Capture of semi-flexible polyelectrolytes by a Nanopore: A Lattice Boltzmann Simulation Study

Although tension-propagation theory indicates that the field-driven translocation time of a polyelectrolyte across a nanopore depends upon its initial conformation, most simulations of this process use equilibrium conformations. During capture, a polymer deforms and orients along the converging field lines. Our Langevin Dynamic (LD) simulations suggest that a long semi-flexible polymer stretches while approaching the pore but then shrinks when it reaches the pore. Rod-like chains, on the other hand, slightly stretch throughout the entire process. In this talk, we compare LD results to those obtained when Hydrodynamic Interactions (HI) and explicit salt are added. The HI are modelled using a Lattice-Boltzmann algorithm and the electrostatic interactions employ the P3M method. We examine how conformations evolve during capture and how much they deviate from equilibrium when translocation start. We also investigate the impact of these "captured conformations" on the translocation process itself. Finally, we investigate the possibility of using time-dependent fields to help end monomers find the nanopore, the last step before translocation. Our simulations are done using ESPResSo.