Skip to main content

Spatial Organization of the Chemical Paradigm and the Specification of Autonomic Systems

  • Chapter
Software-Intensive Systems and New Computing Paradigms

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 5380))

Abstract

The chemical paradigm is an unconventional programming paradigm well fitted to the high-level specification of parallel systems. Based on the fixed point iterations of local rules, its use has been advocated for the programming of autonomic and amorphous systems. However, this model lacks an explicit handling of spatial relationships.

In this contribution, we first show how the chemical paradigm can be extended beyond multisets to arbitrary topological collections. Topological collections handle in a uniform way sophisticated data structures required in algorithmics as well as distributed data structures needed for the programming of autonomic or amorphous systems. Then we adapt a well-known result on multiset ordering to the more general case of topological collections. Well-founded ordering on topological collection can be used to prove the termination of the fixed point iteration of local rules.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., Knight, T.F., Nagpal, R., Rauch, E., Sussman, G.J., Weiss, R.: Amorphous computing. CACM: Communications of the ACM 43 (2000)

    Google Scholar 

  2. Arulanandham, J.J., Calude, C.S., Dinneen, M.J.: Bead-Sort: A natural sorting algorithm. EATCS Bull. 76, 153–162 (2002)

    MathSciNet  MATH  Google Scholar 

  3. Banâtre, J.-P., Coutant, A., Le Metayer, D.: A parallel machine for multiset transformation and its programming style. Future Generation Computer Systems 4, 133–144 (1988)

    Article  Google Scholar 

  4. Brukman, O., Dolev, S., Haviv, Y., Lahiani, L., Kat, R., Schiller, E., Tzachar, N., Yagel, R.: Self-stabilization from theory to practice. Bulletin of the EATCS (94), 130–150 (2008)

    Google Scholar 

  5. Brukman, O., Dolev, S., Haviv, Y., Yagel, R.: Self-stabilization as a foundation for autonomic computing. In: Proc. of the Second IEEE International Conference on Availability, Reliability and Security (ARES 2007), Workshop on Foundation of Fault-tolerance Distributed Computing (FOFDC 2007), pp. 991–998. IEEE, Los Alamitos (2007)

    Chapter  Google Scholar 

  6. Barbier de Reuille, P., Bohn-Courseau, I., Ljung, K., Morin, H., Carraro, N., Godin, C., Traas, J.: Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis. PNAS 103(5), 1627–1632 (2006)

    Article  Google Scholar 

  7. Banâtre, J.-P., Le Métayer, D.: The GAMMA model and its discipline of programming. Science of Computer Programming 15(1), 55–77 (1990)

    Article  MathSciNet  MATH  Google Scholar 

  8. Banâtre, J.-P., Radenac, Y., Fradet, P.: Chemical specification of autonomic systems. In: IASSE, pp. 72–79. ISCA (2004)

    Google Scholar 

  9. Chen, M., Il Choo, Y., Li, J.: Crystal: Theory and Pragmatics of Generating Efficient Parallel Code. In: Szymanski, B.K. (ed.) Parallel Functional Languages and Compilers. Frontier Series, vol. 7, pp. 255–308. ACM Press, New York (1991)

    Google Scholar 

  10. Dershowitz, N., Jouannaud, J.-P.: Rewrite systems. In: Handbook of Theoretical Computer Science, vol. B, pp. 244–320. Elsevier Science, Amsterdam (1990)

    Google Scholar 

  11. Dershowitz, N., Manna, Z.: Proving termination with multiset orderings. Communications of the Association for Computing Machinery 22, 465–476 (1979)

    Article  MathSciNet  MATH  Google Scholar 

  12. Giavitto, J.-L.: Invited talk: Topological collections, transformations and their application to the modeling and the simulation of dynamical systems. In: Nieuwenhuis, R. (ed.) RTA 2003. LNCS, vol. 2706, Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  13. Giavitto, J.-L., Michel, O.: Declarative definition of group indexed data structures and approximation of their domains. In: Proceedings of the 3nd International ACM SIGPLAN Conference on Principles and Practice of Declarative Programming (PPDP 2001). ACM Press, New York (2001)

    Google Scholar 

  14. Giavitto, J.-L., Michel, O.: Data structure as topological spaces. In: Calude, C.S., Dinneen, M.J., Peper, F. (eds.) UMC 2002. LNCS, vol. 2509, pp. 137–150. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  15. Giavitto, J.-L., Michel, O.: The topological structures of membrane computing. Fundamenta Informaticae 49, 107–129 (2002)

    MathSciNet  MATH  Google Scholar 

  16. Giavitto, J.-L., Spicher, A.: Topological rewriting and the geometrization of programming. Physica D 237, 1302–1314 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  17. Henle, M.: A combinatorial introduction to topology. Dover publications, New-York (1994)

    MATH  Google Scholar 

  18. Horn, P.: Autonomic computing: IBM’s perspective on the state of information technology. Technical report, IBM Research (October 2001), http://www.research.ibm.com/autonomic/manifesto/autonomic_computing.pdf

  19. IGEM. Modeling a synthetic multicellular bacterium. Modeling page of the Paris team wiki at iGEM 2007 (2007), http://parts.mit.edu/igem07/index.php/Paris/Modeling

  20. Karp, R.M., Miller, R.E., Winograd, S.: The organization of computations for uniform recurrence equations. Journal of the ACM 14(3), 563–590 (1967)

    Article  MathSciNet  MATH  Google Scholar 

  21. Kovalevsky, V.: Algorithms and data structures for computer topology. In: Digital and image geometry: advanced lectures, pp. 38–58. Springer, New York (2001)

    Chapter  Google Scholar 

  22. Lienhardt, P.: N-dimensional generalized combinatorial maps and cellular quasi-manifolds. International Journal on Computational Geometry and Applications 4(3), 275–324 (1994)

    Article  MathSciNet  MATH  Google Scholar 

  23. Lisper, B.: On the relation between functional and data-parallel programming languages. In: Proc. of the 6th. Int. Conf. on Functional Languages and Computer Architectures. ACM Press, New York (1993)

    Google Scholar 

  24. Michel, O.: There’s plenty of room for unconventional programming languages, or, declarative simulations of dynamical systems (with a dynamical structure). Habilitation Manuscript (December 2007), http://www.ibisc.univ-evry.fr/~michel/Hdr/hdr.pdf

  25. Munkres, J.: Elements of Algebraic Topology. Addison-Wesley, Reading (1984)

    MATH  Google Scholar 

  26. Pǎun, G.: Membrane Computing. An Introduction. Springer, Berlin (2002)

    Google Scholar 

  27. Palmer, R.S., Shapiro, V.: Chain models of physical behavior for engineering analysis and design. In: Research in Engineering Design, vol. 5, pp. 161–184. Springer International, Heidelberg (1993)

    Google Scholar 

  28. Rozenberg, G., Salomaa, A. (eds.): Lindenmayer Systems: Impacts on Theoretical Computer Science, Computer Graphics and Developmental Biology. Springer, Heidelberg (1992)

    MATH  Google Scholar 

  29. Steele, G.L., Hillis, D.: Connection machine LISP: Fine grained parallel symbolic programming. In: Proceedings of the 1986 ACM Conference on LISP and Functional Programming, pp. 279–297. ACM, New York (1986)

    Chapter  Google Scholar 

  30. Suhonen, J., Kohvakka, M., Hännikäinen, M., Hämäläinen, T.D.: Design, implementation, and experiments on outdoor deployment of wireless sensor network for environmental monitoring. In: Vassiliadis, S., Wong, S., Hämäläinen, T.D. (eds.) SAMOS 2006. LNCS, vol. 4017, pp. 109–121. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  31. Spicher, A., Michel, O.: Using rewriting techniques in the simulation of dynamical systems: Application to the modeling of sperm crawling. In: Sunderam, V.S., van Albada, G.D., Sloot, P.M.A., Dongarra, J. (eds.) ICCS 2005. LNCS, vol. 3514, pp. 820–827. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  32. Spicher, A., Michel, O.: Declarative modeling of a neurulation-like process. BioSystems 87(2-3), 281–288 (2007)

    Article  Google Scholar 

  33. Spicher, A., Michel, O., Cieslak, M., Giavitto, J.-L., Prusinkiewicz, P.: Stochastic p systems and the simulation of biochemical processes with dynamic compartments. BioSystems 91(3), 458–472 (2008)

    Article  Google Scholar 

  34. Toffoli, T., Margolus, N.: Cellular automata machines: a new environment for modeling. MIT Press, Cambridge (1987)

    MATH  Google Scholar 

  35. Tonti, E.: The algebraic-topological structure of physical theories. In: Glockner, P.G., Sing, M.C. (eds.) Symmetry, similarity and group theoretic methods in mechanics, Calgary, Canada, pp. 441–467 (August 1974)

    Google Scholar 

  36. Tonti, E.: A direct discrete formulation of field laws: The cell method. Computer Modeling in Engineering & Sciences 2(2), 237–258 (2001)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Giavitto, JL., Michel, O., Spicher, A. (2008). Spatial Organization of the Chemical Paradigm and the Specification of Autonomic Systems. In: Wirsing, M., Banâtre, JP., Hölzl, M., Rauschmayer, A. (eds) Software-Intensive Systems and New Computing Paradigms. Lecture Notes in Computer Science, vol 5380. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-89437-7_15

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-89437-7_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-89436-0

  • Online ISBN: 978-3-540-89437-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics