Driven translocation of a semi-flexible polymer through a nanopore

• Main Authors: Jalal Sarabadani, Timo Ikonen, Harri Mökkönen, Tapio Ala-Nissila, Spencer Carson, Meni Wanunu
• Format: Article
• Language: English
• Published: Nature Publishing Group 2017-08-01
• Series: Scientific Reports
• Online Access: https://doi.org/10.1038/s41598-017-07227-3

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, and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length $${\tilde{{\boldsymbol{\ell }}}}_{{\boldsymbol{p}}}$$ ℓ ˜ p the 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 trans side friction based on MD simulations. Augmented with these two factors, the theory shows that there are three main regimes for the scaling of the average translocation time τ ∝ N α . In the rod $${\boldsymbol{N}}{\boldsymbol{/}}{\tilde{{\boldsymbol{\ell }}}}_{{\boldsymbol{p}}}{\boldsymbol{\ll }}1$$ N / ℓ ˜ p ≪ 1 , Gaussian $${\boldsymbol{N}}{\boldsymbol{/}}{\tilde{{\boldsymbol{\ell }}}}_{{\boldsymbol{p}}}\sim {\bf{1}}{{\bf{0}}}^{{\bf{2}}}$$ N / ℓ ˜ p ∼ 1 0 2 and excluded volume chain $${\boldsymbol{N}}{\boldsymbol{/}}{\tilde{{\boldsymbol{\kappa }}}}_{{\boldsymbol{p}}}$$ N / κ ˜ p  ≫ 10 6 limits, α = 2, 3/2 and 1 + ν, respectively, where ν is the Flory exponent. Our results are in good agreement with available simulations and experimental data.