Thermal bath, hydrogen bonds

Figure 2. The two relaxational mechanisms in hydrogen bonding. F, fast mode S, slow mode B, bending mode TB, thermal bath.

Proteins, however, must function at biological temperatures, and to be useful, the Davydov soliton must survive at these temperatures. The first difficulty faced by the Davydov/Scott model was the question of the thermal stability of the Davydov soliton. The Davydov/Scott Hamiltonian includes two systems one, the amide I vibration, is treated as a quantum mechanical entity and the second, the vibrations of the peptide groups as a whole (or the changes in the hydrogen bond lengths) are very often treated classically, an approximation that shall be designated here as the mixed quantum-classical approximation. The first simulations of the Davydov/Scott model at finite temperature were performed within the mixed quantum/classical model and coupled the classical part of the system to a classical bath. The result was that the localized excitation dispersed in a few picoseconds at biological temperatures. However, this result clashed with another obtained in Monte... 

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