A comparison of experimental bacterial genome mapping data with results from simulation using a coarse-grained dsDNA construct

We design in silico an experimental dual nanopore setup that mimics the original experiment performed by Nooma Bio Inc., to obtain insights into dynamics and conformation of the captured dsDNA at sub-nanometer length scales. We mimic “flossing" in silico using a coarse-grained model of a dsDNA with 2048 beads of diameter 8 nanometers (24 base pairs) that correspond to the experimental 48500 base pair λ-phage DNA with 15 motifs. The simulation results capture the nonequilibrium dynamics of flossing and enable us to make a one-to-one comparison of the dwell time distribution of the individual motifs and the genomic lengths between any two motifs. In addition, by varying the field bias and other controlling factors, we obtain physical insights for the entire translocation process.