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A refinement of Cardelli's brane calculus  is introduced where membrane actions are directed. This modification brings the language closer to biological membranes and also obtains a symmetric set of membrane interactions. An associated structural congruence, termed the projective equivalence, is defined and shown to be preserved under all possible system… (More)
In this work we propose a probabilistic extension of the π-calculus. The main novelty is a probabilistic mixed choice operator, that is, a choice construct with a probability distribution on the branches, and where input and output actions can both occur as guards. We develop the operational semantics of this calculus, and then we investigate its… (More)
We develop a process calculus – the nanoκ calculus – for modeling, analyzing and predicting the properties of molecular devices. The nanoκ calculus is equipped with a simple stochastic model, that we use to model and simulate the behaviour of a molecular shuttle, a basic nano device currently used for building more complex systems.
We introduce a calculus handling complexation of molecules and membranes. The approach is based on adding dynamic interfaces to processes, which induce bonds between molecules. The calculus is then extended with a notion of hierarchy to handle membranes. Introduction In biochemistry, proteins and other molecules have a common way of interacting among… (More)
The nanoκ calculus is a formalism for modelling biochemical systems following a reactive-oriented approach. We study the implementation of nanoκ into the Stochastic Pi Machine that complies with the stochastic behaviors of solutions. Our implementation allows us to use nanoκ as a front-end for a process-oriented simulator, thus being intelligible to… (More)
We develop a process calculus – the nanoκ calculus – for modeling, analyzing and predicting the properties of molecular devices. The nanoκ calculus is equipped with a simple stochastic model, that we use to model and simulate the behavior of a molecular shuttle, a basic nano device currently used for building more complex systems.
A formal approach to the modeling, simulation and analysis of nano-devices.