Lengthening the timescale reach of molecular dynamics

Tanner, David

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

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

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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