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

The behavior 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...

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Principais autores:	Vega, Carlos Alberto Olarte, Chiarugi, Davide, Hermith, Diana, Falaschi, Moreno
Formato:	article
Idioma:	English
Publicado em:	Elsevier
Assuntos:	Biochemical systems Linear logic Spatial Temporal modalities
Endereço do item:	https://repositorio.ufrn.br/jspui/handle/123456789/29759 https://doi.org/10.1016/j.tcs.2016.03.029
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spelling	ri-123456789-297592020-08-02T07:54:43Z A proof theoretic view of spatial and temporal dependencies in biochemical systems Vega, Carlos Alberto Olarte Chiarugi, Davide Hermith, Diana Falaschi, Moreno Biochemical systems Linear logic Spatial Temporal modalities The behavior 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 have a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system 2020-07-30T18:56:10Z 2020-07-30T18:56:10Z 2016 article OLARTE, C.; CHIARUGI, D.; FALASCHI, M.; HERMITH, D.. A proof theoretic view of spatial and temporal dependencies in biochemical systems. Theoretical Computer Science, [S.L.], v. 641, p. 25-42, ago. 2016. Disponível em: https://www.sciencedirect.com/science/article/pii/S0304397516300184?via%3Dihub. Acesso em: 29 jul. 2020. http://dx.doi.org/10.1016/j.tcs.2016.03.029 0304-3975 https://repositorio.ufrn.br/jspui/handle/123456789/29759 https://doi.org/10.1016/j.tcs.2016.03.029 en application/pdf Elsevier
institution	Repositório Institucional
collection	RI - UFRN
language	English
topic	Biochemical systems Linear logic Spatial Temporal modalities
spellingShingle	Biochemical systems Linear logic Spatial Temporal modalities Vega, Carlos Alberto Olarte Chiarugi, Davide Hermith, Diana Falaschi, Moreno A proof theoretic view of spatial and temporal dependencies in biochemical systems
description	The behavior 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 have a strong level of adequacy. Hence, derivations in SELL follow exactly the behavior of the modeled system
format	article
author	Vega, Carlos Alberto Olarte Chiarugi, Davide Hermith, Diana Falaschi, Moreno
author_facet	Vega, Carlos Alberto Olarte Chiarugi, Davide Hermith, Diana Falaschi, Moreno
author_sort	Vega, Carlos Alberto Olarte
title	A proof theoretic view of spatial and temporal dependencies in biochemical systems
title_short	A proof theoretic view of spatial and temporal dependencies in biochemical systems
title_full	A proof theoretic view of spatial and temporal dependencies in biochemical systems
title_fullStr	A proof theoretic view of spatial and temporal dependencies in biochemical systems
title_full_unstemmed	A proof theoretic view of spatial and temporal dependencies in biochemical systems
title_sort	proof theoretic view of spatial and temporal dependencies in biochemical systems
publisher	Elsevier
publishDate	2020
url	https://repositorio.ufrn.br/jspui/handle/123456789/29759 https://doi.org/10.1016/j.tcs.2016.03.029
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A proof theoretic view of spatial and temporal dependencies in biochemical systems

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