Effects of interaction between nanopore and polymer on translocation time

Abdolvahab, Rouhollah; Niknam Hamidabad, Mohammadreza

doi:10.22055/jrmbs.2020.15558

Effects of interaction between nanopore and polymer on translocation time

Document Type : Full length research Paper

Authors

Rouhollah Abdolvahab

Mohammadreza Niknam Hamidabad

Department of Physics, Faculty of Science, Iran University of Science and Technology, Tehran, Iran

10.22055/jrmbs.2020.15558

Abstract

Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and 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 8𝑘𝐵 𝑇 is smaller from the non- equilibrium case even in the small energy of 1𝑘𝐵 𝑇. Moreover, our simulation results show that the translocation velocity decrease by increasing the nanopore diameter from 3𝜎 to 5𝜎, where 𝜎 is the size of a monomer.

Keywords

Polymer Translocation

Nanopore

Molecular Dynamic

Binding energy

20.1001.1.2322231.1399.10.4.12.4

Subjects

Condensed matter

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