Order parameters (OPs) characterizing the nanoscale features of macromolecules are presented. They are generated in a general fashion so that they do not need to be redesigned with each new application. They evolve on time scales much longer than 10−14 s typical for individual atomic collisions/vibrations. The list of OPs can be automatically increased, and completeness can be determined via a correlation analysis. They serve as the basis of a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Smoluchowski/Langevin equations of stochastic OP dynamics. Such OPs and the multiscale analysis imply computational algorithms that we demonstrate in an application to ribonucleic acid structural dynamics for 50 ns.
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28 January 2011
Research Article|
January 24 2011
Order parameters for macromolecules: Application to multiscale simulation
A. Singharoy;
A. Singharoy
Center for Cell and Virus Theory,
Indiana University,
Bloomington, Indiana 47405, USA
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S. Cheluvaraja;
S. Cheluvaraja
Center for Cell and Virus Theory,
Indiana University,
Bloomington, Indiana 47405, USA
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P. Ortoleva
P. Ortoleva
a)
Center for Cell and Virus Theory,
Indiana University,
Bloomington, Indiana 47405, USA
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a)
Author to whom correspondence should be addressed. Electronic mail: [email protected].
J. Chem. Phys. 134, 044104 (2011)
Article history
Received:
May 10 2010
Accepted:
November 13 2010
Citation
A. Singharoy, S. Cheluvaraja, P. Ortoleva; Order parameters for macromolecules: Application to multiscale simulation. J. Chem. Phys. 28 January 2011; 134 (4): 044104. https://doi.org/10.1063/1.3524532
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