An excursion in reaction systems: From computer science to biology

Corolli, Luca; Maj, Carlo; Marini, Fabrizio; Besozzi, Daniela; Mauri, Giancarlo

doi:10.1016/j.tcs.2012.04.003

Cited by 45 publications

(28 citation statements)

References 17 publications

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“…Although the model of reaction systems was inspired by biology, the research on reaction systems is driven by both biological considerations (see, e.g., [2,3,6,7,10,18,19]) and considerations concerned with the understanding of computations taking place in reaction systems which formalise dynamic processes instigated by the interactions of biochemical reactions in the living cell (see, e.g., [8,11,13,14,16,20,[30][31][32]). As a matter of fact, reaction systems turned out to be an interesting novel model of interactive computation.…”

Section: Introductionmentioning

confidence: 99%

Reaction Systems, Transition Systems, and Equivalences

Kleijn

Koutny

Mikulski

et al. 2018

Adventures Between Lower Bounds and Higher Altitudes

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Reaction systems originated as a formal model for processes inspired by the functioning of the living cell. The underlying idea of this model is that the functioning of the living cell is determined by the interactions of biochemical reactions and these interactions are based on the mechanisms of facilitation and inhibition. Since their inception, reaction systems became a well-investigated novel model of computation. Following this line of research, in this paper we discuss a systematic framework for investigating a whole range of equivalence notions for reaction systems. Some of the equivalences are defined directly on reaction systems while some are defined through transition systems associated with reaction systems. In this way we establish a new bridge between reaction systems and transition systems. In order to define equivalences which capture various ways of interacting with an environment, we also introduce models of the environment which evolve in a finite-state fashion.

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Section: Introductionmentioning

confidence: 99%

Reaction Systems, Transition Systems, and Equivalences

Kleijn

Koutny

Mikulski

et al. 2018

Adventures Between Lower Bounds and Higher Altitudes

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“…In one line of research, the focus has been on investigating their mathematical properties, e.g., functions defined by reaction systems, state sequences, effect of limited resources, cycles and attractors, connections to propositional logic, see, e.g., [4,6,7,15,16]. On the other main line of research, the focus has been on the capabilities of reaction systems as a modeling framework, see, e.g., [1,3]. Within this line of research, there is growing interest in model checking for reaction systems.…”

Section: Introductionmentioning

confidence: 99%

Complexity of model checking for reaction systems

Azimi

Gratie

Ivanov³

et al. 2016

Theoretical Computer Science

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Reaction systems are a new mathematical formalism inspired by the living cell and driven by only two basic mechanisms: facilitation and inhibition. As a modeling framework, they differ from the traditional approaches based on ODEs and CTMCs in two fundamental aspects: their qualitative character and the nonpermanency of resources. In this article we introduce to reaction systems several notions of central interest in biomodeling: mass conservation, invariants, steady states, stationary processes, elementary fluxes, and periodicity. We prove that the decision problems related to these properties span a number of complexity classes from P to NP-and coNP-complete to PSPACE-complete.

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“…As consequence of these facts and the capability of RS to capture the main mechanisms of biochemical reactions, the interest and use of RS to study practical problems concerning biological and/or chemical processes [2,1] has grown since their introduction.…”

Section: Introductionmentioning

confidence: 99%

Complexity of the dynamics of reaction systems

Dennunzio

Formenti

Manzoni

et al. 2019

Information and Computation

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Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena that complements the more traditional approaches, for instance those based on differential equations. A comprehensive list of decision problems about the dynamical behavior of reaction systems (such as cycles and fixed/periodic points, attractors, and reachability) is provided along with the corresponding computational complexity, which ranges from tractable problems to PSPACE-complete problems.$ This paper collects, in a more extended/generalized version, both results presented at CiE 2014 conference [10] and the ones presented at DCFS 2014 conference [9]. It also contains a considerable number of further results.

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An excursion in reaction systems: From computer science to biology

Cited by 45 publications

References 17 publications

Reaction Systems, Transition Systems, and Equivalences

Reaction Systems, Transition Systems, and Equivalences

Complexity of model checking for reaction systems

Complexity of the dynamics of reaction systems

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