Slow sites in an exclusion process with limited resources

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

Volumn 82, Issue 5, 2010, Pages

  Brackley, Chris A ^a   Romano, M Carmen ^a,b   Thiel, Marco ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ASYMMETRIC EXCLUSION PROCESS; EXCLUSION PROCESS; HOPPING RATE; MESSENGER RNAS (MRNA); PROTEIN PRODUCTION; SINGLE DEFECT;

AMINO ACIDS; RNA;

QUEUEING THEORY;

EID: 78651370036     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.82.051920     Document Type: Article

References (45)

1. B. Alberts, A. Johnson, P. Walter, and J. Lewis, Molecular Biology of the Cell, 5th ed. (Garland Publishing Inc., New York, 2008).
2. V. Popkov, L. Santen, A. Schadschneider, and G. M. Schütz, J. Phys. A 34, L45 (2001). 10.1088/0305-4470/34/6/103
3. P. Pierobon, in Traffic and Granular Flow '07, edited by, C. Appert-Rolland,,, F. Chevoir,,, P. Gondret,,, S. Lassarre,,, J.-P. Lebacque,, and, M. Schreckenberg, (Springer, Berlin, 2009), p. 679. 10.1007/978-3-540- 77074-9-76
4. C. T. MacDonald, J. H. Gibbs, and A. C. Pipkin, Biopolymers 6, 1 (1968). 10.1002/bip.1968.360060102
5. B. Derrida, E. Domany, and D. Mukamel, J. Stat. Phys. 69, 667 (1992). 10.1007/BF01050430
6. G. Schütz and E. Domany, J. Stat. Phys. 72, 277 (1993). 10.1007/BF01048050
7. R. J. Harris and R. B. Stinchcombe, Phys. Rev. E 70, 016108 (2004). 10.1103/PhysRevE.70.016108
8. M. Robinson, R. Lilley, S. Little, J. Emtage, G. Yarranton, P. Stephens, A. Millican, M. Eaton, and G. Humphreys, Nucleic Acids Res. 12, 6663 (1984). 10.1093/nar/12.17.6663
9. M. A. Sørensen, C. G. Kurland, and S. Pedersen, J. Mol. Biol. 207, 365 (1989). 10.1016/0022-2836(89)90260-X (Pubitemid 19155241)
10. R. Brockmann, A. Beyer, J. J. Heinisch, and T. Wilhelm, PLOS Comput. Biol. 3, e57 (2007). 10.1371/journal.pcbi.0030057 (Pubitemid 46535745)
11. I. J. Purvis, A. J. E. Bettany, T. C. Santiago, J. R. Coggins, K. Duncan, R. Eason, and A. J. P. Brown, J. Mol. Biol. 193, 413 (1987). 10.1016/0022-2836(87)90230-0
12. M. C. Romano, M. Thiel, I. Stansfield, and C. Grebogi, Phys. Rev. Lett. 102, 198104 (2009). 10.1103/PhysRevLett.102.198104
13. T. Chou and G. Lakatos, Phys. Rev. Lett. 93, 198101 (2004). 10.1103/PhysRevLett.93.198101
14. J. Dong, B. Schmittmann, and R. Zia, J. Stat. Phys. 128, 21 (2007). 10.1007/s10955-006-9134-7
15. C. A. Brackley, M. C. Romano, C. Grebogi, and M. Thiel, Phys. Rev. Lett. 105, 078102 (2010). 10.1103/PhysRevLett.105.078102
16. D. A. Adams, B. Schmittmann, and R. K. P. Zia, J. Stat. Mech.: Theory Exp. (2008) P06009. 10.1088/1742-5468/2008/06/P06009
17. L. J. Cook and R. K. P. Zia, J. Stat. Mech.: Theory Exp. (2009) P02012. 10.1088/1742-5468/2009/02/P02012
18. L. J. Cook, R. K. P. Zia, and B. Schmittmann, Phys. Rev. E 80, 031142 (2009). 10.1103/PhysRevE.80.031142
19. A. B. Kolomeisky, G. M. Schütz, E. B. Kolomeisky, and J. P. Straley, J. Phys. A 31, 6911 (1998). 10.1088/0305-4470/31/33/003 (Pubitemid 128118180)
20. M. R. Evans, Braz. J. Phys. 30, 42 (2000). 10.1590/S0103- 97332000000100005
21. V. Popkov and G. M. Schutz, EPL 48, c257 (1999). 10.1209/epl/i1999-00474- 0
22. M. Ha, J. Timonen, and M. den Nijs, Phys. Rev. E 68, 056122 (2003). 10.1103/PhysRevE.68.056122
23. J. J. Dong, B. Schmittmann, and R. K. P. Zia, Phys. Rev. E 76, 051113 (2007). 10.1103/PhysRevE.76.051113 (Pubitemid 350113553)
24. L. B. Shaw, A. B. Kolomeisky, and K. H. Lee, J. Phys. A 37, 2105 (2004). 10.1088/0305-4470/37/6/010
25. G. Tripathy and M. Barma, Phys. Rev. E 58, 1911 (1998). 10.1103/PhysRevE.58.1911
26. L. B. Shaw, J. P. Sethna, and K. H. Lee, Phys. Rev. E 70, 021901 (2004). 10.1103/PhysRevE.70.021901
27. A. B. Kolomeisky, J. Phys. A 31, 1153 (1998). 10.1088/0305-4470/31/4/006 (Pubitemid 128022261)
28. Since in steady state the current must be equal through both lattices the MC phase cannot be mixed with other phases. An LD/HD phase cannot be realized for obvious reasons: an LD region cannot be maintained upstream of an HD region since particles would not be able to leave the LD region and the density there would increase.
29. U. Alon, An Introduction to Systems Biology, 1st ed. (Chapman and Hall/CRC, London, 2006).
30. J. Krug, Phys. Rev. Lett. 67, 1882 (1991). 10.1103/PhysRevLett.67.1882
31. m T ̄ for realistic parameters, an upper bound for J is therefore V / L ⊃′.
32. F. Borel, C. Vincent, R. Leberman, and M. Hartlein, Nucleic Acids Res. 22, 2963 (1994). 10.1093/nar/22.15.2963
33. H. Liu, R. Peterson, J. Kessler, and K. Musier-Forsyth, Nucleic Acids Res. 23, 165 (1995). 10.1093/nar/23.1.165
34. B. Lenhard, S. Filipić, I. Landeka, I. Škrtić, D. Söll, and I. Weygand-Crossed D signurašević, J. Biol. Chem. 272, 1136 (1997). 10.1074/jbc.272.6.3406 (Pubitemid 27066837)
35. C. Francklyn, J. Adamd, and J. Augustine, J. Mol. Biol. 280, 847 (1998). 10.1006/jmbi.1998.1902 (Pubitemid 28345019)
36. Q. Zhang, E. Wang, and Y. Wang, Biochim. Biophys. Acta 1387, 136 (1998). 10.1016/S0167-4838(98)00115-0 (Pubitemid 28529214)
37. P. Fechter, J. Rudinger-Thirion, and A. Theobald-Dietrich, Biochemistry 39, 1725 (2000). 10.1021/bi992276t (Pubitemid 30108963)
38. T. von der Haar, BMC Systems Biology 2, 87 (2008). 10.1186/1752-0509-2-87
39. Y. Arava, Y. Wang, J. D. Storey, C. L. Liu, P. O. Brown, and D. Herschlag, Proc. Natl. Acad. Sci. U.S.A. 100, 3889 (2003). 10.1073/pnas. 0635171100 (Pubitemid 36418127)
40. A. B. Bortz, M. H. Kalos, and J. L. Lebowitz, J. Comput. Phys. 17, 10 (1975). 10.1016/0021-9991(75)90060-1
41. G. Lakatos and T. Chou, J. Phys. A 36, 2027 (2003). 10.1088/0305-4470/36/ 8/302
42. L. B. Shaw, R. K. P. Zia, and K. H. Lee, Phys. Rev. E 68, 021910 (2003). 10.1103/PhysRevE.68.021910
43. L. Ciandrini, I. Stansfield, and M. C. Romano, Phys. Rev. E 81, 051904 (2010). 10.1103/PhysRevE.81.051904
44. MATHEMATICA, Wolfram Research, Inc., 2008.
45. QP → 0 as s → 0.