Jueves 6/9/2012, 14 hs
Aula Seminario, 2do piso, Pabellón I
Structural biology has played a major role in the way we understand the way protein
operates and work. Still the knowledge of the structure alone offers a limited insight
into the protein dynamics. In this respect molecular dynamics can play a major role in
complementing the experiments and in getting precious dynamical information.
However biomolecules are characterized by complex and rough landscapes and their
functionality relies in a delicate balance between enthalpy and entropy. Accurate
sampling of the phase space is therefore necessary but the limited time scale that is
accessible with modern commercially available computers hampers it. Accelerated
sampling techniques are therefore necessary. Here we discuss metadynamics which
allows efficient sampling and permits an accurate reconstruction of the free energy
landscape. We shall show that phenomena that take place on the time scale of
milliseconds can be accurately sampled and subtle phenomena like allosteric
interaction understood in detail.