On Parallel Graph Rewriting Systems

Dragoș Sburlan

Abstract


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.

Keywords


parallel multiset processing, abstract rewriting systems, P systems

Full Text:

PDF

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.




DOI: https://doi.org/10.15837/ijccc.2009.3.2436



Copyright (c) 2017 Dragoș Sburlan

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

CC-BY-NC  License for Website User

Articles published in IJCCC user license are protected by copyright.

Users can access, download, copy, translate the IJCCC articles for non-commercial purposes provided that users, but cannot redistribute, display or adapt:

  • Cite the article using an appropriate bibliographic citation: author(s), article title, journal, volume, issue, page numbers, year of publication, DOI, and the link to the definitive published version on IJCCC website;
  • Maintain the integrity of the IJCCC article;
  • Retain the copyright notices and links to these terms and conditions so it is clear to other users what can and what cannot be done with the  article;
  • Ensure that, for any content in the IJCCC article that is identified as belonging to a third party, any re-use complies with the copyright policies of that third party;
  • Any translations must prominently display the statement: "This is an unofficial translation of an article that appeared in IJCCC. Agora University  has not endorsed this translation."

This is a non commercial license where the use of published articles for commercial purposes is forbiden. 

Commercial purposes include: 

  • Copying or downloading IJCCC articles, or linking to such postings, for further redistribution, sale or licensing, for a fee;
  • Copying, downloading or posting by a site or service that incorporates advertising with such content;
  • The inclusion or incorporation of article content in other works or services (other than normal quotations with an appropriate citation) that is then available for sale or licensing, for a fee;
  • Use of IJCCC articles or article content (other than normal quotations with appropriate citation) by for-profit organizations for promotional purposes, whether for a fee or otherwise;
  • Use for the purposes of monetary reward by means of sale, resale, license, loan, transfer or other form of commercial exploitation;

    The licensor cannot revoke these freedoms as long as you follow the license terms.

[End of CC-BY-NC  License for Website User]


INTERNATIONAL JOURNAL OF COMPUTERS COMMUNICATIONS & CONTROL (IJCCC), With Emphasis on the Integration of Three Technologies (C & C & C),  ISSN 1841-9836.

IJCCC was founded in 2006,  at Agora University, by  Ioan DZITAC (Editor-in-Chief),  Florin Gheorghe FILIP (Editor-in-Chief), and  Misu-Jan MANOLESCU (Managing Editor).

Ethics: This journal is a member of, and subscribes to the principles of, the Committee on Publication Ethics (COPE).

Ioan  DZITAC (Editor-in-Chief) at COPE European Seminar, Bruxelles, 2015:

IJCCC is covered/indexed/abstracted in Science Citation Index Expanded (since vol.1(S),  2006); JCR2018: IF=1.585..

IJCCC is indexed in Scopus from 2008 (CiteScore2018 = 1.56):

Nomination by Elsevier for Journal Excellence Award Romania 2015 (SNIP2014 = 1.029): Elsevier/ Scopus

IJCCC was nominated by Elsevier for Journal Excellence Award - "Scopus Awards Romania 2015" (SNIP2014 = 1.029).

IJCCC is in Top 3 of 157 Romanian journals indexed by Scopus (in all fields) and No.1 in Computer Science field by Elsevier/ Scopus.

 

 Impact Factor in JCR2018 (Clarivate Analytics/SCI Expanded/ISI Web of Science): IF=1.585 (Q3). Scopus: CiteScore2018=1.56 (Q2);

SCImago Journal & Country Rank

Editors-in-Chief: Ioan DZITAC & Florin Gheorghe FILIP.