Research lines

Our research focuses on mesoscopic computational modeling and simulations mainly of biological systems. We attempt to solve new scientific problems by developing new methodologies, software and ideas for bridging between the atomistic scale (femtoseconds, nanometers) and the biological molecular scale (micro- to milli-seconds and hundreds of nanometers).

Research lines:

  1. Equilibrium energetics of molecular systems and protein interactions. Calculations of energetics for molecular systems is of great importance for understanding and controlling protein functions. We apply several techniques for free energy calculations to the understanding of molecular mechanisms like ion permeation, ion binding, ligand binding and protein aggregation. In particular, we are interested to in-silico high-throughput approaches but maintaining thermodynamic accuracy. For this, we are using our GPUGRID.net infrastructure.

  2. Hydronamics-molecular interaction. Building on our previous research for molecular-hydrodynamics interactions, we are looking at resonance patterns of proteins embedded in a hydrodynamics solvent description and how external sound waves can perturb their equilibrium state.

  3. Accelerated and distributed molecular simulation methods. In order to support our research we developed innovate software solutions (ACEMD,http://multiscalelab.org/acemd) for molecular dynamics on accelerator processors (Cell and GPUs), as well as one of the largest distributed computing project worldwide, GPUGRID.net (http://gpugrid.net). This gives us the computational power to tackle problems substantially beyond the state of the art. In fact, whilst the fundamental thermodynamic framework behind the simulation of macromolecules is well characterized, exploration of biological time scales remains beyond the computational capacity routinely available to many researchers. With ACEMD and GPUGRID our group can be considered at the fore front of computational biophysics and biochemistry.

Communications

Talks

  • Gianni De Fabritiis, Impact of GPUs for molecular dynamics simulations: The case of ACEMD and GPUGRID.net, Programming and Tuning Massively Parallel Systems Summer School (PUMPS), July 5-9, 2010 Barcelona.slides

  • I. Buch, T. Giorgino, G. De Fabritiis,Reliable and accurate prediction of ligand binding by high-throughput molecular dynamics simulations, 1st Prize-awarded presentation // XVIII Jornades de Biologia Molecular, Barcelona (Spain), 29-30th June 2010.

  • J. Selent, F.Sanz, M. Pastor, G. De Fabritiis, Sodium ions toggle the rotamer switch in sodium-sensitive dopaminergic G-protein coupled receptors, 28th Camerino-Cyprus-Noordwijkerhout Symposium, Camerino, May 16-20, 2010

  • I. Buch, T. Giorgino, G. De Fabritiis,High-throughput all-atom molecular dynamics simulations using distributed computing (slides), 1st Prize-awarded presentation // 24th Molecular Modeling Workshop, Erlangen (Germany), 15-16th March 2010.

  • J. Selent, F.Sanz, M. Pastor, G. De Fabritiis,Accelerated molecular dynamics simulations in the microseconds time scale: An application to sodium-sensitive G protein-coupled receptors (slides) // Expanding the frontiers of molecular dynamics simulations in biology, Barcelona (Spain), 23-25th November 2009.

  • T. Giorgino, G. De Fabritiis, Submitting and managing distributed computations: the researcher's interface to a BOINC project (slides) // 5th BOINC Workshop, Barcelona (Spain), 22-23th October 2009.

Posters

  • I. Buch, M. Harvey, T. Giorgino, D. Anderson, G. De Fabritiis, A distributed computing system for high-throughput calculations of free energies of binding using molecular dynamics simulations (poster) // Expanding the frontiers of molecular dynamics simulations in biology, Barcelona (Spain), 23-25th November 2009.

  • I. Buch, M. Harvey, T. Giorgino, D. Anderson, G. De Fabritiis, A distributed computing system for high-throughput calculations of free energies of binding using molecular dynamics simulations (poster) // ISC 2010, Hamburg Germany 30th May-3th June 2010.

Courses

Research gallery

Funding acknowledgments

  • Fundació La Marató de TV3
  • Sony Computer Entertainment Spain
  • Nvidia Corporation
  • Ramon y Cajal program
  • EU research program (Virtual Physiological human)
  • National research plan
  • EU Marie Curie program
Copyright 2008-2009. All rights reserved.