Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions

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Journal Title
Journal ISSN
Volume Title
School of Science | A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Date
2012
Major/Subject
Mcode
Degree programme
Language
en
Pages
205104
Series
The Journal of Chemical Physics, Volume 136, Issue 20
Abstract
We study the driven translocation of polymers under time-dependent driving forces using N-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential correlation time, to mimic both plausible experimental setups and naturally occurring biological conditions. In addition, we consider both the case of purely repulsive polymer-pore interactions and the case with additional attractive polymer-pore interactions, typically occurring inside biological pores. We find that the nature of the interaction fundamentally affects the translocation dynamics. For the non-attractive pore, the translocation time crosses over to a fast translocation regime as the frequency of the driving force decreases. In the attractive pore case, because of a free energy well induced inside the pore, the translocation time can be a minimum at the optimal frequency of the force, the so-called resonant activation. In the latter case, we examine the effect of various physical parameters on the resonant activation, and explain our observations using simple theoretical arguments.
Description
Keywords
polymers, polymer translocation, resonant activation, soft matter, free energy, dynamics of biopolymers, DNA
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Citation
Ikonen, T. & Shin, J. & Ala-Nissilä, Tapio & Sung, W. 2012. Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions. The Journal of Chemical Physics. Volume 136, Issue 20. 205104. 0021-9606 (printed). DOI: 10.1063/1.4722080.