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Projective Brane Calculus

  • Vincent Danos
  • Sylvain Pradalier
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3082)

Abstract

A refinement of Cardelli’s brane calculus [1] is introduced where membrane actions are directed. This modification brings the language closer to biological membranes and also obtains a symmetric set of membrane interactions. An associated structural congruence, termed the projective equivalence, is defined and shown to be preserved under all possible system evolutions. Comparable notions of projective equivalence can be developed in other hierarchical process calculi and might be of interest in other applications.

Keywords

Outer Membrane Distinguished Vertex Projective Invariance Process Algebra Membrane Interaction 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Cardelli, L.: Brane calculi. In: Proceedings of BIO-CONCUR 2003, Marseille, France. Electronic Notes in Theoretical Computer Science, vol. ?. Elsevier, Amsterdam (to appear 2003)Google Scholar
  2. 2.
    Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E. (eds.) Pacific Symposium on Biocomputing, vol. 6, pp. 459–470. World Scientific Press, Singapore (2001)Google Scholar
  3. 3.
    Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters (2001)Google Scholar
  4. 4.
    Regev, A., Shapiro, E.: Cells as computation. Nature 419 (September 2002)Google Scholar
  5. 5.
    Danos, V., Laneve, C.: Core formal molecular biology. In: Degano, P. (ed.) ESOP 2003. LNCS, vol. 2618, pp. 302–318. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  6. 6.
    Danos, V., Laneve, C.: Graphs for core molecular biology. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 34–46. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  7. 7.
    Danos, V., Krivine, J.: Formal molecular biology done in CCS. In: Proceedings of BIO-CONCUR 2003, Marseille, France. Electronic Notes in Theoretical Computer Science, vol. ?. Elsevier, Amsterdam (to appear 2003)Google Scholar
  8. 8.
    Chiaverini, M., Danos, V.: A core modeling language for the working molecular biologist (Abstract). In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 166–166. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  9. 9.
    Paun, G.: Membrane Computing. An Introduction. Springer, Heidelberg (2002)CrossRefzbMATHGoogle Scholar
  10. 10.
    Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: Bioambients: An abstraction for biological compartments. Theoretical Computer Science (to appear, 2003)Google Scholar
  11. 11.
    Cardelli, L.: Brane calculi (slides). Slides (2003)Google Scholar
  12. 12.
    Kimball, J.W.: Biology Pages. Online biology textbook (2003), http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/Kimball's
  13. 13.
    Cardelli, L.: Bitonal membrane systems. Draft (2003)Google Scholar
  14. 14.
    Alberts, B., et al.: Essential Cell Biology. International Series on Computer Science. Garland Science, New York (2004)Google Scholar
  15. 15.
    Danos, V., Laneve, C.: Formal molecular biology. Theoretical Computer Science 325(1), 69–110 (2004)CrossRefzbMATHGoogle Scholar
  16. 16.
    Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys. 22, 403–434 (1976)CrossRefGoogle Scholar
  17. 17.
    Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Vincent Danos
    • 1
  • Sylvain Pradalier
    • 2
  1. 1.Université Paris 7 & CNRSFrance
  2. 2.ENS CachanFrance

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