title: Multiscale macromolecular simulation: role of evolving ensembles.
abstract: Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.
authors.affiliation: Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: A
authors.initials: A
authors.lastname: Singharoy
authors.forename: H
authors.initials: H
authors.lastname: Joshi
authors.forename: P J
authors.initials: PJ
authors.lastname: Ortoleva
mesh_terms: D000465:Algorithms; D036022:Capsid Proteins / Q000737:chemistry*; D003198:Computer Simulation; D019020:Directed Molecular Evolution; D052162:Human papillomavirus 16 / Q000737:chemistry*; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D009010:Monte Carlo Method; D013816:Thermodynamics; D014771:Virion / Q000737:chemistry*
chemical_list: D036022:Capsid Proteins