Prediction of the effective force on DNA in a nanopore based on density functional theory

TL;DR

This paper develops a hydrodynamic model combining density functional theory and Navier-Stokes equations to predict the effective force on DNA in a nanopore, accounting for electro-osmotic flow, surface charge, and charge inversion effects.

Contribution

It introduces a novel theoretical framework integrating DFT with continuum fluid dynamics to accurately predict DNA forces in nanopores, including effects overlooked by traditional models.

Findings

Charge inversion reduces electro-osmotic velocity.

Flow reversal occurs at higher salt concentrations.

Model aligns well with experimental data.

Abstract

We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore was presented, in which density functional theory (DFT) combined with the continuum Navier-Stokes (NS) equations is utilized to investigate electro-osmotic flow and the viscous drag force acting on the DNA inside a nanopore. Surface charge on the walls of the nanopore is also taken into account in our model. The consistence between our calculation and the previous experimental measurement indicates that the present theoretical model is an effective tool to predict the hydrodynamic resistance on DNA. Results show that charge inversion, which cannot be obtained by the Poisson-Boltzmann (PB) model, will reduce electro-osmotic velocity, or even lead to flow reversal for higher salt concentration. This is helpful to raise the effective force profoundly in the overscreening region.