Physics – Biological Physics
Scientific paper
2007-03-07
Lecture Notes in Computer Science, 4487 786 (2007)
Physics
Biological Physics
8 pages, 5 figures, to appear in Lecture Notes in Computer Science
Scientific paper
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. Both dynamical and statistical aspects of the translocation process were investigated, 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.
Fyta Maria
Kaxiras Efthimios
Melchionna Simone
Succi Sauro
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