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.
authors.affiliation: Center for Cell and Virus Theory, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: A
authors.initials: A
authors.lastname: Singharoy
authors.forename: S
authors.initials: S
authors.lastname: Cheluvaraja
authors.forename: P
authors.initials: P
authors.lastname: Ortoleva
mesh_terms: D000465:Algorithms; D046911:Macromolecular Substances / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D053758:Nanoparticles / Q000737:chemistry*; D025341:Principal Component Analysis; D013269:Stochastic Processes; D013816:Thermodynamics; D014732:Vibration
chemical_list: D046911:Macromolecular Substances