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Full-Text Articles in Physical Sciences and Mathematics
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-BxC) 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-BxC. Afterward, Hybrid Reverse Monte Carlo (HRMC) technique is used to recreate a-BxC structures. The existing SW potential parameters of Boron are optimized for the α-rhombohedral (Icosahedral B12 …
A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers
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 …
Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman
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 …
Simulation And Software Development To Understand Interactions Of Guest Molecules Inporous Materials, Douglas M. Franz
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
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 …
Tools For Understanding Static Structure Factors And Their Application To Simulations Of Liquids, Travis Mackoy
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 …