Application of a stochastic name-passing calculus to representation and simulation of molecular processes

We describe a novel application of a stochastic name-passing calculus for the study of biomolecular systems. We specify the structure and dynamics of biochemical networks in a variant. of the stochastic pi -calculus, yielding a model which is mathematically well-defined and biologically faithful. We adapt the operational semantics of the calculus to account for both the time and probability of biochemical reactions, and present a computer implementation of the calculus for biochemical simulations. (C) 2001 Elsevier Science B.V. All rights reserved.