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oai:www.ideals.illinois.edu:2142/31144 2023-07-10 col_2142_5131 col_2142_14828 com_2142_5130 com_2142_14827 com_2142_14793 com_2142_8903

Schulten, Klaus J. Schulten, Klaus J. Wraight, Colin A. Grosman, Claudio F. Kale, Laxmikant V. Tanner, David 2012-05-22T00:30:55Z 2012-05-22T00:30:55Z 2012-05 2012-05-22T00:30:55Z 2012-05 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. Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2012-04-17T18:21:36Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Tanner_David.pdf: 9997136 bytes, checksum: 20fb10e496a26640153977887c1e604a (MD5) Made available in DSpace on 2012-05-22T00:30:55Z (GMT). No. of bitstreams: 2 Tanner_David.pdf: 9997136 bytes, checksum: 20fb10e496a26640153977887c1e604a (MD5) license.txt: 4062 bytes, checksum: f1ec24528593fe307d38013d90ab1649 (MD5) http://hdl.handle.net/2142/31144 en Copyright 2012 David Eldon Tanner. molecular dynamics implicit solvent Graphics Processing Units (GPU) High Performance Computing (HPC) flagellum protein translocation Lengthening the timescale reach of molecular dynamics text School of Molecular & Cell Bio 1415 Biophysics & Computnl Biology 0319 University of Illinois at Urbana-Champaign Dissertation Ph.D. PHD:Biophys&Computnl Bio -UIUC 10KS0319PHD