Influence of pore friction on the universal aspects of driven polymer translocation

¹ VTT Technical Research Centre of Finland - P.O. Box 1000, FI-02044 VTT, Finland, EU
² Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science P.O. Box 11000, FI-00076 Aalto, Espoo, Finland, EU
³ Department of Physics, University of Central Florida - Orlando, FL 32816-2385, USA
⁴ Department of Physics, Box 1843, Brown University - Providence, RI 02912-1843, USA
⁵ Department of Physics, Pohang University of Science and Technology - Pohang 790-784, South Korea

Received: 6 May 2013
Accepted: 25 July 2013

Abstract

We derive a scaling ansatz for the mean first passage time (MFPT) τ of a driven polymer chain through a nanopore as a function of the chain length N, the external bias f, and the effective pore-polymer friction η, and demonstrate that the pore-polymer interaction, which we introduce as a correction term to asymptotic scaling, is responsible for the dominant finite-size effect. This ansatz provides a simple procedure to extract the asymptotic τ in the large-N limit from a finite chain length data (obtained either from experiment or simulation) by eliminating the correction-to-scaling term. We validate the ansatz applying it on a large set of data for τ obtained using Brownian dynamics (BD) and Brownian dynamics tension propagation (BDTP) simulation results (Ikonen T. et al., Phys. Rev. E, 85 (2012) 051803; J. Chem. Phys., 137 (2013) 085101) for a variety of combination for N, f, and η. As an important practical application we demonstrate how the rescaling procedure can be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we extend the BDTP theory to incorporate Zimm dynamics and find that the asymptotic results for τ (or the translocation exponent) remains unaltered with the inclusion of the hydrodynamics interactions (HI), although the convergence is slower than what we observe for Rouse dynamics. Using the rescaling ansatz we find that these new findings are in good agreement with the existing experimental results as well as with lattice Boltzmann results for driven polymer translocation (PT) for small N.