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).

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. Hydrodynamics-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

  • Structure-Based Drug Design conference, BIO-IT, 19-21 June 2013, Cambridge, Massachusetts, USA.

  • Conference of the Russian Biophysical society, 3-7 June 2013, Moscow, Russia.
  • Conference of the american chemical society, 8-11 April 2013 New Orleans,USA.

  • Biomolecular Simulation 2013, 25-27 March 2013, Nottingham, UK.

  • G. De Fabritiis, Fragment based drug discovery by simulation, CDDD, computationally driven drug discovery, 4-6 February (2013).

  • G. De Fabritiis, Fragment based drug discovery by simulation, Drug Design 2012, Oxford, UK 26-28 September (2012).

  • G. De Fabritiis, Molecular recognition by simulations, 2nd Aegean Conference on Molecular Recognition, 5-10 June 2012.

  • G. De Fabritiis, Fragment-based drug design using molecular dynamics, 2012 Workshop on Free Energy Methods in Drug Design,May 21-23, Cambridge, Massachusetts, USA.

  • T. Giorgino, I. Buch, G. De Fabritiis, Molecular recognition of SH2-phosphopeptide by molecular dynamics, XI Jornadas de Bioinformática, Barcelona, Spain, 23-25 Jan (2012).

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations,Combining Experimental and Computational Techniques to Study Protein Behavior, Lugano, Swiss, 26-29 Sept 2011.

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, SEQT XVI, Valencia, 18-21 Sept (2011).

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of a protein-ligand binding process by molecular dynamics simulations, Molecular kinetics, Berlin, 4-6 Sept (2011).

  • I. Buch, T. Giorgino, G. De Fabritiis, Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, Frontiers in Protein Research, Lisbon, 4-7 May (2011).

  • M. Harvey, I. Buch, T. Giorgino, G. De Fabritiis, High-throughput molecular dynamics simulations on GPUs using ACEMD, Exploiting New Computer Architectures in Molecular Dynamics Simulations, London UK March 23 2011.

  • I. Buch, T. Giorgino, Gianni De Fabritiis, Reconstructing an enzyme-inhibitor binding process by molecular dynamics simulations, Breakthroughs in Molecular Simulations, Albany 2011, The 17th Conversation, Albany, NY, USA, June 14-18 2011.

  • Gianni De Fabritiis, Towards high-throughput molecular simulations, Exascale Challenges in Computational Biology, 13-15 December, 2010 - Barcelona, Spain.

  • I. Buch, T. Giorgino, G. De Fabritiis, Energetics, kinetics and binding pathway reconstruction for enzyme-inhibitor complex from high-throughput molecular dynamics simulations, Prize-awarded presentation // UK Young Modellers Forum 2010, London (UK), 10th December 2010.

  • Gianni De Fabritiis, Workshop on parallel applications in HPC, Zaragoza, Spain, 30th November 2010,

  • Toni Giorgino, M. D'Abramo, F. Gervasio, G. De Fabritiis. Exploring the kinetics of drug binding to the hERG channel through large-scale simulations, VPH2010, Bruxelles, Belgium, 30th September-1st October, 2010.

  • I. Buch, T. Giorgino, G. De Fabritiis, Energetics, kinetics and binding pathway reconstruction for enzyme-inhibitor complex from high-throughput molecular dynamics simulations // IV Meeting on High Performance Computing in Molecular Simulations, Madrid (Spain), 30th September-1st October 2010.

  • Gianni De Fabritiis, High-throughput molecular dynamics simulations using ACEMD on GPUs, Bio-molecular Simulations Workshop on Future Computing Architectures, Oak Ridge National Laboratory, Oak Ridge, USA, 16-17th September 2010.

  • 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

  • HPC-EUROPA2
  • 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
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