In the preceding chapter, we have derived the generalized Langevin equations that describe the structural fluctuation of a biomolecule and the density fluctuation of water, which are coupled together. The most essential finding in the theory is that the free energy surface to produce the restoring force is quadratic with respect to the structural fluctuation or the displacement, which indicates that the structural fluctuation of a biomolecule in water is harmonic, and that the probability distribution of the fluctuation is Gaussian. It is a common strategy in the theoretical physics and chemistry to apply the harmonic analysis to such a process that is taking place on a quadratic surface. By performing the harmonic analysis, or solving an eigen value problem, one may decompose a multi-dimensional free-energy-surface into independent quadratic surfaces with different curvatures, which are hierarchically ordered.