Stochastic chemical kinetics: A review of the modelling and simulation approaches

Biophysical Reviews

Volumn 5, Issue 4, 2013, Pages 323-345

  Lecca, Paola ^a  

^a UNIVERSITY OF TRENTO   (Italy)

Author keywords

Biochemical systems; Chemical kinetics; Hybrid simulation methods; Markov processes; Spatio temporal algorithms; Stochastic simulation algorithms

Indexed keywords

ALGORITHM; CATALYST; CHEMICAL REACTION; CHEMICAL REACTION KINETICS; DENSITY FUNCTIONAL THEORY; ENZYME KINETICS; GILLESPIE ALGORITHM; HYBRID ALGORITHM; LANGEVIN EQUATION; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; POISSON TIMESTEP; PROBABILITY; REVIEW; SIMULATION ALGORITHM; SPATIO TEMPORAL ALGORITHM; STATISTICAL ANALYSIS; STOCHSIM ALGORITHM; T LEAP METHOD; TEMPERATURE;

EID: 84893014850     PISSN: 18672450     EISSN: 18672469     Source Type: Journal    
DOI: 10.1007/s12551-013-0122-2     Document Type: Review

References (52)

1. Gillespie DT (1976) J Comp Physics 22: 403.
2. Gillespie DT (1977) J Stat Phys 16(3).
3. Gillespie DT, Petzold LR (2003) Journal of Chemcial Physics 119: 8299.
4. Gillespie DT (2000) Journal of Chemcial Physics 113: 297.
5. GIllespie DT (1977) J Phys Chem 81(25).
6. Gillespie DT (1992) Markov processes. Academic Press.
7. McQuarrie DA (1967) J Appl Prob 4: 413.
8. GIllespie DT (1992) Physica A 188: 404.
9. Gillespie DT (2001) J Chem Phys 115: 1716.
10. Gillespie DT (2007) Annual Review of Physical Chemistry 58: 35.
11. Burrage K, Burrage PM, Leier A, Marquez-Lago T, Jr (2011) Stochastic simulation for spatial modelling of dynamic processes in a living cell. In: Koeppl H et al. (eds) Design and analysis of biomolecular circuits: engineering approaches to systems and synthetic biology chap. 2. Springer Science + Business Media, LLC.
12. Cao Y, Samuels DC (2009) Methods Enzymol 454: 115.
13. Ramaswamy R, González-Segredo N, Sbalzarini IF (2009) Journal of Chemical Physics 130(24): 244104.
14. Cao Y, Li H, Petzold L (2004) Journal of Chemical Physics 121(9): 4059.
15. Liu WED, Vanden-Eijnden E (2007) Journal of computational physics 221(1): 158.
16. van Kampfen NG (1992) Stochastic processes in physics and chemistry. Elsevier, Amsterdam.
17. Jöberg PS (2005) Numerical solution of the Fokker-Planck approximation of the Chemical Master Equation. Master's thesis, Dept. of Information Technology, Uppsala University.
18. Wolkenhauer WKO, Ullah M, Cho K (2004) IEEE Trans NanoBiosci. Special issue molecular and sub-cellular system biology.
19. Gibson M, Bruck J (2000) J Phys Chem A 104.
20. Lecca P (2006) In: SAC ACM'06.
21. Lecca P (2006) Int. Journal of Data Mining and Bioinformatics 1(4).
22. Lu T, Volfson LTD (2004) J Hasty Syst Biol 1.
23. Pahle J (2009) Briefings in Bioinformatics 10(1): 53.
24. Anderson DF (2008) Journal of Chemcial Physics 128: 054103.
25. Anderson DF, Ganguly A, Kurtz TG (2011) Ann Appl Probab 21(6): 2226.
26. Cao Y, Gillespie DT, Petzold LR (2005) Journal of Chemcial Physics 123: 054104.
27. Cao Y, Gillespie DT, Petzold LR (2006) Journal of Chemical Physics 124: 044109.
28. Chatterjee A, Mayawala K, Edwards JS, Vlachos DG (2005) Bioinformatics 21(9): 2136.
29. Morton-Firth CJ (1998) Stochastic simulation of cell signaling pathways. Ph. D. thesis, University of Cambridge, Cambridge, UK.
30. Shimizu TS, Bray D (2001) In: Kitano H (ed) Foundation of system biology, chap. 10.
31. Kitano H, Foundations of system biology (The MIT Press Cambridge, 2001), chap. System biology: toward system-level understanding of biological systems.
32. Shimizu TS (2002) The spatial organisation of cell signaling pathways-a computer based study. PhD thesis, University of Cambridge.
33. Elf J, Doncic A, Eherenberg M (2003) In: Proceedings of SPIE 5110, pp. 114-124.
34. Stundzia AB, Lumsden CJ (1996) J Comput Phys 127: 196.
35. Bartol TM, Stiles JR (2002) M-cell, http://www. MCell. cnl. salk. edu.
36. Lecca P, Ihekwaba AEC, Dematté L, Priami C (2010) Journal of Integrative Bioinformatics 7(1): 150.
37. Lecca P, Morpurgo D (2012) BMC Bioinformatics 13(14): 514.
38. Erdi P, Barna G (1993) Lecture notes in bioinformatics 71.
39. Horsthemke W, Hanson L (1993) J. Chem. Phys. 81.
40. Hasty J, Issacs F (2001) CHAOS 11(1): 207.
41. Bundschuh FHR, Javaprakash C (2003) Biophys J 84: 1606.
42. Haseltine EL, Rawlings JB (2002) J Chem Phys 117: 6959.
43. Puchalka J, Kierzek AM (2004) Biophys J 86: 1357.
44. Kiehl TR, Mattheyses RM, Simmons MK (2004) Bioinformatics 20: 316.
45. Alur R, Belta C, Ivancic F, Kumar V, Mintz M, Pappas G, Rubin H, Schug J (2001) In: Hybrid system. Computation and control, 4th International Workshop, HSCC, Rome Italy.
46. H. Matsuno, A. Doj, M. Nagasaki, S. Miyano (2000) in Pac. Symp. Biocomput, pp. (5) -333-349.
47. Bockmayr A, Courtois A (2002) In: 18th International Conference on Logic Programming, ICLP02. Springer, LNCS 2401, pp. 85-99.
48. Liu Z, Cao Y (2008) IET Syst Biol 5(5): 334.
49. Kalantzis G (2009) Computational Biology and Chemistry 33(3): 205.
50. Resat H, Petzold L, Pettigrew MF (2009) Methods Mol Biol 541: 311.
51. Salis H, Kaznessis Y (2005) Kinetic Modeling of Biological Systems 122(5): 54103.
52. Rossinelli D, Bayati B, Koumoutsakos P (2008) Chemical Physics Letters 451(1-3): 136.