University of groningen molecular dynamics simulation. In this thesis, a suttonchen potential was chosen to describe the manybody. Thesis title molecular dynamics simulations of escherichia coli ammonia channel amtb thesis submitted june 2007 department of chemistry technical university of denmark dtu, kgs. Molecular dynamics simulation study of peobased polymer electrolytes in aqueous solution by zhi tao dissertation submitted to the faculty of the graduate school of vanderbilt university in partial fulfillment of the requirements for the degree of doctor of philosophy in chemical engineering 052008 nashville, tennessee approved. The work described in this thesis was made possible.
Michiel bosch 5 2 theory in order to setup a representative simulation and to be able to interpret the data generated from the md simulations, the theory involved must first be carefully understood. At, just tell us what you are looking for and our representative will provide you with the optimum and molecular dynamics simulations phd thesis utmost dependable service molecular dynamics simulations phd thesis you could have asked for. Molecular dynamics approach to mica surface reconstruction. Molecular dynamics studies of metallic glasses caltechthesis. Molecular dynamics simulations of hematite nanoparticle deposition onto a substrate by dana r. A masters thesis presented to the graduate college of. Molecular dynamics is a technique in which the trajectories of a group of particles are calculated as a function of time by integrating the equations of motion. Hamiltonian thermostatting techniques for molecular dynamics. Hamiltonian thermostatting techniques for molecular dynamics simulation. This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. English pdf migrated pdf a conversion from original format. A molecular dynamics study of the gibbs elasticity of interfaces.
Molecular dynamics provides a computational framework to simulate the movement of interacting atoms in response to external perturbations, such as changes in temperature or pressure. The work described in this thesis was supported by and performed at unilever re. In this thesis, i discuss the results of molecular dynamics md simulations of the native and thermal sio2 substrates which are used in the plasmaenhanced. Marina which were there for me from the beginning and continue to. Graduate thesis or dissertation molecular dynamics at. Molecular dynamics simulation of nanoporous graphene for. Also in this thesis, molecular dynamics md simulation is used to estimate gas phase diffusion coefficients based on meansquare displacement methods and results are compared with chapmanenksog theory. Molecular dynamics simulation of damage cascade formation in ion bombarded solids. Molecular dynamics simulations of rna bulges, loops and base. Modeling real world phenomena using molecular dynamics and.
Effects of confinement on water structure and dynamics. Each of these chapters will be a summary of corresponding publications published by the author during the course of his graduate study. I hereby declare that the thesis entitled molecular dynamics simulations of nano. Molecular dynamics md is a computer simulation method for analyzing the physical movements of atoms and molecules. Encyclopedia of bioinformatics and computational biology, 2019. While the translational dynamics is modelled well by a product of a isf representing short time incage vibrations and long time cage relaxation processes, the rotational dynamics is an aspect we shall study in this thesis. These direct molecular dynamics simulation of piezoelectric and. Stabilisation of fusarium solani pisi cutinase against anionic surfactants. Molecular dynamics simulation study of peobased polymer.
Exploration of the phase field framework marmot to include anisotropic grain boundaries with molecular dynamics by aaron s. Mica has a layered silicate sheet structure and is widely used as a substrate for imaging biological samples. In this thesis, all the subjects mentioned in the previous section are revised, except neighbor searching and integration. Various analysis methods were used in order to investigate structural and dynamical properties and solve particular problems for different systems. Hamiltonian thermostatting techniques for molecular. The first one will investigate the neck growth in the laser sintering of differentsize gold 100 nanoparticles under different heating rates. Pdf the molecular dynamics and rheology of polymer melts. In this thesis we study the use of molecular dynamics for atoms in a crystal. Molecular dynamics simulations of rna bulges, loops and. Pdf theoretical analysis of spectral lineshapes from. Various analysis methods were used in order to investigate structural and dynamical properties. Inter molecular and intra molecular forces are incorporated in these simulations using the lennardjones 126 and a torsional potential. Study of slow dynamics in supercooled water by molecular.
In this thesis the structure and dynamics of different rna molecules have been studied by molecular dynamics md simulations. Molecular dynamics investigation on the fracture behavior of nanocrystalline fe antoine n. Pdf molecular dynamics simulations on a 17 residues peptide of the nterm of ubiquitin, using two forcefields amber99sb and. Pdf of hh pair during cooling down at room temperature for 600 ev page 43. Molecular dynamics simulations of escherichia coli ammonia. Each atom i at position r i, is treated as a point with a mass m i and a fixed charge q i. My phd thesis could not have been executed if not for my two wonderful parents kleanthis and. As a result, an obvious alternative to classical uid dynamics is molecular dynamics md. Graduate student theses jila exploring the frontiers of. The pennsylvania state university droplet vaporization of n. We utilize molecular dynamics md simulations and show. A growing collection from over 500 graduate student theses produced at jila. University of groningen the application of molecular dynamics. Piezoelectric materials are crystals which display a.
The research presented in this thesis investigates the viability of using both md and cfd to obtain solutions for small systems. Graduate student theses jila exploring the frontiers. Force fields for molecular dynamics three major force fields are used for md charmm, amber, oplsaa multiple versions of each do not confuse charmm and amber force fields with charmm and amber software packages they all use strikingly similar functional forms common heritage. Xu, muyi ant 2014 molecular dynamics approach to mica surface reconstruction. The function of membranes and membrane proteins are determined by their structure, and the central focus of this thesis is the use of computational molecular dynamics simulations to study experimentally inaccessible details of membrane structure. Largescale molecular dynamics simulations for highly. Levin was the supervisor for this portion of the thesis only. Molecular dynamics simulation of sputtering caltechthesis. The dynamics of supercooled water can be decoupled into a product of translational and rotational dynamics. A molecular dynamics and experimental study a thesis submitted to the graduate faculty of the north dakota state university of agriculture and applied science by md zillur rahman patwary in partial fulfillment for the degree of master of science major department. The thermodynamic, structural, and mechanical properties of metallic glasses are studied using molecular dynamics simulations. Molecular dynamics trajectories that sample from a gibbs, or canonical, distribution can be generated by introducing a modi. Molecular dynamics simulation of amphiphilic aggregates public file details depositor rkati date uploaded 20190415 date modified 20190415 fixity check fixity checks have not yet been run on this object. Three studies are presented that are intended to improve our ability to simulate larger systems more realistically.
This work was done wholly or mainly while in candidature for a research degree at this university. A molecular dynamics simulationisothermal titration calorimetry study of antimicrobial peptidepeptide interaction by shaghayegh vafaei a thesis presented to the university of guelph in partial ful. In the second part of this thesis, we present the results of three di. Base flipping is studied by umbrella sampling in two of the papers. Masters thesis, memorial university of newfoundland. A study of bending deformations in carbon nanotubes using the objective molecular dynamics method a thesis submitted to the faculty of the graduate school of the university of minnesota by ilia a. Latapie thesis submitted to the faculty of the virginia polytechnic institute and state university in partial fulfillment of the requirement for the degree of master of science in materials science and engineering dr. Publishers pdf, also known as version of record publication date. I am indebted to visiting professor pietro poesio from the university of brescia for contributing to the code used in this thesis. Jul 19, 2012 molecular dynamics md simulation is a powerful computational method for delineating motions of proteins at an atomicscale via theoretical and empirical principles in physical chemistry. Molecular dynamics an overview sciencedirect topics. Molecular dynamics simulations of membranes and membrane. In this dissertation, molecular dynamics simulations were performed for systems containing amphiphilic aggregates, such as monolayers, bilayers, and reverse micelles. Molecular dynamics simulations on phospholipid membranes.
In this thesis, two scenarios of simulations are studied by molecular dynamics md method. Presented in this thesis are the results from an integrated experimental and modeling study on damage cascade formation in ion bombarded solids. This investigation has been carried out by performing classical molecular dynamics simulations using atomistic manybody potential energy functions at many different sinr sheet lengths and widths, at. A comparison study of two and threebody potential models. Results at 298 k show the formation of a wellordered structure constituted by water layers parallel to the graphite surfaces. Due to its high thermal stability and negatively charged features, it is interesting to investigate whether the mica substrate will affect sample surface structure by enabling interactions between biological systems.
Oriented, semicrystalline polylactic acid a thesis in. This thesis consists of molecular dynamics studies of several sputtering topics not directly related to each other and is organized accordingly into separate chapters. Molecular dynamics simulations paul sabatier thesesups. Introduction to molecular dynamics simulation michael p. Molecular dynamics simulation of amphiphilic aggregates public file details depositor rkati date uploaded 20190415 date modified 20190415 fixity check fixity checks have not. In this thesis the question of nonlinear scaling is explored with classical molecular dynamics md. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. The modelling of electronic effects in molecular dynamics. The molecular dynamic simulation of neutral argon particles.
Speci cally, we are interested in characteristics of viscous. The vaporization of a nheptane c 7h16 droplet is investigated using molecular dynamics md. The thesis is focused on investigating the effect of strain on the thermal conductivity of piezoelectric materials. Molecular dynamics simulations in rational protein design. Molecular dynamics simulation of an engineered t4 lysozyme. Molecular dynamics and continuum simulations of fluid flows with slip boundary conditions by anoosheh niavaranikheiri microuidics is a rapidly developing. University of groningen molecular dynamics simulations in. University of groningen molecular dynamics simulation methods. Molecular dynamics simulation methods revised research. The pennsylvania state university droplet vaporization. This thesis is concerned with the molecular dynamics and rheology of polymer melts in the vicinity of a hard flat surface. Molecular dynamics simulation of dna lesions by matthew brian ernst a thesis submitted in partial ful. One initial motivation is the desire to better understand the phenomenon.
His enthusiasm for the new subject of molecular dynamics was infectious. Where any part of this thesis has previously been submitted for. The method is especially suitable for simulations of dynamics of large groups of atoms, and therefore it has been used for impact simulations for as long as computers have been routinely used in physics research. Where any part of this thesis has previously been submitted for a degree or. Nikiforov in partial fulfillment of the requirements for the degree of master of science september, 2010.
Molecular dynamics simulations of enforced functional protein motions. The thesis is based on four papers where the rna structures contain nucleotides that do not form watsoncrick base pairs. This thesis builds upon a previous implementation of an accelerator for performing the reciprocalspace portion. In the first part of this thesis, structural properties of sinr sheets have been investigated. Eindhoven university of technology master a molecular. Synthesis of amorphous hydrogenated boron carbide from. Pdf molecular dynamics simulation in virus research. Molecular dynamics simulations of nanofluids and their. During each integration step the structure of the molecule is maintained by constraining bond lengths. Extensive comparisons with experimental diffraction and nmr data were made to validate the structure models. Molecular dynamics simulations on phospholipid membranes academic dissertation to be presented with the assent of the faculty of science, university of oulu, for public discussion in auditorium go101, linnanmaa, on april 20th, 2001, at 12 noon.
Many attempts have been made to improve the performance of molecular dynamics md simulations by implementing portions of the computation in hardware, but few approaches consider longrange electrostatic interactions. Molecular dynamics simulations calculate the motion of the atoms in a molecular assembly using newtonian dynamics to determine the net force and acceleration experienced by each atom. A comparison study of two and threebody potential models for liquid and amorphous si0. Molecular dynamics md is a technique where the time evolution of a set of interacting atoms is followed by numerical integration of newtons equation of motion adcock and mccammon, 2006. In this thesis, i have studied the atomic level structure of rare earth doped silicate and aluminophosphate glasses by using molecular dynamics simulations. A molecular dynamics study to understand behavior of corrosion inhibitors in bulk aqueous phase and near metalwater interface. Molecular dynamics investigation on the fracture behavior. A 3d convolution engine for computing the reciprocalspace. Molecular dynamics simulation of nanosintering processes. You are advised to consult the publishers version publishers pdf if you wish. A molecular dynamics simulationisothermal titration. Hereby i declare that this thesis proposal is my original authorial work, which i have. Allen centre for scientic computing and department of physics, university of warwick, coventry cv4 7al, united kingdom email.
Md simulation is also used to model evaporation of solvents into air and relative solvent drying times based on simulation. A study of bending deformations in carbon nanotubes using the. Algorithms, biology, biomolecules, biophysics, chemistry, cuda, molecular dynamics, nvidia, nvidia geforce gtx 480, physics, thesis august 26, 2017 by hgpu openclbased implementation of an fpga accelerator for molecular dynamics simulation. Dissertation or thesis molecular dynamics simulation of. Graduate thesis or dissertation molecular dynamics. In the second part of this work, two types of experimental systems have been modeled, with an aim to replicate the results of experiments and study the dynamics of the respective systems in a more detailed manner.
By means of a set of advanced md simulation methods, this thesis ad dresses various types of transitions. This thesis presents a study of applications and techniques for molecular dynamics simulations. A molecular dynamics study to understand behavior of. This masters thesis is the result of a study performed at the department of. Molecular dynamics simulations of the structures of. Molecular dynamics extends the use of computational chemistry to describe behaviors in a chemical. I, jing cao, declare that this thesis titled, molecular dynamics study of polymer melts and the work presented in it are my own.
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