Driven translocation of a semi-flexible polymer through a nanopore

Abstract

We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory (IFTP), and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length $\tilde{\ell}_p$ the {\it trans} side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance $R_N$ as a function of the chain length $N$ must be known. To this end, we first derive a semi-analytic scaling form for $R_N$, which reproduces the limits of a rod, an ideal chain, and an excluded volume chain in the appropriate limits. We then quantitatively characterize the nature of the {\it trans} side friction based on MD simulations of semi-flexible chains. Augmented with these two factors, the modified IFTP theory shows that there are three main regimes for the scaling of the average translocation time $\tau \propto N^{\alpha}$. In the stiff chain (rod) limit $N/\tilde{\ell}_p \ll 1$, {$\alpha = 2$}, which continuously crosses over in the regime $ 1 < N/\tilde{\ell}_p < 4$ towards the ideal chain behavior with {$\alpha = 3/2$}, which is reached in the regime $N/\tilde{\ell}_p \sim 10^2$. Finally, in the limit $N/\tilde{\ell}_p \gg 10^6$ the translocation exponent approaches its symptotic value $1+\nu$, where $\nu$ is the Flory exponent. Our results are in good agreement with available simulations and experimental data.