Polymer translocation dynamics in the quasi-static limit

Journal of Chemical Physics

Volumn 138, Issue 17, 2013, Pages

  Polson, James M ^a   McCaffrey, Anthony C M ^a  

^a UNIVERSITY OF PRINCE EDWARD ISLAND   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS SIMULATION; FREE ENERGY FUNCTION; FRICTION COEFFICIENTS; MONTE CARLO SIMULATIONS; OSCILLATION AMPLITUDE; POLYMER TRANSLOCATION; QUANTITATIVE AGREEMENT; QUASI-STATIC REGIME;

FREE ENERGY; FRICTION; MONOMERS; MONTE CARLO METHODS; NANOPORES;

POLYMERS;

EID: 84877781484     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4803022     Document Type: Article

References (88)

1. M. Muthukumar, Polymer Translocation (CRC Press, Boca Raton, 2011).
2. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walters, Molecular Biology of the Cell, 5th ed. (Garland Science, New York, 2008).
3. H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, A. Bretscher, H. Ploegh, A. Amon, and M. P. Scott, Molecular Cell Biology, 7th ed. (W. H. Freeman and Company, New York, 2012).
4. 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
5. S. Bezrukov, I. Vodyanoy, R. Brutyan, and J. Kasianowicz, Macromolecules 29, 8517 (1996). 10.1021/ma960841j
6. M. Akeson, D. Branton, J. Kasianowicz, E. Brandin, and D. Deamer, Biophys. J. 77, 3227 (1999). 10.1016/S0006-3495(99)77153-5
7. A. Meller, L. Nivon, E. Brandin, J. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000). 10.1073/pnas.97.3.1079
8. A. Meller, J. Phys.: Condens. Matter 15, R581 (2003). 10.1088/0953-8984/15/17/202
9. H. Wang, J. Dunning, A. Huang, J. Nyamwanda, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 101, 13472 (2004). 10.1073/pnas.0405568101
10. T. Z. Butler, J. H. Gundlach, and M. A. Troll, Biophys. J. 90, 190 (2006). 10.1529/biophysj.105.068957
11. C. T. A. Wong and M. Muthukumar, J. Chem. Phys. 128, 154903 (2008). 10.1063/1.2897932
12. C. T. A. Wong and M. Muthukumar, J. Chem. Phys. 133, 045101 (2010). 10.1063/1.3464333
13. J. Li, M. Gershow, D. Stein, E. Brandin, and J. Golovchenko, Nature Mater. 2, 611 (2003). 10.1038/nmat965
14. P. Chen, J. Gu, E. Brandin, Y. R. Kim, Q. Wang, and D. Branton, Nano Lett. 4, 2293 (2004). 10.1021/nl048654j
15. D. Fologea, J. Uplinger, B. Thomas, D. McNabb, and J. Li, Nano Lett. 5, 1734 (2005). 10.1021/nl051063o
16. D. Fologea, M. Gershow, B. Ledden, D. McNabb, J. Golovchenko, and J. Li, Nano Lett. 5, 1905 (2005). 10.1021/nl051199m
17. A. J. Storm, C. Storm, J. Chen, H. Zandbergen, J.-F. Joanny, and C. Dekker, Nano Lett. 5, 1193 (2005). 10.1021/nl048030d
18. A. Storm, J. Chen, H. Zandbergen, and C. Dekker, Phys. Rev. E 71, 051903 (2005). 10.1103/PhysRevE.71.051903
19. R. Purnell, K. Mehta, and J. Schmidt, Nano Lett. 8, 3029 (2008). 10.1021/nl802312f
20. D. Branton, Nat. Biotechnol. 26, 1146 (2008). 10.1038/nbt.1495
21. B. M. Venkatesan and R. Bashir, Nat. Nanotechnol. 6, 615 (2011). 10.1038/nnano.2011.129
22. M. Wanunu, Phys. Life Rev. 9, 125 (2012). 10.1016/j.plrev.2012.05.010
23. S. Kowalczyk, D. Wells, A. Aksimentiev, and C. Dekker, Nano Lett. 12, 1038 (2012). 10.1021/nl204273h
24. A. Milchev, J. Phys.: Condens. Matter 23, 103101 (2011). 10.1088/0953-8984/23/10/103101
25. W. Sung and P. J. Park, Phys. Rev. Lett. 77, 783 (1996). 10.1103/PhysRevLett.77.783
26. M. Muthukumar, J. Chem. Phys. 111, 10371 (1999). 10.1063/1.480386
27. M. Muthukumar, Phys. Rev. Lett. 86, 3188 (2001). 10.1103/PhysRevLett.86. 3188
28. M. Muthukumar, J. Chem. Phys. 118, 5174 (2003). 10.1063/1.1553753
29. E. Slonkina and A. B. Kolomeisky, J. Chem. Phys. 118, 7112 (2003). 10.1063/1.1560932
30. C. Y. Kong and M. Muthukumar, J. Chem. Phys. 120, 3460 (2004). 10.1063/1.1642588
31. D. Keijan, Z. Furu, C. Dongqin, and Y. Zengliang, Biochem. Biophys. Res. Commun. 341, 139 (2006). 10.1016/j.bbrc.2005.12.154
32. A. Mohan, A. B. Kolomeisky, and M. Pasquali, J. Chem. Phys. 133, 024902 (2010). 10.1063/1.3458821
33. S. Yang and A. V. Neimark, J. Chem. Phys. 136, 214901 (2012). 10.1063/1.4720505
34. C. Rasmussen, A. Vishnyakov, and A. Neimark, J. Chem. Phys. 137, 144903 (2012). 10.1063/1.4754632
35. S. Mirigian, Y. Wang, and M. Muthukumar, J. Chem. Phys. 137, 064904 (2012). 10.1063/1.4742970
36. H. Qian, L.-Z. Sun, and M.-B. Luo, J. Chem. Phys. 137, 034903 (2012). 10.1063/1.4737929
37. M. G. Gauthier and G. W. Slater, J. Chem. Phys. 128, 065103 (2008). 10.1063/1.2826339
38. M. G. Gauthier and G. W. Slater, J. Chem. Phys. 128, 205103 (2008). 10.1063/1.2927878
39. H. W. de Haan and G. W. Slater, J. Chem. Phys. 134, 154905 (2011). 10.1063/1.3580769
40. P.-G. de Gennes, Scaling Concept in Polymer Physics (Cornell University Press, London, 1979).
41. L.-Z. Sun, W.-P. Cao, and M.-B. Luo, J. Chem. Phys. 131, 194904 (2009). 10.1063/1.3264944
42. Y.-C. Chen, C. Wang, Y.-L. Zhou, and M.-B. Luo, J. Chem. Phys. 130, 054902 (2009). 10.1063/1.3071198
43. C. Rasmussen, A. Vishnyakov, and A. Neimark, J. Chem. Phys. 135, 214109 (2011). 10.1063/1.3657438
44. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic Press, London, 2002), Chap. 7.
45. M. Fatehi Hassanabad and J. M. Polson, Phys. Can. 65, 126 (2009).
46. J. M. Polson, M. Fatehi Hassanabad, and A. C. M. McCaffrey, J. Chem. Phys. 138, 024906 (2013). 10.1063/1.4774118
47. J. Chuang, Y. Kantor, and M. Kardar, Phys. Rev. E 65, 011802 (2001). 10.1103/PhysRevE.65.011802
48. Y. Kantor and M. Kardar, Phys. Rev. E 69, 021806 (2004). 10.1103/PhysRevE.69.021806
49. D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 19, 432202 (2007). 10.1088/0953-8984/19/43/432202
50. 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
51. H. W. de Haan and G. W. Slater, J. Chem. Phys. 136, 154903 (2012). 10.1063/1.3699979
52. J. L. A. Dubbeldam, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis, EPL 79, 18002 (2007). 10.1209/0295-5075/79/18002
53. H. Vocks, D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 20, 095224 (2008). 10.1088/0953-8984/20/9/095224
54. T. Sakaue, Phys. Rev. E 76, 021803 (2007). 10.1103/PhysRevE.76.021803
55. T. Sakaue, Phys. Rev. E 81, 041808 (2010). 10.1103/PhysRevE.81.041808
56. T. Saito and T. Sakaue, Eur. Phys. J. E 34, 135 (2011). 10.1140/epje/i2011-11135-3
57. P. Rowghanian and A. Y. Grosberg, J. Phys. Chem. B 115, 14127 (2011). 10.1021/jp204014r
58. J. L. A. Dubbeldam, V. G. Rostiashvili, A. Milchev, and T. A. Vilgis, Phys. Rev. E 85, 041801 (2012). 10.1103/PhysRevE.85.041801
59. T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012). 10.1103/PhysRevE.85.051803
60. T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, J. Chem. Phys. 137, 085101 (2012). 10.1063/1.4742188
61. T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, preprint arXiv:1211.7043 (2012).
62. A. Milchev, K. Binder, and A. Bhattacharya, J. Chem. Phys. 121, 6042 (2004). 10.1063/1.1785776
63. S. Tsuchiya and A. Matsuyama, Phys. Rev. E 76, 011801 (2007). 10.1103/PhysRevE.76.011801
64. K. Luo, T. Ala-Nissila, and S.-C. Ying, J. Chem. Phys. 124, 034714 (2006). 10.1063/1.2161189
65. J. K. Wolterink, G. T. Barkema, and D. Panja, Phys. Rev. Lett. 96, 208301 (2006). 10.1103/PhysRevLett.96.208301
66. S. Guillouzic and G. W. Slater, Phys. Lett. A 359, 261 (2006). 10.1016/j.physleta.2006.06.042
67. I. Huopaniemi, K. Luo, T. Ala-Nissila, and S.-C. Ying, Phys. Rev. E 75, 061912 (2007). 10.1103/PhysRevE.75.061912
68. D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 20, 075101 (2008). 10.1088/0953-8984/20/7/075101
69. D. Wei, W. Yang, X. Jin, and Q. Liao, J. Chem. Phys. 126, 204901 (2007). 10.1063/1.2735627
70. K. 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
71. V. V. Lehtola, R. P. Linna, and K. Kaski, Phys. Rev. E 78, 061803 (2008). 10.1103/PhysRevE.78.061803
72. V. V. Lehtola, R. P. Linna, and K. Kaski, EPL 85, 58006 (2009). 10.1209/0295-5075/85/58006
73. K. Luo, T. Ala-Nissila, S.-C. Ying, and R. Metzler, EPL 88, 68006 (2009). 10.1209/0295-5075/88/68006
74. M. G. Gauthier and G. W. Slater, Phys. Rev. E 79, 021802 (2009). 10.1103/PhysRevE.79.021802
75. A. Bhattacharya, W. H. Morrison, K. Luo, T. Ala-Nissila, S.-C. Ying, A. Milchev, and K. Binder, Eur. Phys. J. E 29, 423 (2009). 10.1140/epje/i2009- 10495-5
76. F. Kapahnke, U. Schmidt, D. W. Heermann, and M. Weiss, J. Chem. Phys. 132, 164904 (2010). 10.1063/1.3400650
77. H. W. de Haan and G. W. Slater, Phys. Rev. E 81, 051802 (2010). 10.1103/PhysRevE.81.051802
78. J. L. A. Dubbeldam, V. G. Rostiashvili, A. Milchev, and T. A. Vilgis, Phys. Rev. E 83, 011802 (2011). 10.1103/PhysRevE.83.011802
79. K. Luo, I. Huopaniemi, T. Ala-Nissila, and S.-C. Ying, J. Chem. Phys. 124, 114704 (2006). 10.1063/1.2179792
80. K. Luo and R. Metzler, Phys. Rev. E 82, 021922 (2010). 10.1103/PhysRevE.82.021922
81. A. Bhattacharya and K. Binder, Phys. Rev. E 81, 041804 (2010). 10.1103/PhysRevE.81.041804
82. J. Feng, Y. Shang, L. Zhou, H. Liu, and Y. Hu, Chin. J. Chem. Eng. 20, 231 (2012). 10.1016/S1004-9541(12)60383-8
83. A. Cacciuto and E. Luitjen, Phys. Rev. Lett. 96, 238104 (2006). 10.1103/PhysRevLett.96.238104
84. K. Zhang and K. Luo, J. Chem. Phys. 136, 185103 (2012). 10.1063/1.4712618
85. V. V. Lehtola, K. Kaski, and R. P. Linna, Phys. Rev. E 82, 031908 (2010). 10.1103/PhysRevE.82.031908
86. D. Panja and G. T. Barkema, J. Chem. Phys. 132, 014902 (2010). 10.1063/1.3281641
87. BT N, and this problem does not arise.
88. As noted in Ref., the oscillations in the free energy require very sharp boundaries at the nanopore edge. Nanopores used in experiments are unlikely to satisfy this requirement. However, oscillations arising from energetic interactions between the polymer and the nanopore wall could very well be present.