It doesn't appear to be ab initio simulated (e.g. QED up) if that's what you're asking. They appear to swoop in at higher scales (molecular level) and simulate molecular interactions across "hundreds of molecular species" and "thousands of reactions."

Apparently the interface between molecules uses the Chemical Master Equations (CME) and Reaction-Diffusion Master Equations (RDME) both of which I'm unfamiliar with: http://faculty.scs.illinois.edu/schulten/lm/download/lm23/Us...