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Polymer translocation out of planar confinements

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Panja, Debabrata, Barkema, Gerard T. and Ball, Robin. (2008) Polymer translocation out of planar confinements. Journal of Physics: Condensed Matter, Vol.20 (No.7). Article no. 075101. ISSN 0953-8984

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Official URL: http://dx.doi.org/10.1088/0953-8984/20/7/075101

Abstract

Polymer translocation in three dimensions out of planar confinements is studied in this paper. Three membranes are located at z = -h, z = 0 and z = h(1). These membranes are impenetrable, except for the middle one at z = 0, which has a narrow pore. A polymer with length N is initially sandwiched between the membranes placed at z = -h and z = 0 and translocates through this pore. We consider strong confinement (small h), where the polymer is essentially reduced to a two-dimensional polymer, with a radius of gyration scaling as R-g((2D)) similar to N-nu 2D; here, nu(2D) = 0.75 is the Flory exponent in two dimensions. The polymer performs Rouse dynamics. On the basis of theoretical analysis and high-precision simulation data, we show that in the unbiased case h = h(1), the dwell time tau(d) scales as N2+nu 2D, in perfect agreement with our previously published theoretical framework. For h(1) = infinity, the situation is equivalent to field-driven translocation in two dimensions. We show that in this case tau(d) scales as N-2 nu 2D, in agreement with several existing numerical results in the literature. This result violates the earlier reported lower bound N1+nu for tau(d) for field-driven translocation. We argue, on the basis of energy conservation, that the actual lower bound for tau(d) is N-2 nu and not N1+nu. Polymer translocation in such theoretically motivated geometries thus resolves some of the most fundamental issues that have been the subject of much heated debate in recent times.

Item Type:	Journal Article
Subjects:	Q Science > QA Mathematics Q Science > QP Physiology
Divisions:	Faculty of Science > Physics
Library of Congress Subject Headings (LCSH):	Polymers -- Physiological transport -- Mathematical models
Journal or Publication Title:	Journal of Physics: Condensed Matter
Publisher:	IOP Publishing Ltd
ISSN:	0953-8984
Official Date:	2008
Volume:	Vol.20
Number:	No.7
Number of Pages:	9
Page Range:	Article no. 075101
Identification Number:	10.1088/0953-8984/20/7/075101
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access
References:	[1] B. Dreiseikelmann, Microbiol. Rev. 58, 293 (1994). [2] J. P. Henry et al., J. Membr. Biol. 112, 139 (1989). [3] J. Akimaru et al., PNAS USA 88, 6545 (1991). [4] D. Goerlich and T. A. Rappaport, Cell 75, 615 (1993). [5] G. Schatz and B. Dobberstein, Science 271, 1519 (1996). [6] I. Szab`o et al. J. Biol. Chem. 272, 25275 (1997). [7] B. Hanss et al., PNAS USA 95, 1921 (1998). [8] Yun-Long Tseng et al., Molecular Pharm. 62, 864 (2002). [9] J. Kasianowicz et al., PNAS USA 93, 13770 (1996). [10] J. J. Nakane, M. Akeson, A. Marziali, J. Phys.: Cond. Mat. 15, R1365 (2003). [11] J. Buchner, FASEB J. 10, 10 (1996); M. Magzoub, A. Pramanik and A. Gr¨aslund, Biochemistry 44, 14890 (2005); W. T. Wickner and H. F. Lodisch, Science 230, 400 (1995); S. M. Simon and G. Blobel, Cell 65, 1 (1991); D. Goerlich and I. W. Mattaj, Science 271, 1513 (1996); K. Verner and G. Schatz, Science 241, 1307 (1988); G. J. L. Wuite et al., Nature 404, 103 (2000). [12] B. H. Leighton et al., J. Biol. Chem. 281, 29788 (2006). [13] Y. Kafri, D. K. Lubensky, D. R. Nelson, Biophys. J. 86, 3373 (2004). [14] W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996); S. K. Lee and W. Sung, Phys. Rev. E 63, 012115 (2001); K. Lee andW. Sung, Phys. Rev. E 64, 041801 (2001); M. Muthukumar, J. Chem. Phys. 111, (1999); M. Muthukumar, J. Chem. Phys. 118, 5174 (2003); M. Muthukumar, Phys. Rev. Lett. 86, 3188 (2001); M. Muthukumar, Electrophoresis 23, 2697 (2002); E. A. DiMarzio and J. J. Kasianowicz, J. Chem. Phys. 119, 6378 (2003); E. Slonkina and A. B. Kolomeisky, J. Chem. Phys. 118, 7112 (2003). [15] J. Chuang et al., Phys. Rev. E 65, 011802 (2001). [16] Y. Kantor and M. Kardar, Phys. Rev. E 69, 021806 (2004). [17] K. Luo et al., J. Chem. Phys. 124, 034714 (2006). [18] D. Wei et al., J. Chem. Phys. 126, 204901 (2006). [19] J. Klein Wolterink, G. T. Barkema and D. Panja, Phys. Rev. Lett. 96, 208301 (2006). [20] A. Milchev, K. Binder, and A. Bhattacharya, J. Chem. Phys. 121, 6042 (2004). [21] J. L. A. Dubbeldam et al., Phys. Rev. E 76, 010801(R) (2007). [22] K. Luo et al., J. Chem. Phys. 124, 114704 (2006); I. Huopaniemi et al., J. Chem. Phys. 125 124901 (2006); K. Luo et al., e-print arxiv 0708.1147. [23] A. Cacciuto and E. Luijten, Phys. Rev. Lett. 96, 238104 (2006). [24] J. L. A. Dubbeldam et al., Europhys. Lett. 79, 18002 (2007). [25] R. Metzler and J. Klafter, Biophys. J. 85 2776 (2003). [26] D. Panja, G. T. Barkema and R. C. Ball, e-print arXiv: cond-mat/0703404; to appear in J. Phys.: Cond. Mat. (2007). [27] D. Panja, G. T. Barkema and R. C. Ball, e-print arXiv: cond-mat/0610671 (version 2). [28] D. Panja and G. T. Barkema, e-print arXiv: 0706.3969; to appear in Biophys. J. (2007). [29] E. F. Casassa, J. Polym. Sci., Part B: Polym. Lett. 5, 773 (1967); S. F. Edwards and K. F. Freed, J. Phys. A 2, 145 (1969). [30] P.-G. de Gennes, Scaling concepts in polymer physics (Cornell University Press, New York, 1979). [31] P.-G. de Gennes, Proc. Natl. Acad. Sci. USA 96, 7262 (1999); D. E. Smith. et al., Nature 413, 748 (2001); J. Arsuaga et al., Proc. Natl. Acad. Sci. USA 102, 9165 (2005). [32] 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).
URI:	http://wrap.warwick.ac.uk/id/eprint/30617