How effective is graphene nanopore geometry on DNA sequencing?

TL;DR

This study uses molecular dynamics simulations to analyze how different geometries of graphene nanopores influence DNA translocation, highlighting the importance of pore shape and symmetry for sequencing efficiency.

Contribution

It provides a comparative analysis of various graphene nanopore geometries and their effects on DNA pulling dynamics, proposing optimal pore design for sequencing.

Findings

Symmetric circular nanopores facilitate DNA translocation.

Pore shape and symmetry significantly affect free energy barriers.

High pulling velocity enhances sequencing potential.

Abstract

In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assessed. Simulation results demonstrate the strong effect of the pore shape as well as geometrical symmetry on free energy barrier, orientations and dynamic of DNA translocation through graphene nanopore. Our study proposes that the symmetric circular geometry of monolayer graphene nanopore with high pulling velocity can be used for DNA sequencing.