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, and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a...

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Autores principales:	Jalal Sarabadani, Timo Ikonen, Harri Mökkönen, Tapio Ala-Nissila, Spencer Carson, Meni Wanunu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dd49193fd36245c5a19c5189f4478cb8
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spelling	oai:doaj.org-article:dd49193fd36245c5a19c5189f4478cb82021-12-02T15:06:15ZDriven translocation of a semi-flexible polymer through a nanopore10.1038/s41598-017-07227-32045-2322https://doaj.org/article/dd49193fd36245c5a19c5189f4478cb82017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07227-3https://doaj.org/toc/2045-2322Abstract 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.Jalal SarabadaniTimo IkonenHarri MökkönenTapio Ala-NissilaSpencer CarsonMeni WanunuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-8 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jalal Sarabadani Timo Ikonen Harri Mökkönen Tapio Ala-Nissila Spencer Carson Meni Wanunu Driven translocation of a semi-flexible polymer through a nanopore
description	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.
format	article
author	Jalal Sarabadani Timo Ikonen Harri Mökkönen Tapio Ala-Nissila Spencer Carson Meni Wanunu
author_facet	Jalal Sarabadani Timo Ikonen Harri Mökkönen Tapio Ala-Nissila Spencer Carson Meni Wanunu
author_sort	Jalal Sarabadani
title	Driven translocation of a semi-flexible polymer through a nanopore
title_short	Driven translocation of a semi-flexible polymer through a nanopore
title_full	Driven translocation of a semi-flexible polymer through a nanopore
title_fullStr	Driven translocation of a semi-flexible polymer through a nanopore
title_full_unstemmed	Driven translocation of a semi-flexible polymer through a nanopore
title_sort	driven translocation of a semi-flexible polymer through a nanopore
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/dd49193fd36245c5a19c5189f4478cb8
work_keys_str_mv	AT jalalsarabadani driventranslocationofasemiflexiblepolymerthroughananopore AT timoikonen driventranslocationofasemiflexiblepolymerthroughananopore AT harrimokkonen driventranslocationofasemiflexiblepolymerthroughananopore AT tapioalanissila driventranslocationofasemiflexiblepolymerthroughananopore AT spencercarson driventranslocationofasemiflexiblepolymerthroughananopore AT meniwanunu driventranslocationofasemiflexiblepolymerthroughananopore
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Driven translocation of a semi-flexible polymer through a nanopore

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