Order parameters for macromolecules: Application to multiscale simulation

Abhishek Singharoy, S. Cheluvaraja, P. Ortoleva

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number044104
JournalJournal of Chemical Physics
Volume134
Issue number4
DOIs
StatePublished - Jan 28 2011
Externally publishedYes

Fingerprint

Macromolecules
macromolecules
Liouville equation
Structural dynamics
simulation
RNA
ribonucleic acids
Atoms
atomic collisions
Liouville equations
dynamic structural analysis
completeness
lists
vibration
atoms

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Order parameters for macromolecules : Application to multiscale simulation. / Singharoy, Abhishek; Cheluvaraja, S.; Ortoleva, P.

In: Journal of Chemical Physics, Vol. 134, No. 4, 044104, 28.01.2011.

Research output: Contribution to journalArticle

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