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

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  • Biology
  • Chemistry
  • Linguistics
  • Mathematics
  • Medicine

Abstract

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 P-­calculus, yielding a model which is mathematically well­defined 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.

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