Mohammadreza Niknam Hamidabad

arXiv2019

Translocation through a narrow pore under a puling force

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.

physics.comp-ph↗

arXiv2018

Effects of interaction between nanopore and polymer on translocation time

Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non-equilibrium initial condition shows that the translocation time is very sensitive to the initial condition. Translocation time of the relaxed polymers for interaction energy of 8k_B T is smaller from the non-equilibrium case even in the small energy of 1k_B T.

physics.comp-ph↗