Mitsuru Nakata

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This paper first presents basic Petri net components representing molecular interactions and mechanisms of signalling pathways, and introduces a method to construct a Petri net model of a signalling pathway with these components. Then a simulation method of determining the delay time of transitions, by using timed Petri nets - i.e. the time taken in fi ring(More)
The purpose of this paper is to discuss how to model and analyze signaling pathways by using Petri net. Firstly, we propose a modeling method based on Petri net by paying attention to the molecular interactions and mechanisms. Then, we introduce a new notion "activation transduction component" in order to describe an enzymic activation process of reactions(More)
T-invariants represent periodic behaviors of Petri nets and elementary T-invariants represent fundamental periodic behaviors that can’t be divided into smaller ones anymore. To reveal dynamic behaviors of a system modeled by a Petri net, generating elementary T-invariants is indispensable. For a given Petri net, there may have enormous elementary(More)
In this paper we discuss the formulation and the analysis of a signaling pathway by Petri nets. In order to explicitly and formally describe the molecular mechanisms and pathological characteristics of signaling pathways, we propose a new modeling method to construct signaling pathways on the basis of formal representation of Petri net. Our proposed(More)