Analytical and numerical studies of sequence dependence of passage times for translocation of heterobiopolymers through nanopores

Journal of Chemical Physics

Volumn 129, Issue 23, 2008, Pages

  Abdolvahab, R H ^a   Roshani, Farinaz ^b,c   Nourmohammad, Armita ^d   Sahimi, Muhammad ^e   Tabar, M Reza Rahimi ^a,f  

^a SHARIF UNIVERSITY OF TECHNOLOGY   (Iran)

^b ALZAHRA UNIVERSITY   (Iran)

^c INSTITUTE FOR STUDIES IN THEORETICAL PHYSICS AND MATHEMATICS IPM   (Iran)

^d UNIVERSITY OF COLOGNE   (Germany)

^e University of Southern California ^*  (United States)

^f UNIVERSITY OF OLDENBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; BIOPOLYMERS; MONOMERS; MONTE CARLO METHODS; NUMERICAL ANALYSIS; POLYMERS; PROBABILITY; PROBABILITY DISTRIBUTIONS; TRELLIS CODES;

ANALYTICAL RESULTS; GAUSSIAN; MASTER EQUATIONS; MONTE CARLO SIMULATIONS; NONTRIVIAL DEPENDENCES; NUMERICAL STUDIES; PASSAGE TIME DISTRIBUTIONS; PASSAGE TIMES; PROBABILITY DENSITIES; TRANSLOCATION TIMES;

PROBABILITY DENSITY FUNCTION;

BIOPOLYMER; NANOMATERIAL;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; METABOLISM; MONTE CARLO METHOD; NANOTECHNOLOGY; POROSITY; PROBABILITY; QUANTUM THEORY; TIME;

BIOPOLYMERS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; NANOSTRUCTURES; NANOTECHNOLOGY; POROSITY; PROBABILITY; QUANTUM THEORY; TIME FACTORS;

EID: 57849139730     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3040267     Document Type: Article

References (47)

1. B. Alberts, D. Bray, J. Lewis, Molecular Biology of the Cell (Garland, New York, 2002).
2. J. P. Henry, J. F. Chich, D. Goldschmidt, and M. Thieffry, J. Membr. Biol. 0022-2631 10.1007/BF01871275 112, 139 (1989); J. Akimaru, S. Matsuyama, H. Tokuda, and S. Mizushima, Proc. Natl. Acad. Sci. U.S.A. 88, 6545 (1991) 0027-8424; E. Di Marzio and J. J. Kasianowicz, J. Chem. Phys. 0021-9606 10.1063/1.1603725 119, 6378 (2003).
3. Y. -L. Tseng, J. -J. Liu, and R. -L. Hong, Mol. Pharmacol. 0026-895X 10.1124/mol.62.4.864 62, 864 (2002); J. M. Tsutsui, F. Xie, and R. T. Porter, Cardiovasc. Ultrasound 2, 23 (2004). 1476-7120
4. J. Han, S. W. Turner, and G. H. Craighead, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.83.1688 83, 1688 (1999); S. W. P. Turner, M. Cabodi, and H. G. Craighead, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.88.128103 88, 128103 (2002).
5. M. Bukrinsky, Mol. Med. 10, 1 (2004). 1076-1551
6. W. Liebermeister, T. A. Rapoport, and R. Heinrich, J. Mol. Biol. 305, 643 (2001). 0022-2836
7. W. T. Wickner and H. F. Lodish, Science 0036-8075 10.1126/science.4048938 230, 400 (1985); K. Verner and G. Schatz, Science 0036-8075 10.1126/science.2842866 241, 1307 (1988); D. Georlich and I. W. Mattaj, Science 271, 1513 (1991). 0036-8075
8. J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.93.24.13770 93, 13770 (1996).
9. L. Song, M. R. Hobaugh, C. Shustak, S. Cheley, H. Barley, and J. E. Gouaux, Science 0036-8075 10.1126/science.274.5294.1859 274, 1859 (1996).
10. Y. Jung, H. Bayley, and L. Movileanu, J. Am. Chem. Soc. 0002-7863 10.1021/ja065827t 128, 15332 (2006); S. M. Bezrukov and J. J. Kasianowicz, Eur. Biophys. J. 0175-7571 10.1007/s002490050101 26, 471 (1997); M. Pastoriza-Gallego, G. Oukhaled, J. Math́, B. Thíbot, J. M. Bretton, L. Auvray, and J. Pelta, FEBS Lett. 0014-5793 10.1016/j.febslet.2007.06.036 581, 3371 (2007).
11. M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer, Biophys. J. 77, 3227 (1999) 0006-3495; A. Aksimentiev, J. B. Heng, G. Timp, and K. Schulten, Biophys. J. 0006-3495 10.1529/biophysj.104.042960 87, 2086 (2004); S. E. Henrickson, M. Misakian, B. Robertson, and J. J. Kasianowicz, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.85.3057 85, 3057 (2000); A. Meller, L. Nivon, and D. Branton, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.86.3435 86, 3435 (2001).
12. A. Meller, L. Nivon, E. Brandin, J. A. Golovchenko, and D. Branton, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.97.3.1079 97, 1079 (2000).
13. A. Meller and D. Branton, Electrophoresis 0173-0835 10.1002/1522- 2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H 23, 2583 (2002); A. F. Sauer-Budge, J. A. Nyamwanda, D. K. Lubensky, and D. Branton, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.90.238101 90, 238101 (2003); J. Math́, H. Visram, V. Visnoff, Y. Rubin, and A. Meller, Biophys. J. 0006-3495 10.1529/biophysj.104.047274 87, 3205 (2004).
14. W. Sung and P. J. Park, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett. 77.783 77, 783 (1996); M. Muthukumar, J. Chem. Phys. 0021-9606 10.1063/1.480386 111, 10371 (1999); M. Muthukumar, J. Chem. Phys. 0021-9606 10.1063/1.1553753 118, 5174 (2003).
15. J. -F. Chauwin, G. Oster, and B. S. Glick, Biophys. J. 74, 1732 (1998) 0006-3495; T. C. Elston, Biophys. J. 82, 1239 (2002) 0006-3495; T. Ambjörnsson and R. Metzler, Phys. Biol. 1478-3975 10.1088/1478-3967/1/2/004 1, 77 (2004); T. Ambjörnsson, M. A. Lomholt, and R. Metzler, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/17/47/021 17, S3945 (2005).
16. M. Muthukumar, Electrophoresis 0173-0835 10.1002/1522-2683(200205)23: 10<1417::AID-ELPS1417>3.0.CO;2-O 23, 1417 (2002).
17. B. Slonkina and A. B. Kolomeisky, J. Chem. Phys. 0021-9606 10.1063/1.1560932 118, 7112 (2003).
18. A. J. Storm, C. Storm, J. Chen, H. Zandbergen, J. -F. Joanny, and C. Dekker, Nano Lett. 1530-6984 10.1021/nl048030d 5, 1193 (2005); P. J. Park and W. Sung, J. Chem. Phys. 0021-9606 10.1063/1.475688 108, 3013 (1998); D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999). 0006-3495
19. J. Chuang, Y. Kantor, and M. Kardar, Phys. Rev. E 1063-651X 10.1103/PhysRevE.65.011802 65, 011802 (2001); Y. Kantor and M. Kardar, Phys. Rev. E 1063-651X 10.1103/PhysRevE.69.021806 69, 021806 (2004); A. Milchev, K. Binder, and A. Bhattacharya, J. Chem. Phys. 0021-9606 10.1063/1.1785776 121, 6042 (2004); A. Corsi, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis, Macromolecules 0024-9297 10.1021/ma060920n 39, 7115 (2006).
20. A. Baumgärtner and J. Skolnick, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.74.2142 74, 2142 (1995); R. Bundschuh and U. Gerland, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.95.208104 95, 208104 (2006); S. Matysiak, A. Montesi, M. Pasquali, A. B. Kolomeisky, and C. Clementi, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.96.118103 96, 118103 (2006).
21. S. F. Simon, C. S. Peskin, and G. F. Oster, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.89.9.3770 89, 3770 (1992); A. Meller, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/15/17/202 15, R581 (2003); Y. Kafri, D. K. Lubensky, and D. R. Nelson, Biophys. J. 0006-3495 10.1529/biophysj.103.036152 86, 3373 (2004).
22. T. Ambjörnsson, S. P. Apell, Z. Konkoli, E. A. DiMarzio, and J. J. Kasainowicz, J. Chem. Phys. 0021-9606 10.1063/1.1486208 117, 4063 (2002); C. T. A. Wong and M. Muthukumar, J. Chem. Phys. 0021-9606 10.1063/1.2897932 128, 154903 (2008); R. Metzler and J. Klafter, Biophys. J. 85, 2776 (2003) 0006-3495; U. Gerland, R. Bundschuh, and T. Hwa, Phys. Biol. 1478-3975 10.1088/1478-3967/1/1/002 1, 19 (2004).
23. K. F. Luo, T. Ala-Nissila, and S. -Ch. Ying, J. Chem. Phys. 0021-9606 10.1063/1.2161189 124, 034714 (2006); K. F. Luo, I. Huopaniemi, T. Ala-Nissila, and S. -Ch. Ying, J. Chem. Phys. 0021-9606 10.1063/1.2179792 124, 114704 (2006); I. Huopaniemi, K. F. Luo, T. Ala-Nissila, and S. -Ch. Ying, J. Chem. Phys. 0021-9606 10.1063/1.2357118 125, 124901 (2006); I. Huopaniemi, K. F. Luo, T. Ala-Nissila, and S. -Ch. Ying, Phys. Rev. E 1063-651X 10.1103/PhysRevE.75.061912 75, 061912 (2007).
24. C. Y. Kong and M. Muthukumar, Electrophoresis 0173-0835 10.1002/1522-2683(200208)23:16<2697::AID-ELPS2697>3.0.CO;2-M 23, 2697 (2002); C. Y. Kong and M. Muthukumar, J. Am. Chem. Soc. 0002-7863 10.1021/ja055695o 127, 18252 (2005); M. Muthukumar and C. Y. Kong, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0510725103 103, 5273 (2006).
25. S. -S. Chern, A. E. Cardenas, and R. D. Coalson, J. Chem. Phys. 0021-9606 10.1063/1.1392367 115, 7772 (2001); M. G. Gauthier and G. W. Slater, J. Chem. Phys. 0021-9606 10.1063/1.2826339 128, 065103 (2008); H. C. Loebl, R. Randel, S. P. Goodwin, and C. C. Mathai, Phys. Rev. E 1063-651X 10.1103/PhysRevE.67.041913 67, 041913 (2003).
26. H. Salman, D. Zbaida, Y. Rabin, D. Chatenay, and M. Elbaum, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.121067698 98, 7247 (2001); Z. Farkas, I. Derenyi, and T. Vicsek, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/15/18/310 15, S1767 (2003); J. K. Wolterink, G. T. Barkema, and D. Panja, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.96.208301 96, 208301 (2006).
27. R. Zandi, D. Reguera, J. Rudnick, and W. M. Gelbart, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.1533334100 100, 8649 (2003).
28. D. Klotsa, R. A. Romer, and M. S. Turner, Biophys. J. 0006-3495 10.1529/biophysj.105.064014 89, 2187 (2005); A. Rodriguez, R. A. Römer, and M. S. Turner, Phys. Status Solidi B 0370-1972 10.1002/pssb.200562703 243, 373 (2006).
29. M. M. Inamdar, W. M. Gelbart, and R. Phillips, Biophys. J. 0006-3495 10.1529/biophysj.105.070532 91, 411 (2006).
30. A. Gopinathan and Y. W. Kim, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.99.228106 99, 228106 (2007).
31. A. B. Fulton, Cell 0092-8674 10.1016/0092-8674(82)90231-8 30, 345 (1982).
32. M. Muthukumar, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.86.3188 86, 3188 (2001).
33. Y. R. Chemla, K. Aathavan, J. Michaelis, S. Grimes, P. J. Jardine, D. W. Anderson, and C. Bustamante, Cell 0092-8674 10.1016/j.cell.2005.06.024 122, 683 (2005); J. P. Rickgauer, D. N. Fuller, S. Grimes, P. J. Jardine, D. L. Anderson, and D. K. Smith, Biophys. J. 94, 159 (2008). 0006-3495
34. T. Ambjörnsson, S. K. Banik, O. Krichevsky, and R. Metzler, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.97.128105 97, 128105 (2006).
35. K. Luo, T. Ala-Nissila, S. -Ch. Ying, and A. Bhattacharya, J. Chem. Phys. 0021-9606 10.1063/1.2719198 126, 145101 (2007); K. Luo, T. Ala-Nissila, S. -Ch. Ying, and A. Bhattacharya, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.100. 058101 100, 058101 (2008).
36. M. Slutsky, M. Kardar, and L. A. Mirny, Phys. Rev. E 1063-651X 10.1103/PhysRevE.69.061903 69, 061903 (2004).
37. P. Romiszowski and A. Sikorski, Comput. Mater. Sci. 0927-0256 10.1016/j.commatsci.2006.02.014 38, 533 (2007).
38. M. G. Gauthier and G. W. Slater, J. Chem. Phys. 0021-9606 10.1063/1.2912069 128, 175103 (2008).
39. O. Flomenbom and J. Klafter, Phys. Rev. E 1063-651X 10.1103/PhysRevE.68. 041910 68, 041910 (2003); O. Flomenbom and J. Klafter, Biophys. J. 0006-3495 10.1529/biophysj.103.037580 86, 3576 (2004).
40. N. G. Van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1992); T. Ambjörnsson and R. Metzler, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/17/20/013 17, S1841 (2005).
41. U. Gerland, J. D. Moroz, and T. Hwa, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.192693599 99, 12015 (2002).
42. C. W. Gardiner, Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences (Springer, New York, 2002).
43. I. R. Epstein, Biophys. Chem. 0301-4622 10.1016/0301-4622(78)80015-5 8, 327 (1978).
44. M. Abramowitz and I. A. Stegun, Handbook of Mathematical Functions (Dover, New York, 1972).
45. B. D. Hughes, Random Walks and Random Environments (Oxford University Press, London, 1995), Vol. 1.
46. C. Chatelain, Y. Kantor, and M. Kardar, Phys. Rev. E 1063-651X 10.1103/PhysRevE.78.021129 78, 021129 (2008).
47. S. Redner, A Guide to First-Passage Time Processes (Cambridge University Press, London, 2001).