Stochastic simulation of chemically reacting systems using multi-core processors

Journal of Chemical Physics

Volumn 136, Issue 1, 2012, Pages

  Gillespie, Colin S ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM PARTITION; BIOCHEMICAL NETWORK; CHEMICALLY REACTING SYSTEMS; COMPLEX DYNAMICS; MULTI-CORE MACHINES; MULTI-CORE PROCESSOR; SIMULATION ALGORITHMS; STOCHASTIC APPROACH; STOCHASTIC SIMULATIONS; STOCHASTICITY; SUBMODELS;

ALGORITHMS; PROGRAM PROCESSORS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

COMPUTER SIMULATION;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; STATISTICS;

ALGORITHMS; COMPUTER SIMULATION; STOCHASTIC PROCESSES;

EID: 84855546582     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3670416     Document Type: Article

References (33)

1. B. Ingalls, in Essays in Biochemistry - Systems Biology, edited by, O. Wolkenhauer, P. Wellstead, and, C. Kwang-Hyun, (Portland Press, London, 2008), pp. 177-193.
2. D. Endy and R. Brent, Nature (London) 409, 391 (2001). 10.1038/35053181 (Pubitemid 32151252)
3. H. Kitano, Nature (London) 420, 206 (2002). 10.1038/nature01254 (Pubitemid 35340131)
4. E. S. Marland and J. E. Keizer, in Computational Cell Biology, 3rd ed., edited by, C. P. Fall, E. S. Marland, J. M. Wagner, and, J. J. Tyson, (Springer, New York, 2005), Chap., pp. 53-76.
5. A. Arkin, J. Ross, and H. H. McAdams, Genetics 149, 1633 (1998).
6. W. J. Blake, M. Kaern, C. R. Cantor, and J. J. Collins, Nature (London) 422, 633 (2003). 10.1038/nature01546 (Pubitemid 36460419)
7. D. T. Gillespie, J Phys. Chem. 81, 2340 (1977). 10.1021/j100540a008
8. J. M. McCollum, G. D. Peterson, C. D. Cox, M. L. Simpson, and N. F. Samatova, Comput. Biol. Chem. 30, 39 (2006). 10.1016/j.compbiolchem.2005.10.007 (Pubitemid 43144430)
9. A. Slepoy, A. P. Thompson, and S. J. Plimpton, J Chem. Phys. 128, 205101 (2008). 10.1063/1.2919546 (Pubitemid 351771348)
10. M. A. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000). 10.1021/jp993732q
11. D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001). 10.1063/1.1378322 (Pubitemid 32715518)
12. Y. Cao and L. R. Petzold, Comput. Methods Appl. Mech. Eng. 197, 3472 (2008). 10.1016/j.cma.2008.02.024
13. N. G. van Kampen, Stochastic Processes in Physics and Chemistry, 3rd ed. (North-Holland, Amsterdam, 2007).
14. I. Krishnarajah, A. R. Cook, G. Marion, and G. Gibson, Bull. Math. Biol. 67, 855 (2005). 10.1016/j.bulm.2004.11.002 (Pubitemid 40707615)
15. C. S. Gillespie, IET Sys. Biol. 3, 52 (2009). 10.1049/iet-syb:20070031
16. P. Milner, C. S. Gillespie, and D. J. Wilkinson, Math. Biosci. 231, 99 (2011). 10.1016/j.mbs.2011.02.006
17. C. J. Proctor, C. Soti, R. J. Boys, C. S. Gillespie, D. P. Shanley, D. J. Wilkinson, and T. B.L. Kirkwood, Mech. Ageing Dev. 126, 119 (2005). 10.1016/j.mad.2004.09.031 (Pubitemid 40018485)
18. T. R. Kiehl, R. M. Mattheyses, and M. K. Simmons, Bioinformatics 20, 316 (2004). 10.1093/bioinformatics/btg409 (Pubitemid 38262762)
19. H. Salis and Y. Kaznessis, J. Chem. Phys. 122, 54103 (2005). 10.1063/1.1835951 (Pubitemid 41047527)
20. L. Harris and P. Clancy, J Chem. Phys. 125, 144107 (2006). 10.1063/1.2354085 (Pubitemid 44570773)
21. J. A. Papin, J. L. Reed, and B. O. Palsson, Trends Biochem. Sci. 29, 641 (2004). 10.1016/j.tibs.2004.10.001 (Pubitemid 39491262)
22. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, Science 298, 824 (2002). 10.1126/science.298.5594.824 (Pubitemid 35231534)
23. F. Li, I. Thiele, N. Jamshidi, and B. O. Palsson, PLOS Comput. Biol. 5, e1000292 (2009). 10.1371/journal.pcbi.1000292
24. C. G. Bowsher, J. R. Soc., Interface 8, 186 (2011). 10.1098/rsif.2010. 0287
25. C. G. Bowsher, Bioinformatics 27, 584 (2011). 10.1093/bioinformatics/ btq694
26. N. Le Novre, B. Bornstein, A. Broicher, M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. M. Sauro, M. Schilstra, B. Shapiro, J. Snoep, and M. Hucka, Nucleic Acids Res. 34, D689 (2006). 10.1093/nar/gkj092
27. A. Deckard, F. T. Bergmann, and H. M. Sauro, Bioinformatics 22, 2966 (2006). 10.1093/bioinformatics/btl520 (Pubitemid 44811576)
28. D. T. Gillespie and L. R. Petzold, J. Chem. Phys. 119, 8229 (2003). 10.1063/1.1613254
29. Y. Cao and L. R. Petzold, J. Comput. Phys. 212, 6 (2006). 10.1016/j.jcp.2005.06.012
30. J. Pahle, Briefings Bioinf. 10, 53 (2009). 10.1093/bib/bbn050
31. Y. Zhou, J. Liepe, X. Sheng, M. P. H. Stumpf, and C. Barnes, Bioinformatics 27, 874 (2011). 10.1093/bioinformatics/btr015
32. R Development Core Team, R: A Language and Environment for Statistical Computing, Vienna, Austria (2009); see http://www.r-project.org.
33. H. Wickham, ggplot2: Elegant Graphics for Data Analysis (Springer, New York, 2009). ISBN 978-0-387-98140-6