RESUMO
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.
RESUMO
The first study in which stochastic simulations of a two-component molecular machine are performed in the mass-action regime is presented. This system is an autonomous molecular pump consisting of a photoactive axle that creates a directed flow of rings through it by exploiting light energy away from equilibrium. The investigation demonstrates that the pump can operate in two regimes, both experimentally accessible, in which light-driven steps can be rate-determining or not. The number of photons exploited by an individual molecular pump, as well as the precision of cycling and the overall efficiency, critically rely on the operating regime of the machine. This approach provides useful information not only to guide the chemical design of a self-assembling molecular device with desired features, but also to elucidate the effect of the environment on its performance, thus facilitating its experimental investigation.