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dc.contributor.advisor Ortoleva, Peter J en Miao, Yinglong en 2010-06-16T17:42:10Z en 2012-03-23T21:30:49Z en 2012-03-23T21:32:51Z 2010-06-16T17:42:10Z en 2009 en
dc.identifier.uri en
dc.description Thesis (Ph.D.) - Indiana University, Chemistry, 2009 en
dc.description.abstract Viruses are composed of millions of atoms functioning on supra-nanometer length scales over timescales of milliseconds or greater. In contrast, individual atoms interact on scales of angstroms and femtoseconds. Thus they display dual microscopic/macroscopic characteristics involving processes that span across widely-separated time and length scales. To address this challenge, we introduced automatically generated collective modes and order parameters to capture viral large-scale low-frequency coherent motions. With an all-atom multiscale analysis (AMA) of the Liouville equation, a stochastic (Fokker-Planck or Smoluchowski) equation and equivalent Langevin equations are derived for the order parameters. They are shown to evolve on timescales much larger than the 10^(-14)-second timescale of fast atomistic vibrations and collisions. This justifies a novel multiscale Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX) approach, which propagates viral atomistic and nanoscale dynamics simultaneously by solving the Langevin equations of order parameters implicitly without the need to construct thermal-average forces and friction/diffusion coefficients. In MD/OPX, a set of short replica MD runs with random atomic velocity initializations estimate the ensemble average rate of change in order parameters, extrapolation of which is then used to project the system over long time. The approach was implemented by using NAMD as the MD platform. Application of MD/OPX to cowpea chlorotic mottle virus (CCMV) capsid revealed that its swollen state undergoes significant energy-driven shrinkage in vacuum during 200ns simulation, while for the native state as solvated in a host medium at pH 7.0 and ionic strength I=0.2M, the N-terminal arms of capsid proteins are shown to be highly dynamic and their fast fluctuations trigger global expansion of the capsid. Viral structural transitions associated with both processes are symmetry-breaking involving local initiation and front propagation. MD/OPX accelerates MD for long-time simulation of viruses, as well as other large bionanosystems. By using universal inter-atomic force fields, it is generally applicable to all dynamical nanostructures and avoids the need of parameter recalibration with each new application. With our AMA method and MD/OPX, viral dynamics are predicted from laws of molecular physics via rigorous statistical mechanics. en
dc.language.iso EN en
dc.publisher [Bloomington, Ind.] : Indiana University en
dc.subject cowpea chlorotic mottle virus en
dc.subject collective modes en
dc.subject structural transitions en
dc.subject molecular dynamics/order parameter extrapolation en
dc.subject all-atom multiscale analysis en
dc.subject viral dynamics en
dc.subject.classification Chemistry, Physical en
dc.subject.classification Biology, Virology en
dc.subject.classification Biophysics, General en
dc.title All-Atom Multiscale Computational Modeling Of Viral Dynamics en
dc.type Doctoral Dissertation en

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