Influence of pore friction on the universal aspects of driven polymer translocation

Timo Ikonen, A. Bhattacharya, T. Ala-Nissilä, W. Sung

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Abstract

We derive a scaling ansatz for the mean first passage time (MFPT) τ of a driven polymer chain through a nanopore as a function of the chain length N, the external bias f, and the effective pore-polymer friction η, and demonstrate that the pore-polymer interaction, which we introduce as a correction term to asymptotic scaling, is responsible for the dominant finite-size effect. This ansatz provides a simple procedure to extract the asymptotic τ in the large-N limit from a finite chain length data (obtained either from experiment or simulation) by eliminating the correction-to-scaling term. We validate the ansatz applying it on a large set of data for τ obtained using Brownian dynamics (BD) and Brownian dynamics tension propagation (BDTP) simulation results (Ikonen T. et al., Phys. Rev. E, 85 (2012) 051803; J. Chem. Phys., 137 (2013) 085101) for a variety of combination for N, f, and η. As an important practical application we demonstrate how the rescaling procedure can be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we extend the BDTP theory to incorporate Zimm dynamics and find that the asymptotic results for τ (or the translocation exponent) remains unaltered with the inclusion of the hydrodynamics interactions (HI), although the convergence is slower than what we observe for Rouse dynamics. Using the rescaling ansatz we find that these new findings are in good agreement with the existing experimental results as well as with lattice Boltzmann results for driven polymer translocation (PT) for small N.
Original languageEnglish
Article number38001
JournalEurophysics Letters
Volume103
Issue number3
DOIs
Publication statusPublished - 2013
MoE publication typeA1 Journal article-refereed

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friction
porosity
polymers
scaling
propagation
simulation
interactions
hydrodynamics
exponents
inclusions
estimates

Cite this

Ikonen, Timo ; Bhattacharya, A. ; Ala-Nissilä, T. ; Sung, W. / Influence of pore friction on the universal aspects of driven polymer translocation. In: Europhysics Letters. 2013 ; Vol. 103, No. 3.
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Influence of pore friction on the universal aspects of driven polymer translocation. / Ikonen, Timo; Bhattacharya, A.; Ala-Nissilä, T.; Sung, W.

In: Europhysics Letters, Vol. 103, No. 3, 38001, 2013.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Influence of pore friction on the universal aspects of driven polymer translocation

AU - Ikonen, Timo

AU - Bhattacharya, A.

AU - Ala-Nissilä, T.

AU - Sung, W.

PY - 2013

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N2 - We derive a scaling ansatz for the mean first passage time (MFPT) τ of a driven polymer chain through a nanopore as a function of the chain length N, the external bias f, and the effective pore-polymer friction η, and demonstrate that the pore-polymer interaction, which we introduce as a correction term to asymptotic scaling, is responsible for the dominant finite-size effect. This ansatz provides a simple procedure to extract the asymptotic τ in the large-N limit from a finite chain length data (obtained either from experiment or simulation) by eliminating the correction-to-scaling term. We validate the ansatz applying it on a large set of data for τ obtained using Brownian dynamics (BD) and Brownian dynamics tension propagation (BDTP) simulation results (Ikonen T. et al., Phys. Rev. E, 85 (2012) 051803; J. Chem. Phys., 137 (2013) 085101) for a variety of combination for N, f, and η. As an important practical application we demonstrate how the rescaling procedure can be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we extend the BDTP theory to incorporate Zimm dynamics and find that the asymptotic results for τ (or the translocation exponent) remains unaltered with the inclusion of the hydrodynamics interactions (HI), although the convergence is slower than what we observe for Rouse dynamics. Using the rescaling ansatz we find that these new findings are in good agreement with the existing experimental results as well as with lattice Boltzmann results for driven polymer translocation (PT) for small N.

AB - We derive a scaling ansatz for the mean first passage time (MFPT) τ of a driven polymer chain through a nanopore as a function of the chain length N, the external bias f, and the effective pore-polymer friction η, and demonstrate that the pore-polymer interaction, which we introduce as a correction term to asymptotic scaling, is responsible for the dominant finite-size effect. This ansatz provides a simple procedure to extract the asymptotic τ in the large-N limit from a finite chain length data (obtained either from experiment or simulation) by eliminating the correction-to-scaling term. We validate the ansatz applying it on a large set of data for τ obtained using Brownian dynamics (BD) and Brownian dynamics tension propagation (BDTP) simulation results (Ikonen T. et al., Phys. Rev. E, 85 (2012) 051803; J. Chem. Phys., 137 (2013) 085101) for a variety of combination for N, f, and η. As an important practical application we demonstrate how the rescaling procedure can be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we extend the BDTP theory to incorporate Zimm dynamics and find that the asymptotic results for τ (or the translocation exponent) remains unaltered with the inclusion of the hydrodynamics interactions (HI), although the convergence is slower than what we observe for Rouse dynamics. Using the rescaling ansatz we find that these new findings are in good agreement with the existing experimental results as well as with lattice Boltzmann results for driven polymer translocation (PT) for small N.

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