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J Chem Phys. 2011 Jan 28;134(4):044104. doi: 10.1063/1.3524532.

Order parameters for macromolecules: application to multiscale simulation.

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  • 1Center for Cell and Virus Theory, Indiana University, Bloomington, Indiana 47405, USA.


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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