Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways

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

Volumn 74, Issue 5, 2006, Pages

  Chiam, K H ^a   Tan, Chee Meng ^a,b   Bhargava, Vipul ^a,c   Rajagopal, Gunaretnam ^a  

^a BIOINFORMATICS INSTITUTE   (Singapore)

^b Duke University   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; PROTEINS; RANDOM PROCESSES; REACTION KINETICS;

INTRACELLULAR SIGNALING PATHWAYS; PHOSPHORYLATION; SIGNALING MOLECULES;

DIFFUSION;

MULTIENZYME COMPLEX; PROTEOME;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CELL FUNCTION; COMPUTER SIMULATION; DIFFUSION; METABOLISM; PHYSIOLOGY; SIGNAL TRANSDUCTION; STATISTICAL MODEL; STATISTICS;

ALGORITHMS; CELL PHYSIOLOGY; COMPUTER SIMULATION; DIFFUSION; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MULTIENZYME COMPLEXES; PROTEOME; SIGNAL TRANSDUCTION; STOCHASTIC PROCESSES;

EID: 33751113261     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.74.051910     Document Type: Article

References (50)

1. R. J. Ellis and A. P. Minton, Nature (London) NATUAS 0028-0836 10.1038/425027a 425, 27 (2003).
2. A. S. Verkman, Trends Biochem. Sci. TBSCDB 0167-7640 10.1016/S0968- 0004(01)02003-5 27, 27 (2002).
3. D. Gerlich and J. Ellenberg, Nat. Cell Biol. NCBIFN 1465-7392 5, S14 (2003).
4. E. A. Finch and G. J. Augustine, Nature (London) NATUAS 0028-0836 10.1038/25541 396, 753 (1998).
5. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science SCIEAS 0036-8075 10.1126/science.1070919 297, 1183 (2002).
6. W. J. Blake, M. Kærn, C. R. Cantor, and J. J. Collins, Nature (London) NATUAS 0028-0836 10.1038/nature01546 422, 633 (2003).
7. Mads Kærn, T. C. Elston, W. J. Blake, and J. J. Collins, Nat. Rev. Genet. NRGAAM 1471-0056 10.1038/nrg1615 6, 451 (2005).
8. M. Sasai and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2627987100 100, 2374 (2003).
9. J. Paulsson, Nature (London) NATUAS 0028-0836 10.1038/nature02257 427, 415 (2004).
10. C. V. Rao, D. M. Wolf, and A. P. Arkin, Nature (London) NATUAS 0028-0836 10.1038/nature01258 420, 231 (2002).
11. O. G. Berg, J. Paulsson, and M. Ehrenberg, Biophys. J. BIOJAU 0006-3495 79, 1228 (2000).
12. R. Metzler and P. G. Wolynes, Chem. Phys. CMPHC2 0301-0104 10.1016/S0301-0104(02)00674-2 284, 469 (2002).
13. M. Thattai and A. van Oudenaarden, Biophys. J. BIOJAU 0006-3495 82, 2943 (2002).
14. J. Paulsson, O. G. Berg, and M. Ehrenberg, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.110057697 97, 7148 (2000).
15. J. Paulsson and M. Ehrenberg, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.84.5447 84, 5447 (2000).
16. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1983).
17. D. T. Gillespie, J. Phys. Chem. A JPCAFH 1089-5639 81, 2340 (1977).
18. D. T. Gillespie, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1378322 115, 1716 (2001).
19. D. T. Gillespie and L. R. Petzold, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1613254 119, 8229 (2003).
20. M. Rathinam, L. R. Petzold, Y. Cao, and D. T. Gillespie, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1627296 119, 12784 (2003).
21. Y. Cao, D. T. Gillespie, and L. R. Petzold, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1824902 122, 014116 (2005).
22. F. Baras and M. M. Mansour, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.54.6139 54, 6139 (1996).
23. A. B. Stundzia and C. J. Lumsden, J. Comput. Phys. JCTPAH 0021-9991 10.1006/jcph.1996.0168 127, 196 (1996).
24. M. D. Levin, T. S. Shimizu, and D. Bray, Biophys. J. BIOJAU 0006-3495 82, 1809 (2002).
25. T. S. Shimizu, S. V. Aksenov, and D. Bray, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(03)00437-6 329, 291 (2003).
26. U. S. Bhalla, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.040469 87, 733 (2004).
27. S. S. Andrews and D. Bray, Phys. Biol. PBHIAT 1478-3975 10.1088/1478-3967/1/3/001 1, 137 (2004).
28. J. Elf, A. Dončić, and M. Ehrenberg, Proc. SPIE PSISDG 0277-786X 5110, 114 (2003).
29. J. Elf and M. Ehrenberg, Systems Biology 1, 230 (2004).
30. R. Metzler, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.87. 068103 87, 068103 (2001).
31. E. L. Haseltine and J. B. Rawlings, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1505860 117, 6959 (2002).
32. C. V. Rao and A. P. Arkin, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1545446 118, 4999 (2003).
33. J. Puchałka and A. M. Kierzek, Biophys. J. BIOJAU 0006-3495 86, 1357 (2004).
34. D. A. Lauffenburger and J. J. Linderman, Receptors: Models for Binding, Trafficking and Signaling (Oxford University Press, Oxford, 1993).
35. B. Schoeberl, C. Eichler-Jonsson, E. D. Gilles, and G. Müller, Nat. Biotechnol. NABIF9 1087-0156 10.1038/nbt0402-370 20, 370 (2002).
36. G. L. Nelsestuen and M. B. Martinez, Biochemistry BICHAW 0006-2960 36, 9081 (1997).
37. M. Eigen, Quantum Statistical Mechanics In The Natural Sciences (Plenum, New York, 1974), Chap. Diffusion control in biochemical reactions, pp. 37-61.
38. G. I. Bell, Science SCIEAS 0036-8075 200, 618 (1978).
39. W. R. Burack and A. S. Shaw, Curr. Opin. Cell Biol. COCBE3 0955-0674 12, 211 (2000).
40. J. E. Ferrell, Jr., Science Signal Transduction Knowledge Environment 2000, PE1 (2000).
41. D. K. Morrison and R. J. Davis, Annu. Rev. Cell Dev. Biol. ARDBF8 1081-0706 19, 91 (2003).
42. E. A. Elion, J. Cell. Sci. JNCSAI 0021-9533 114, 3967 (2001).
43. S.-H. Park, A. Zarrinpar, and W. A. Lim, Science SCIEAS 0036-8075 299, 1061 (2003).
44. D. Bray and S. Lay, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.25.13493 94, 13493 (1997).
45. A. Levchenko, J. Bruck, and P. W. Sternberg, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.97.11.5818 97, 5818 (2000).
46. A. Goldbeter and D. E. Koshland, Jr., Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.78.11.6840 78, 6840 (1981).
47. E. Lee, A. Salic, R. Krüger, R. Heinrich, and M. W. Kirschner, PLoS Biol. PBLIBG 1545-7885 1, 116 (2004).
48. M. Hucka, Bioinformatics BOINFP 1367-4803 19, 524 (2003).
49. M. A. Gibson and J. Bruck, J. Phys. Chem. A JPCAFH 1089-5639 10.1021/jp993732q 104, 1876 (2000).
50. W. H. Press, B. P. Glannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes: The Art of Scientific Computing (Cambridge University Press, Cambridge, England, 1989).