title: Dynamics of a nonconserving Davydov monomer.
abstract: The Davydov-Scott model describes the transfer of energy along hydrogen-bonded chains, like those that stabilize the structure of alpha helices. It is based on the hypothesis that amide I excitations are created (by the hydrolysis of ATP, for instance) and kept in the system. Recent experimental results confirm that the energy associated with amide I excitations does indeed last for tens of picoseconds in proteins and model systems. However, the Davydov-Scott model cannot describe the conversion of that energy into work, because it conserves the number of excitations. With the aim of describing conformational changes, we consider, in this paper, a nonconserving generalization of the model, which is found to describe essentially a contraction of the hydrogen bond adjacent to the site where an excitation is present. Unlike the one-site Davydov-Scott model, that contraction is time dependent because the number of excitations is not conserved. However, considering the time average of the dynamical variables, the results reported here tend to the known results of the Davydov-Scott model.
authors.affiliation: CCMAR and FCT, University of Algarve, Campus de Gambelas, 8000 Faro, Portugal.
authors.forename: P A S
authors.initials: PA
authors.lastname: Silva
authors.forename: L
authors.initials: L
authors.lastname: Cruzeiro
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry*; D000577:Amides / Q000737:chemistry*; D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D013816:Thermodynamics
chemical_list: D000577:Amides; D000255:Adenosine Triphosphate