A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

Journal of Chemical Physics

Volumn 125, Issue 14, 2006, Pages

  Harris, Leonard A ^a   Clancy, Paulette ^a  

^a Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTION DYNAMICS; MODEL-INDEPENDENT PARAMETERS; MULTISCALE SIMULATION; SPECIES POPULATIONS;

ACOUSTIC NOISE; ALGORITHMS; COMPUTATIONAL METHODS; COSTS; PARAMETER ESTIMATION; RANDOM PROCESSES; REACTION KINETICS;

MOLECULAR DYNAMICS;

BIOLOGICAL MODEL; CHEMICAL MODEL; COMPUTER SIMULATION; REVIEW; STATISTICAL ANALYSIS; STATISTICS;

COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; MODELS, CHEMICAL; MODELS, GENETIC; STOCHASTIC PROCESSES;

EID: 33749989765     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2354085     Document Type: Article

References (42)

1. H. H. McAdams and A. Arkin, Proc. Natl. Acad. Sci. U.S.A. 94, 814 (1997).
2. A. P. Arkin, J. Ross, and H. H. McAdams, Genetics 149, 1633 (1998).
3. H. H. McAdams and A. Arkin, Trends Genet. 15, 65 (1999).
4. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science 297, 1183 (2002).
5. N. Fedoroff and W. Fontana, Science 297, 1129 (2002).
6. C. V. Rao, D. M. Wolf, and A. P. Arkin, Nature (London) 420, 231 (2002).
7. M. Krn, T. C. Elston, W. J. Blake, and J. J. Collins, Nat. Rev. Genet. 6, 451 (2005).
8. J. M. Raser and E. K. O'Shea, Science 309, 2010 (2005).
9. J. D. Plummer and P. B. Griffin, Nucl. Instrum. Methods Phys. Res. B 102, 160 (1995).
10. S. Roy and A. Asenov, Science 309, 388 (2005).
11. The International Technology Roadmap for Semiconductors, 2001 ed., http://public.itrs.net
12. D. T. Gillespie, J. Comput. Phys. 22, 403 (1976).
13. M. A. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000).
14. Y. Cao, H. Li, and L. Petzold, J. Chem. Phys. 121, 4059 (2004).
15. H. Resat, H. S. Wiley, and D. A. Dixon, J. Phys. Chem. B 105, 11026 (2001).
16. D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001).
17. D. T. Gillespie and L. R. Petzold, J. Chem. Phys. 119, 8229 (2003).
18. M. Rathinam, L. R. Petzold, Y. Cao, and D. T. Gillespie, J. Chem. Phys. 119, 12784 (2003).
19. Y. Cao, L. R. Petzold, M. Rathinam, and D. T. Gillespie, J. Chem. Phys. 121, 12169 (2004).
20. Y. Cao, D. T. Gillespie, and L. R. Petzold, J. Chem. Phys. 123, 054104 (2005).
21. M. Rathinam, L. R. Petzold, Y. Cao, and D. T. Gillespie, Multiscale Model. Simul. 4, 867 (2005).
22. Y. Cao, D. T. Gillespie, and L. R. Petzold, J. Chem. Phys. 124, 044109 (2006).
23. T. Tian and K. Burrage, J. Chem. Phys. 121, 10356 (2004).
24. A. Chatterjee, D. G. Vlachos, and M. A. Katsoulakis, J. Chem. Phys. 122, 024112 (2005).
25. E. L. Haseltine and J. B. Rawlings, J. Chem. Phys. 117, 6959 (2002).
26. K. Burrage, T. Tian, and P. Burrage, Prog. Biophys. Mol. Biol. 85, 217 (2004).
27. J. Puchaka and A. M. Kierzek, Biophys. J. 86, 1357 (2004).
28. K. Vasudeva and U. S. Bhalla, Bioinformatics 20, 78 (2004).
29. T. R. Kiehl, R. M. Mattheyses, and M. K. Simmons, Bioinformatics 20, 316 (2004).
30. H. Salis and Y. Kaznessis, J. Chem. Phys. 122, 054103 (2005).
31. C. V. Rao and A. P. Arkin, J. Chem. Phys. 118, 4999 (2003).
32. Y. Cao, D. T. Gillespie, and L. R. Petzold, J. Chem. Phys. 122, 014116 (2005).
33. Y. Cao, D. Gillespie, and L. Petzold, J. Comput. Phys. 206, 395 (2005).
34. J. Goutsias, J. Chem. Phys. 122, 184102 (2005).
35. A. Samant and D. G. Vlachos, J. Chem. Phys. 123, 144114 (2005).
36. H. Salis and Y. N. Kaznessis, J. Chem. Phys. 123, 214106 (2005).
37. D. T. Gillespie, J. Chem. Phys. 113, 297 (2000).
38. D. T. Gillespie, Physica A 188, 404 (1992).
39. Y. Cao and L. Petzold, J. Comput. Phys. 212, 6 (2006).
40. D. Endy and R. Brent, Nature (London) 409, 391 (2001).
41. D. T. Gillespie, Markov Processes: An Introduction for Physical Scientists (Academic, San Diego, 1992).
42. See, e. g., W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C, The Art of Scientific Computing, 2nd ed. (Cambridge University Press, New York, NY, 1999).