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Un calcul de réécriture de graphes : applications à la biologie et aux systèmes autonomes

Abstract : The objective of this thesis is to explore formal descriptions for the structure and functioning of biological systems, as well as formal tools for reasoning about their behavior. This work takes place in the overall prospective to study safe computational models where computations are expressed via rewriting, and where we can rely on formal verification to express and validate suitable properties. In this thesis we develop a higher-order calculus rewriting for describing molecules, reaction patterns, and biochemical network generation. The calculus is based on the chemical metaphor by describing the computations in terms of chemical solutions in which molecules representing data freely interact according to reaction rules. This way we obtained an Abstract Biochemical Calculus as an extension of the higher-order chemical model by considering structured molecules. The calculus is provided with a natural specification of concurrency and of controlling mechanisms by expressing rewrite strategies as molecules. The description of molecular complexes or chemical reactants belong to specific classes of graphs. We define the structure of port graphs and we show how the principles of the biochemical calculus instantiated for port graphs are expressive enough for modeling autonomous systems and biochemical networks. In addition, strategic rewriting techniques open the way to reason about the computations and to verify properties of the modeled systems
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https://hal.univ-lorraine.fr/tel-01748694
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Oana-Maria Andrei. Un calcul de réécriture de graphes : applications à la biologie et aux systèmes autonomes. Autre [cs.OH]. Institut National Polytechnique de Lorraine, 2008. Français. ⟨NNT : 2008INPL058N⟩. ⟨tel-01748694⟩

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