A Numerical Investigation of Analyte Size Effects in Nanopore Sensing Systems

TL;DR

This study uses numerical simulations to explore how the size of DNA molecules affects ionic current signals in nanopore sensing, revealing size-dependent polarization effects that explain discrepancies with simpler models.

Contribution

It introduces a detailed electrokinetic model to analyze analyte size effects in nanopore sensing, addressing limitations of previous infinite pore assumptions.

Findings

Shorter DNA molecules produce smaller ionic currents at low salt concentrations.

Ion cloud polarization causes opposing electric dipole fields affecting current.

Results explain discrepancies between simplified models and experimental data.

Abstract

We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the relative length of the translocating molecule. Our simulations show a significantly smaller ionic current for DNA molecules that are shorter than the pore at low salt concentrations. These effects can be ascribed to the polarization of the ion cloud along the DNA that leads to an opposing electric dipole field. Our results for DNA shine light on the observed discrepancy between infinite pore models and experimental data on various sized DNA complexes.