhibitor of MAO-B (IC50 = 198 nM). Acacetin 7-methyl ether (also known as 5-hydroxy-40, 7-dimethoxyflavone) is a naturally occurring flavone that is present in many plants and vegetables. Acacetin 7-methyl ether was four-fold less potent as an inhibitor of MAO-B when compared to acacetin (IC50 = 50 nM). However, acacetin 7-methyl ether was >500-fold selective against MAO-B over MAO-A as compared …

Direct Polymer Grafting As A Method Of Maintaining The Mechanical Properties Of Cellulose Nanocrystals In The Presence Of Moisture, Mary Elizabeth Breen-Lyles

Graduate Research Theses & Dissertations

Cellulose nanocrystals (CNCs) are a distinctive nanomaterial derived from cellulose, the most abundant natural polymer on Earth, and the primary reinforcing structural component of cellulose fibrils found within the plant cell wall. These nanocrystals exhibit mechanical properties comparable to synthetic aramid fibers but are advantageous as they are biodegradable, renewable, and can be produced sustainably as they are predominantly extracted from naturally occurring cellulosic materials. These qualities make it a sustainable, highly renewable and environmentally friendly material to be used in place of synthetic materials in a variety of applications. With their high surface area to volume ratio, low level …