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A refinement of Cardelli's brane calculus [1] 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)

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)

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