Eur. Phys. J. E (2009) 28: 385-393
https://doi.org/10.1140/epje/i2008-10429-9

Regular Article

Polymer translocation in a double-force arrangement

¹ Department of Applied Physics, Helsinki University of Technology, P.O. Box 1100, FIN-02015, Espoo, Finland
² Department of Physics, Brown University, Box 1843, 02912-1843, Providence, Rhode Island, USA

^* e-mail: santtu.ollila@tkk.fi
^** e-mail: tapio.ala-nissila@tkk.fi

Received: 19 June 2008
Revised: 30 October 2008
Accepted: 21 January 2009
Published online: 27 March 2009

Abstract

Using Langevin dynamics simulations, we investigate the translocation dynamics of an externally driven polymer chain through a nanopore, where a pulling force F is exerted on the first monomer whilst there is an opposing force F _E < F within the pore. Such a double-force arrangement has been proposed recently to allow better dynamical control of the translocation process in order to sequence biopolymers. We find that in the double-force arrangement translocation becomes slower as compared to the case under a single monomer pulling force of magnitude F - F _E , but scaling of the translocation time as a function of the chain length ∼ N ² does not change. The waiting time (m) for monomer m to exit the pore is found to be a monotonically increasing function of the bead number almost until m N , which indicates relatively well-defined slowing down and control of the chain velocity during translocation. We also study the waiting time distributions for the beads in the chain, and characterize in detail fluctuations in the bead positions and their transverse position coordinates during translocation. These data should be useful in estimating position-dependent sequencing errors in double-force experiments.