Simple Reaction Systems and Their Classification

Manzoni, Luca; Poças, Diogo; Porreca, Antonio E.

doi:10.1142/s012905411440005x

Cited by 23 publications

(16 citation statements)

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“…It is also of definite interest to develop the theory without this assumption. This gives rise to many interesting constructions, also concerning stepwise simulation, see [6].…”

Section: Definitions and Earlier Resultsmentioning

confidence: 99%

Two-Step Simulations of Reaction Systems by Minimal Ones

Salomaa¹

2015

Acta Cybern

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Reaction systems were introduced by Ehrenfeucht and Rozenberg with biochemical applications in mind. The model is suitable for the study of subset functions, that is, functions from the set of all subsets of a finite set into itself. In this study the number of resources of a reaction system is essential for questions concerning generative capacity. While all functions (with a couple of trivial exceptions) from the set of subsets of a finite set S into itself can be defined if the number of resources is unrestricted, only a specific subclass of such functions is defined by minimal reaction systems, that is, the number of resources is smallest possible. On the other hand, minimal reaction systems constitute a very elegant model. In this paper we simulate arbitrary reaction systems by minimal ones in two derivation steps. Various techniques for doing this consist of taking names of reactions or names of subsets as elements of the background set. In this way also subset functions not at all definable by reaction systems can be generated. We follow the original definition of reaction systems, where both reactant and inhibitor sets are assumed to be nonempty

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“…It is also of definite interest to develop the theory without this assumption. This gives rise to many interesting constructions, also concerning stepwise simulation, see [6].…”

Section: Definitions and Earlier Resultsmentioning

confidence: 99%

Two-Step Simulations of Reaction Systems by Minimal Ones

Salomaa¹

2015

Acta Cybern

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“…The research on minimal systems is by now rich and broader than what we could cover in this section. Typical research topics in this area are: simulation of state sequences [43]; functions defined by minimal reaction systems [41]; computational complexity of various problems in such systems [40], [25]; normal forms [32]; connections to Boolean lattices [31].…”

Section: Corollary 3 ([13]mentioning

confidence: 99%

Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell

Ehrenfeucht¹,

Petre²,

Rozenberg³

2017

The Role of Theory in Computer Science

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Reaction systems is a model of computation inspired by the functioning of the living cell. It formalizes the interactions between biochemical reactions which form the basic mechanism (the skeleton) underlying this functioning. This paper is a tutorial style introduction to reaction systems-it introduces the basic notions and reviews a number of research directions which are motivated either by biological considerations or by the need of understanding the basic formal processes (computations) underlying the dynamic behavior of reaction systems.

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“…As a arXiv:1904.07445v1 [cs.FL] 15 Apr 2019 computational model, they (and their dynamics) occupy an interesting intermediate position between Boolean Automata Networks [3,4] and Cellular Automata [5,6]. The theoretical exploration is flourishing, with the investigation of combinatorial properties [7,8], complexity of establishing the presence of dynamical behaviours [9,10,11], causal dynamics [12,13,14], and the classification of reaction systems according to the relation of mutual simulability [15]. Reaction systems, however, have also been employed to model real-world systems [16,17].…”

Section: Introductionmentioning

confidence: 99%

The Many Roads to the Simulation of Reaction Systems

Ferretti

Leporati

Manzoni

et al. 2019

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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.

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Simple Reaction Systems and Their Classification

Cited by 23 publications

References 0 publications

Two-Step Simulations of Reaction Systems by Minimal Ones

Two-Step Simulations of Reaction Systems by Minimal Ones

Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell

The Many Roads to the Simulation of Reaction Systems

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