A time-dependent extension of Gillespie algorithm for biochemical stochastic π - Calculus

Proceedings of the ACM Symposium on Applied Computing

Volumn 1, Issue , 2006, Pages 137-144

  Lecca, Paola ^a  

^a UNIVERSITY OF TRENTO   (Italy)

Author keywords

Biochemical systems modeling; Chemical kinetics simulation; Gillespie algorithm; Passive transport; Stochastic calculus

Indexed keywords

ALGEBRA; BIOCHEMISTRY; COMPUTER SCIENCE; COMPUTER SIMULATION; RANDOM PROCESSES;

BIOCHEMICAL SYSTEMS MODELING; CHEMICAL KINETICS SIMULATION; GILLESPIE ALGORITHMS; PASSIVE TRANSPORT; STOCHASTIC Π-CALCULUS;

ALGORITHMS;

EID: 33751065165     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1141277.1141310     Document Type: Conference Paper

References (15)

1. R. Barburi, A. Maggiolo-Schettini, P. Milazzo, and A. Troina. An alternative to gillespie's algorithm for simulating chemical reactions. In Procs of Computational Methods in Systems Biology, Edinburg, April 2005.
2. A. Bloch, B. Haagensen, M. K. Hoyer, and S. U. Knudsen. The stopi-calculus and simulator. http://www.cs.aau.dk/~bh/education.html?education, 2003.
3. D. T. Gillespie. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem, 81(25):2340-2361, 1977.
4. D. T. Gillespie. A rigorous derivation of the chemical master equation. Physica A, (188):404-425, 1992.
5. S. A. Isaacson and C. S. Peskin. Incorporating diffusion in complex geometries into stochastic chemical kinetics simulations. Downloadable from http://www.math.nyu.edu/phd_students/isaacsas/, 2005.
6. C. Kuttler, J. Niehren, and R. Blossey. Gene regulation in the pi calculus: Simulating cooperativity at the lambda switch. In Proceedings of BioConcur 2004, London, 2004.
7. P. Lecca, C. Priami, P. Quaglia, B. Rossi, C. Laudanna, and G. Costantin. A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment. SIMULATION: Transactions of the society for modelling and simulation international, 80:273-288, 2004.
8. G. E. Lienhard, J. W. Slot, D. E. James, and M. M. Mueckler. How cells absorb glucose. Scientific American, April 1992.
9. T. Lu, D. Volfson, L. Tsimring, and J. Hasty. Cellular growth and division in the gillespie algorithm. Syst. Biol., 1(1), 2004.
10. E. Marland and J. E. Keizer. Computational Cell Biology, chapter 3. Transporters and Pumps. Springer-Verlag New York Inc, 2001.
11. A. Phillips and L. Cardelli. A correct abstract machine for the stochastic pi-calculus. In Procs of BioConcur 2004, London, 2004.
12. C. Priami. Stochastic π-calculus. The Computer Journal, 38(6):578-589, 1995.
13. A. Regev, W. Silverman, and E. Shapiro. Representation and simulation of biochemical processes using the pi-calculus process algebra. In Proceedings of PSB2001, volume 6, pages 459-470, 2001.
14. M. Schwehm. Fast stochastic simulation of metabolic networks. In German Conference on Bioinformatics, pages 223-226, 2001.
15. E. Weinan, D. Liu, and E. Vanden-Eijinden. Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. www.math.nyu.edu/~diliu/kmc1.pdf.