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1
Content available remote Reaction Systems and Enabling Equivalence
Kleijn Jetty, Koutny Maciej, Mikulski Łukasz
Fundamenta Informaticae
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2020
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Vol. 171, nr 1-4
261--277
EN
Reaction systems were introduced in order to provide an abstract model for the study of the biochemical processes that take place in the living cell. Processes of this kind are the result of the interactions between reactions and may be influenced by the environment. Thus, reaction systems can be considered as a model of (interactive) computation. In previous works, various equivalences defined directly on reaction systems and processes had been proposed and compared. These equivalences were all based on functional equivalence that compares a system’s behaviour at every stage of its execution. In this paper, in contrast, we investigate enabling equivalence which focuses on the system behaviour only in specific stages of its evolution, namely those where all of its reactions are active. We discuss the effect of such an approach and, in particular, its relationship to a transition system representation of the system’s behaviour.
2
Content available remote Linking Reaction Systems with Rough Sets
Dutta Soma, Rozenberg Grzegorz, Jankowski Andrzej, Skowron Andrzej
Fundamenta Informaticae
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2019
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Vol. 165, nr 3-4
283--302
EN
Reaction system is a model of interactive computations which was motivated by the functioning of the living cell. It is an idealized mathematical model, also because it abstracts from the complex nature of the physical systems where only partial, incomplete information is available (e.g., about their states). The framework of rough sets was developed to deal with such incomplete information. In this paper we establish a connection between reaction systems and rough sets. This is done in a somewhat broader perspective of the relationship between “pure” mathematical models and “realistic models” that take into account the limitation of perceiving physical reality.
3
Content available remote Verification of Linear-Time Temporal Properties for Reaction Systems with Discrete Concentrations
Męski A., Koutny M., Penczek W.
Fundamenta Informaticae
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2017
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Vol. 154, nr 1/4
289--306
EN
Reaction systems are a formal model for computational processes inspired by the functioning of the living cell. This paper introduces reaction systems with discrete concentrations, which are an extension of reaction systems allowing for quantitative modelling. We demonstrate that although reaction systems with discrete concentrations are semantically equivalent to the original qualitative reaction systems, they provide much more succinct representations in terms of the number of entities being used. We define a variant of Linear Time Temporal Logic interpreted over models of reaction systems with discrete concentrations. We provide its suitable encoding in SMT, together with bounded model checking, and present experimental results demonstrating the scalability of the verification method for reaction systems with discrete concentrations.
4
Content available remote Efficient Simulation of Reaction Systems on Graphics Processing Units
Nobile M. S., Porreca A. E., Spolaor S., Manzoni L., Cazzaniga P., Mauri G., Besozzi D.
Fundamenta Informaticae
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2017
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Vol. 154, nr 1/4
307--321
EN
Reaction systems represent a theoretical framework based on the regulation mechanisms of facilitation and inhibition of biochemical reactions. The dynamic process defined by a reaction system is typically derived by hand, starting from the set of reactions and a given context sequence. However, this procedure may be error-prone and time-consuming, especially when the size of the reaction system increases. Here we present HERESY, a simulator of reaction systems accelerated on Graphics Processing Units (GPUs). HERESY is based on a fine-grained parallelization strategy, whereby all reactions are simultaneously executed on the GPU, therefore reducing the overall running time of the simulation. HERESY is particularly advantageous for the simulation of large-scale reaction systems, consisting of hundreds or thousands of reactions. By considering as test case some reaction systems with an increasing number of reactions and entities, as well as an increasing number of entities per reaction, we show that HERESY allows up to 29× speed-up with respect to a CPU-based simulator of reaction systems. Finally, we provide some directions for the optimization of HERESY, considering minimal reaction systems in normal form.
5
Content available remote Bridging Membrane and Reaction Systems : Further Results and Research Topics
Păun G., Pérez-Jiménez M.J., Rozenberg G.
Fundamenta Informaticae
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2013
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Vol. 127, nr 1-4
99--114
EN
This paper continues an investigation into bridging two research areas concerned with natural computing: membrane computing and reaction systems. More specifically, the paper considers a transfer of two assumptions/axioms of reaction systems, non-permanency and the threshold assumption, into the framework of membrane computing. It is proved that: (1) spiking neural P systems with non-permanency of spikes assumption characterize the semilinear sets of numbers, and (2) symport/antiport P systems with threshold assumption (translated as ω multiplicity of objects) can solve SAT in polynomial time. Also, several open research problems are stated.
6
Content available remote Właściwości fizykochemiczne kompozytów TiO2/SiO2 otrzymanych w wyniku nukleacji układu reakcyjnego
Siwińska-Stefańska K., Paukszta D., Jesionowski T.
Przemysł Chemiczny
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2011
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T. 90, nr 5
1009-1019
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