30/10/2013

Thesis defence of Nils Jan Daniel Drechsel: “Development of a multiscale protocol for the study of energetic of protein dynamics”

On October 31st, Nils Jan Daniel Drechsel, member of the Computational Biochemistry group of GRIB (IMIM-UPF) will defend his thesis at 10.00 at the PRBB Seminar´s room 473.10. You are all invited to this event.

Abstract:

Multiscale Molecular Dynamics is a popular trend in the field of computational chemistry and physics. Coarse-grained force-fields have been around for years, and used independently, but used cooperatively with all-atom force-fields combines their advantages and cancels their disadvantages. This seems to be the case, however, only when they are both compatible. In this thesis, a Multiscale Molecular Dynamics Protocol is introduced, based on earlier work by Benjamin Messer, Z. Fan, Arieh Warshel, and in other parts by Christopher Fennel and Ken Dill. The protocol consists of the following tool-set:

• A parametrization machinery that created a new coarse-grained force-field named AmberCG.
• A multiscale thermodynamic cycle utilized within a free energy perturbation context to cooperatively use the best of coarse-grained and all-atom force-fields.

• A collective variable that performs a linearization of the phase space to improve separation of product and reactant states.
• A new algorithm to calculate functional quantities on spheres bounded by complicated solvent accessible surface areas - which as a special case calculates the amount of solvent accessible surface area.
• A novel algorithm based on simple one dimensional Depth-Buffers, to identify atoms which actively form the boundary of the solvent accessible surface areas.