Publications

**I. Buch, K. Sadiq and G. De Fabritiis, Optimized potential of mean force calculations of standard binding free energy, in press J. Chem. Theory Comput. (2011). pdf

T. Giorgino and G. De Fabritiis, A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, in press J. Chem. Theory Comput. (2011). pdf

***I. Buch, T. Giorgino and G. De Fabritiis,Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations, in press PNAS (2011). pdf

M. J. Harvey and G. De Fabritiis, Swan: A tool for porting CUDA programs to OpenCL, Comp. Phys. Commun. 182, 1093 (2010). pdf

*** J. Selent, F. Sanz, M. Pastor and G. De Fabritiis, Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors, PLOS Computational Biology, 6, e1000884 (2010) pdf.

K. Sadiq and G. De Fabritiis,Explicit solvent dynamics and energetics of HIV-1 protease flap-opening and closing, Proteins 78, 2873 (2010) pdf.

J Cooper,F Cervenansky, G De Fabritiis, J Fenner, D Friboulet, T Giorgino, S Manos, Y Martelli, J Villa-Freixa, S Zasada, S Lloyd, K Mccormack and P V Coveney, The Virtual Physiological Human Toolkit, Phil. Trans. R. Soc. A 368(1925) 3925-3936 (2010).pdf

**T. Giorgino, M. J. Harvey and G. De Fabritiis, Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations, Comp. Phys. Commun. 181, 1402 (2010).pdf

**I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis, High-throughput all-atom molecular dynamics simulations using distributed computing, J. Chem. Inf. and Mod. 50, 397 (2010). pdf

A. Lopez Garcıa de Lomana, Q. K. Beg, G. De Fabritiis and J. Villa-Freixa, Global Connectivity and Activity Distributions in Cellular Networks, J. Comp. Bio. 17(7), 869 (2010). pdf

** M. J. Harvey and G. De Fabritiis, An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware, J. Chem. Theory Comput., 5, 2371–2377 (2009).pdf

*** M. Harvey, G. Giupponi and G. De Fabritiis, ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale, J. Chem. Theory and Comput. 5, 1632 (2009). pdf

** F. X. Guix, G. Ill-Raga, R. Bravo, T. Nakaya, G. De Fabritiis, M. Coma, G. P. Miscione, J. Villà-Freixa, T. Suzuki, X. Fernàndez-Busquets, M. A. Valverde, B. de Strooper and F. J. Muñoz, Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation, Brain 132, 1335 (2009).pdf

Notes:
Andrea Rinaldi. Science wikinomics. Mass networking through the web creates new forms of scientific collaboration, EMBO reports 10, 5, 439–443 (2009) doi:10.1038/embor.2009.79

Play me a molecule, Science 12 September 2008, Vol. 321. no. 5895, p. 14251

*** G. Giupponi, M. Harvey and G. De Fabritiis, The impact of accelerator processors for high-throughput molecular modeling and simulation, Drug Discovery Today 13, 1052 (2008). pdf or journal link

M. Harvey, G. De Fabritiis and G. Giupponi, Accuracy of the Lattice Boltzmann method on the Cell processor, Phys. Rev. E 78, 056702 (2008). pdf (http://www.multiscalelab.org/CellLB)

*** G. De Fabritiis, S. Geroult, P. V. Coveney and G. Waksman, Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain, 72, 1290 Proteins (2008). journal link

R. Delgado-Buscalioni, P. V. Coveney and G. De Fabritiis Towards multiscale modelling of complex liquids, Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science, 222, 769 (2008). pdf

** G. De Fabritiis, P. V. Coveney and J. Villa-Freixa, Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics, 73, 184 Proteins (2008).pdf

** STEP Consortium. Seeding the Euro Physiome: A Roadmap to the Virtual Physiological Human. [Online] 5 July 2007, editor and expert.pdf

R. Delgado-Buscalioni and G. De Fabritiis, Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids, Phys. Rev. E 76, 036709 (2007).pdf

** M. Harvey, G. Giupponi, J. Villa-Freixa and G. De Fabritiis, PS3GRID.NET: Building a distributed supercomputer using the Playstation 3, Distributed & Grid Computing – Science Made Transparent for Everyone. Principles, Applications and Supporting Communities (2007).pdf

G. Giupponi, G. De Fabritiis and P. V. Coveney, Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules , J. Chem. Phys. 126, 154903 (2007). pdf

*** G. De Fabritiis, Performance of the Cell processor for biomolecular simulations, Comp. Phys. Commun. 176, 670 (2007).pdf

G. De Fabritiis and J. Villa-Freixa and P. V. Coveney, Multiscale modelling of permeation through membrane channels using pregenerated molecular dynamics trajectories , Int. J. Mod. Phys. C, 18, 511 (2007).pdf

G. Giupponi, G. De Fabritiis and P. V. Coveney, A coupled molecular-continuum hybrid model for the simulation of macromolecular dynamics, Int. J. Mod. Phys. C, 18, 520 (2007).pdf

** G. De Fabritiis, M. Serrano, R. Delgado-Buscalioni and P. V. Coveney, Fluctuating hydrodynamic modelling of fluids at the nanoscale, Phys. Rev. E 75, 026307 (2007).pdf

S. Lloyd, D. Gavaghan, A. Simpson, M. Mascord, C. Seneurine, G. Williams, J. Pitt-Francis, D. Boyd, D. M. Randal, L. Sastry, S. Nagella, K. Weeks, R. Fowler,D. Hanlon, J. Handley, G. De Fabritiis, Integrative Biology: The Challenges of Developing a Collaborative Research Environment for Heart and Cancer Modelling, Future Generation Computer Systems, 23, 457-465 (2007)

*** G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, Multiscale Modeling of Liquids with Molecular Specificity, Phys. Rev. Lett. 97, 134501 (2006). pdf

P. V. Coveney, G. De Fabritiis, M. Harvey, S. Pickles and A. Porter, Coupling applications on distributed resources, Comp. Phys. Commun. 175, 389 (2006). pdf

M. Serrano, G. De Fabritiis, P. Espanol and P. V. Coveney, A stochastic Trotter integration scheme for dissipative particle dynamics, Math. Comput. Simul. 72, 190 (2006).pdf

** G. De Fabritiis, M. Serrano, P. Espanol and P. V. Coveney, Efficient numerical integrators for stochastic models, Physica A 361, 429 (2006). pdf

P. V. Coveney, G. De Fabritiis, M. Harvey, S. Pickles and A. Porter, On steering coupled models, proceeding’s of UK e-science AHM2005, (2005).pdf

R. Delgado-Buscalioni, G. De Fabritiis, P. V. Coveney, Determination of the chemical potential using energy biased sampling, J. Chem. Phys. 123, 054105 (2005).pdf

** G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, Energy controlled insertion of polar molecules in dense fluids, J. Chem. Phys. 121, 12139 (2004). Selected for the Virtual Journal of Biological Physics Research, December 15, 2004 Volume 8, Issue 12.pdf

*** G. De Fabritiis, F. Pammolli and M. Riccaboni, On size and growth of business firms, Physica A 324, 38-44 (2003). pdf

** G. De Fabritiis and P. V. Coveney, Dynamical geometry for multiscale dissipative particle dynamics, Computer Physics Communications, 153(2), 209-226 (2003). pdf

M. Serrano, G. De Fabritiis, P. Espanol, E. G. Flekkøy and P. V. Coveney, Mesoscopic dynamics of Voronoi fluid particles, J. Phys. A: Math. Gen. 35, 1605 (2002); pdf

G. De Fabritiis, P. V. Coveney and E.G. Flekkøy, Multiscale dissipative particle dynamics, Phil. Trans. R. Soc. Lond. A 360, 317 (2002). pdf

G. De Fabritiis, S. Succi and P. V. Coveney, Electronic structure calculations using Voronoi multiscale basis functions, J. Stat. Phys. 107, 159 (2002). pdf

** E.G. Flekkøy, P.V. Coveney and G. De Fabritiis, Foundations of Dissipative Particle Dynamics, Phys. Rev. E 62, 2140 (2000). pdf

R.Gorenflo, G. De Fabritiis and F. Mainardi, Discrete random walk models for symmetric Levy-Feller diffusion processes, Physica A 269, 79-89 (1999). pdf

G. De Fabritiis, A. Mancini, D. Mansutti and S. Succi, Mesoscopic models of liquid/solid phase transitions, Int. J. Mod. Phys. C 9, 1405-1415 (1998). pdf

P.V.Coveney, G. De Fabritiis, E.G. Flekkøy and J. Christopher, From Molecular Dynamics to Dissipative Particle Dynamics, SIMU newsletter, 1, 73-98 (2000).

G. De Fabritiis, P.V. Coveney and E.G. Flekkøy, Multiscale modelling of complex fluids, Proceedings of 5th European SGI/Cray MPP Workshop, Bologna, Italy (1999).

G. Bellanca, P. bassi, G. Erbacci, G. De Fabritiis and R. Roccari, Bringing home HPCN: implementation of a FD-TD code for microwave ovens design on a PC cluster, 7th Inter. Conf. on Microwave and High Frequency heating, Valencia, Spain (1999).

G.Bellanca, P.Bassi, G.Erbacci, G. De Fabritiis and R.Roccari, Supercomputer optimized micro-wave domestic oven design via FD-TD, Proceedings of VEC-PAR98 Porto, Portugal (1998).

G. De Fabritiis, Stochastic dynamics of mesoscopic fluids, Ph.D. thesis (2002).
G. De Fabritiis, Cellular Automata in Fluid Dynamics, tesi di laurea (in Italian) 1997.