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Generalized contexts for reaction systems: definition and study of dynamic causalities

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Abstract

Reaction systems are a qualitative formalism for the modelling of systems of biochemical reactions. In their original formulation, a reaction system executes in an environment (or context) that can supply it with new objects at each evolution step. The context drives the behaviour of a reaction system: it can provide different inputs to the system that can lead to different behaviours. In order to more faithfully deal with open systems, in this paper we propose a more powerful notion of context having not only the capability to provide objects, but also to absorb (or remove) objects at each evolution step. For such reaction systems with generalized context we investigate properties of dynamic causality by revising the previously proposed concept of formula based predictor. A formula based predictor is a Boolean formula characterising all contexts that lead to the production of a certain object after a given number of steps. In this paper, we revise the theory of formula based predictors in order to deal with reaction systems executed in a context of the new kind. As applications, we show an example of interaction between biochemical pathways and a reaction system modelling cell metabolism and respiration.

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Notes

  1. Note that in a generalized context sequence we have \(C_i \cap \overline{C}_i = \emptyset \) for each step i.

References

  1. Barbuti, R., Gori, R., Levi, F., Milazzo, P.: Specialized predictor for reaction systems with context properties. In: Proceedings of the 24th International Workshop on Concurrency, Specification and Programming, CS&P 2015, pp. 31–43 (2015)

  2. Barbuti, R., Gori, R., Levi, F., Milazzo, P.: Investigating dynamic causalities in reaction systems. Theor. Comput. Sci. 623, 114–145 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  3. Barbuti, R., Gori, R., Levi, F., Milazzo, P.: Specialized predictor for reaction systems with context properties. Fundam. Inf. 147(2–3), 173–191 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  4. Bodei, C., Gori, R., Levi, F.: An analysis for causal properties of membrane interactions. Electr. Notes Theor. Comput. Sci. 299, 15–31 (2013)

    Article  MATH  Google Scholar 

  5. Bodei, C., Gori, R., Levi, F.: Causal static analysis for Brane Calculi. Theor. Comput. Sci. 587, 73–103 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  6. Brijder, R., Ehrenfeucht, A., Main, M.G., Rozenberg, G.: A tour of reaction systems. Int. J. Found. Comput. Sci. 22(7), 1499–1517 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  7. Brijder, R., Ehrenfeucht, A., Rozenberg, G.: A note on causalities in reaction systems. Electronic Communications of the EASST 30 (2010). doi:10.14279/tuj.eceasst.30.429

  8. Brown, F.M.: Boolean Reasoning: The Logic of Boolean Equations. Kluwer, Amsterdam (1990)

    Book  MATH  Google Scholar 

  9. De Castro, L.N.: Fundamentals of Natural Computing: Basic Concepts, Algorithms, and Applications. CRC Press, Boca Raton (2006)

    MATH  Google Scholar 

  10. Dietmeyer, D.: Logic Design of Digital Systems. Allyn and Bacon, Boston (1978)

    MATH  Google Scholar 

  11. Ehrenfeucht, A., Rozenberg, G.: Reaction systems. Fundam. Inf. 75(1–4), 263–280 (2007)

    MathSciNet  MATH  Google Scholar 

  12. Fujita, M., Matsunaga, Y.: Multi-level logic minimization based on minimal support and its application to the minimization of look-up table type FPGAS. In: 1991 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 1993, Santa Clara, CA, USA, November 11–14, 1991. Digest of Technical Papers, pp. 560–563 (1991)

  13. Gori, R., Levi, F.: Abstract interpretation based verification of temporal properties for bioambients. Inf. Comput. 208(8), 869–921 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  14. Halatsis, C., Gaitanis, N.: Irredundant normal forms and minimal dependece sets of a Boolean function. IEEE Trans. Comput. 27(11), 1064–1068 (1978)

    Article  MathSciNet  MATH  Google Scholar 

  15. Hassoun, S., Sasao, T. (eds.): Logic Synthesis and Verification. Kluwer, Amsterdam (2002)

    Google Scholar 

  16. Kambayashi, Y.: Logic design of programmable logic arrays. IEEE Trans. Comput. 28(9), 609–617 (1979)

    Article  MathSciNet  MATH  Google Scholar 

  17. Kari, L., Rozenberg, G.: The many facets of natural computing. Commun. ACM 51(10), 72–83 (2008)

    Article  Google Scholar 

  18. Konieczny, P., Jóźwiak, L.: Minimal input support problem and algorithms to solve it. Eindhoven University of Thechnology Reaserch Report, pp. 1–55 (1995)

  19. Păun, G.: Computing with membranes. J. Comput. Syst. Sci. 61(1), 108–143 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  20. Păun, G.: Membrane Computing: An Introduction. Natural Computing Series. Springer, Berlin (2002)

    Book  MATH  Google Scholar 

  21. Sonveaux, P., Végran, F., Schroeder, T., Wergin, M.C., Verrax, J., Rabbani, Z.N., De Saedeleer, C.J., Kennedy, K.M., Diepart, C., Jordan, B.F., et al.: Targeting lactate-fueled respiration selectively kills hypoxic tumor cells in mice. J. Clin. Investig. 118(12), 3930–3942 (2008)

    Google Scholar 

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Authors and Affiliations

  1. Dipartimento di Informatica, Università di Pisa, Pisa, Italy

    Roberto Barbuti, Roberta Gori, Francesca Levi & Paolo Milazzo

Authors
  1. Roberto Barbuti
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  2. Roberta Gori
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  3. Francesca Levi
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  4. Paolo Milazzo
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Correspondence to Roberta Gori.

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Barbuti, R., Gori, R., Levi, F. et al. Generalized contexts for reaction systems: definition and study of dynamic causalities. Acta Informatica 55, 227–267 (2018). https://doi.org/10.1007/s00236-017-0296-3

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  • DOI: https://doi.org/10.1007/s00236-017-0296-3

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