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International Journal for Multiscale Computational Engineering

ISSN for PRINT: 1543-1649

Institutional price:	$747.00
Issues per year:	6

Best Paper Award Selection - Editorial Board Site

2008, Volume6

114 pages

DOI: 10.1615/IntJMultCompEng.v6.i1

Issue price - $150.00

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, Professor
Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA

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.