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1

The Many Roads to the Simulation of Reaction Systems

Ferretti Claudio, Leporati Alberto, Manzoni Luca, Porreca Antonio E.

Fundamenta Informaticae

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2020

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Vol. 171, nr 1-4

175--188

EN

Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool for biochemical systems, but in order to be able to employ them effectively in the field the presence of efficient and widely available simulators is essential. Here we explore three different algorithms and implementations of the simulation, comparing them to the current state of the art. We also show that we can obtain performances comparable to GPU-based simulations on real-world systems by using a carefully tuned CPU-based simulator.

2

Reaction systems with precipitation

Rogalski M.

Journal of Theoretical and Applied Computer Science

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2015

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Vol. 9, nr 4

26--34

EN

This article proposes expanding Reaction Systems of Ehrenfeucht and Rozenberg by incorporating precipitation reactions into it. This improves the computing power of Reaction Systems by allowing us to implement a stack. This addition enables us to implement a Deterministic Pushdown Automaton.

3

Model Checking Temporal Properties of Reaction Systems

Męski A., Penczek W., Rozenberg G.

Prace Instytutu Podstaw Informatyki Polskiej Akademii Nauk

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2014

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Nr 1028

1--28

EN

This paper defines a temporal logic for reaction systems (RSTL). The logic is interpreted over the models for the context restricted reaction systems that generalize standard reaction systems by controlling context sequences. Moreover, a translation from the context restricted reaction systems into boolean functions is defined in order to be used for a symbolic model checking for RSTL over these systems. Finally, model checking for RSTL is proved to be PSPACE-complete.

PL

Praca wprowadza logikę temporalną dla systemów reakcyjnych (RSTL), która jest interpretowana w modelach dla systemów reakcyjnych z ograniczeniami kontekstów. Systemy te uogólniają standardowe systemy reakcyjne przez wprowadzenie ograniczeń kontrolujących dopuszczalne konteksty. Ponadto, przedstawiono translację z systemów reakcyjnych z ograniczeniami kontekstów do formuł boolowskich, która umożliwia symboliczną weryfikację modelową dla tych systemów oraz RSTL. Wykazano również, że problem weryfikacji modelowej dla RSTL jest problemem PSPACE-zupełnym.

4

Reaction System Models for the Heat Shock Response

Azimi S., Iancu B., Petre I.

Fundamenta Informaticae

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2014

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Vol. 131, nr 3-4

299--312

EN

Reaction systems are a formal framework for modeling processes driven by biochemical reactions. They are based on the mechanisms of facilitation and inhibition. A main assumption is that if a resource is available, then it is present in sufficient amounts and as such, several reactions using the same resource will not compete concurrently against each other; this makes reaction systems very different as a modeling framework than traditional frameworks such as ODEs or continuous time Markov chains. We demonstrate in this paper that reaction systems are rich enough to capture the essential characteristics of ODE-based models. We construct a reaction system model for the heat shock response in such a way that its qualitative behavior correlates well with the quantitative behavior of the corresponding ODE model. We construct our reaction system model based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We conclude with a discussion on the expressivity of reaction systems as compared to that of ODE-based models.

5

Membrane Systems with Qualitative Evolution Rules

Kleijn J., Koutny M.

Fundamenta Informaticae

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2011

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Vol. 110, nr 1-4

217-230

EN

In membrane systems, biochemical reactions taking place in the compartments of a cell are abstracted to evolution rules that specify which and how many objects are consumed and produced. The recently proposed reaction systems also investigate processes carried by biochemical reactions, but the resulting computational model is remarkably different. A key difference is that in reaction systems, biochemical reactions are modeled using a qualitative rather than a quantitative approach. In this paper, we introduce so-called set membrane systems, a variant of membrane systems with qualitative evolution rules inspired by reaction systems. We then relate set membrane systems to Petri nets which leads to a new class of Petri nets: set-nets with localities. This Petri net model provides a faithful match with the operational semantics of set membrane systems.

6

Reaction Systems

Ehrenfeucht A., Rozenberg G.

Fundamenta Informaticae

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2007

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Vol. 75, nr 1-4

263-280

EN

Interactions between biochemical reactions lie at the heart of functioning of a living cell. In order to formalize these interactions we introduce reaction systems. We motivate them by explicitely stating a number of assumptions/axioms that (we believe) hold for a great number of biochemical reactions - we point out that these assumptions are very different from the ones underlying traditional models of computation. The paper provides the basic definitions, illustrates them by biology and computer science oriented examples, relates reaction systems to some traditional models of computation, and proves some basic properties of reaction systems.