Abstract

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. Joint work with: E. Lai (Cambridge), N. Oury (Edinburgh, CSBE ) and J. Ollivier (Edinburgh, CSBE and McGill)