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Address:
Computational Biochemistry and Biophysics Lab (GRIB), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Dr. Aiguader 88, 08003, Barcelona, Spain.
e m a i l:
- gianni.defabritiis at upf.edu
Profile:
I am currently a Ramon y Cajal scientist at Universitat Pompeu Fabra (UPF) based at the Computational Biochemistry and Biophysics Laboratory in the Research Unit on Biomedical Informatics (GRIB) and teacher at two courses at the Master of bioinformatics for health sciences in Barcelona. The laboratory is located within the new Barcelona Biomedical Research Park (PRBB). I am also a co-founder and scientific advisor for a new technology company Acellera focused on the use of the Cell processor and GPGPU for industrial and scientific applications.
Lookup the PS3GRID.NET project which aims at using it for molecular simulations with the help of BOINC and the Cell MD software.
Preprints
Performance of the Cell processor for bio-molecular simulations
The new Cell processor represents a turning point for computing intensive applications. Here, I show that for molecular dynamics it is possible to reach an impressive sustained performance in excess of 30 Gflops with a peak of 45 Gflops for the non-bonded force calculations, well over an order of magnitude faster than a single core standard processor. G. De Fabritiis, Performance of the Cell processor for bio-molecular simulations, preprint (2006). pdf
A general commentary from HPCwire on Commodity Processor Chaos or Convergence? referencing this paper.
Multiscale modelling of liquids with molecular specificity
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the full molecular nature of the system where it is of interest and coarse-graining it elsewhere. This is made possible by coupling molecular dynamics with a mesoscopic description of realistic liquids based on Landau's fluctuating hydrodynamics. We show that our scheme correctly couples hydrodynamics and that fluctuations, at both the molecular and continuum levels, are thermodynamically consistent. Hybrid simulations of sound waves in bulk water and reflected by a lipid monolayer are presented as illustrations of the scheme. G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, Modelling the mesoscale with molecular specificity, Phys. Rev. Lett. 97, 134501 (2006). pdf