Dynamics of driven translocation of semiflexible polymers

Abstract

We study translocation of semiflexible polymers driven by force $f_d$ inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time $\tau$ increases with increasing bending rigidity $\kappa$. Similarly, the exponent $\beta$ for the scaling of $\tau$ with polymer length $N$, $\tau \sim N^{\beta }$, increases with increasing $\kappa$ as well as with increasing $f_d$. By comparing waiting times between semiflexible and fully flexible polymers we show that for realistic $f_d$ translocation dynamics is to a large extent, but not completely, determined by the polymer's elastic length measured in number of Kuhn segments $N_{\mathrm{Kuhn}}$. Unlike in driven translocation of flexible polymers, friction related to the polymer segment on the trans side has a considerable effect on the resulting dynamics. This friction is intermittently reduced by buckling of the polymer segment in the vicinity of the pore opening on the trans side. We show that in the experimentally relevant regime, where viscosity is higher than in computer simulation models, the probability for this buckling increases with increasing $f_d$, giving rise to larger contribution to trans side friction at small $f_d$. Similarly to flexible polymers, we find significant center of mass diffusion of the cis side polymer segment. This speeds up translocation, which effect is larger for smaller $f_d$. However, this speed-up is smaller than the slowing down due to the trans side friction. At large enough $N_{\mathrm{Kuhn}}$, the roles can be seen to be reversed and the dynamics of flexible polymers be reached. However, for example, polymers used in translocation experiments of DNA, are elastically so short, that the finite-length dynamics outlined here applies.

10 pages, 9 figures

References in corpus (14)

• Fast DNA translocation through a solid-state nanopore
• Nonequilibrium dynamics of polymer translocation and straightening
• Unifying model of driven polymer translocation
• Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations
• Dynamics of forced biopolymer translocation
• How long does it take to pull an ideal polymer into a small hole?
• Driven translocation of a polymer: fluctuations at work
• Using a Péclet Number for the Translocation of Polymer through a Nanopore to Tune Coarse-Grained Simulations to Experimental Conditions
• Criteria for minimal model of driven polymer translocation
• Quantification of tension to explain bias dependence of driven polymer translocation dynamics
• Driven polymer translocation in good and bad solvent: effects of hydrodynamics and tension propagation
• Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics
• Rigidity-induced scale invariance in polymer ejection from capsid
• Polymer ejection from strong spherical confinement

Cited by in corpus (1)

• Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions