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Lookup NU author(s): Artur Meski, Professor Maciej KoutnyORCiD, Dr Lukasz Mikulski
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
Reaction systems are a formal model for computational processing in which reactions operate on sets of entities (molecules) providing a framework for dealing with qualitative aspects of biochemical systems.This paper is concerned with reaction systems in which entities can have discrete concentrations, and so reactions operate on multisets rather than sets of entities.The resulting framework allows one to deal with quantitative aspects of reaction systems, and a bespoke linear-time temporal logicallows one to express and verify a wide range of key behavioural system properties.In practical applications, a reaction system with discrete concentrationsmay only be partially specified, and the possibility of an effective automated calculation of the missing details provides an attractive design approach.With this idea in mind, the current paper discusses parametric reaction systems withparameters representing unknown parts of hypothetical reactions.The main result is a method aimed at replacing the parameters in such a way thatthe resulting reaction system operating in a specified external environment satisfies a given temporal logic formula.This paper provides an encoding of parametric reaction systems in SMT, and outlines a synthesis procedure based on bounded model checking for solving the synthesis problem.It also reports on the initial experimental results demonstrating the feasibility of thenovel synthesis method.
Author(s): Meski A, Koutny M, Mikulski L, Penczek W
Publication type: Article
Publication status: Published
Journal: Natural Computing
Year: 2024
Volume: 23
Pages: 323-343
Online publication date: 24/07/2024
Acceptance date: 18/04/2024
Date deposited: 19/04/2024
ISSN (print): 1567-7818
ISSN (electronic): 1572-9796
Publisher: Springer Dordrecht
URL: https://doi.org/10.21203/rs.3.rs-3592339/v1
DOI: 10.21203/rs.3.rs-3592339/v1
Data Access Statement: Our experimental results can be reproduced by cloning the repository with ReactICS (https://github.com/arturmeski/reactics/) and running the shell script from the experiments/reaction_mining_mutex directory.
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