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  A proof theoretic view of spatial and temporal dependencies in biochemical systems

Olarte, C., Chiarugi, D., Falaschi, M., & Hermith, D. (2016). A proof theoretic view of spatial and temporal dependencies in biochemical systems. Theoretical Computer Science, 641, 25-42. doi:10.1016/j.tcs.2016.03.029.

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Olarte, C., Author
Chiarugi, D.1, Author           
Falaschi, M., Author
Hermith, D., Author
Affiliations:
1Angelo Valleriani, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863324              

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Free keywords: Biochemical systems; Linear logic; Spatial and temporal modalities; Verification of P systems
 Abstract: The behaviour of biochemical systems such as metabolic and signaling pathways may depend on either the location of the reactants or on the time needed for a reaction to occur. In this paper we propose a formalism for specifying and verifying properties of biochemical systems that combines, coherently, temporal and spatial modalities. To this aim, we consider a fragment of intuitionistic linear logic with subexponentials (SELL). The subexponential signature allows us to capture the spatial relations among the different components of the system and the timed constraints. We illustrate our approach by specifying some well-known biological systems and verifying properties of them. Moreover, we show that our framework is general enough to give a logic-based semantics to P systems. We show that the proposed logical characterizations has a strong level of adequacy. Hence, derivations in \SELL\ follow exactly the behavior of the modeled system.

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 Dates: 2016-04-042016
 Publication Status: Issued
 Pages: -
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 Rev. Type: -
 Identifiers: DOI: 10.1016/j.tcs.2016.03.029
BibTex Citekey: Olarte2016
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Title: Theoretical Computer Science
Source Genre: Journal
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Publ. Info: Amsterdam : Elsevier
Pages: - Volume / Issue: 641 Sequence Number: - Start / End Page: 25 - 42 Identifier: ISSN: 0304-3975