University of Illinois Urbana-Champaign

Lengthening the timescale reach of molecular dynamics

Tanner, David

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Tanner_David.pdf

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https://hdl.handle.net/2142/31144

Description

Title
Lengthening the timescale reach of molecular dynamics
Author(s)
Tanner, David
Issue Date
2012-05-22T00:30:55Z
Director of Research (if dissertation) or Advisor (if thesis)
Schulten, Klaus J.
Doctoral Committee Chair(s)
Schulten, Klaus J.
Committee Member(s)
  • Wraight, Colin A.
  • Grosman, Claudio F.
  • Kale, Laxmikant V.
Department of Study
School of Molecular & Cell Bio
Discipline
Biophysics & Computnl Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Date of Ingest
2012-05-22T00:30:55Z
Keyword(s)
  • molecular dynamics
  • implicit solvent
  • Graphics Processing Units (GPU)
  • High Performance Computing (HPC)
  • 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.
Graduation Semester
2012-05
Permalink
http://hdl.handle.net/2142/31144
Copyright and License Information
Copyright 2012 David Eldon Tanner.

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