Memory effects during the unbiased translocation of a polymer through a nanopore

Journal of Chemical Physics

Volumn 136, Issue 15, 2012, Pages

  De Haan, Hendrick W ^a   Slater, Gary W ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENT TIME SCALE; HIGH VISCOSITIES; LANGEVIN DYNAMICS; LOCAL MINIMUMS; LOW VISCOSITY; MEMORY EFFECTS; PHYSICAL PICTURES; QUASI-STATIC; STANDARD MEASUREMENTS; TRANSLOCATION PROCESS;

PHYSICAL CHEMISTRY; PHYSICS;

MOLECULAR DYNAMICS;

POLYMER;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; NANOPORE; SURFACE PROPERTY; VISCOSITY;

MOLECULAR DYNAMICS SIMULATION; NANOPORES; POLYMERS; SURFACE PROPERTIES; VISCOSITY;

EID: 84860134319     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3699979     Document Type: Article

References (34)

1. B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson, Molecular Biology of the Cell (Garland Publishing, New York, 1989).
2. S. Howorka and Z. Siwy, Chem. Soc. Rev. 38, 2360-2384 (2009). 10.1039/b813796j
3. W. Sung and P. J. Park, Phys. Rev. Lett. 77 (4), 783-786 (1996). 10.1103/PhysRevLett.77.783
4. M. Muthukumar, J. Chem. Phys. 111 (22), 10371-10374 (1999). 10.1063/1.480386
5. J. Chuang, Y. Kantor, and M. Kardar, Phys. Rev. E 65, 011802 (2001). 10.1103/PhysRevE.65.011802
6. J. K. Wolterink, G. T. Barkema, and D. Panja, Phys. Rev. Lett. 96, 208301 (2006). 10.1103/PhysRevLett.96.208301
7. A. Aksimentiev, J. B. Heng, G. Timp, and K. Schulten, Biophys. J. 87, 2086-2097 (2004). 10.1529/biophysj.104.042960
8. 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
9. M. G. Gauthier and G. W. Slater, Phys. Rev. E 79, 021802 (2009). 10.1103/PhysRevE.79.021802
10. 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
11. D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 19, 432202 (2007). 10.1088/0953-8984/19/43/432202
12. J. L. A. Dubbeldam, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis, J. Phys.: Condens. Matter 21, 098001 (2009). 10.1088/0953-8984/21/9/098001
13. D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 21, 098002 (2009). 10.1088/0953-8984/21/9/098002
14. H. W. de Haan and G. W. Slater, J. Chem. Phys. 134, 154905 (2011). 10.1063/1.3580769
15. K. Luo, T. Ala-Nissial, and S. C. Ying, J. Chem. Phys. 124, 124901 (2006). 10.1063/1.2176605
16. S. Guillouzic and G. W. Slater, Phys. Lett. A 359, 261-264 (2006). 10.1016/j.physleta.2006.06.042
17. D. Wie, W. Yang, X. Jin, and Q. Liao, J. Chem. Phys. 126, 204901 (2007). 10.1063/1.2735627
18. M. G. Gauthier and G. W. Slater, Eur. Phys. J. E 25, 17-23 (2008). 10.1140/epje/i2007-10257-5
19. H. W. de Haan and G. W. Slater, Phys. Rev. E 81, 051802 (2010). 10.1103/PhysRevE.81.051802
20. V. V. Lehtola, R. P. Linna, and K. Kaski, Phys. Rev. E 81, 031803 (2010). 10.1103/PhysRevE.81.031803
21. A. Bhattacharya and K. Binder, Phys. Rev. E. 81, 041804 (2010). 10.1103/PhysRevE.81.041804
22. K. Luo, T. Ala-Nissial, and S. C. Ying, J. Chem. Phys. 124, 034714 (2006). 10.1063/1.2161189
23. K. Luo, T. Ala-Nissila, S.-C. Ying, and R. Metzler, Europhys. Lett. 88, 68006 (2009). 10.1209/0295-5075/88/68006
24. R. Metzler and J. Klafter, Phys. Rep. 339, 1 (2000). 10.1016/S0370- 1573(00)00070-3
25. R. Metzler and J. Klafter, Biophys. J. 85, 2776 (2003). 10.1016/S0006-3495(03)74699-2
26. J. L. A Dubbeldam, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis, Europhys. Lett. 79 (1) 18002 (2007). 10.1209/0295-5075/79/18002
27. G. W. Slater, C. Holm, M. V. Chubynsky, H. W. de Haan, A. Dub, K. Grass, O. Hickey, C. Kingsburry, D. Sean, T. N. Shendruk, and L. Zhan, Electrophoresis 30 (5), 792-818 (2009). 10.1002/elps.200800673
28. J. D. Weeks, D. Chandler, and H. C. Anderson, J. Chem. Phys. 54, 5237-5247 (1978). 10.1063/1.1674820
29. G. S. Grest and K. Kremer, Phys. Rev. A. 33, 3628-3631 (1986). 10.1103/PhysRevA.33.3628
30. H. J. Limbach, A. Arnold, B. A. Mann, and C. Holm, Comput. Phys. Commun. 174, 704-727 (2006). 10.1016/j.cpc.2005.10.005
31. J. L. A Dubbeldam, V. G. Rostiashvili, A. Milchev, and T. A. Vilgis, Phys. Rev. E 83, 011802 (2011). 10.1103/PhysRevE.83.011802
32. B. Lu, F. Albertorio, D. P. Hoogerheide, and J. A. Golovchenko, Biophys. J. 101, 70-79 (2011). 10.1016/j.bpj.2011.05.034
33. M. G. Gauthier and G. W. Slater, J. Chem. Phys. 128, 065103 (2008). 10.1063/1.2826339
34. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14, 33-38 (1996). 10.1016/0263-7855(96)00018-5