title: Translocation dynamics with attractive nanopore-polymer interactions.
abstract: Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time tau approximately tau1+tau2+tau3 corresponding to the initial filling of the pore, transfer of polymer from the cis side to the trans side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from nonactivated to activated in nature as the strength of the attractive interaction increases, and tau3 becomes the dominant contribution to the total translocation time for strong attraction. This leads to nonuniversal dependence of tau as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a plausible explanation for the different scaling behavior observed in solid state nanopores vs that for the natural alpha-hemolysin channel.
authors.affiliation: Physics Department, Technical University of Munich, D-85748 Garching, Germany. luokaifu@gmail.com
authors.forename: Kaifu
authors.initials: K
authors.lastname: Luo
authors.forename: Tapio
authors.initials: T
authors.lastname: Ala-Nissila
authors.forename: See-Chen
authors.initials: SC
authors.lastname: Ying
authors.forename: Aniket
authors.initials: A
authors.lastname: Bhattacharya
mesh_terms: D001693:Biological Transport, Active; D055592:Biophysical Phenomena; D001704:Biopolymers / Q000737:chemistry* / Q000378:metabolism*; D008954:Models, Biological; D008956:Models, Chemical; D015394:Molecular Structure; D049329:Nanostructures / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D001704:Biopolymers