Abstract
Brane calculi are a family of biologically inspired process calculi proposed in [3] for modeling the interactions of dynamically nested membranes.
In [3] a basic calculus for membranes interactions – called Phago/Exo/ Pino – is proposed, whose primitives are inspired by endocytosis and exocytosis. An alternative basic calculus – called Mate/Bud/Drip and inspired by membrane fusion and fission – is also outlined and shown to be encodable in Phago/Exo/Pino in [3].
In this paper we investigate and compare the expressiveness of such two calculi w.r.t. their ability to act as computational devices.
We show that (a fragment of) the Phago/Exo/Pino calculus is Turing powerful, by providing an encoding of Random Access Machines.
On the other hand, we show the impossibility to define a “faithful” encoding of Random Access Machines in the Mate/Bud/Drip calculus, by providing a proof of the decidability of the existence of a divergent computation in Mate/Bud/Drip.
Revised and full version of the extended abstract in Proc. Workshop on Computational Methods in Systems Biology, Edinburgh, April 2005.
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Busi, N.: On the Computational Power of the Mate/Bud/Drip Brane Calculus: Interleaving vs. Maximal Parallelism. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 144–158. Springer, Heidelberg (2006)
Busi, N., Zavattaro, G.: On the expressive power of movement and restriction in pure mobile ambients. Theoretical Computer Science 322, 477–515 (2004)
Cardelli, L.: Brane Calculi - Interactions of biological membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
Cardelli, L.: Abstract Machines for System Biology. Draft (2005)
Cardelli, L., Gordon, A.D.: Mobile Ambients. Theoretical Computer Science 240(1), 177–213 (2000)
Cardelli, L., Păun, G.: An universality result for a (Mem) Brane Calculus based on mate/drip operations. International Journal of Foundations of Computer Science (to appear)
Danos, V., Pradalier, S.: Projective Brane Calculus. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 134–148. Springer, Heidelberg (2005)
Finkel, A., Schnoebelen, P.: Well-Structured Transition Systems Everywhere! Theoretical Computer Science 256, 63–92 (2001)
Freund, R.: Asynchronous P Systems and P Systems Working in the Sequential Mode. In: Mauri, G., Păun, G., Jesús Pérez-Jímenez, M., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 36–62. Springer, Heidelberg (2005)
Higman, G.: Ordering by divisibility in abstract algebras. In: Proc. London Math. Soc., vol. 2, pp. 236–366 (1952)
Ibarra, O.H.: Some Recent Results Concerning Deterministic P Systems. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 49–54. Springer, Heidelberg (2006)
Minsky, M.L.: Computation: finite and infinite machines. Prentice-Hall, Englewood Cliffs (1967)
Păun, G.: Membrane Computing. An Introduction. Springer, Heidelberg (2002)
Păun, G.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)
Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic passing-name calculus to representation and simulation of molecular processes. Information Processing Letter 80, 25–31 (2001)
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: An Abstraction for Biological Compartments. Theoretical Computer Science 325(1), 141–167 (2004)
Shepherdson, J.C., Sturgis, J.E.: Computability of recursive functions. Journal of the ACM 10, 217–255 (1963)
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Busi, N., Gorrieri, R. (2006). On the Computational Power of Brane Calculi. In: Priami, C., Plotkin, G. (eds) Transactions on Computational Systems Biology VI. Lecture Notes in Computer Science(), vol 4220. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11880646_2
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DOI: https://doi.org/10.1007/11880646_2
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