Transport of biopolymers through nanopores offers significant prospects to human health, such as label-free DNA sequencing, mapping, and barcoding, analysis of protein unfolding, understanding post-translational modification of proteins, and various other applications.  Despite significant progress in the last three decades of nanopore sensing in designing engineered protein nanopores and thin solid-state nanopores our understanding of the piecewise translocation dynamics is far from complete due to lack of resolution in deciphering sub-chain conformations and dynamics. In this talk we will present Brownian dynamics (BD) simulation results for translocation dynamics using coarse-grained (CG) models for a solitary as well as for a dual nanopore, to demonstrate how simulations studies can be helpful to understand experimental data using fundamental physics at a smaller length scale difficult to gather experimentally [1, 2].  I will use the theoretical ideas of the nonequilibrium tension propagation theory to interpret simulation results. I will discuss how the velocity of the motifs on a DNA construct is altered so that the genomic length measurements are underscored. Next, I will show the dwell time characteristics of neutral and charged motifs. Finally, I will validate and demonstrate the practical usefulness of these numerical studies by comparing simulation results with those recently obtained experimentally for a dual-nanopore system [3,4]. These examples will demonstrate how simulation studies of nanopore sensing can be effectively used to understand discrimination of motifs on a dsDNA.  I will discuss how the electric field affects the capture process and show modes of translocation of DNA fold through a nanopore.

1. Swarnadeep Seth and Aniket Bhattacharya, DNA Barcodes using a Cylindrical Nanopore, RSC Advances, 11 20781-20787 (2021).

2. Swarnadeep Seth and Aniket Bhattacharya, DNA Barcodes using a Double Nanopore System, Scientific Reports 11, 9799 (2021).

3. X. Liu, Y. Zhang, R. Nagel, W. Reisner, and W. Dunbar, Controlling DNA Tug-of-War in a Dual Nanopore Device, Small 15, 1901704 (2019).

4. X. Liu, P. Zimny, Y. Zhang, A. Rana, A, R. Nagel, W. Reisner, and W. Dunbar, Flossing DNA in a Dual Nanopore Device, Small 16, 1905379 (2020).