On Parallel Graph Rewriting Systems
Keywords:
parallel multiset processing, abstract rewriting systems, P systemsAbstract
In this paper we introduce a new theoretical paradigm, called PGR systems, which can be used to model in a discrete manner some natural phenomena occurring in-vivo/in-vitro en- vironments. PGR systems make use of graphs to describe the spatial structure of space of individuals, while the system dynamics caused by the movement/interaction of individuals is captured by the parallel applications of some graph rewriting rules. In this frame, an il- lustrative example is studied and based on it, an eloquent comparison between the abstract rewriting machines and PGR systems is done. Several further ideas to overcome the global computational effort needed for simulations, but still maintaining the overall ability for mod- eling are finally proposed.References
D. Besozzi, G. Mauri, D. Pescini, C. Zandron, Dynamical Probabilistic P Systems. Int. J. Found. Comput. Sci., 17, 1 (2006), pp. 183-204.
D. Besozzi, P. Cazzaniga, G. Mauri, D. Pescini, Modelling Metapopulations with Stochastic Membrane Systems, BioSystems, 91 (2008), pp. 499-514. http://dx.doi.org/10.1016/j.biosystems.2006.12.011
B. Bollobas, Modern Graph Theory, Springer, 1991.
M. Cavaliere, I.I. Ardelean, Modeling Biological Processes by Using a Probabilistic P Sys- tem Software, Natural Computing, 2, 2 (2003), pp. 173-197. http://dx.doi.org/10.1023/A:1024943605864
H. Ehrig, Introduction to the Algebraic Theory of Graph Grammars, Lecture Notes in Com- puter Science 73 (1979), pp. 1-69. http://dx.doi.org/10.1007/BFb0025714
P. Frisco, The Conformon-P System: A Molecular and Cell Biology-Inspired Computability Model, Theoretical Computer Science, 312, 2-3 (2004), pp. 295-319.
P. Frisco, R.T. Gibson, A Simulator and an Evolution Program for Conformon-P Systems, Proc. of the 7th Int. Symp. on Symbolic and Numeric Algorithms for Scientific Computing, 2005, pp. 427-430. http://dx.doi.org/10.1109/SYNASC.2005.14
D.T. Gillespie, Exact Simulation of Coupled Chemical Reactions, J. Physical Chemistry, 81 (1977), pp. 2340-2361. http://dx.doi.org/10.1021/j100540a008
V. Manca, L. Bianco, Biological Networks in Metabolic P Systems. Biosystems, 91, 3(2008), pp. 489-498. http://dx.doi.org/10.1016/j.biosystems.2006.11.009
G. Păun, Membrane Computing. An Introduction, Springer, Berlin, 2002. http://dx.doi.org/10.1007/978-3-642-56196-2
D. Sburlan, Parallel Graph Rewriting Systems, Proc. of the 7th BWMC, Seville, Spain, 2009, in print.
Y. Suzuki, H. Tanaka, S. Tsumoto, Analysis of Cycles in Symbolic Chemical System Based on Abstract Rewriting System on Multisets, Proceedings of International Conference on Artificial Life 5 (Alife 5), 1996, pp. 482-489.
Y. Suzuki, J. Takabayashi, H. Tanaka, Investigation of Tritrophic System in Ecological Systems by Using an Artificial Chemistry, J. Artif. Life Robot., 6 (2002), pp. 129-132. http://dx.doi.org/10.1007/BF02481327
Y. Suzuki, H. Tanaka, Modelling p53 Signaling Pathways by Using Multiset Processing, Applications of Membrane Computing (G. Ciobanu, G. Păun, M. Pérez-Jiménez, Eds.), Springer, Berlin, 2006, pp. 203-214.
Published
Issue
Section
License
ONLINE OPEN ACCES: Acces to full text of each article and each issue are allowed for free in respect of Attribution-NonCommercial 4.0 International (CC BY-NC 4.0.
You are free to:
-Share: copy and redistribute the material in any medium or format;
-Adapt: remix, transform, and build upon the material.
The licensor cannot revoke these freedoms as long as you follow the license terms.
DISCLAIMER: The author(s) of each article appearing in International Journal of Computers Communications & Control is/are solely responsible for the content thereof; the publication of an article shall not constitute or be deemed to constitute any representation by the Editors or Agora University Press that the data presented therein are original, correct or sufficient to support the conclusions reached or that the experiment design or methodology is adequate.
