1,155 research outputs found
Higher-Dimensional Timed Automata
We introduce a new formalism of higher-dimensional timed automata, based on
van Glabbeek's higher-dimensional automata and Alur's timed automata. We prove
that their reachability is PSPACE-complete and can be decided using zone-based
algorithms. We also show how to use tensor products to combat state-space
explosion and how to extend the setting to higher-dimensional hybrid automata
Petri nets for systems and synthetic biology
We give a description of a Petri net-based framework for
modelling and analysing biochemical pathways, which uni¯es the qualita-
tive, stochastic and continuous paradigms. Each perspective adds its con-
tribution to the understanding of the system, thus the three approaches
do not compete, but complement each other. We illustrate our approach
by applying it to an extended model of the three stage cascade, which
forms the core of the ERK signal transduction pathway. Consequently
our focus is on transient behaviour analysis. We demonstrate how quali-
tative descriptions are abstractions over stochastic or continuous descrip-
tions, and show that the stochastic and continuous models approximate
each other. Although our framework is based on Petri nets, it can be
applied more widely to other formalisms which are used to model and
analyse biochemical networks
Analysing oscillatory trends of discrete-state stochastic processes through HASL statistical model checking
The application of formal methods to the analysis of stochastic oscillators
has been at the focus of several research works in recent times. In this paper
we provide insights on the application of an expressive temporal logic
formalism, namely the Hybrid Automata Stochastic Logic (HASL), to that issue.
We show how one can take advantage of the expressive power of the HASL logic to
define and assess relevant characteristics of (stochastic) oscillators
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