Literature DB >> 23004778

Unifying model of driven polymer translocation.

T Ikonen1, A Bhattacharya, T Ala-Nissila, W Sung.   

Abstract

We present a Brownian dynamics model of driven polymer translocation, in which nonequilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, based on the idea suggested by Sakaue [Phys. Rev. E 76, 021803 (2007)]. We validate the model by numerical comparisons with high-accuracy molecular dynamics simulations, showing excellent agreement in a wide range of parameters. Our results show that the dynamics of driven translocation is dominated by the nonequilibrium TP along the cis side subchain. Furthermore, by solving the model for chain lengths up to 10^{10} monomers, we show that the chain lengths probed by experiments and simulations are typically orders of magnitude below the asymptotic limit. This explains both the considerable scatter in the observed scaling of translocation time with respect to chain length, and some of the shortcomings of present theories. Our study shows that for a quantitative theory of polymer translocation, explicit consideration of finite chain length effects is required.

Entities:  

Year:  2012        PMID: 23004778     DOI: 10.1103/PhysRevE.85.051803

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  8 in total

1.  Translocation of a heterogeneous polymer.

Authors:  Stephen Mirigian; Yanbo Wang; Murugappan Muthukumar
Journal:  J Chem Phys       Date:  2012-08-14       Impact factor: 3.488

2.  Pore translocation of knotted DNA rings.

Authors:  Antonio Suma; Cristian Micheletti
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-28       Impact factor: 11.205

3.  Role of non-equilibrium conformations on driven polymer translocation.

Authors:  H H Katkar; M Muthukumar
Journal:  J Chem Phys       Date:  2018-01-14       Impact factor: 3.488

4.  Driven translocation of a semi-flexible polymer through a nanopore.

Authors:  Jalal Sarabadani; Timo Ikonen; Harri Mökkönen; Tapio Ala-Nissila; Spencer Carson; Meni Wanunu
Journal:  Sci Rep       Date:  2017-08-07       Impact factor: 4.379

5.  Active translocation of a semiflexible polymer assisted by an ATP-based molecular motor.

Authors:  A Fiasconaro; J J Mazo; F Falo
Journal:  Sci Rep       Date:  2017-06-23       Impact factor: 4.379

6.  RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration.

Authors:  Matteo Becchi; Pietro Chiarantoni; Antonio Suma; Cristian Micheletti
Journal:  J Phys Chem B       Date:  2021-01-26       Impact factor: 2.991

7.  Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore.

Authors:  Nicholas A W Bell; Kaikai Chen; Sandip Ghosal; Maria Ricci; Ulrich F Keyser
Journal:  Nat Commun       Date:  2017-08-30       Impact factor: 14.919

8.  Simulation of nano elastic polymer chain displacement under pressure gradient/electroosmotic flow with the target of less dispersion of transition.

Authors:  Ramin Zakeri; Eon Soo Lee
Journal:  Sci Rep       Date:  2021-10-04       Impact factor: 4.379

  8 in total

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