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国际多尺度计算工程期刊
影响因子: 1.016 5年影响因子: 1.194 SJR: 0.554 SNIP: 0.68 CiteScore™: 1.18

ISSN 打印: 1543-1649
ISSN 在线: 1940-4352

国际多尺度计算工程期刊

DOI: 10.1615/IntJMultCompEng.v6.i1.30
pages 25-37

Parallel Multiscale Modeling of Biopolymer Dynamics with Hydrodynamic Correlations

Maria Fyta
Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
Jayanta Sircar
Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
Efthimios Kaxiras
Harvard University
Simone Melchionna
SOFT-INFM-CNR and Department of Physics, University of Rome La Sapienza, P. le A. Moro 2, 00185, Rome, Italy
Massimo Bernaschi
Istituto Applicazioni Calcolo, CNR, Viale del Policlinico 137, 00161, Rome, Italy
Sauro Succi
Istituto Applicazioni Calcolo, CNR, Viale del Policlinico 137, 00161, Rome, Italy

ABSTRACT

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic molecular dynamics with a mesoscopic lattice Boltzmann method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. We describe an efficient parallel implementation of the method that exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.