The Library

Pore-blockade times for field-driven polymer translocation

Tools

Vocks, Henk, Panja, Debabrata, Barkema, Gerard T. and Ball, Robin. (2008) Pore-blockade times for field-driven polymer translocation. Journal of Physics-Condensed Matter, Vol.20 (No.9). pp. 1-7. ISSN 0953-8984

Preview

PDF
WRAP_Ball_Pore_blockade_times.pdf - Accepted Version - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Download (337Kb)

Official URL: http://dx.doi.org/10.1088/0953-8984/20/9/095224

Abstract

We study pore-blockade times for a translocating polymer of length N, driven by a field E across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical interactions. We find that the typical time for which the pore remains blocked during a translocation event scales as similar to N(1+ 2 nu)/(1+nu)/E, where nu similar or equal to 0.588 is the Flory exponent for the polymer. We show, in line with our previous work, that this scaling behavior stems from polymer dynamics in the immediate vicinity of the pore - in particular, the memory effects in the polymer chain tension imbalance across the pore. This result, like numerical results from several other groups, violates the lower bound similar to N1+nu/E suggested earlier in the literature. We discuss why this lower bound is incorrect and show, on the basis of the conservation of energy, that the correct lower bound for the pore-blockade time for field-driven translocation is given by eta N-2 nu/E, where eta is the viscosity of the medium surrounding the polymer.

Item Type:

Journal Article

Subjects:

Q Science > QC Physics

Divisions:

Faculty of Science > Physics

Library of Congress Subject Headings (LCSH):

Biophysics, Translocation (Genetics), Polymers

Journal or Publication Title:

Journal of Physics-Condensed Matter

Publisher:

IOP Publishing

ISSN:

0953-8984

Official Date:

5 March 2008

Dates:

Date	Event
5 March 2008	Published

Volume:

Vol.20

Number:

No.9

Number of Pages:

Page Range:

pp. 1-7

Identification Number:

10.1088/0953-8984/20/9/095224

Status:

Peer Reviewed

Publication Status:

Published

Access rights to Published version:

Open Access

References:

B. Dreiseikelmann, Microbiol. Rev. 58, 293 (1994).
J. P. Henry et al., J. Membr. Biol. 112, 139 (1989).
J. Akimaru et al., PNAS USA 88, 6545 (1991).
D. Goerlich and T. A. Rappaport, Cell 75, 615 (1993).
G. Schatz and B. Dobberstein, Science 271, 1519 (1996).
I. Szab`o et al. J. Biol. Chem. 272, 25275 (1997).
B. Hanss et al., PNAS USA 95, 1921 (1998).
Yun-Long Tseng et al., Molecular Pharm. 62, 864 (2002).
J. J. Nakane, M. Akeson, A. Marziali, J. Phys.: Cond. Mat. 15, R1365 (2003).
J. Kasianowicz et al., PNAS USA 93, 13770 (1996); E. Henrickson et al., Phys. Rev. Lett. 85, 3057
(2000); A Meller et al., Phys. Rev. Lett. 86, 3435 (2001); M. Akeson et al., Biophys. J. 77, 3227
(1999); A. Meller et al., PNAS USA 97, 1079 (2000); A. Meller and D. Branton, Electrophoresis
23, 2583 (2002).
A. J. Storm et al., Nanoletters 5, 1193 (2005).
I. Szab`o et al., FASEB J. 12, 495 (1998); S. Horowka et al. PNAS 98, 12996 (2001); S. Howorka,
S. Cheley and H. Bayley, Nature Biotechnol. 19, 636 (2001).
D. Panja, G. T. Barkema and R. C. Ball, e-print arxiv cond-mat/0610671.
A. van Heukelum and G. T. Barkema, J. Chem. Phys. 119, 8197 (2003); A. van Heukelum et
al., Macromol. 36, 6662 (2003); J. Klein Wolterink et al., Macromol. 38, 2009 (2005); J. Klein
Wolterink and G. T. Barkema, Mol. Phys. 103, 3083 (2005).
Y. Kantor and M. Kardar, Phys. Rev. E 69, 021806 (2004).
J. Chuang et al., Phys. Rev. E 65, 011802 (2001).
D. Panja, G. T. Barkema and R. C. Ball, J. Phys.: Condens. Mattter 19, 432202 (2007).
D. Panja, G. T. Barkema and R. C. Ball, e-print arXiv:0710.0147, J. Phys.: Cond. Mat., in press.
D. Panja and G. T. Barkema, e-print arXiv: 0706.3969; to appear in Biophys. J.
K. Luo et al., J. Chem. Phys. 124, 114704 (2006); I. Huopaniemi et al., J. Chem. Phys. 125,
124901 (2006).
A. Cacciuto and E. Luijten, Phys. Rev. Lett. 96, 238104 (2006).
D. Wei et al., J. Chem. Phys. 126, 204901 (2006).
A. Milchev, K. Binder, and A. Bhattacharya, J. Chem. Phys. 121, 6042 (2004).
J. L. A. Dubbeldam et al., Europhys. Lett. 79, 18002 (2007).
P.-G. de Gennes, Scaling Concepts in Polymer Physics, Cornell University Press, Ithaca, 1979.
R. Metzler and J. Klafter, Biophys. J. 85, 2776 (2003).
J. L. A. Dubbeldam et al., Phys. Rev. E 76, 010801(R) (2007).