INVESTIGADORES
MILLÁN RaÚl Daniel
congresos y reuniones científicas
Título:
Nonlinear dimensionality reduction for accelerated molecular dynamics calculations
Autor/es:
BEHROOZ HASHEMIAN; DANIEL MILLÁN; CARLOS BRAGA; MARINO ARROYO
Lugar:
Barcelona
Reunión:
Simposio; IRB Barcelona PhD Student Symposium; 2011
Institución organizadora:
Institute for Research in Biomedicine
Resumen:
Free energy is the central thermodynamic function in biological systems as it provides the relevant
thermodynamic forces that drive structural processes for biomacromolecules. Molecular Dynamics (MD)
simulations allow the calculation of these properties in a potentially precise manner. Notwithstanding,
extracting such thermodynamic information from a MD simulation is often a very challenging process
described by the presence of a large configuration space with many metastable basins. A spate of
methods has been proposed to overcome this difficulty either by enhancing the sampling of the phase space, or by focusing instead on the transition paths between specific conformations. A family of
successful methods relies on a judicious identification of the reaction coordinates along which the chemical
transformation takes place, and applies an appropriate bias along them to overcome the energy barriers.
The unambiguous identification of the relevant reaction coordinates for a given chemical process is often
not immediately apparent. We propose a method that automatically identifies low dimensional nonlinear
reaction co-ordinates on the basis of MD trajectories or other ensembles characterizing the large deviation
flexibility of the molecule. These data-driven (as opposed to insight-driven) reaction coordinates provide
a mechanistic description of the conformational transitions, and are the basis of accelerated MD.