Molecular Dynamics Simulation of ss-DNA Translocation between Copper Nanoelectrodes Incorporating Electrode Charge Dynamics

Abstract

Molecular dynamics simulations have been performed to study the translocation of single-stranded (ss)-DNA through the nanoscale gap between the nanoscale electrodes of a proposed genomic sequencing device. Using a fixed gap width between the electrodes and a small sample segment of ss-DNA as initial starting points in this project, the effect of applied electric fields on translocation velocity was studied. To describe the electrostatic interactions of the water, ions, and ss-DNA with the nanoscale electrodes, we applied the electrode charge dynamics (ECD) method. Through the density profile and comparison of translocation velocities to extrapolated experimental data, we found the ECD potential to be a better descriptor of the metal/nonmetal electrostatic interactions compared to the commonly used universal force field (UFF). Translocation velocities obtained using the ECD potential were consistent with simulated bulk data.