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Computation 2015, 3(1), 29-57; doi:10.3390/computation3010029

A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization

1
Department of Applied Mathematics and Statistics, Colorado School of Mines, 1500 Illinois St, Golden, CO 80401, USA
2
Center for Cell and Virus Theory, Indiana University, 800 E Kirkwood Ave, Bloomington, IN 47405, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Constantinos Theodoropoulos
Received: 20 August 2014 / Revised: 14 January 2015 / Accepted: 26 January 2015 / Published: 5 February 2015
(This article belongs to the Special Issue Multiscale Modeling and Simulation in Computational Biology)
View Full-Text   |   Download PDF [5675 KB, uploaded 5 February 2015]   |  

Abstract

Many mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. Due to the large number of atoms involved and the need to simulate over long time periods of biological interest, traditional computational tools, like molecular dynamics, are often infeasible for such systems. Hence, in the current review article, we present and discuss two recent multiscale methods, stemming from the N-atom formulation and an underlying scale separation, that can be used to study such systems in a friction-dominated regime: multiscale perturbation theory and multiscale factorization. These novel analytic foundations provide a self-consistent approach to yield accurate and feasible long-time simulations with atomic detail for a variety of multiscale phenomena, such as viral structural transitions and macromolecular self-assembly. As such, the accuracy and efficiency of the associated algorithms are demonstrated for a few representative biological systems, including satellite tobacco mosaic virus (STMV) and lactoferrin. View Full-Text
Keywords: multiscale perturbation theory; Fokker–Planck equation; Langevin equation; multiscale factorization; lactoferrin; satellite tobacco mosaic virus multiscale perturbation theory; Fokker–Planck equation; Langevin equation; multiscale factorization; lactoferrin; satellite tobacco mosaic virus
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Pankavich, S.; Ortoleva, P. A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization. Computation 2015, 3, 29-57.

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