In this paper, we described a novel formalism for computational simulation by modeling the regulatory behavior of muscle thin filaments as an example. By using computer graphics, we can create a ``surrogate reality'' in the sense that (1) each finite automaton in our computational system corresponds to a protein molecule on the thin filament; (2) the location of the finite automaton with respect to other finite automata corresponds to the physical location of the protein molecule with respect to other constituent molecules on the thin filament; (3) the state of a finite automaton in the model represented by a geometric shape corresponds to a certain configuration of a protein molecule on the thin filament; (4) the state transition of a finite automaton in the model represented by a change of its geometric shape corresponds to the configurational change of a protein molecule on the filament; (5) the connection of the finite automaton with its neighbors represented by the contact of the geometric shapes and by the local disturbance caused by the change of shapes corresponds to the physical interactions between the protein molecules on the filament; and (6) the law that we used to describe the computational model, i.e. Eqs. 1 and 2 are in the exactly same form as that we use to describe the behavior of the thin filament in biochemical experiments.
Much experimental and theoretical work has be done on the structure, function and interaction of constituent molecules of muscle. Our model can serve as a efficient knowledge organization scheme in which all type of results can be integrated into a coherent description of the system as a whole. Meanwhile it also provide a powerful tool by which we can explore and test various hypotheses about the unknown aspect of muscle both quantitatively and visually.