Artificial biochemistry

Natural Computing Series

Volumn , Issue 9783540888680, 2009, Pages 429-462

  Cardelli, Luca ^a  

^a MICROSOFT RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84986570296     PISSN: 16197127     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-88869-7_22     Document Type: Article

References (26)

1. Auxiliary materials for this article. http://lucacardelli.name
2. Cardelli L (2008) On process rate semantics. Theor Comput Sci 391(3):190-215. http://dx.doi.org/10.1016/j.tcs.2007.11.012
3. Cardelli L, Zavattaro G (2008) On the computational power of biochemistry. In: Third international conference on algebraic biology, AB 2008, July 2008, Linz
4. Fontana W, Buss LW (1996) The barrier of objects, from dynamical systems to bounded organization. In: Casti J, Karlqvist A (eds) Boundaries and barriers. Addison-Wesley, Reading, pp 56-116
5. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361
6. Jahnke T, Huisinga W (2007) Solving the chemical master equation for monomolecular reaction systems analytically. Math Biol 54(1):1-26
7. Harel D (1987) Statecharts: a visual formalism for complex systems. Sci Comput Program 8:231-274
8. Harel D, Efroni S, Cohen IR (2003) Reactive animation. In: Proceedings of FMCO 2002. LNCS, vol 2852. Springer, Berlin, pp 136-153
9. Hillston J (1996) A compositional approach to performance modelling. Cambridge University Press, Cambridge
10. House JE (2007) Principles of chemical kinetics. Academic Press, New York
11. Huang C-YF, Ferrell JE Jr (1996) Ultrasensitivity in the mitogen-activated protein cascade. Proc Natl Acad Sci USA 93:10078-10083
12. Kitano H (2003) A graphical notation for biochemical networks. BioSilico 1(5):169-176
13. Lerman K, Galstyan A (2004) Automatically modeling group behavior of simple agents. In: Agent modeling workshop, AAMAS-04, New York
14. Meinke MH, Bishops JS, Edstrom RD (1986) Zero-order ultrasensitivity in the regulation of glycogen phosphorylase. Proc Natl Acad Sci USA 83:2865-2868
15. Milner R (1999) Communicating and mobile systems: the π-calculus. Cambridge University Press, Cambridge
16. Phillips A, Cardelli L (2004) A correct abstract machine for the stochastic pi-calculus. In: Proceedings of BioConcur’04
17. Phillips A, Cardelli L, Castagna G (2006) A graphical representation for biological processes in the stochastic pi-calculus. Trans Comput Syst Biol VII:123-152
18. Priami C (1995) Stochastic π-calculus. Comput J 38:578-589
19. Priami C, Regev A, Shapiro E, Silverman W (2001) Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf Process Lett 80:25-31
20. Regev A, Shapiro E (2004) The π-calculus as an abstraction for biomolecular systems. In: Ciobanu G, Rozenberg G (eds) Modelling in molecular biology. Springer, Berlin, pp 219-266
21. Regev A, Shapiro E (2002) Cellular abstractions: cells as computation. Nature 419:343
22. Sauroa HM, Kholodenko BN (2004) Quantitative analysis of signaling networks. Prog Biophys Mol Biol 86:5-43
23. Soloveichik D, Cook M, Winfree E, Bruck J (2007) Computation with finite stochastic chemical reaction networks. http://www.dna.caltech.edu/DNAresearch_publications.html
24. Tumer K, Wolpert D (2004) A survey of collectives. In: Collectives and the design of complex systems. Springer, Berlin, pp 1-42
25. Wolkenhauer O, Ullah M, Kolch W, Cho K (2004) Modelling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans Nanobiosci 3:200-207
26. Vilar JMG, Kueh HY, Barkai N, Leibler S (2002) Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci 99(9):5988-5992