Literature DB >> 14995482

Anomalous dynamics of forced translocation.

Yacov Kantor1, Mehran Kardar.   

Abstract

We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two segments are in equilibrium. The dynamics of s(t) in such a limit would be diffusive, with a mean translocation time scaling as N2 in the absence of a force, and proportional to N when a force is applied. We demonstrate that the assumption of equilibrium must break down for sufficiently long polymers (more easily when forced), and provide lower bounds for the translocation time by comparison to unimpeded motion of the polymer. These lower bounds exceed the time scales calculated on the basis of equilibrium, and point to anomalous (subdiffusive) character of translocation dynamics. This is explicitly verified by numerical simulations of the unforced translocation of a self-avoiding polymer. Forced translocation times are shown to strongly depend on the method by which the force is applied. In particular, pulling the polymer by the end leads to much longer times than when a chemical potential difference is applied across the membrane. The bounds in these cases grow as N2 and N1+nu, respectively, where nu is the exponent that relates the scaling of the radius of gyration to N. Our simulations demonstrate that the actual translocation times scale in the same manner as the bounds, although influenced by strong finite size effects which persist even for the longest polymers that we considered (N=512).

Entities:  

Year:  2004        PMID: 14995482     DOI: 10.1103/PhysRevE.69.021806

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


  24 in total

1.  Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

Authors:  Matthias Weiss; Markus Elsner; Fredrik Kartberg; Tommy Nilsson
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

2.  Polymer translocation through alpha-hemolysin pore with tunable polymer-pore electrostatic interaction.

Authors:  Chiu Tai Andrew Wong; M Muthukumar
Journal:  J Chem Phys       Date:  2010-07-28       Impact factor: 3.488

3.  Cooperative translocation dynamics of biopolymer chains through nanopores in a membrane: Slow dynamics limit.

Authors:  Hai-Jun Wang; Fang Gu; Xiao-Zhong Hong; Xin-Wu Ba
Journal:  Eur Phys J E Soft Matter       Date:  2010-10-31       Impact factor: 1.890

4.  Presentation of large DNA molecules for analysis as nanoconfined dumbbells.

Authors:  Kristy L Kounovsky-Shafer; Juan P Hernández-Ortiz; Kyubong Jo; Theo Odijk; Juan J de Pablo; David C Schwartz
Journal:  Macromolecules       Date:  2013-10-22       Impact factor: 5.985

5.  Ionic current blockades from DNA and RNA molecules in the alpha-hemolysin nanopore.

Authors:  Tom Z Butler; Jens H Gundlach; Mark Troll
Journal:  Biophys J       Date:  2007-08-03       Impact factor: 4.033

6.  Passage times for polymer translocation pulled through a narrow pore.

Authors:  Debabrata Panja; Gerard T Barkema
Journal:  Biophys J       Date:  2007-10-19       Impact factor: 4.033

7.  How subdiffusion changes the kinetics of binding to a surface.

Authors:  Irwin M Zaid; Michael A Lomholt; Ralf Metzler
Journal:  Biophys J       Date:  2009-08-05       Impact factor: 4.033

8.  Nonexponential kinetics of DNA escape from alpha-hemolysin nanopores.

Authors:  Matthew Wiggin; Carolina Tropini; Vincent Tabard-Cossa; Nahid N Jetha; Andre Marziali
Journal:  Biophys J       Date:  2008-09-05       Impact factor: 4.033

9.  Scaling exponents of forced polymer translocation through a nanopore.

Authors:  A Bhattacharya; W H Morrison; K Luo; T Ala-Nissila; S-C Ying; A Milchev; K Binder
Journal:  Eur Phys J E Soft Matter       Date:  2009-08-08       Impact factor: 1.890

10.  Enzyme-modulated DNA translocation through a nanopore.

Authors:  Ajay S Panwar; M Muthukumar
Journal:  J Am Chem Soc       Date:  2009-12-30       Impact factor: 15.419

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