Molecular Dynamics Simulation Study of Transverse and Longitudinal Ionic Currents in Solid-State Nanopore DNA Sequencing

We report all-atom molecular dynamics (MD) simulations of single-stranded DNA (ssDNA) translocation in 1 M KCl solution through a silicon nitride solid-state nanopore with one or two nanochannels perpendicular to the nanopore. We measure the longitudinal and transverse ionic currents generated through the pores under voltage biases applied longitudinally and transversely across the pores. During fast translocation of homo-oligonucleotides through the pore, the characteristic signals of nucleotides resulting from ion-nucleotide interactions cannot be distinguished. These signals are buried in fluctuations of the ions caused by thermal energy at high sampling frequency. A pattern recognition neural network shows that the averaged transverse and longitudinal ionic currents and their combination enable the canonical A, G, T, and C nucleotide classifications to be recognized with an accuracy of 81.4%. Further improvements can be explored with machine learning algorithms, larger databases, and slower translocation rates at lower voltages biases that would require greater computer resources.