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

    14 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 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 l p1, Gaussian l p 1 0 2 and excluded volume chain 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.

    Original languageEnglish
    Article number7423
    Number of pages8
    JournalScientific Reports
    Volume7
    Issue number1
    DOIs
    Publication statusPublished - 1 Dec 2017
    MoE publication typeA1 Journal article-refereed

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    polymers
    scaling
    rods
    friction
    molecular dynamics
    simulation
    exponents
    propagation

    Cite this

    Sarabadani, J., Ikonen, T., Mökkönen, H., Ala-Nissila, T., Carson, S., & Wanunu, M. (2017). Driven translocation of a semi-flexible polymer through a nanopore. Scientific Reports, 7(1), [7423]. https://doi.org/10.1038/s41598-017-07227-3
    Sarabadani, Jalal ; Ikonen, Timo ; Mökkönen, Harri ; Ala-Nissila, Tapio ; Carson, Spencer ; Wanunu, Meni. / Driven translocation of a semi-flexible polymer through a nanopore. In: Scientific Reports. 2017 ; Vol. 7, No. 1.
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    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 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 l p1, Gaussian l p 1 0 2 and excluded volume chain 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.",
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    Sarabadani, J, Ikonen, T, Mökkönen, H, Ala-Nissila, T, Carson, S & Wanunu, M 2017, 'Driven translocation of a semi-flexible polymer through a nanopore', Scientific Reports, vol. 7, no. 1, 7423. https://doi.org/10.1038/s41598-017-07227-3

    Driven translocation of a semi-flexible polymer through a nanopore. / Sarabadani, Jalal; Ikonen, Timo; Mökkönen, Harri; Ala-Nissila, Tapio; Carson, Spencer; Wanunu, Meni.

    In: Scientific Reports, Vol. 7, No. 1, 7423, 01.12.2017.

    Research output: Contribution to journalArticleScientificpeer-review

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    AU - Carson, Spencer

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    Sarabadani J, Ikonen T, Mökkönen H, Ala-Nissila T, Carson S, Wanunu M. Driven translocation of a semi-flexible polymer through a nanopore. Scientific Reports. 2017 Dec 1;7(1). 7423. https://doi.org/10.1038/s41598-017-07227-3