There in a correspondence between the discrete set of complexes and their concentrations, to the phase space of the underlying physical system and its probability density distribution. The complexes in a system correspond to energy equivalence classes of the phase space, or phase “cells” (see [
van Kampen (2007) p. 108]). Whether such a description is appropriate for biological cellular processes is not a simple question to answer. Such processes often involve many actors, with an overflow of chemical detail, and it is not always clear how to divide the phase space into energetically-equivalent “cells”. Many cellular processes are however compartmentalized, macroscopically confined in time and space[
Mitrea et al. (2016)]. We may theorize that these compartments are small enough to present a uniform (well mixed) environment in which chemical reactions occur, so that the complexes are well-defined energetically, but large enough to use the tools of statistical mechanics. We then will assume the localized steady-states are perturbed, e.g. by changing the boundary conditions, followed by return to equilibration. Whether the system reaches equilibrium or a nonequilibrium steady state depends on the properties of the system and the reactions (see
3.3.4. Steady state and equilibrium).