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Lengthening the timescale reach of molecular dynamics

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Title: Lengthening the timescale reach of molecular dynamics
Author(s): Tanner, David
Director of Research: Schulten, Klaus J.
Doctoral Committee Chair(s): Schulten, Klaus J.
Doctoral Committee Member(s): Wraight, Colin A.; Grosman, Claudio F.; Kale, Laxmikant V.
Department / Program: School of Molecular & Cell Bio
Discipline: Biophysics & Computnl Biology
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: Ph.D.
Genre: Dissertation
Subject(s): molecular dynamics implicit solvent graphics processing units (gpu) high-performance computing flagellum protein translocation
Abstract: Molecular dynamics (MD) is a computational method employed for studying the dynamics of nanoscale biological systems on nanosecond to microsecond timescales. Using MD, researchers can utilize experimental data from crystallography and cryo-electron microscopy to explore the functional dynamics of biological systems. The timescale reach of the molecular dynamics tool is limited by how fast femtosecond timesteps can be sequentially integrated; today's fast computers allow simulation speeds of tens of nanoseconds of simulation time per day, which typically limits simulation lengths to hundreds of nanoseconds. This work explores three ways whereby the timescale reach of molecular dynamics can be lengthened beyond nanoseconds, to the millisecond timescales of cellular processes. First, a theoretical model of flagellin translocation allows nanosecond timescale MD simulations to explore the hour-long process of bacterial flagellum elongation. Second, a generalized Born model of implicit solvent accelerates simulation through reduced computational expense as well as increased conformational sampling due to reduced viscosity of the implicit solvent. Finally, advanced computing technologies, such as graphics processing units, accelerate simulation speeds of hybrid GB/SA implicit solvent models, thereby directly increasing simulation lengths.
Issue Date: 2012-05-22
URI: http://hdl.handle.net/2142/31144
Rights Information: Copyright 2012 David Eldon Tanner.
Date Available in IDEALS: 2012-05-22
Date Deposited: 2012-05
 

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