Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm

Journal of Chemical Physics

Volumn 123, Issue 14, 2005, Pages

  Samant, A ^a   Vlachos, D G ^a  

^a University of Delaware   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL SAVINGS; PARTIAL EQUILIBRIUM; PERTURBED SYSTEMS; STOCHASTIC SIMULATION ALGORITHMS (SSA);

ALGORITHMS; COMPUTATIONAL METHODS; COMPUTER SIMULATION; MONTE CARLO METHODS; PERTURBATION TECHNIQUES; PROBABILITY DISTRIBUTIONS; SAMPLING; STIFFNESS;

RANDOM PROCESSES;

EID: 26944450876     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2046628     Document Type: Article

References (28)

1. E. M. Ozbudak, M. Thattai, I. Kurtser, A. D. Grossman, and A. van Oudenaarden, Nat. Genet. 31, 69 (2002).
2. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science 297, 1183 (2002).
3. C. V. Rao, D. M. Wolf, and A. P. Arkin, Nature (London) 420, 231 (2002).
4. H. H. McAdams and A. Arkin, Trends Genet. 15, 65 (1999).
5. N. Federoff and W. Fontana, Science 297, 1129 (2002).
6. D. T. Gillespie, J. Comput. Phys. 22, 403 (1976).
7. D. T. Gillespie, J. Phys. Chem. 81, 2340 (1977).
8. A. Chatterjee, D. G. Vlachos, and M. A. Katsoulakis, J. Chem. Phys. 122, 024112 (2005).
9. T. Tian and K. Burrage, J. Chem. Phys. 121, 10356 (2004).
10. D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001).
11. M. Rathinam, L. R. Petzold, Y. Cao, and D. T. Gillespie, J. Chem. Phys. 119, 12784 (2003).
12. C. V. Rao and A. P. Arkin, J. Chem. Phys. 118, 4999 (2003).
13. E. L. Haseltine and J. B. Rawlings, J. Chem. Phys. 117, 6959 (2002).
14. J. Goutsias, J. Chem. Phys. 122, 184102 (2005).
15. Y. Cao, D. T. Gillespie, and L. R. Petzold, J. Chem. Phys. 122, 014116 (2005).
16. J. He, H. Zhang, J. Chen, and Y. Yang, Macromolecules 30, 8010 (1997).
17. H. Resat, H. S. Wiley, and D. A. Dixon, J. Chem. Phys. 105, 11026 (2001).
18. D. G. Vlachos, Chem. Eng. Sci. 53, 157 (1998).
19. M. A. Snyder, A. Chatterjee, and D. G. Vlachos, Comput. Chem. Eng. 29, 701 (2005).
20. D. G. Vlachos, Adv. Chem. Eng. (to be published).
21. E. Vanden-Eijnden, Commun. Math. Sci. 1 (2), 385 (2003).
22. E. Weinan, B. Engquist, and Z. Y. Huang, Phys. Rev. B 67, 092101 (2003).
23. R. Rico-Martinez, C. W. Gear, and I. G. Kevrekidis, J. Comput. Phys. 196, 474 (2004).
24. I. G. Kevrekidis, C. W. Gear, and G. Hummer, AIChE J. 50 (7), 1346 (2004).
25. D. G. Vlachos, Chem. Eng. Sci. 51 (16), 3979 (1996).
26. D. G. Vlachos, AIChE J. 43 (11), 3031 (1997).
27. A. Chatterjee and D. G. Vlachos, (unpublished).
28. J. S. Reese, S. Raimondeau, and D. G. Vlachos, J. Comp. Physiol. 173 (1), 302 (2001).