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 approximate to tau(1)+tau(2)+tau(3) 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 tau(3) 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.
Physical Review E
Luo, Kaifu; Ala-Nissila, Tapio; Ying, See-Chen; and Bhattacharya, Aniket, "Translocation dynamics with attractive nanopore-polymer interactions" (2008). Faculty Bibliography 2000s. 660.