Abstract
We put forward a method to map stochastic π-calculus processes in chemical ground form into hybrid automata, a class of dynamical systems with both discrete and continuous evolution. The key ingredient is the separation of control and molecular terms, which turns out to be related to the conservation properties of the system.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bortolussi, L.: A master equation approach to differential approximations of stochastic concurrent constraint programming. In: Proceedings of QAPL 2008 (2008)
Bortolussi, L., Policriti, A.: Dynamical systems and stochastic programming I - ordinary differential equations. Trans. of Comp. Sys. Bio. (submitted, 2008)
Bortolussi, L., Policriti, A.: Stochastic concurrent constraint programming and differential equations. In: Proceedings of QAPL 2007. ENTCS, vol. 16713 (2007)
Bortolussi, L., Policriti, A.: Hybrid approximation of stochastic concurrent constraint programming. In: Proceedings of IFAC 2008 (2008)
Bortolussi, L., Policriti, A.: Modeling biological systems in concurrent constraint programming. Constraints 13(1) (2008)
Calder, M., Gilmore, S., Hillston, J.: Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. Trans. of Comp. Sys. Bio. 4230, 1–23 (2006)
Cardelli, L.: From processes to ODEs by chemistry (2006), http://lucacardelli.name/
Cardelli, L.: On process rate semantics. In: TCS (2007)
Garey, M.R., Johnson, D.S.: Computers and Intractability: a Guide to the Therory of NP-Completeness. Freeman, New York (1979)
Gillespie, D.: The Chemical Langevin Equation. Jo. of Chem. Phys. 113(1), 297–306 (2000)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. of Phys. Chem. 81(25) (1977)
Haseltine, E.L., Rawlings, J.B.: On the origins of approximations for stochastic chemical kinetics. J. Chem. Phys. 123 (2005)
Henzinger, T.A.: The theory of hybrid automata. In: Proceedings of LICS 1996 (1996)
Hillston, J.: A Compositional Approach to Performance Modelling. Cambridge University Press, Cambridge (1996)
Hillston, J.: Fluid flow approximation of PEPA models. In: Proceedings of QEST 2005 (2005)
Kitano, H.: Computational systems biology. Nature 420, 206–210 (2002)
Neogi, N.A.: Dynamic partitioning of large discrete event biological systems for hybrid simulation and analysis. In: Alur, R., Pappas, G.J. (eds.) HSCC 2004. LNCS, vol. 2993, pp. 463–476. Springer, Heidelberg (2004)
Priami, C., Quaglia, P.: Modelling the dynamics of biosystems. Briefings in Bioinformatics 5(3), 259–269 (2004)
Regev, A., Shapiro, E.: Cellular abstractions: Cells as computation. Nature 419 (2002)
Ross, S.M.: Stochastic Processes. Wiley, New York (1996)
Wilkinson, D.J.: Stochastic Modelling for Systems Biology. Chapman & Hall, Boca Raton (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bortolussi, L., Policriti, A. (2008). Hybrid Semantics for Stochastic π-Calculus. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds) Algebraic Biology. AB 2008. Lecture Notes in Computer Science, vol 5147. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85101-1_4
Download citation
DOI: https://doi.org/10.1007/978-3-540-85101-1_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85100-4
Online ISBN: 978-3-540-85101-1
eBook Packages: Computer ScienceComputer Science (R0)