title: Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions.
abstract: 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 Péclet 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 Péclet control parameter, λ, 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 τ 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 τ distributions is obtained for the in-pore force but not for the pulling force.
authors.affiliation: Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1H 7K4, Canada.
authors.forename: Hendrick W
authors.initials: HW
authors.lastname: de Haan
authors.affiliation: Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Sean
authors.affiliation: Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: Gary W
authors.initials: GW
authors.lastname: Slater
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D004058:Diffusion; D008956:Models, Chemical; D058608:Nanopores; D011108:Polymers / Q000737:chemistry*; D014780:Viruses
chemical_list: D011108:Polymers; D004247:DNA