A Logic for Constrained Process Calculi with Applications to Molecular Biology

Linear implication can represent state transitions, but real transition systems operate under temporal, stochastic or probabilistic constraints that are not directly representable in ordinary linear logic. We propose a general modal extension of intuitionistic linear logic where logical truth is indexed by constraints and hybrid connectives combine constraint reasoning with logical reasoning. The logic has a focused cut-free sequent calculus that can be used to internalize the rules of particular constrained transition systems; we illustrate this with an adequate encoding of the synchronous stochastic pi-calculus that has been used to encode a number of biochemical reaction systems. We also discuss direct encodings of biochemical reactions in suitable (temporal and stochastic) fragments of the logic.