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

Computation

Stephen Pankavich¹  Peter Ortoleva² 

[1] Department of Applied Mathematics and Statistics, Colorado School of Mines, 1500 Illinois St, Golden, CO 80401, USA;Center for Cell and Virus Theory, Indiana University, 800 E Kirkwood Ave, Bloomington, IN 47405, USA; E-Mail:

关键词: multiscale perturbation theory;    Fokker–Planck equation;    Langevin equation;    multiscale factorization;    lactoferrin;    satellite tobacco mosaic virus;   

DOI  :  10.3390/computation3010029

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland