Literature DB >> 15740298

Coarse-grained computations for a micellar system.

Dmitry I Kopelevich1, Athanassios Z Panagiotopoulos, Ioannis G Kevrekidis.   

Abstract

We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms), and atomistic simulations of the Larson model of micelle formation. The procedure hinges on the (expected) evolution of a few slow, coarse-grained mesoscopic observables of the Monte Carlo simulation, and on (computational) time scale separation between these and the remaining "slaved," fast variables. Short bursts of appropriately initialized atomistic simulation are used to estimate the (coarse grained, deterministic) local dynamics of the evolution of the observables. These estimates are then in turn used to accelerate the evolution to computational stationarity through traditional continuum algorithms (forward Euler integration, Newton-Raphson fixed point computation). This "equation-free" framework, bypassing the derivation of explicit, closed equations for the observables (e.g., equations of state), may provide a computational bridge between direct atomistic/stochastic simulation and the analysis of its macroscopic, system-level consequences. (c) 2005 American Institute of Physics.

Year:  2005        PMID: 15740298     DOI: 10.1063/1.1839173

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  3 in total

1.  Coarse-grained analysis of stochasticity-induced switching between collective motion states.

Authors:  Allison Kolpas; Jeff Moehlis; Ioannis G Kevrekidis
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-27       Impact factor: 11.205

2.  Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

Authors:  Weihua Zheng; Michael Andrec; Emilio Gallicchio; Ronald M Levy
Journal:  J Phys Chem B       Date:  2009-08-27       Impact factor: 2.991

3.  Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

Authors:  Weihua Zheng; Emilio Gallicchio; Nanjie Deng; Michael Andrec; Ronald M Levy
Journal:  J Phys Chem B       Date:  2011-01-21       Impact factor: 2.991

  3 in total

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