Order parameters for macromolecules: Application to multiscale simulation

A. Singharoy; S. Cheluvaraja; P. Ortoleva

doi:10.1063/1.3524532

Order parameters for macromolecules: Application to multiscale simulation

A. Singharoy, S. Cheluvaraja, P. Ortoleva

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

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 language	English (US)
Article number	044104
Journal	Journal of Chemical Physics
Volume	134
Issue number	4
DOIs	https://doi.org/10.1063/1.3524532
State	Published - Jan 28 2011
Externally published	Yes

ASJC Scopus subject areas

Physics and Astronomy(all)
Physical and Theoretical Chemistry

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10.1063/1.3524532

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title = "Order parameters for macromolecules: Application to multiscale simulation",

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.",

author = "A. Singharoy and S. Cheluvaraja and P. Ortoleva",

note = "Funding Information: We appreciate efforts of the JCP editor and reviewers whose suggestions greatly improved the manuscript. We thank Professor Srini Iyengar for fruitful discussions on extended Lagrangian approaches. This project was supported in part by the National Science Foundation (Collaborative Research in Chemistry program), National Institutes of Health (NIBIB), Department of Energy (Office of Basic Science), METAcyt through the Center of Cell and Virus Theory, and Indiana University College of Arts and Sciences.",

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AB - 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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Order parameters for macromolecules: Application to multiscale simulation

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