Hydrodynamic effects on the translocation rate of a polymer through a pore

Journal of Chemical Physics

Volumn 131, Issue 4, 2009, Pages

  Hernández Ortiz, Juan P ^a   Chopra, Manan ^b   Geier, Stephanie ^b   De Pablo, Juan J ^b  

^a UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^b University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOUNDARY EFFECTS; DNA MOLECULES; FULL COUPLING; HYDRODYNAMIC EFFECT; HYDRODYNAMIC INTERACTION; MOLECULAR CONFORMATION; MULTI-SCALE SIMULATION; MULTIPLE ORDERS; NARROW PORES;

HYDRODYNAMICS; NUCLEIC ACIDS; RATE CONSTANTS;

FLUID DYNAMICS;

DNA; POLYMER;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; KINETICS; POROSITY; TRANSPORT AT THE CELLULAR LEVEL;

BIOLOGICAL TRANSPORT; COMPUTER SIMULATION; DNA; KINETICS; POLYMERS; POROSITY;

EID: 68249099629     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3184798     Document Type: Article

References (76)

1. M. Zwolak and M. Di-Ventra, Rev. Mod. Phys. 0034-6861 80, 141 (2008). 10.1103/RevModPhys.80.141
2. J. Jing, J. Reed, J. Huang, X. Hu, V. Clarke, J. Edington, D. Housman, T. Anantharaman, E. Huff, B. Mishra, B. Porter, A. Shenker, E. Wolfson, C. Hiort, R. Kantor, C. Aston, and D. C. Schwartz, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 95, 8046 (1998). 10.1073/pnas.95.14.8046 (Pubitemid 28326063)
3. C. W. Kan, C. P. Fredlake, E. A. S. Doherty, and A. E. Barron, Electrophoresis 0173-0835 25, 3564 (2004). 10.1002/elps.200406161 (Pubitemid 40012113)
4. M. G. Roper, C. J. Easley, and J. P. Landers, Anal. Chem. 0003-2700 77, 3887 (2005). 10.1021/ac050756m (Pubitemid 40848055)
5. C. -F. Chou, R. H. Austin, O. Bakajin, J. O. Tegenfeldt, J. A. Castelino, S. S. Chan, E. C. Cox, H. Craighead, N. Darnton, T. Duke, J. Han, and S. Turner, Electrophoresis 0173-0835 21, 81 (2000). 10.1002/(SICI)1522- 2683(20000101)21:1<81::AID-ELPS813.0.CO;2-#
6. J. Han and H. G. Craighead, Science 0036-8075 288, 1026 (2000). 10.1126/science.288.5468.1026 (Pubitemid 30324230)
7. M. Streek, F. Schmid, T. T. Duong, D. Anselmetti, and A. Ros, Phys. Rev. E 1063-651X 71, 011905 (2005). 10.1103/PhysRevE.71.011905
8. A. J. Storm, J. H. Chen, H. W. Zandbergen, and C. Dekker, Phys. Rev. E 1063-651X 71, 051903 (2005). 10.1103/PhysRevE.71.051903 (Pubitemid 41480966)
9. K. Luo, T. Ala-Nissila, S. -C. Ying, and A. Bhattacharya, Phys. Rev. Lett. 0031-9007 99, 148102 (2007). 10.1103/PhysRevLett.99.148102 (Pubitemid 47519539)
10. K. Luo, T. Ala-Nissila, S. -C. Ying, and A. Bhattacharya, Phys. Rev. Lett. 0031-9007 100, 058101 (2008). 10.1103/PhysRevLett.100.058101 (Pubitemid 351220690)
11. J. Chuang, Y. Kantor, and M. Kardar, Phys. Rev. E 1063-651X 65, 011802 (2001). 10.1103/PhysRevE.65.011802
12. Y. Kantor and M. Kardar, Phys. Rev. E 1063-651X 69, 021806 (2004). 10.1103/PhysRevE.69.021806
13. D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 0953-8984 19, 432202 (2007). 10.1088/0953-8984/19/43/432202 (Pubitemid 47574744)
14. M. G. Gauthier and G. W. Slater, J. Chem. Phys. 0021-9606 128, 065103 (2008). 10.1063/1.2826339 (Pubitemid 351264601)
15. M. G. Gauthier and G. W. Slater, J. Chem. Phys. 0021-9606 128, 205103 (2008). 10.1063/1.2927878 (Pubitemid 351770649)
16. M. Muthukumar and C. Y. Kong, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 5273 (2006). 10.1073/pnas.0510725103
17. 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 1063-651X 78, 050901 (R) (2008). 10.1103/PhysRevE.78.050901
18. C. Forrey and M. Muthukumar, J. Chem. Phys. 0021-9606 127, 015102 (2007). 10.1063/1.2746246 (Pubitemid 47248494)
19. A. Izmitli, D. C. Schwartz, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 0021-9606 128, 085102 (2008). 10.1063/1.2831777 (Pubitemid 351328732)
20. M. G. Gauthier and G. W. Slater, Eur. Phys. J. E 1292-8941 25, 17 (2008). 10.1140/epje/i2007-10257-5
21. M. Fyta, S. Melchionna, S. Succi, and E. Kaxiras, Phys. Rev. E 1063-651X 78, 036704 (2008). 10.1103/PhysRevE.78.036704
22. D. A. Hoagland and R. K. Prudhomme, Macromolecules 0024-9297 22, 775 (1989). 10.1021/ma00192a044
23. D. C. Schwartz, X. Li, L. Hernandez, S. Ramnarain, E. Huff, and Y. Wang, Science 0036-8075 262, 110 (1993). 10.1126/science.8211116
24. A. Lim, E. T. Dimalanta, K. D. Potamousis, G. Yen, J. Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. Hackett, F. R. Blattner, T. S. Anantharaman, B. Mishra, and D. C. Schwartz, Genome Res. 1088-9051 11, 1584 (2001). 10.1101/gr.172101 (Pubitemid 32894685)
25. N. Perna, G. Plunkett III, V. Burland, B. Mau, J. Glasner, D. Rose, G. Mayhew, P. Evans, J. Gregor, H. Kirkpatrick, G. Pósfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner, Nature (London) 0028-0836 409, 529 (2001). 10.1038/35054089 (Pubitemid 32144360)
26. S. Zhou, E. Kvikstad, A. Kile, J. Severin, D. Forrest, R. Runnheim, C. Churas, J. Hickman, C. Mackenzie, M. Choudhary, T. Donohue, S. Kaplan, and D. C. Schwartz, Genome Res. 1088-9051 13, 2142 (2003). 10.1101/gr.1128803 (Pubitemid 37161771)
27. E. T. Dimalanta, A. Lim, R. Runnheim, C. Lamers, C. Churas, D. K. Forrest, J. J. de Pablo, M. D. Graham, S. N. Coppersmith, S. Goldstein, and D. C. Schwartz, Anal. Chem. 0003-2700 76, 5293 (2004). 10.1021/ac0496401 (Pubitemid 39249409)
28. Y. -L. Chen, M. D. Graham, J. J. de Pablo, G. C. Randall, M. Gupta, and P. S. Doyle, Phys. Rev. E 1063-651X 70, 060901 (R) (2004). 10.1103/PhysRevE.70. 060901 (Pubitemid 40213899)
29. J. P. Hernández-Ortiz, H. Ma, J. J. de Pablo, and M. D. Graham, Phys. Fluids 1070-6631 18, 123101 (2006). 10.1063/1.2397571 (Pubitemid 46055914)
30. J. B. Anderson, Adv. Chem. Phys. 0065-2385 91, 381 (1995). 10.1002/9780470141502.ch5
31. W. E, R. Weiqing, and E. Vanden-Eijnden, J. Phys. Chem. B 1089-5647 109, 6688 (2005). 10.1021/jp0455430 (Pubitemid 40552536)
32. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 0066-426X 53, 291 (2002). 10.1146/annurev.physchem.53.082301.113146 (Pubitemid 35336255)
33. C. Dellago, P. G. Bolhuis, and P. L. Geissler, Adv. Chem. Phys. 0065-2385 123, 1 (2002). 10.1002/0471231509.ch1
34. T. S. van Erp and P. G. Bolhuis, J. Comput. Phys. 0021-9991 205, 157 (2005). 10.1016/j.jcp.2004.11.003
35. R. J. Allen, P. B. Warren, and P. R. ten Wolde, Phys. Rev. Lett. 0031-9007 94, 018104 (2005). 10.1103/PhysRevLett.94.018104
36. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 0021-9606 124, 024102 (2006). 10.1063/1.2140273 (Pubitemid 43100174)
37. G. E. Crooks and D. Chandler, Phys. Rev. E 1063-651X 64, 026109 (2001). 10.1103/PhysRevE.64.026109
38. A. Warmflash, P. Bhimalapuram, and A. Dinner, J. Chem. Phys. 0021-9606 127, 154112 (2007). 10.1063/1.2784118 (Pubitemid 351260747)
39. Y. Li, T. Zhao, P. Bhimalapuram, and A. Dinner, J. Chem. Phys. 0021-9606 128, 074102 (2008). 10.1063/1.2828505 (Pubitemid 351304938)
40. R. Bird, C. Curtiss, R. Armstrong, and O. Hassager, Dynamics of Polymer Liquids: Kinetic Theory, 2nd ed. (Wiley, New York, 1987), Vol. 2.
41. H. -C. Öttinger, Stochastic Processes in Polymeric Fluids (Springer, New York, 1996).
42. M. Allen and D. Tildesley, Computer Simulation of Liquids (Oxford Science, Oxford, 1987).
43. D. Frenkel and B. Smith, Understanding Molecular Simulations-From Algorithms to Applications (Academic, New York, 1996).
44. H. Risken, The Fokker-Planck Equation, 2nd ed. (Springer, New York, 1989).
45. C. Gardiner, Handbook of Stochastic Methods (Springer, New York, 1985).
46. H. -C. Öttinger, Beyond Equilibrium Thermodynamics (Wiley-Interscience, New York, 2005).
47. L. Reichl, A Modern Course in Statistical Physics, 2nd ed. (Wiley-Interscience, New York, 1998).
48. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, Oxford, 2001).
49. R. M. Jendrejack, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 0021-9606 113, 2894 (2000). 10.1063/1.1305884 (Pubitemid 30917793)
50. R. M. Jendrejack, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 0021-9606 116, 7752 (2002). 10.1063/1.1466831 (Pubitemid 34599089)
51. R. M. Jendrejack, D. C. Schwartz, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 0021-9606 119, 1165 (2003). 10.1063/1.1575200
52. J. P. Hernández-Ortiz, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 0021-9606 125, 164906 (2006). 10.1063/1.2358344 (Pubitemid 44658418)
53. P. J. Mucha, S. -Y. Tee, D. A. Weitz, B. I. Shraiman, and M. P. Brenner, J. Fluid Mech. 0022-1120 501, 71 (2004). 10.1017/S0022112003006967 (Pubitemid 38431409)
54. H. Hasimoto, J. Fluid Mech. 0022-1120 5, 317 (1959). 10.1017/ S0022112059000222
55. J. P. Hernández-Ortiz, J. de Pablo, and M. D. Graham, Phys. Rev. Lett. 0031-9007 98, 140602 (2007). 10.1103/PhysRevLett.98.140602 (Pubitemid 46557435)
56. C. Pozrikidis, Boundary Integral and Singularity Methods for Linearized Viscous Flow (Cambridge University Press, Cambridge, 1992).
57. M. Deserno and C. Holm, J. Chem. Phys. 0021-9606 109, 7678 (1998). 10.1063/1.477414 (Pubitemid 128678339)
58. M. Deserno and C. Holm, J. Chem. Phys. 0021-9606 109, 7694 (1998). 10.1063/1.477415 (Pubitemid 128678340)
59. U. Essmann, L. Perera, and M. Berkowitz, J. Chem. Phys. 0021-9606 103, 8577 (1995). 10.1063/1.470117
60. R. W. Hockney and J. W. Eastwood, Computer Simulation using Particles (Taylor & Francis, London, 1988).
61. H. Power and L. C. Wrobel, Boundary Integral Methods in Fluid Mechanics (Computational Mechanics, Southampton, 1995).
62. J. P. Hernández-Ortiz, H. Ma, J. J. de Pablo, and M. D. Graham, Korea-Aust. Rheol. J. 1226-119X 20, 143 (2008).
63. T. A. Osswald and J. P. Hernández-Ortiz, Polymer Processing: Modeling and Simulation (Carl Hanser-Verlag, Munich, 2006).
64. J. W. Demmel, S. C. Eisenstat, J. R. Gilbert, X. S. Li, and J. W. H. Liu, SIAM J. Matrix Anal. Appl. 0895-4798 20, 720 (1999). 10.1137/S0895479895291765
65. J. W. Demmel, J. R. Gilbert, and X. S. Li, SIAM J. Matrix Anal. Appl. 0895-4798 20, 915 (1999). 10.1137/S0895479897317685
66. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in Fortran 77, 2nd ed. (Cambridge University Press, Cambridge, 1992).
67. M. Fixman, J. Chem. Phys. 0021-9606 69, 1527 (1978). 10.1063/1.436725
68. P. Grassia, E. Hinch, and L. Nitsche, J. Fluid Mech. 0022-1120 282, 373 (1995). 10.1017/S0022112095000176
69. M. Fixman, Macromolecules 0024-9297 19, 1204 (1986). 10.1021/ma00158a043
70. R. M. Jendrejack, E. T. Dimalanta, D. C. Schwartz, M. D. Graham, and J. J. de Pablo, Phys. Rev. Lett. 0031-9007 91, 038102 (2003). 10.1103/PhysRevLett. 91.038102
71. R. M. Jendrejack, D. C. Schwartz, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 0021-9606 120, 2513 (2004). 10.1063/1.1637331
72. A. J. Banchio and J. F. Brady, J. Chem. Phys. 0021-9606 118, 10323 (2003). 10.1063/1.1571819
73. C. Stoltz, J. J. de Pablo, and M. D. Graham, J. Rheol. 0148-6055 50, 137 (2006). 10.1122/1.2167468 (Pubitemid 43269366)
74. J. Blake, Proc. Cambridge Philos. Soc. 0068-6735 70, 303 (1971). 10.1017/S0305004100049902
75. H. B. Ma and M. D. Graham, Phys. Fluids 1070-6631 17, 083103 (2005). 10.1063/1.2011367 (Pubitemid 41226568)
76. C. G. Stoltz, J. J. de Pablo, and M. D. Graham, J. Chem. Phys. 0021-9606 126, 124906 (2007). 10.1063/1.2712182 (Pubitemid 46517171)