Translocation through a narrow pore under a puling force

Abstract

We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces. In order to see the polymer and pore interaction effects on translocation time, we studied 9 different interaction energies. Moreover, to better understand the simulation results we investigate polymer center of mass, shape factor and the monomer distribution through the translocation. Our results unveil that while increasing the polymer-pore interaction energy slows down the translocation, expanding the pore diameter, makes the translocation faster. The shape analysis of the results reveals that the polymer shape is very sensitive to the interaction energy. In high interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last.