Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes

Electronic Notes in Theoretical Computer Science

Volumn 194, Issue 3, 2008, Pages 165-180

  Versari, Cristian ^a   Busi, Nadia ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Calculus; process calculi; stochastic simulation

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; SEMANTICS; STOCHASTIC MODELS;

MULTIPLE VARIABLE VOLUMES; STOCHASTIC SIMULATION;

BIOLOGICAL SYSTEMS;

EID: 38649136925     PISSN: 15710661     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.entcs.2007.12.012     Document Type: Article

References (24)

1. Cao Y., Li H., and Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. J. Chem. Phys. 121 (2004) 4059-4067
2. Carbone M., and Maffeis S. On the expressive power of polyadic synchronisation in pi-calculus. Nord. J. Comput. 10 (2003) 70-98
3. Cardelli, L., Brane calculi., in: Danos and Schächter [6], pp. 257-278
4. Cleaveland R., Lüttgen G., and Natarajan V. Priority in process algebra. In: Bergstra J., Ponse A., and Smolka S. (Eds). Handbook of Process Algebra (2001), Elsevier Science Publishers 711-765
5. Danos V., and Laneve C. Formal molecular biology. Theor. Comput. Sci. 325 (2004) 69-110
6. In: Danos V., and Schächter V. (Eds). Computational Methods in Systems Biology, International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers. Lecture Notes in Computer Science 3082 (2005), Springer
7. Elf J., and Ehrenberg M. Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Systems Biology 1 (2004) 230-236. http://link.aip.org/link/?BDJ/1/230/1 URL
8. Gibson M., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. Journal of Physical Chemistry A 104 (2000) 1876-1889. http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp993732q URL
9. Gillespie D.T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22 (1976) 403-434. http://dx.doi.org/10.1016/0021-9991(76)90041-3 URL
10. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
11. Kuttler, C., C. Lhoussaine and J. Niehren, A stochastic pi calculus for concurrent objects, in: Proceedings of the Second International Conference on Algebraic Biology, Lecture Notes in Computer Science (2007)
12. Lecca, P., A time-dependent extension of gillespie algorithm for biochemical stochastic π-calculus, in: SAC '06: Proceedings of the 2006 ACM symposium on Applied computing (2006), pp. 137-144
13. Lu, T., D. Volfson, L. Tsimring and J. Hasty, Cellular growth and division in the gillespie algorithm, in: Systems Biology, IEE Proceedings, 2004, pp. 121-128
14. Milner R. Communicating and mobile systems: the π-calculus (1999), Cambridge University Press, New York, NY, USA
15. Milner R., Parrow J., and Walker D. A calculus of mobile processes, i. Inf. Comput. 100 (1992) 1-40
16. Milner R., Parrow J., and Walker D. A calculus of mobile processes, ii. Inf. Comput. 100 (1992) 41-77
17. Phillips, A. and L. Cardelli, A correct abstract machine for the stochastic pi-calculus, in: Bioconcur'04 (2004)
18. Priami C. Stochastic pi-calculus. Comput. J. 38 (1995) 578-589
19. Priami, C. and P. Quaglia, Beta binders for biological interactions, in: Danos and Schächter [6], pp. 20-33
20. Priami C., Regev A., Shapiro E.Y., and Silverman W. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Process. Lett. 80 (2001) 25-31
21. Regev A., Panina E.M., Silverman W., Cardelli L., and Shapiro E.Y. Bioambients: an abstraction for biological compartments. Theor. Comput. Sci. 325 (2004) 141-167
22. Regev, A., W. Silverman and E.Y. Shapiro, Representation and simulation of biochemical processes using the pi-calculus process algebra., in: Pacific Symposium on Biocomputing, 2001, pp. 459-470
23. Versari, C., A core calculus for a comparative analysis of bio-inspired calculi, European Symposium on Programming (2007), available at http://www.cs.unibo.it/~versari/files/cversari-esop07.pdf
24. Versari, C. and N. Busi, Stochastic simulation of biological systems with dynamical compartment structure, in: CMSB, 2007, available at http://www.cs.unibo.it/~versari/files/cversari-cmsb07.pdf. URL http://www.cs.unibo.it/~versari/files/cversari-cmsb07.pdf