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 τ increases with increasing bending rigidity κ. Similarly, the exponent β for the scaling of τ with polymer length N,τ∼N^{β}, increases with increasing κ 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_{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 a larger contribution to the trans side friction at small f_{d}. Similarly to flexible polymers, we find significant center-of-mass diffusion of the cis side polymer segment which speeds up translocation. This effect is larger for smaller f_{d}. However, this speedup is smaller than the slowing down due to the trans side friction. At large enough N_{Kuhn}, the roles can be seen to be reversed, and the dynamics of flexible polymers can be reached. However, for example, polymers used in translocation experiments of DNA are elastically so short that the finite-length dynamics outlined here applies.

Driven translocation of semiflexible polyelectrolyte through a nanopore

“…A large v p,c indicates that more monomers of polyelectrolyte go forward along with the driven monomer inside the pore, that is, the length of the stretched part is larger for larger k θ . The result is in agreement with the finding that the length of polymer monomers causing friction increases with k θ . This is also consistent with long persistence length of the stiff polyelectrolyte.…”

“…Figure shows the dependence of the translocation time τ on the bending modulus k θ for the polyelectrolyte of length N = 64. We find τ increases with k θ , in agreement with previous simulation . However, τ increases fast at small k θ and it tends to saturation at large k θ .…”

“…Whereas we find the exponent δ = 0.97 for the stiff polyelectrolyte chain with k θ = 100. Suhonen et al got δ = 0.92, 1.02, and 1.04 for k θ = 0, 10, and 20 for the polymer of length N = 200 using LD simulation, that is, a trend for δ to approach 1 with increasing k θ was observed . We will show later that the conformation of the flexible polyelectrolyte during the translocation changes more obviously than that of the stiff one.…”

“…There are also many notable works on the translocation of semiflexible polymer chains . For instance, Lam and Zhen applied the TP theory proposed by Sakaue for completely flexible polymer to the case of the translocation of a semiflexible polymer .…”

“…While experimental data as well as coarse‐grained (CG) model simulation showed α = 1.37 for DNA or semiflexible polymer translocation . Recently, simulation showed that τ increases with increasing the bending rigidity and the scaling exponent α increases with increasing bending rigidity as well as with increasing driving force …”