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LSU Doctoral Dissertations

Molecular dynamics simulation

Publication Year

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Full-Text Articles in Mechanical Engineering

Molecular Dynamics Simulation Study Of Single Dna Nucleotides Transport Through Nanoslits, Kai Xia Jan 2015

Molecular Dynamics Simulation Study Of Single Dna Nucleotides Transport Through Nanoslits, Kai Xia

LSU Doctoral Dissertations

There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with 2 or more detectors. Molecular dynamics simulation of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits was performed. Electric field strength (E) varied from 0.0 to 0.6 V/nm. Slit walls were smooth or had a roughness similar to nucleotide size. Multiple nucleotide-wall adsorptions occurred. The electric field did not influence the nucleotide adsorption and desorption mechanism for E ¡Ü 0.1 V/nm, but influenced nucleotide orientation relative to the field direction ...


Molecular Dynamics Simulation Studies Of Interaction Of Amphiphilic Molecules With Lipid Bilayers, Jieqiong Lin Jan 2013

Molecular Dynamics Simulation Studies Of Interaction Of Amphiphilic Molecules With Lipid Bilayers, Jieqiong Lin

LSU Doctoral Dissertations

We use molecular dynamics simulations to investigate the behavior of various amphiphilic molecules in aqueous solutions in the presence of vitamin E or lipid bilayers. Our research studies focus on two molecular systems. First, we investigate the effect of DMSO on structural properties of DMPC bilayers and calculate bilayers permeability coefficients for both water and DMSO molecules at low DMSO concentration. The simulations show that the increase of DMSO concentration in solution leads to an increase of the permeability of water through the bilayers. The permeability increase might explain the unusual ability of DMSO, even at relatively low concentrations, to ...


Molecular Dynamics Simulation Studies Of Surface-Stress Effects In Metallic Nanostructures, Jijun Lao Jan 2011

Molecular Dynamics Simulation Studies Of Surface-Stress Effects In Metallic Nanostructures, Jijun Lao

LSU Doctoral Dissertations

Using molecular dynamics (MD) simulations we investigate the surface-stress-induced structural transformations and pseudoelastic behavior in palladium (Pd) crystalline nanowires. For a <100> initial crystal orientation our studies indicate that the surface stress can cause Pd nanowires to spontaneously undergo structural changes with characteristics that are determined by the wire cross-sectional area. Specifically, when the cross-sectional area is below 2.18nm x 2.18nm the wire changes spontaneously its crystal structure from the initial fcc structure to a body-centered-tetragonal (bct) structure. In wires of larger cross-sectional area (i.e., 2.57nm x 2.57nm) the structural transformation is achieved via a spontaneous ...


The Effect Of Anisotropic Surface Energy On The Stability Of Micro And Nano Wires, Ping Du Jan 2010

The Effect Of Anisotropic Surface Energy On The Stability Of Micro And Nano Wires, Ping Du

LSU Doctoral Dissertations

A liquid thread of radius R will break up into drops if the axial wavelength of the surface perturbation L > 2πR. If L < 2πR, the thread is stable and will remain intact. This is Rayleigh’s stability criterion based on a continuum model. We use molecular dynamics to simulate the evolution of Lennard-Jones liquid threads with equilibrium radius R = 2.3-6.6, where R has been non-dimensionalized by the distance at which the Lennard-Jones potential equals zero. We find that if R is fixed, the wavelength L is bounded by Lmin and Lmax. For L > Lmax the thread always breaks up and stays as drops, and for L < Lmin the thread remains intact. However, for Lmin < L < Lmax, the thread oscillates continuously among several shapes. The appearance of various shapes can be explained by the energy fluctuation of the system.

We also simulate the evolution of Lennard-Jones nanowires with equilibrium radius R = 1.57, 2.58, 3.59, and 4.60 by molecular dynamics. The ...