Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

Journal of Chemical Physics

Volumn 128, Issue 4, 2008, Pages

  Morelli, Marco J ^a   Allen, Rosalind J ^b   Tanase Nicola, Sorin ^a,c   Ten Wolde, Pieter Rein ^a  

^a FOM INSTITUTE AMOLF   (Netherlands)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL NETWORKS; COARSE-GRAINING METHODS; GENETIC SWITCH; STOCHASTIC SIMULATIONS;

COMPUTER SIMULATION; DISTRIBUTION FUNCTIONS; DNA; PROTEINS; RANDOM PROCESSES;

BIOCHEMISTRY;

DNA; PROTEIN;

ARTICLE; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; GENETICS; METABOLISM; PROBABILITY; STATISTICS; TIME;

BINDING SITES; COMPUTER SIMULATION; DNA; MODELS, GENETIC; PROBABILITY; PROTEINS; STOCHASTIC PROCESSES; TIME FACTORS;

EID: 38849117209     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2821957     Document Type: Article

References (41)

1. D. T. Gillespie, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(76) 90041-3 22, 403 (1976).
2. D. T. Gillespie, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100540a008 81, 2340 (1977).
3. E. L. Haseltine and J. B. Rawlings, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1505860 117, 6959 (2002).
4. T. Shibata, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1603738 119, 6629 (2003).
5. R. Bundschuh, F. Hayot, and C. Jayaprakash, Biophys. J. BIOJAU 0006-3495 84, 1606 (2003).
6. C. V. Rao and A. P. Arkin, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1545446 118, 4999 (2003).
7. J. Puchalka and A. M. Kierzek, Biophys. J. BIOJAU 0006-3495 86, 1357 (2004).
8. Y. Cao, D. T. Gillespie, and L. R. Petzold, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1824902 122, 014116 (2005).
9. H. Salis and Y. N. Kaznessis, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2131050 123, 214106 (2005).
10. W. E, D. Liu, and E. Vanden-Eijnden, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2109987 123, 194107 (2005).
11. J. Elf and M. Ehrenberg, Syst. Biol. SBYIAB 1741-2471 10.1049/sb:20045021 2, 230 (2004).
12. M. Ander, P. Beltrao, B. D. Ventura, J. Ferkinghoff-Borg, M. Foglierini, A. Kaplan, C. Lemerle, I. Tomas-Oliveira, and L. Serrano, Syst. Biol. SBYIAB 1741-2471 10.1049/sb:20045017 1, 129 (2004).
13. J. S. van Zon and P. R. ten Wolde, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.128103 94, 128103 (2005).
14. J. S. van Zon and P. R. ten Wolde, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2137716 123, 234910 (2005).
15. T. R. Kiehl, R. M. Mattheyses, and M. K. Simmons, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/btg409 20, 316 (2004).
16. K. Takahashi, K. Kaizu, B. Hu, and M. Tomita, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/btg442 20, 538 (2004).
17. D. T. Gillespie, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1378322 115, 1716 (2001).
18. H. Salis and Y. N. Kaznessis, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1992483 123, 054103 (2005).
19. Y. N. Kaznessis, Chem. Eng. Sci. CESCAC 0009-2509 10.1016/j.ces.2005.06. 033 61, 940 (2005).
20. R. J. Allen, P. B. Warren, and P. R. ten Wolde, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.018104 94, 018104 (2005).
21. A. M. Walczak, J. N. Onuchic, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0509547102 102, 18926 (2005).
22. J. L. Cherry and F. R. Adler, J. Theor. Biol. JTBIAP 0022-5193 10.1006/jtbi.2000.1068 203, 117 (2000).
23. T. B. Kepler and T. C. Elston, Biophys. J. BIOJAU 0006-3495 81, 3116 (2001).
24. P. B. Warren and P. R. ten Wolde, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.92.128101 92, 128101 (2004).
25. P. B. Warren and P. R. ten Wolde, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp045523y 109, 6812 (2005).
26. T. Ushikubo, W. Inoue, M. Yoda, and M. Sasai, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2006.08.114 430, 139 (2006).
27. A. Lipshtat, A. Loinge, N. Q. Balaban, and O. Biham, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.188101 96, 188101 (2006).
28. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2140273 124, 024102 (2006).
29. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2198827 124, 194111 (2006).
30. M. J. Morelli, R. J. Allen, S. Tnase-Nicola, and P. ten Wolde, Biophys. J. (in press).
31. M. Ptashne, A Genetic Switch: Gene Control and λ Phage (Cell Press and Blackwell Scientific, Cambridge, MA, 1986).
32. P. J. Darling, J. M. Holt, and G. K. Ackers, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.2000.4050 302, 625 (2000).
33. D. K. Hawley and W. R. McClure, Cell CELLB5 0092-8674 10.1016/0092-8674(83)90452-X 32, 327 (1983).
34. D. S. Burz, D. Beckett, N. Benson, and G. K. Ackers, Biochemistry BICHAW 0006-2960 10.1021/bi00194a003 33, 8399 (1994).
35. P. B. Warren, S. Tnase-Nicola, and P. R. ten Wolde, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2356472 125, 144904 (2006).
36. W. Press, S. Teukolsky, W. Vetterling, and B. Flannery, Numerical Recipes in C, 2nd ed. (Academic, Cambridge, 1992).
37. C. Valeriani, R. J. Allen, M. Morelli, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2767625 127, 114109 (2007).
38. J. W. Little, D. P. Shepley, and D. W. Wert, EMBO J. EMJODG 0261-4189 10.1093/emboj/18.15.4299 18, 4299 (1999).
39. E. Aurell, S. Brown, J. Johanson, and K. Sneppen, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.65.051914 65, 051914 (2002).
40. E. Aurell and K. Sneppen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.88.048101 88, 048101 (2002).
41. P. G. Bolhuis, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1562614 118, 7762 (2003).