Driven translocation of a semi-flexible polymer through a nanopore

Jalal Sarabadani, Timo Ikonen, Harri Mökkönen, Tapio Ala-Nissila, Spencer Carson, Meni Wanunu

Research output: Contribution to journalArticleScientificpeer-review

36 Citations (Scopus)

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 ℓp 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 RN as a function of the chain length N must be known. To this end, we first deriveF a semi-analytic scaling form for RN, 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∞Nα . In the rod N/ℓp «1, Gaussian N/ℓp~1 0 2 and excluded volume chain N/κp «106 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.
Original languageEnglish
Article number7423
Number of pages8
JournalScientific Reports
Volume7
Issue number1
DOIs
Publication statusPublished - 7 Aug 2017
MoE publication typeA1 Journal article-refereed

Funding

This work was supported by the Academy of Finland through its Centers of Excellence Program under Project Nos 251748 and 284621. The numerical calculations were performed using computer resources from the Aalto University School of Science “Science-IT” project, and from CSC - Center for Scientific Computing Ltd. This research was funded in part by the National Institutes of Health (R01-HG009186, M.W.).

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