Polymer translocation out of confined environments

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 80, Issue 2, 2009, Pages

  Luo, Kaifu ^a   Metzler, Ralf ^a   Ala Nissila, Tapio ^b,c   Ying, See Chen ^c  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b AALTO UNIVERSITY   (Finland)

^c BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHOICE OF PARAMETERS; CONFINED ENVIRONMENT; FLORY EXPONENT; LANGEVIN DYNAMICS; POLYMER TRANSLOCATION; SCALING EXPONENT; THREE-DIMENSIONAL (3D) ENVIRONMENTS; TIME-SCALES;

THREE DIMENSIONAL;

EID: 70349553927     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.80.021907     Document Type: Article

References (46)

1. B. Alberts, D. Bray, J. Lewis, M. Raff, and J. D. Watson, Molecular Biology of the Cell (Garland, New York, 1994).
2. J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996). 10.1073/pnas.93.24.13770
3. A. Meller, J. Phys.: Condens. Matter 15, R581 (2003). 10.1088/0953-8984/15/17/202
4. M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer, Biophys. J. 77, 3227 (1999). 10.1016/S0006-3495(99)77153-5
5. A. Meller, L. Nivon, E. Brandin, J. A. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000). 10.1073/pnas.97.3.1079
6. A. Meller, L. Nivon, and D. Branton, Phys. Rev. Lett. 86, 3435 (2001). 10.1103/PhysRevLett.86.3435
7. A. Evilevitch, L. Lavelle, C. M. Knobler, E. Raspaud, and W. M. Gelbart, Proc. Natl. Acad. Sci. U.S.A. 100, 9292 (2003). 10.1073/pnas.1233721100
8. W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996). 10.1103/PhysRevLett.77.783
9. P. J. Park and W. Sung, Phys. Rev. E 57, 730 (1998). 10.1103/PhysRevE.57. 730
10. M. Muthukumar, J. Chem. Phys. 111, 10371 (1999). 10.1063/1.480386
11. M. Muthukumar, Phys. Rev. Lett. 86, 3188 (2001). 10.1103/PhysRevLett.86. 3188
12. D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999). 10.1016/S0006-3495(99)77027-X
13. R. Metzler and J. Klafter, Biophys. J. 85, 2776 (2003). 10.1016/S0006-3495(03)74699-2
14. T. Ambjörnsson and R. Metzler, Phys. Biol. 1, 77 (2004) 10.1088/1478-3967/1/2/004
15. T. Ambjörnsson, M. A. Lomholt, and R. Metzler, J. Phys.: Condens. Matter 17, S3945 (2005). 10.1088/0953-8984/17/47/021
16. R. Zandi, D. Reguera, J. Rudnick, and W. M. Gelbart, Proc. Natl. Acad. Sci. U.S.A. 100, 8649 (2003). 10.1073/pnas.1533334100
17. J. Chuang, Y. Kantor, and M. Kardar, Phys. Rev. E 65, 011802 (2001) 10.1103/PhysRevE.65.011802
18. Y. Kantor and M. Kardar, Phys. Rev. E 76, 061121 (2007) 10.1103/PhysRevE.76.061121
19. C. Chatelain, Y. Kantor, and M. Kardar, Phys. Rev. E 78, 021129 (2008). 10.1103/PhysRevE.78.021129
20. Y. Kantor and M. Kardar, Phys. Rev. E 69, 021806 (2004). 10.1103/PhysRevE.69.021806
21. A. Yu. Grosberg, S. Nechaev, M. Tamm, and O. Vasilyev, Phys. Rev. Lett. 96, 228105 (2006). 10.1103/PhysRevLett.96.228105
22. A. Cacciuto and E. Luijten, Phys. Rev. Lett. 96, 238104 (2006). 10.1103/PhysRevLett.96.238104
23. D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 20, 075101 (2008). 10.1088/0953-8984/20/7/075101
24. A. Gopinathan and Y. W. Kim, Phys. Rev. Lett. 99, 228106 (2007). 10.1103/PhysRevLett.99.228106
25. J. L. A. Dubbeldam, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis, Phys. Rev. E 76, 010801 (R) (2007) 10.1103/PhysRevE.76.010801
26. J. L. A. Dubbeldam, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis, Europhys. Lett. 79, 18002 (2007). 10.1209/0295-5075/79/18002
27. A. Milchev, K. Binder, and A. Bhattacharya, J. Chem. Phys. 121, 6042 (2004). 10.1063/1.1785776
28. K. F. Luo, T. Ala-Nissila, and S. C. Ying, J. Chem. Phys. 124, 034714 (2006). 10.1063/1.2161189
29. I. Huopaniemi, K. F. Luo, T. Ala-Nissila, and S. C. Ying, Phys. Rev. E 75, 061912 (2007). 10.1103/PhysRevE.75.061912
30. K. F. Luo, I. Huopaniemi, T. Ala-Nissila, and S. C. Ying, J. Chem. Phys. 124, 114704 (2006) 10.1063/1.2179792
31. I. Huopaniemi, K. F. Luo, T. Ala-Nissila, and S. C. Ying, J. Chem. Phys. 125, 124901 (2006). 10.1063/1.2357118
32. K. F. Luo, T. Ala-Nissila, S. C. Ying, and A. Bhattacharya, J. Chem. Phys. 126, 145101 (2007) 10.1063/1.2719198
33. K. F. Luo, T. Ala-Nissila, S. C. Ying, and A. Bhattacharya, Phys. Rev. Lett. 99, 148102 (2007) 10.1103/PhysRevLett.99.148102
34. K. F. Luo, T. Ala-Nissila, S. C. Ying, and A. Bhattacharya, Phys. Rev. Lett. 100, 058101 (2008) 10.1103/PhysRevLett.100.058101
35. K. F. Luo, T. Ala-Nissila, S. C. Ying, and A. Bhattacharya, Phys. Rev. E 78, 061911 (2008) 10.1103/PhysRevE.78.061911
36. K. F. Luo, T. Ala-Nissila, S. C. Ying, and A. Bhattacharya, Phys. Rev. E 78, 061918 (2008). 10.1103/PhysRevE.78.061918
37. K. F. Luo, S. T. T. Ollila, I. Huopaniemi, T. Ala-Nissila, P. Pomorski, M. Karttunen, S. C. Ying, and A. Bhattacharya, Phys. Rev. E 78, 050901 (R) (2008). 10.1103/PhysRevE.78.050901
38. S. T. T. Ollila, K. F. Luo, T. Ala-Nissila, and S. C. Ying, Eur. Phys. J. E 28, 385 (2009). 10.1140/epje/i2008-10429-9
39. Recent numerical results show that for translocation with driving force localized in the pore, the translocation velocity v scales as 1/ Nβ with β≈0.8 in 3D instead of 1/N for highly nonequilibrium translocation processes [A. Bhattacharya, W. Morrison, K. Luo, T. Alanissila, S. Ying, A. Milchev, and K. Binder, e-print arXiv:0808.1868
40. K. Luo (unpublished)].
41. P. G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979)
42. M. Daoud and P. G. de Gennes, J. Phys. (Paris) 38, 85 (1977).
43. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Clarendon, Oxford, 1986).
44. M. Rubinstein and R. Colby, Polymer Physics (Oxford University Press, Oxford, 2003).
45. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
46. D. L. Ermak and H. Buckholz, J. Comput. Phys. 35, 169 (1980). 10.1016/0021-9991(80)90084-4