English

Pore-blockade Times for Field-Driven Polymer Translocation

Soft Condensed Matter 2008-02-15 v4 Statistical Mechanics Biological Physics Biomolecules

Abstract

We study pore blockade times for a translocating polymer of length NN, driven by a field EE across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical interactions. We find that the typical time the pore remains blocked during a translocation event scales as N(1+2ν)/(1+ν)/E\sim N^{(1+2\nu)/(1+\nu)}/E, where ν0.588\nu\simeq0.588 is the Flory exponent for the polymer. In line with our previous work, we show that this scaling behaviour stems from the polymer dynamics at the immediate vicinity of the pore -- in particular, the memory effects in the polymer chain tension imbalance across the pore. This result, along with the numerical results by several other groups, violates the lower bound N1+ν/E\sim N^{1+\nu}/E suggested earlier in the literature. We discuss why this lower bound is incorrect and show, based on conservation of energy, that the correct lower bound for the pore-blockade time for field-driven translocation is given by ηN2ν/E\eta N^{2\nu}/E, where η\eta is the viscosity of the medium surrounding the polymer.

Keywords

Cite

@article{arxiv.0710.4940,
  title  = {Pore-blockade Times for Field-Driven Polymer Translocation},
  author = {Henk Vocks and Debabrata Panja and Gerard T. Barkema and Robin C. Ball},
  journal= {arXiv preprint arXiv:0710.4940},
  year   = {2008}
}

Comments

14 pages, 6 figures, slightly shorter than the previous version; to appear in J. Phys.: Cond. Mat

R2 v1 2026-06-21T09:36:34.649Z