Totally asymmetric exclusion process with extended objects: A model for protein synthesis

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

Volumn 68, Issue 2 1, 2003, Pages

  Shaw, Leah B ^a   Zia, R K P ^b   Lee, Kelvin H ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DIFFERENTIAL EQUATIONS; MATHEMATICAL MODELS; MONTE CARLO METHODS; PROBABILITY DISTRIBUTIONS; PROTEINS;

DIFFUSION EQUATION; EXCLUSION PROCESS; PARTICLE DENSITY; PROTEIN SYNTHESIS;

BIOSYNTHESIS;

EID: 42749107428     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (53)

1. L. Stryer, Biochemistry, 4th ed. (W.H. Freeman, New York, 1995).
2. F. Neidhardt and H. Umbarger, in Escherichia coli and Salmonella, 2nd ed. edited by F. C. Neidhardt (ASM Press, Washington, D.C., 1996).
3. B. Derrida, E. Domany, and D. Mukamel, J. Stat. Phys. 69, 667 (1992).
4. G. Schütz and E. Domany, J. Stat. Phys. 72, 277 (1993).
5. R. Heinrich and T. Rapoport, J. Theor. Biol. 86, 279 (1980).
6. C. Kang and C. Cantor, J. Mol. Struct. 181, 241 (1985).
7. C. MacDonald, J. Gibbs, and A. Pipkin, Biopolymers 6, 1 (1968).
8. C. MacDonald and J. Gibbs, Biopolymers 7, 707 (1969).
9. G. Schütz, in Phase Transitions and Critical Phenomena, edited by C. Domb and J. L. Lebowitz (Academic Press, San Diego, 2000).
10. A. Kolomeisky, G. Schütz, E. Kolomeisky, and J. Straley, J. Phys. A 31, 6911 (1998).
11. S. Gygi, Y. Rochon, B. Franza, and R. Aebersold, Mol. Cell. Biol. 19, 1720 (1999).
12. T. Ideker, V. Thorsson, J. Ranish, R. Christmas, J. Buhler, J. Eng, R. Bumgarner, D. Goodlett, R. Aebersold, and L. Hood, Science 292, 929 (2001).
13. A. Bortz, M. Kalos, and J. Lebowitz, J. Comput. Phys. 17, 10 (1975).
14. J. Krug, Phys. Rev. Lett. 67, 1882 (1991).
15. B. Derrida, J. Stat. Phys. 31, 433 (1983).
16. For generalizations and more recent studies, see, e.g., A. Kolomeisky and M. Fisher, J. Chem. Phys. 113, 10867 (2000), and references therein.
17. S. Janowsky and J. Lebowitz, Phys. Rev. A 45, 618 (1992).
18. S. Janowsky and J. Lebowitz, J. Stat. Phys. 77, 35 (1994).
19. T. Seppäläinen, J. Stat. Phys. 102, 69 (2001).
20. A. Kolomeisky, J. Phys. A 31, 1153 (1998).
21. G. Tripathy and M. Barma, Phys. Rev. E 58, 1911 (1998).
22. M. Bengrine, a. Benyoussef, H. Ez-Zahraouy, J. Krug, M. Loulidi, and F. Mhirech, J. Phys. A 32, 2527 (1999).
23. J. Krug, Braz. J. Phys. 30, 97 (2000); e-print cond-mat/9912411.
24. V. Becker and H. Janssen, J. Stat. Phys. 96, 817 (1999).
25. K. Lauritsen and H. Fogedby, Phys. Rev. E 47, 1563 (1993).
26. B. Derrida, Phys. Rep. 301, 65 (1998), and references therein.
27. T. Sasamoto and M. Wadati, J. Phys. A 31, 6057 (1998).
28. F. Alcaraz and R. Bariev, Phys. Rev. E 60, 79 (1999).
29. A. Ferreira and F. Alcaraz, Phys. Rev. E 65, 052102 (2002).
30. G. Lakatos and T. Chou, J. Phys. A 36, 2027 (2003).
31. D. Mukamel, in Soft and Fragile Matter: Nonequilibrium Dynamics, Metastability and Flow, edited by M. Evans and M. Cates (Scottish Universities Summer School in Physics, St. Andrews, 2000); e-print cond-mat/0003424.
32. F. Spitzer, Adv. Math. 5, 246 (1970).
33. C″→C in the master equation. Specifically, every C cnsists of (one or more) solid "trains" of ribosomes. Let C′ be the result of the "leading" ribosome of one of these trains hopping forwards. Then C″ differs from C by the "trailing" ribosoome being a single site behind the end of this train.
34. P.-M. Binder, M. Paczuski, and M. Barma, Phys. Rev. E 49, 1174 (1994).
35. G.M. Schutz, R. Ramaswamy, and M. Barma, J. Phys. A 29, 837 (1996).
36. r, etc., and taking the logarithm leads to the expression here.
37. B. Derrida, J. Lebowitz, and E. Speer, J. Stat. Phys. 107, 599 (2002)
38. L. Bertini, A. De Sole, D. Gabrielli, G. Jona-Lasinio, and C. Landim, Phys. Rev. Lett. 87, 040601 (2001)
39. L. Bertini, A. De Sole, D. Gabrielli, G. Jona-Lasinio, and C. Landim, J. Stat. Phys. 107, 635 (2002).
40. Note that it is always possible to achieve a linear profile (in these one-dimensional systems) by an appropriate transformation of the density variable, as long as the effective "diffusion constant" is a single valued function of ρ*.
41. V. Popkov and G. Schütz, Europhys. Lett. 48, 257 (1999).
42. J. Hager, J. Krug, V. Popkov, and G. Schütz, Phys. Rev. E 63, 056110 (2001).
43. J. Hager, Phys. Rev. E 63, 067103 (2001).
44. In this section, we will use only the N → ∞ limit of Eq. (5).
45. B. Derrida, J. Lebowitz, and E. Speer, e-print cond-mat/0205353.
46. B. Derrida, J. Lebowitz, and E. Speer, Phys. Rev. Lett. 89, 030601 (2002).
47. D. Boal, B. Schmittmann, and R. Zia, Phys. Rev. A 43, 5214 (1991).
48. J. Solomovici, T. Lesnik, and C. Reiss, J. Theor. Biol. 185, 511 (1997).
49. J. Bergmann and H. Lodish, J. Biol. Chem. 254, 11927 (1979).
50. E. coli Genome Project at the University of Wisconsin-Madison, http://www.genome.wisc.edu/sequencing/k12.htm
51. T. Lesnik, J. Solomovici, A. Deana, R. Erhlich, and C. Reiss, J. Theor. Biol. 202, 175 (2000).
52. L. Santen and C. Appert, J. Stat. Phys. 106, 187 (2002).
53. Y. Cenatiempo, Biochimie 68, 505 (1986).