Using a Peclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions

Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Peclet number for translocation, P-t, to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach overestimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using double stranded DNA (dsDNA). By defining a Peclet control parameter, lambda, we are able to correct this and tune the simulations to replicate the experimental P-t (for dsDNA and other scenarios). To show the effect that a particular P-t can have on the dynamics of translocation, we perform simulations across a wide range of P-t values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As P-t brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time tau on P-t and a steep rise in the probability of translocating. Comparing the two force cases illustrates the impact of the crowding effects that occur on the trans side: a non-monotonic dependence of the width of the t distributions is obtained for the in-pore force but not for the pulling force.