The paper presents a new calculus suitable to describe mi-crobiological systems and their evolution. We use the calculus to model interactions among bacteria and bacteriophage viruses, and to reason on their properties.
We introduce a probabilistic algorithm for the simulation of chemical reactions, which can be used as an alternative to the well-established stochastic algorithm proposed by D.T. Gillespie in the '70s. We show that the probabilistic evolution of systems derived by means of our algorithm can be compared to the stochastic time evolution of chemical reactive… (More)
The Calculus of Looping Sequences (CLS) is a calculus suitable to describe biological systems and their evolution. CLS terms are constructed by starting from basic constituents and composing them by means of operators of concatenation, looping, containment and parallel composition. CLS terms can be transformed by applying rewrite rules. We give a labeled… (More)
The paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable to describe microbiological systems, such as cellular pathways, and their evolution. Systems are represented by terms. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping… (More)
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems. The main simplification consists in the removal of the sequencing operator, thus lightening the formal treatment of the… (More)
The calculus of looping sequences is a formalism for describing evolution of biological systems by means of term rewriting rules. We propose to enrich this calculus with type disciplines to guarantee the soundness of reduction rules with respect to interesting biological properties.
We propose an extension of the Applied Pi–calculus by introducing nondeterministic and probabilistic choice operators. The semantics of the resulting model, in which probability and nondetermin-ism are combined, is given by Segala's Probabilistic Automata driven by schedulers which resolve the nondeterministic choice among the probability distributions over… (More)
We are interested in describing timed systems that exhibit probabilistic behaviors. To this purpose, we define a model of probabilistic timed automata and give a concept of weak bisimulation together with an algorithm to decide it. We use this model for describing and analyzing a probabilistic non-repudiation protocol in a timed setting.