Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows

Abstract

We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

10 pages, 9 figures, to appear in Computing in Science and Engineering

References in corpus (9)

• Fast DNA translocation through a solid-state nanopore
• Polymer Translocation througha Pore in a Membrane
• Driven Polymer Translocation Through a Narrow Pore
• Minimal entropic kinetic models for simulating hydrodynamics
• Fluctuating lattice Boltzmann
• Design of quasi-symplectic propagators for Langevin dynamics
• Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore
• Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations
• Simulating Colloid Hydrodynamics with Lattice Boltzmann