Cruzeiro, Leonor2017-04-072017-04-072016-050942-9352http://hdl.handle.net/10400.1/9502This work started as a (biased) review of the state of the art of the Davydov/Scott model for energy transfer in proteins via the propagation of amide I excitations and of how this initial quantum stage may lead to protein conformational changes. It is not a traditional review because certain results reported in the literature have been complemented by extra simulations which revealed, for instance, a new class of possible states for the amide I excitation, here designated as double discrete breathers. The issue of the thermal stability of the Davydov soliton is discussed, as well as the deeper question of how to simulate the non-equilibrium regime of a mixed quantum-classical system at finite temperature. While an exact answer to the latter question is not yet available, a specific formalism that is able to reproduce the correct canonical ensemble is described. Finally, the question of how a quantum amide I excitation can generate of the specific protein conformational changes known to be associated with function is also explored. Indeed, computer simulations indicate that a local action can lead to reproducible conformational changes. The paper ends with a discussion of some of the open questions that plague/stimulate this field and with a suggestion for an experiment to test the basic assumption of the Davydov/Scott model.engjournal article10.1515/zpch-2015-0714