Using a Péclet Number for the Translocation of 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 endeavour 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 over-estimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using dsDNA. By defining a coarse-graining 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 $\tau$ distributions is obtained for the in-pore force but not for the pulling force.

arXiv comment8 pages, 5 figures, 1 table

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Cited by in corpus (6)

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• Polymer translocation under a pulling force: scaling arguments and threshold forces
• Dynamics of driven translocation of semiflexible polymers
• Quantification of tension to explain bias dependence of driven polymer translocation dynamics
• Reducing the variance in the translocation times by pre-stretching the polymer