Polymer translocation through a nanopore: a geometry dependence study

The translocation of a single stranded nucleic acid polymer through a nanopore, by an external electric field applied across the pore, may be well described by a 1-D drift-diffusion model. Translocation times and velocities are calculated for a homopolymer driven through a nanopore, where the polymer-pore interaction dominates the polymer dynamics. In this model a purely electrostatic polymer-pore interaction is introduced, calculated from atomic charges on the polymer and pore. Simulation results show that the peak repulsion force occurs on the polymer during entry into the pore. In addition, the peak polymer-pore interaction is shown to decrease with polymer length for homopolymers with less than 20 nucleotides. The modeling results offer an explanation for the enhanced drift velocities experimentally observed for such short polymers. The dependence of the polymer translocation time on the pore geometry is investigated. For increasing pore radius the translocation velocity approaches the free space drift velocity for the surrounding ionic solution.