Hamiltonian equation atomic reaction systems

The chemical master equation (CME) for a given system invokes the same rate constants as the associated deterministic kinetic model. Yet the CME is more fundamental than the deterministic kinetic view. Just as Schrodinger s equation is the fundamental equation for modeling motions of atomic and subatomic particle systems, the CME is the fundamental equation for reaction systems. Remember that Schrodinger s equation is not a model for a specific mechanical system. Rather, it is a theoretical framework upon which models for particular systems can be developed. In order to write down a model for an atomic system based on Schrodinger s equation, one needs to know how to write down the Hamiltonian a priori. Similarly, the CME is not a model for a specific biochemical reaction system it is a theoretical framework. To determine the CME model for a reaction system, one must know what are the possible elementary reactions and the associated rate constants. 

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