Abstract
Genetic Systems are a formalism inspired by genetic regulatory networks, suitable for modeling the interactions between genes and proteins, acting as regulatory products. The evolution is driven by genetic gates: a new object (representing a protein) is produced when all activator objects are available in the system, and no inhibitor object is present. Activators are not consumed by the application of such a rule. Objects disappear because of degradation: each object is equipped with a lifetime, and the object decays when such a lifetime expires.
We investigate the computational expressiveness of Genetic Systems with interleaving semantics (a single action is executed in a computational step): we show that they are Turing equivalent by providing a deterministic encoding of Random Access Machines in Genetic Systems. We also show that the computational power strictly decreases when moving to Genetic Systems where either the degradation or the inhibition mechanism are absent.
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
Blossey, R., Cardelli, L., Phillips, A.: A Compositional Approach to the Stochastic Dynamics of Gene Networks. In: Priami, C., Cardelli, L., Emmott, S. (eds.) Transactions on Computational Systems Biology IV. LNCS (LNBI), vol. 3939. Springer, Heidelberg (2006)
Busi, N., Pinna, G.M.: A Causal Semantics for Contextual P/T nets. In: Proc. ICTCS 1995, pp. 311–325. World Scientific, Singapore (1995)
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. Springer, Heidelberg (2006)
Busi, N., Zandron, C.: Computing with Genetic Gates, Proteins and Membranes. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361. Springer, Heidelberg (2006)
Busi, N., Zandron, C.: On the computational power of Genetic Gates with interleaving semantics: The power of inhibition and degradation, www.cs.unibo.it/%7Ebusi/FCT07long.pdf
Busi, N., Zandron, C.: Computing with Genetic Gates. In: Proc. Third Conference on Computability in Europe. Computation and Logic in the Real World (CiE 2007). LNCS, vol. 4497. Springer, Heidelberg 2007 (to appear)
Cardelli, L.: Brane Calculi - Interactions of Biological Membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–280. Springer, Heidelberg (2005)
De Jong, H.: Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. Journal of Computatonal Biology 9, 67–103 (2002)
Finkel, A., Schnoebelen, Ph.: 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., Pérez-Jiménez, M.J., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 36–62. Springer, Heidelberg (2005)
Minsky, M.L.: Computation: Finite and Infinite Machines. Prentice-Hall, Englewood Cliffs (1967)
Montanari, U., Rossi, F.: Contextual Nets. Acta Inform. 32(6), 545–596 (1995)
Păun, G.: Membrane Computing. An Introduction. Springer, Heidelberg (2002)
Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing. New computing paradigms. Springer, Heidelberg (1998)
Reisig, W.: Petri nets: An Introduction. In: EATCS Monographs in Computer Science, Springer, Heidelberg (1985)
Shepherdson, J.C., Sturgis, J.E.: Computability of Recursive Functions. Journal of the ACM 10, 217–255 (1963)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Busi, N., Zandron, C. (2007). On the Computational Power of Genetic Gates with Interleaving Semantics: The Power of Inhibition and Degradation. In: Csuhaj-Varjú, E., Ésik, Z. (eds) Fundamentals of Computation Theory. FCT 2007. Lecture Notes in Computer Science, vol 4639. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74240-1_16
Download citation
DOI: https://doi.org/10.1007/978-3-540-74240-1_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-74239-5
Online ISBN: 978-3-540-74240-1
eBook Packages: Computer ScienceComputer Science (R0)