Simulation studies of nonequilibrium dynamics of charged motifs in a dual nanopore device

Accurate detection of DNA motifs has essential applications in taxonomical research, conserving biodiversity, characterizing unknown species, identifying disease vectors, authenticating herbal products, and unambiguously labeling food specimens. We use Brownian dynamics simulation to study the detailed translocation process of a coarse-grain DNA scanning through a double nanopore setup using an extended electric field. We use a 48kbp long dsDNA with seven motifs (spherical/elongated) with different partial change content. Our study explains the origin of the asymmetric distribution of the dwell time observed experimentally in lambda-phage DNA with seven motifs (X. Liu et al., Small 2020). We demonstrate that the electric field inside and beyond the pores is critical to discriminate protein tags based on their effective charges and can be a viable method directly applicable to experiments. Our mesoscopic simulation provides a complete description of the time-of-flight velocity variation along the chain arising from the non-equilibrium tension propagation in presence of the extended electric field.