Publications

Find below the publications related to projects awarded in the PRACE 1st Regular Call.


Investigating the effects of quantum nuclear motion in an enzyme that employs hydrogen tunnelling

Project leader: Prof. Dr. Dominik Marx (Professor of Chemistry), Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, Germany
Research field: Chemistry and Material Sciences

Publications:

  • This project was featured in the PRACE Scientific Annual Report in 2012: Garlo, Nina (2012, June). “Nature’s subway: Do enzymes use tunnelling to take a shortcut?” PRACE Scientific Annual Report, 13–15.

Theses:

  • Theodros Zelleke, MSc thesis, Computer Simulation of Methylamine Dehydrogenase (February 2011), Theodros Zelleke, PhD (expected 2014)

Invited talks:

  • S.D. Ivanov, Path Integral QM/MM Simulations of Quantum Effects in Proteins, DEISA PRACE Symposium 2011, April 13–14, Helsinki, Finland
  • T Zelleke, Analysis of Reaction Pathways for Deprotonation in Methylamine Dehydrogenase, Mulliken Center for Theoretical Chemistry, Universitaet Bonn, 07.11.2013, Bonn, Germany
  • D. Marx, TBA, “International Supercomputing Conference ISC 2012”, June 17-21, Hamburg, Germany.

Turbulent entrainment due to a plume impinging on a density interface

Project leader: Maarten van Reeuwijk, Dept. Of Civil and Environmental Engineering, Imperial College London
Research field: Engineering and Energy

Publications:

  • VAN REEUWIJK, M, HUNT, G.R. AND JONKER, H.J.J (2011) Direct simulation of turbulent entrainment due to a plume impinging on a density interface, Advances in Turbulence XIII, 4 pages

Talks:

  • 2011: Direct simulation of turbulent entrainment due to a plume impinging on a density interface, 13th European Turbulence Conference, Warsaw, Poland
  • 2012: Direct Simulation of Turbulent entrainment, Imperial College Turbulence Seminars, London UK.
  • 2012: Direct Simulation of Turbulent entrainment,University of Southampton Turbulence seminars, UK.
  • 2012: Symposium on Turbulence, Heat and Mass Transfer, Palermo Italy,

Entrainment Effects in Rough-wall Boundary Layers

Project leader: Javier Jiménez Sendín, Universidad Politécnica de Madrid
Research field: Engineering and Energy

Publications:

  • Guillem Borrell, Juan A. Sillero and Javier Jiménez. “Direct Numerical Simulation of Turbulent Boundary Layers at High Reynolds Numbers in BG/P Supercomputers”. Computers and Fluids. Submitted September 2011

Theses:

  • Guillem Borrell. Entrainment effects in turbulent boundary layers (in progress)

Talks:

  • “Wall bounded turbulence simulation in the BG/P” Scicomp 17. Paris May 12th. Paris FR. 2011 (Borrell)
  • “Direct numerical simulation of turbulent boundary layers at high Reynolds numbers” XXXII ParCFD. May 20th. Barcelona ES. 2011 (Borrell)
  • “Hybrid OpenMP-MPI turbulent boundary layer code over 32k cores” EuroMPI 17. September 18-21. Santorini GR. 2011 (Sillero)
  • “Direct numerical simulation of a high-entrainment turbulent boundary layer” APS Div. Fluid Dynamics meeting November 20-22. Baltimore USA. 2011 (Borrell)

Large scale high resolution blood flow simulations in realistic vessel geometries

Project leader: Federico Toschi, Mesoscopic Transport Phenomena, Department of Applied Physics, TU Eindhoven
Research field: Fundamental Physics

Publications:

  • F. Janoschek, J. Harting, F. ToschiTowards a continuum model for particle-induced velocity fluctuations in suspension flow through a stenosed geometryarXiv:1311.2900 (2013)
  • F. Janoschek, J. Harting, F. ToschiAccurate lubrication corrections for spherical and non-spherical particles in discretized fluid simulationsarXiv:1308.6482 (2013)
  • T. Krüger, S. Frijters, F. Günther, B. Kaoui, J. Harting”Numerical simulations of complex ?uid-?uid interface dynamics”European Physical Journal Special Topics 222, Number 1, 177-198 (2013)
  • B. Kaoui, T. Krüger, J. Harting”How does confinement affect the dynamics of viscous vesicles and red blood cells?”Soft Matter 8, 9246-9252, 2012
  • J. Harting, F. Janoschek, B. Kaoui, T. Krüger, F. Toschi”Simplified models for coarse-grained hemodynamics simulations”3rd European Conference on Microfluidics, submitted, 2012
  • F. Janoschek, F. Toschi, J. Harting. “Simulations of Blood Flow in Plain Cylindrical and Constricted Vessels with Single Cell Resolution”. Macromolecular Theory and Simulations, 20, 7, 562, August 2011
  • F. Günther, F. Janoschek, S. Frijters, J. Harting. “Lattice Boltzmann simulations of anisotropic particles at liquid interfaces” Computers and Fluids 80, 184-189 (2013)
  • D. Groen, O. Henrich, F. Janoschek, P. V. Coveney, J. Harting. “Lattice-Boltzmann Methods in Fluid Dynamics: Turbulence and Complex Colloidal Fluids”. Jülich Blue Gene/P Extreme Scaling Workshop 2011, ed. Bernd Mohr, Wolfgang Frings, FZJJSC-IB-2011-02, 17, April 2011
  • J. Harting, S. Frijters, F. Janoschek, F. Günther. “Coupled Lattice Boltzmann and Molecular Dynamics simulations on massively parallel computers”. Technical Report, Forschungszentrum Juelich, 2011

Talks:

  • “Simplified particulate model for coarse-grained hemodynamics simulations” Lorentz Center Workshop “Multiscale fluid dynamics with the Lattice Boltzmann method”, February 2011, Leiden (The Netherlands)
  • “Simplified particulate model for coarse-grained hemodynamics simulations” DPG Spring Meeting, March 2011, Dresden (Germany)
  • “Large Scale High Resolution Blood Flow Simulations” DEISA/PRACE Symposium, April 2011, Helsinki (Finland)
  • “Simplified particulate model for coarse-grained hemodynamics simulations” TM’s 1st world cardiovascular, diabetes, and obesity online conference, September 2011

Ab initio molecular dynamics study of proton transport in a biological ion channel

Project leader: Prof. Dr. Paolo Carloni, German Research School for Simulations Science, FZ Jülich and RWTH Aachen
Research field: Medicine and Life Sciences

Publications:

  • Dreyer J., C. Zhang, E. Ippoliti, P. Carloni, Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer. Journal of Chemical Theory and Computation 2013. 9(8): p. 3826–3831.

Theses:

  • Chao Zhang, Doctoral Candidate, RWTH Aachen University. Thesis title “Computational studies on ions in biochemical systems”.

Talks:

  • J. Dreyer, 13.10.2011, 1st CAS-HGF Workshop on Supercomputing, Beijing, China, High Performance Computing Applications in Biophysics.
  • J. Dreyer, 11.11.2011, RWTH Wissenschaftsnacht, Aachen, Mit Supercomputern auf der Spur von Parkinson, AIDS und Krebs: Können Computersimulationen helfen, Krankheiten besser zu verstehen?
  • J. Dreyer, 05.12.2011, XL REUNION ANNUAL SOCIEDAD ARGENTINA DE BIOFISICA, Buenos Aires, Argentina, Large-Scale Ab Initio Applications in Biophysics.
  • J. Dreyer, 26.04.2012, Joint Institute for Computational Sciences (JICS) German Research School (GRS) Joint Workshop on Large-scale Computer Simulation Oak Ridge, USA, Large-Scale Ab Initio Applications in Biophysics.
  • J. Dreyer, 21.05.2012, I3TM Seminar, AICES/CCES, Aachen, Large-Scale Ab Initio Applications in Biophysics
  • P. Carloni, 13.09.2012, Seminar at Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique, Paris, France, Multiscale modeling of membrane and membrane proteins
  • J. Dreyer, 04.10.2012, AICES Annual Retreat, Monschau, Computational Molecular Biophysics
  • J. Dreyer, 09.11.2012, BioScience 2012, Forschungszentrum Jülich Physical basis for efficient proton conduction in the Gramicidin A ion channel
  • P. Carloni, 05.12.2012, Seminar at University of Prague, Czech Republic, Multiscale modeling of membrane and membrane proteins
  • P. Carloni, 10.12.2012, Seminar at KTH Stockholm, Sweden, Multiscale modeling of membrane and membrane proteins
  • P. Carloni, 18.02.2013, Car-Parrinello Special Symposium at the King and Prince Resort on historic St. Simons Island, Georgia, USA, Proton Transport in Biological Systems by Large-scale Car-Parrinello Simulations
  • J. Dreyer, 20.03.2013, Seminar for Students of the “Studienstiftung des deutschen Volkes” from Göttingen, German Research School for Simulation Sciences, Jülich. Computational Biomedicine
  • P. Carloni, 15.05.2013, XXXVI National Meeting on Condensed Matter Physics (ENFMC), Sao Paulo, Brazil, Proton Transport in Biological Systems by Large-scale Ab initio Molecular Dynamics Simulations
  • J. Dreyer, 28.08.2013, ONETEP Workshop, Cambridge, UK, Ab initio molecular dynamics simulations of biological systems
  • J. Dreyer, 06.09.2013, CPMD Conference, Leipzig, Role of the membrane dipole potential for proton transport in the Gramicidin A biological channel.
  • P. Carloni, 10.09.2013, ?k-CECAM Research Conference on Multi-Scale Modeling from First Principles, Platja d’Aro, Spain, Membrane biophysics investigated by multi-scale methods
  • P. Carloni, 18.09.2013, BDEBATE-BSC-IRB “Towards In Silico Humans” Barcelona, Spain.
  • P. Carloni, 24.09.2013, XCIX Congresso Nazionale, Trieste, Italy, Investigating proton transport in biological systems by HPC-based molecular simulation

QCD Thermodynamics with Wilson fermions

Project leader: G. Endrodi (Eotvos University, Budapest, later Regensburg University)
Research field: Fundamental Physics

Publications:

  • Sz. Borsanyi, Z. Fodor, C. Hoelbling, S.D. Katz, S. Krieg, D. Nogradi, B.C. Toth, K.K. Szabo, N. Trombitas, “QCD thermodynamics with Wilson fermions” presented at the lattice 2011 conference, to appear in PosLat2011, arXiv:1111.3500
  • Szabolcs Borsanyi, Stephan Durr, Zoltan Fodor, Christian Hoelbling, Sandor D. Katz, Stefan Krieg, Daniel Nogradi, Kalman K. Szabo, Balint C. Toth, Norbert Trombitas. “QCD thermodynamics with continuum extrapolated Wilson fermions I” JHEP 1208 (2012) 126

Theses:

  • Norbert Trombitas completed his diploma thesis based on this work in 2011. The title of the thesis was “Studying the phase transition of Quantum-Chromodynamics with Wilson fermions”

Talks:

  • D. Nogradi, “QCD Thermodynamics from the lattice” Strong Interactions in Quantum Field Theory Workshop, Furstenfeld, Austria, 04-06.05.2011
  • D. Nogradi, “Lattice QCD with Wilson fermions” Lattice 2011 conference, Squaw Valley, USA, 10-16.07.2011
  • S.D. Katz, “QCD Thermodynamics on the lattice” STRONGNET Workshop, Trento, 04-07.10.2011
  • D. Nogradi “QCD thermodynamics with continuum extrapolated Wilson fermions” Lattice 2012, Cairns, Australia, June 24-29, 2012
  • D. Nogradi, “QCD thermodynamics with Wilson fermions”, Theory Seminar, CERN, 21.11.2011
  • S.D. Katz: “Recent lattice results on the QCD phase diagram” Zimanyi School, Budapest, 27.11-01.12, 2011
  • S. D. Katz “Recent lattice results on the QCD phase diagram” CBM Physics, Workshop, GSI, Darmstadt, Germany, March 28,2012.
  • S. D. Katz “QCD thermodynamics with dynamical fermions” SFB Workshop, Graz, Austria, September 27-28, 2012
  • D. Nogradi “QCD thermodynamics with continuum extrapolated Wilson fermions” Lattice 2012, Cairns, Australia, June 24-29, 2012

Predictive full-scale fast ignition with PW plasma amplified laser pulses

Project leader: Luís Silva (IST/Portugal)
Research field: Engineering and Energy

Publications:

  • F. Fiuza et al., Full-scale simulations of fast ignition of fusion targets, to be submitted to Physical Review Letters;
  • F. Fiuza et al., Control of thermal and collisional effects for efficient Raman amplification in plasmas, to be submitted to Physical Review Letters
  • F. Fiuza et al., Laser-driven shock acceleration of monoenergetic ion beams, to be submitted to Physical Review Letters
  • F. Fiuza, R. A. Fonseca, J. Tonge, W. B. Mori, and L. O. Silva, Weibel mediated collisionless shocks in laboratory with ultraintense lasers, submitted to Physical Review Letters
  • E. P. Alves, T. Grismayer, S. F. Martins, F. Fiuza, R. A. Fonseca, L. O. Silva, Large-scale magnetic field generation via the Kelvin-Helmholtz instability, The Astrophysical Journal Letters, accepted for publication
  • N. Shukla, A. Stockem, F. Fiuza, L. O. Silva, Enhancement in the electromagnetic beam-plasma instability due to ion streaming, Journal of Plasma Physics, accepted for publication
  • D. Haberberger, S. Tochitsky, F. Fiuza, C. Gong, R. A. Fonseca, L. O. Silva, W. B. Mori, C. Joshi, Collisionless shocks in a laser produced plasma generate monoenergetic high energy proton beams, Nature Physics 8, 95, January 2012
  • F. Fiuza, R. A. Fonseca, L. O. Silva, J. Tonge, J. May, and W. B. Mori, Three-dimensional simulations of laser-plasma interaction at ultrahigh intensities, IEEE Transactions on Plasma Science, Special Issue on Images in Plasma Science, 39, 2618, November 2011
  • R. Trines, F. Fiuza, R. A. Fonseca, L. O. Silva, R. Bingham, R. A. Cairns, and P. A. Norreys, Numerical simulations of plasma-based Raman amplification of laser pulse
    s to petawatt powers, IEEE Transactions on Plasma Science, Special Issue on Images in Plasma Science, 39, 2622, November 2011
  • S. Jacquemot, F. Amiranoff, S.D. Baton, J.C. Chanteloup, C. Labaune, M. Koenig, D.T. Michel, F. Perez, H.P. Schlenvoigt, B. Canaud, C. Cherfils Clérouin, G. Debras, S. Depierreux, J. Ebrardt, D. Juraszek, S. Lafitte, P. Loiseau, J.L. Miquel, F. Philippe, C. Rousseaux, N. Blanchot, C.B. Edwards, P. Norreys, S. Atzeni, A. Schiavi, J. Breil, J.L. Feugeas, L. Hallo, M. Lafon, X. Ribeyre, J.J. Santos, G. Schurtz, V. Tikhonchuk, A. Debayle, J.J. Honrubia, M. Temporal, D. Batani, J.R. Davies, F. Fiuza, R.A. Fonseca, L.O. Silva, L.A. Gizzi, P. Koester, L. Labate, J. Badziak and O. Klimo, Studying ignition schemes on European laser facilities, Nuclear Fusion 51, 094025, September 2011
  • R. Trines, F. Fiuza, R. Bingham, R. A. Fonseca, L. O. Silva, R. A. Cairns, and P. A. Norreys, Production of picosecond, kilojoule, petawatt laser pulses via Raman amplification of nanosecond pulses, Physical Review Letters 107, 105002, August 2011;
  • F. Fiuza, M. Marti, R. A. Fonseca, L. O. Silva, J. Tonge, J. May, and W. B. Mori, Efficient modeling of laser plasma interactions in high energy density scenarios, Plasma Physics and Controlled Fusion 53, 074004, July 2011;

Theses:

  • Frederico Fiúza, PhD thesis will be submitted in the first semester of 2012, tentative title Multi-scale plasma simulations of high energy density scenarios
  • Joana L. Martins, PhD thesis will be submitted in the first semester of 2012, tentative title: Radiation sources from laser plasma interactions
  • Marija Vranic, PhD thesis in progress (expected 2014), tentative title: Radiation reaction effects at ultra-high laser intensities

Invited talks:

  • L. O. Silva, Intense lasers in plasmas: from accelerators to relativistic shocks, Colloquim, International Workshop on Laser-Plasma Interaction at Ultra-High Intensity, Dresden (Germany), 2012
  • L. O. Silva, Collisionless shocks driven by lasers: ion acceleration and relativistic astrophysics, 25. Symposium on the Plasma Physics and Technology in Prague, June, 2012
  • F. Fiuza, Weibel mediated collisionless shocks: from astrophysics to laboratory, 9th International High Energy Density Laboratory Astrophysics Conference, Florida (USA), 2012;
  • F. Fiuza, Multi-scale PIC modeling of high energy density scenarios, Mathematical and Computer Science Approaches to High Energy Density Physics, Los Angeles (USA), 2012;
  • L. O. Silva, Monoenergetic ion acceleration with shock waves, Optical Acceleration of Ions and Perspective for Biomedicine, Bologna (Italy), 2011
  • F. Fiuza, Multi-scale PIC modeling of laser-plasma interactions in high density scenarios, International Conference on Ultraintense Laser Interaction Science, Lisbon (Portugal), 2011;
  • L. O. Silva, Relativistic collisionless shocks in astrophysics and with lasers, Pleanry talk, Anomalous Absorption Conference, San Diego (USA), 2012
  • F. Fiuza, Multi-scale PIC modeling of high energy density scenarios: from laboratory to astrophysics, International Conference on Numerical Simulation of Plasmas, Long Branch (USA), 2011;
  • L. O. Silva, Monoenergetic 10’s MeV proton acceleration with moderate laser intensities, International Conference on High Energy Density Physics, Lisbon (Portugal), 2011
  • F. Fiuza, Full-scale simulations of fast ignition of fusion targets, International Conference on High Energy Density Physics, Lisbon (Portugal), 2011;
  • F. Fiuza, Efficient Raman amplification into the multi-PW regime, Harnessing Relativistic Plasma Waves as Novel Radiation Sources from Terahertz to X-rays and Beyond, SPIE Conference Optics and Optoelectronics, Prague (Czech Republic), 2011;

Talks:

  • F. Fiuza, R. A. Fonseca, L. O. Silva, J. Tonge, W. B. Mori, Weibel mediated collisionless shocks in laboratory with ultraintense lasers, 53nd APS Division of Plasma Physics, Salt Lake City (USA), 2011;
  • F. Fiuza, M. Marti, R. A. Fonseca, L. O. Silva, J. Tonge, J. May, W. B. Mori, Full-scale PIC simulations of fast ignition of ICF targets, 7th Inertial Fusion Sciences and Applications, Bordeaux (France), 2011;
  • F. Fiuza, R. A. Fonseca, L. O. Silva, J. Tonge, W. B. Mori, Weibel mediated collisionless shocks in laboratory with ultraintense lasers, 38th EPS Conference on Plasma Physics, Strasbourg (France), 2011;
  • F. Fiuza, R. A. Fonseca, L. O. Silva, J. Tonge, W. B. Mori, Three-dimensional multi-scale modeling of ion acceleration in laser-plasma interactions, Laser Acceleration of Electrons, Protons and Ions, SPIE Conference Optics and Optoelectronics, Prague (Czech Republic), 2011;
  • F. Fiuza, M. Marti, R. A. Fonseca, L. O. Silva, J. Tonge, J. May, W. B. Mori, Full-scale modeling of fast ignition with ultra-intense lasers, ELI: Ultrarelativistic Laser-Matter Interactions and Petawatt Photonics, SPIE Conference Optics and Optoelectronics, Prague (Czech Republic), 2011;
  • F. Fiuza, R. A. Fonseca, L. O. Silva, J. Tonge, and W. B. Mori, Multi-scale simulation techniques for laboratory and astrophysical shocks, ISSI meeting on Fermi Shock Acceleration Process: From Non-Relativistic to Ultra-Relativistic Shocks, Bern (Switzerland), 2011;
  • F. Fiuza, R. Trines, R. A. Fonseca, L. O. Silva, R. Bingham, A. Cairns, and P. Norreys, Simulations of efficient Raman amplification into the multi-petawatt regime, Alpha-X Meeting, Lisbon (Portugal), 2011;
  • F. Fiuza, R. Trines, R. A. Fonseca, L. O. Silva, R. Bingham, A. Cairns, and P. Norreys, Simulations of efficient Raman amplification into the multi-petawatt regime, Christmas High Power Laser Science Community Meeting, Abingdon (UK), 2010;

Awards:

  • Frederico Fiuza was awarded the Oscar Buneman Prize 2011 for best visualization of scientific data, for a visualization of the simulation work performed at JUGENE and our simulations also lead to the cover of the 2012 January issue of nature Physics and the cover of the 2011 Central Laser Facilty report of the Rutherford Appleton Laboratory (see enclosed images)

Droplet growth by coalescence in turbulent clouds: kinetics, fluctuations, and Universality

Project leader: Jérémie BEC, Laboratoire Cassiopée, Université de Nice-Sophia Antipolis, CNRS. Observatoire de la Côte d’Azur, Nice, France
Research field: Fundamental Physics

Publications:

  • J. Bec, H. Homann, and S.S. Ray, “Gravitational settling of heavy particles in turbulent flow,” submitted to the Journal of Fluid Mechanics, 2011.
  • J. Bec, S. Musacchio, and S.S. Ray, “Sticky elastic collisons between inertial particles,” submitted to the Journal of Fluid Mechanics, 2011.
  • J. Bec, H. Homann, S. Musacchio, and S.S. Ray, “Distribution of large velocity differences between heavy particles,” in preparation.
  • J. Bec, H. Homann, and S.S. Ray, “Turbulent enhancement of droplet growth by coalescence,” in preparation.

Talks:

  • J. Bec, “Finite?size effect in the dynamics of particles in turbulent flow”, COST Conference on Particles in Turbulence, Potsdam, Germany, March 2011.
  • S. Musacchio, “Sticky Elastic Collisions”, COST Conference on Particles in Turbulence, Potsdam, Germany, March 2011.
  • J. Bec, “Dynamics and statistics of inertial particles in turbulent flow”, Physics Colloquium ENS Lyon, France, May 2011.
  • S.S. Ray, “Sticky Elastic Collisions”, Fluid Dynamics Day, Nice, October 2011.<
    /li>
  • J. Bec, “Dynamics and statistics of inertial particles in turbulent flow”, Condensed Matter Colloquium, Nice, France, November 2011.
  • J. Bec, “Direct numerical simulations of particles suspended in a turbulent flow”, Discussion Meeting on “Defining Guidelines for Future Extreme Simulations of Three-dimensional Fluid and Magnetohydrodynamic Turbulence”, Bangalore, India, December 2011.