Tagged-moiety viewpoint of chemical reaction networks.

In this work we consider mass action chemical reaction networks, either closed or open, and focus on the hopping path that a tagged moiety makes from molecule to molecule because of the occurrence of the reactions. We develop the tool for simulating the stochastic paths by means of a Gillespie-like algorithm and provide examples of the master equation counterpart for simple archetype problems of general interest. Both stationary and transient conditions are taken into account. An explanatory case is adopted to illustrate the approach.