research-article

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

Authors:

D. HermithAuthors Info & Claims

Theoretical Computer Science, Volume 641, Issue C

Pages 25 - 42

https://doi.org/10.1016/j.tcs.2016.03.029

Published: 16 August 2016 Publication History

Abstract

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.

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Cited By

Blaisdell EKanovich MKuznetsov SPimentel EScedrov A(2022)Non-associative, Non-commutative Multi-modal Linear LogicAutomated Reasoning10.1007/978-3-031-10769-6_27(449-467)Online publication date: 8-Aug-2022
https://dl.acm.org/doi/10.1007/978-3-031-10769-6_27
Bernini ABrodo LDegano PFalaschi MHermith D(2018)Process calculi for biological processesNatural Computing: an international journal10.1007/s11047-018-9673-217:2(345-373)Online publication date: 1-Jun-2018
https://dl.acm.org/doi/10.1007/s11047-018-9673-2

Index Terms

A proof theoretic view of spatial and temporal dependencies in biochemical systems
1. Computing methodologies
  1. Symbolic and algebraic manipulation
    1. Symbolic and algebraic algorithms
      1. Theorem proving algorithms
2. Theory of computation
  1. Logic
    1. Proof theory
  2. Models of computation
    1. Computability

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cover image Theoretical Computer Science

Theoretical Computer Science Volume 641, Issue C

August 2016

115 pages

ISSN:0304-3975

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Copyright © Elsevier B.V.

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Elsevier Science Publishers Ltd.

United Kingdom

Publication History

Published: 16 August 2016

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Cited By

Blaisdell EKanovich MKuznetsov SPimentel EScedrov A(2022)Non-associative, Non-commutative Multi-modal Linear LogicAutomated Reasoning10.1007/978-3-031-10769-6_27(449-467)Online publication date: 8-Aug-2022
https://dl.acm.org/doi/10.1007/978-3-031-10769-6_27
Bernini ABrodo LDegano PFalaschi MHermith D(2018)Process calculi for biological processesNatural Computing: an international journal10.1007/s11047-018-9673-217:2(345-373)Online publication date: 1-Jun-2018
https://dl.acm.org/doi/10.1007/s11047-018-9673-2

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