Molecular Modeling: Mapping Biochemical State Space
At this point in our journey we should generally agree about the central element of biophysical chemical study: The important biological observables of function and action in a biological state space are a direct consequence of the coordinate structure of the physical elements (mass, energy, and forces) of biomolecules. We have used this concept to construct potential energy surfaces that connect the position of the physical elements in space with a measurable interaction (i.e., force or energy). How this helps us with our interest in function is as follows: The observed function of a system is simply its perceived interaction with elements within the system and with the observer (whether strongly or weakly coupled to the system). All interactions require energy. If no force or action is exerted between elements of a system, the system can have no function. Furthermore, if no force is exerted by the system on the observer, it is impossible to assign function to the system.
KeywordsForce Field Harmonic Function Molecular Modeling Potential Energy Surface Empirical Method
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