THe invention is the development of a simulation capability that allows the prediction of concentrations of chemical species, rates, and energy requirements of systems of coupled reactions that does not require the use of rate constants. The technology, often refered to as simulations of state or state simulations, is based on the concept of simulation states (outcomes of reactions) rather than reactions themselves. This approach has been widely used to model equilibrium states. We are adopting it to model non-equilibrium states. This technology is particularly attractive for the domain of biology because the determination of rate parameters for a simulation (rate constants) is incredibly difficult. Other approaches, specifically flux-based approaches, have limited predictive power and are actually more apporpriately described as high-end data analysis methods.