Energy as Syntax - an attempt at a thermodynamical framework for combinatorial molecular networks.
Rule-based approaches (as in our own Kappa, or BNGL, or many other propositions allowing the consideration of "reaction classes") offer some means to capture combinatorial molecular interactions. This is trying to fill a need that seems ever more pressing - as molecular biology uncovers more amazing combinational structures. Here, we propose to pair these approaches with the use of a class of local energy functionals to guarantee their thermodynamical correctness. In so doing we get a more physically realistic, less parameter-hungry, and more structured approach to the modeling/programming of combinatorial molecular networks.
The formalism we present is related to Saiz and Vilar's energy-based description of macro-molecular assemblies (“Stochastic dynamics of macromolecular-assembly networks”, Mol Syst Biol - 2006); it is also related and eminently inspired by Julien Ollivier’s ANC - a general allosteric language for protein networks.