Molecular dynamics simulation of a nanoscale device for fast sequencing of DNA.

Abstract

We report a molecular-simulation based modeling of transport and orientation properties of single-stranded DNA molecules in a nanoscale channel as a part of a larger nanoscale device designed for rapid DNA sequencing. The proposed novel nanotechnology concept modeled in these simulations offers the possibility of unprecedented rapidity in the detection of DNA sequences. The proposed device consists of a detection gate, created by two metal nano-electrodes separated by approximately two to five nanometers, placed between two nonconductive plates. The DNA molecules in aqueous solution contained between the plates will be driven by an electric field through the detection gate. Individual base pairs within the DNA sequence are to be determined experimentally by examining the variations in the tunneling conductance as the DNA passes through the gate. We are conducting large-scale molecular dynamics simulations to study the transport and orientation of the DNA segment as it passes through the nanogate. Molecular dynamics is used to determine feasible and ideal gate widths, optimal applied electric field magnitude, and strand length effects. Results from these molecular dynamics simulations are presented and compared to bulk simulation results. Additionally, we present compelling evidence of the applicability of a recently developed model for the interaction between metal nanostructures and charged species, electrode charge dynamics (ECD), over the commonly applied such model, based on the universal force field (UFF).