Beta Binders for Biological Interactions

  • Corrado Priami
  • Paola Quaglia
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3082)

Abstract

This paper presents binders and operators, in the process calculi tradition, to reason about biological interactions.

Special binders are added to wrap a process just as membranes enclose some living matter and hence to mimick biological interfaces. A few operators are then added to the pi-calculus kernel to describe the dynamics of those interfaces.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular biology of the cell. IVth ed., Garland science (2002)Google Scholar
  2. 2.
    Berry, G., Boudol, G.: The chemical abstract machine. Theoretical Computer Science 96(1), 217–248 (1992)CrossRefMATHGoogle Scholar
  3. 3.
    Cardelli, L.: Membrane interactions. In: BioConcur 2003, Workshop on Concurrent Models in Molecular Biology (2003)Google Scholar
  4. 4.
    Danos, V., Krivine, J.: Formal molecular biology done in CCS-R. In: BioConcur 2003, Workshop on Concurrent Models in Molecular Biology (2003)Google Scholar
  5. 5.
    Danos, V., Laneve, C.: Core formal molecular biology. In: Degano, P. (ed.) ESOP 2003 and ETAPS 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.
    Milner, R. (ed.): Communication and Concurrency. International Series in Computer Science. Prentice-Hall, Englewood Cliffs (1989)MATHGoogle Scholar
  8. 8.
    Milner, R.: Communicating and mobile systems: the π-calculus. Cambridge Universtity Press, Cambridge (1999)MATHGoogle Scholar
  9. 9.
    Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic passing-name calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)CrossRefMATHGoogle 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.
    Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Proceedings of the Pacific Symposium of Biocomputing 2001, vol. 6, pp. 459–470 (2001)Google Scholar
  12. 12.
    Sangiorgi, D., Walker, D.: The π-calculus: a Theory of Mobile Processes. Cambridge Universtity Press, Cambridge (2001)MATHGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Corrado Priami
    • 1
  • Paola Quaglia
    • 1
  1. 1.Dipartimento di Informatica e TelecomunicazioniUniversità di TrentoItaly

Personalised recommendations