Advertisement

DCBA: Simulating Population Dynamics P Systems with Proportional Object Distribution

  • Miguel A. Martínez-del-Amor
  • Ignacio Pérez-Hurtado
  • Manuel García-Quismondo
  • Luis F. Macías-Ramos
  • Luis Valencia-Cabrera
  • Álvaro Romero-Jiménez
  • Carmen Graciani
  • Agustín Riscos-Núñez
  • Mari A. Colomer
  • Mario J. Pérez-Jiménez
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7762)

Abstract

Population Dynamics P systems provide a formal framework for ecological modelling having a probabilistic (while keeping the maximal parallelism). Several simulation algorithms have been developed always trying to reach higher reliability in the way they reproduce the behaviour of the ecosystems being modelled.

It is natural for those algorithms to classify the rules into blocks, comprising rules that share identical left-hand side. Previous algorithms, such as the Binomial Block Based (BBB) or the Direct Non Deterministic distribution with Probabilities (DNDP), do not define a deterministic behaviour for blocks of rules competing for the same resources. In this paper we introduce the Direct distribution based on Consistent Blocks Algorithm (DCBA), a simulation algorithm which addresses that inherent non-determinism of the model by distributing proportionally the resources.

Keywords

Membrane Computing Population Dynamics P systems Simulation Algorithm Probabilistic P systems DCBA P-Lingua pLinguaCore 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Bianco, L., Manca, V., Marchetti, L., Petterlini, M.: Psim: a simulator for biomolecular dynamics based on P systems. In: IEEE Congress on Evolutionary Computation, pp. 883–887 (2007)Google Scholar
  2. 2.
    Cardona, M., Colomer, M.A., Margalida, A., Palau, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A computational modeling for real ecosystems based on P systems. Natural Computing 10(1), 39–53 (2011)MathSciNetzbMATHCrossRefGoogle Scholar
  3. 3.
    Cardona, M., Colomer, M.A., Margalida, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A P System Based Model of an Ecosystem of Some Scavenger Birds. In: Păun, G., Pérez-Jiménez, M.J., Riscos-Núñez, A., Rozenberg, G., Salomaa, A. (eds.) WMC 2009. LNCS, vol. 5957, pp. 182–195. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  4. 4.
    Cardona, M., Colomer, M.A., Pérez-Jiménez, M.J., Sanuy, D., Margalida, A.: Modeling Ecosystems Using P Systems: The Bearded Vulture, a Case Study. In: Corne, D.W., Frisco, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2008. LNCS, vol. 5391, pp. 137–156. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  5. 5.
    Cheruku, S., Păun, A., Romero-Campero, F.J., Pérez-Jiménez, M.J., Ibarra, O.H.: Simulating FAS-induced apoptosis by using P systems. Progress in Natural Science 17(4), 424–431 (2007)MathSciNetzbMATHCrossRefGoogle Scholar
  6. 6.
    Colomer, M.A., Lavín, S., Marco, I., Margalida, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D., Serrano, E., Valencia-Cabrera, L.: Modeling Population Growth of Pyrenean Chamois (Rupicapra p. pyrenaica) by Using P-Systems. In: Gheorghe, M., Hinze, T., Păun, G., Rozenberg, G., Salomaa, A. (eds.) CMC 2010. LNCS, vol. 6501, pp. 144–159. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  7. 7.
    Colomer, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos-Núñez, A.: Comparing simulation algorithms for multienvironment probabilistic P system over a standard virtual ecosystem. Natural Computing 11(3), 369–379 (2012)zbMATHCrossRefGoogle Scholar
  8. 8.
    García-Quismondo, M., Gutiérrez-Escudero, R., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos-Núñez, A.: An Overview of P-Lingua 2.0. In: Păun, G., Pérez-Jiménez, M.J., Riscos-Núñez, A., Rozenberg, G., Salomaa, A. (eds.) WMC 2009. LNCS, vol. 5957, pp. 264–288. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  9. 9.
    Martínez-del-Amor, M.A., Karlin, I., Jensen, R.E., Pérez-Jiménez, M.J., Elster, A.C.: Parallel Simulation of Probabilistic P Systems on Multicore Platforms. In: Proceedings of the Tenth Brainstorming Week on Membrane Computing, vol. II, pp. 17–26 (2012)Google Scholar
  10. 10.
    Martínez-del-Amor, M.A., Pérez-Hurtado, I., Gastalver-Rubio, A., Elster, A.C., Pérez-Jiménez, M.J.: Population Dynamics P Systems on CUDA. In: Gilbert, D., Heiner, M. (eds.) CMSB 2012. LNCS, vol. 7605, pp. 247–266. Springer, Heidelberg (2012)CrossRefGoogle Scholar
  11. 11.
    Martínez-del-Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos-Núñez, A., Sancho-Caparrini, F.: A simulation algorithm for multienvironment probabilistic P systems: A formal verification. International Journal of Foundations of Computer Science 22(1), 107–118 (2011)MathSciNetzbMATHCrossRefGoogle Scholar
  12. 12.
    Martínez-del-Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Riscos-Núñez, A., Colomer, M.A.: A new simulation algorithm for multienvironment probabilistic P systems. In: Proceedings of the 5th IEEE International Conference on Bio-Inspired Computing: Theories and Applications, vol. 1, pp. 59–68 (2010)Google Scholar
  13. 13.
    Păun, G.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000); Turku Center for Computer Science-TUCS Report No 208MathSciNetzbMATHCrossRefGoogle Scholar
  14. 14.
    Păun, G., Romero-Campero, F.J.: Membrane Computing as a Modeling Framework. Cellular Systems Case Studies. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 168–214. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  15. 15.
    Păun, G., Rozenberg, G., Salomaa, A. (eds.): The Oxford Handbook of Membrane Computing (2010)Google Scholar
  16. 16.
    Terrazas, G., Krasnogor, N., Gheorghe, M., Bernardini, F., Diggle, S., Cámara, M.: An Environment Aware P-System Model of Quorum Sensing. In: Cooper, S.B., Löwe, B., Torenvliet, L. (eds.) CiE 2005. LNCS, vol. 3526, pp. 479–485. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  17. 17.
    The GNUplot web page, http://www.gnuplot.info
  18. 18.
    The P-Lingua web page, http://www.p-lingua.org
  19. 19.
    The Bearded Vulture ecosystem model in P-Lingua, http://www.p-lingua.org/wiki/index.php/bvBWMC12

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Miguel A. Martínez-del-Amor
    • 1
  • Ignacio Pérez-Hurtado
    • 1
  • Manuel García-Quismondo
    • 1
  • Luis F. Macías-Ramos
    • 1
  • Luis Valencia-Cabrera
    • 1
  • Álvaro Romero-Jiménez
    • 1
  • Carmen Graciani
    • 1
  • Agustín Riscos-Núñez
    • 1
  • Mari A. Colomer
    • 2
  • Mario J. Pérez-Jiménez
    • 1
  1. 1.Research Group on Natural Computing Department of Computer Science and Artificial IntelligenceUniversity of SevilleSevillaSpain
  2. 2.Department of MathematicsUniversity of LleidaLleidaSpain

Personalised recommendations