Foundational aspects of multiscale modeling of biological systems with process algebras

AbstractWe propose a variant of the CCS process algebra with new features aiming at allowing multiscale modeling of biological systems. In the usual semantics of process algebras for modeling biological systems actions are instantaneous. When different scale levels of biological systems are considered in a single model, one should take into account that actions at a level may take much more time than actions at a lower level. Moreover, it might happen that while a component is involved in one long lasting high level action, it is involved also in several faster lower level actions. Hence, we propose a process algebra with operations and with a semantics aimed at dealing with these aspects of multiscale modeling. We give both a reduction semantics and an SOS semantics for our new algebra with a result of operational correspondence between the two. Moreover, we study behavioral equivalences for such an algebra and give some examples

Foundational aspects of multiscale modeling of biological systems with process algebras

We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modeling of biological systems. In the usual semantics of process algebras for modeling biological systems actions are instantaneous. When different scale levels of biological systems are considered in a single model, one should take into account that actions at a level may take much more time than actions at a lower level. Moreover, it might happen that while a component is involved in one long lasting high level action, it is involved also in several faster lower level actions. Hence, we propose a process algebra with operations and with a semantics aimed at dealing with these aspects of multiscale modeling. We give both a reduction semantics and an SOS semantics for our new algebra with a result of operational correspondence between the two. Moreover, we study behavioral equivalences for such an algebra and give some examples. \ua9 2011 Elsevier B.V. All rights reserved

Probabilistic Semantics: Metric and Logical Character¨ations for Nondeterministic Probabilistic Processes

In this thesis we focus on processes with nondeterminism and probability in the PTS model, and we propose novel techniques to study their semantics, in terms of both classic behavioral relations and the more recent behavioral metrics. Firstly, we propose a method for decomposing modal formulae in a probabilistic extension of the Hennessy-Milner logic. This decomposition method allows us to derive the compositional properties of probabilistic (bi)simulations. Then, we propose original notions of metrics measuring the disparities in the behavior of processes with respect to (decorated) trace and testing semantics. To capture the differences in the expressive power of the metrics we order them by the relation `makes processes further than'. Thus, we obtain the first spectrum of behavioral metrics on the PTS model. From this spectrum we derive an analogous one for the kernels of the metrics, ordered by the relation `makes strictly less identification than'. Finally, we introduce a novel technique for the logical characterization of both behavioral metrics and their kernels, based on the notions of mimicking formula and distance on formulae. This kind of characterization allows us to obtain the first example of a spectrum of distances on processes obtained directly from logics. Moreover, we show that the kernels of the metrics can be characterized by simply comparing the mimicking formulae of processes