4th Project Access Call – Publications

Find below the publications related to projects awarded in the PRACE 4th Regular Call.


PETASCALE QUANTUM MONTE CARLO SIMULATIONS FOR THE CHEMISTRY OF ALZHEIMER’S DISEASE

Project leader: Michel Caffarel, UMR 5626 CNRS-Univers. Paul Sabatier – Lab. Chimie et Physique Quantiques, France
Research field: Chemistry and Material Sciences

Publications:

  • “Biochemistry with quantum Monte Carlo: Exploring the impact of the Fixed-Node approximation”, A. Scemama, E. Giner, M. Caffarel, C. Hureau, and P. Faller

Theses:

  • GINER Emmanuel: “Development of perturbatively selected interaction configuration wavefunctions for quantum Monte Carlo” (University of Toulouse, France) (2014)

Talks:

  • 10th International Meeting on High-Performance Computing for Computational Science (VECPAR 2012) 17-20 July 2012, Kobe (Japan). “QMC=Chem: a quantum Monte Carlo program for large-scale simulations in chemistry at the petascale level and beyond” A. Scemama, M. Caffarel, E. Oseret, and W. Jalby
  • CECAM Tutorial: “Atomistic and molecular simulations on massively parallel architectures” July 16, 2013 – July 19, 2013. Location : Chimie ParisTech, Paris, France “Quantum Monte Carlo with QMC=Chem: Basic concepts” by M. Caffarel and A. Scemama

Invited talks:

  • Colloque « Curie, un an après » 21 mai 2013, TGCC, Bruyères?le?Châtel “Simulations petascales sur CURIE pour la biochimie”
  • Institut Henri Poincaré June 24, 2013: MINI-WORKSHOP “Mathematical and numerical challenges in quantum chemistry”, “Toward systematic improvment of the Fixed-Node approximation in diffusion Monte Carlo methods”
  • “EVOLVE 2013: A Bridge between Probability, Set-Oriented Numerics, and Evolutionary Computation” 11-13 July 2013, Leiden, Netherlands. Key Note Invited Conference: “Stochastic Approaches for Electronic Structure Theory”

Vertical axis wind turbines for future large offshore farms

Project leader: Philippe Chatelain, Université catholique de Louvain – Institute of Mechanics, Materials and Civil Engineering, Belgium
Research field: Engineering and Energy

Talks:

  • S. Backaert, P. Chatelain, and G. Winckelmans. Vortex particle-mesh with immersed lifting lines for aerospace and wind engineering. In Symposium on Particle Methods in Fluid Mechanics, October 15-17 2012, DTU Copenhagen, Procedia IUTAM. IUTAM, 2012.
  • S. Backaert, P. Chatelain, G. Winckelmans, S. Kern, T. Maeder, D. von Terzi, W. M. van Rees, and P. Koumoutsakos. Vertical axis wind turbine flows using a vortex particle-mesh method: from near to very far wakes. In 65th Annual Meeting of the Division of Fluid Dynamics, November 18-20, San Diego. American Physical Society, Nov 2012.

Characterization of the bacterial membrane and its interaction with antimicrobial peptides

Project leader: Matteo Dal Peraro, Ecole Polytechnique Federale de Lausanne, EPFL – Institute of Bioengineering, School of Life Sciences, Switzerland.
Research field: Medicine and Life Sciences

Publications:

  • T. Lemmin, C. Bovigny, D. Lancon and M. Dal Peraro “Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes”, J. Chem. Theory Comput., 9 (1), 670, 2013.
  • C. Bovigny, G. Tamo, T Lemmin and M. Dal Peraro, “LipidBuilder: a tool to build realistic models of the bacterial membrane”, in preparation.
  • – C. Bovigny, T. Lemmin and M. Dal Peraro, “Characterization of E. coli membrane and its interactions with defensin anti-microbial peptides”, in preparation.

Theses:

  • Lemmin Thomas, thesis title “Molecular modeling of membrane embedded proteins”, defended in April 2013
  • Bovigny Christophe, thesis title “Biophysical chraracterization of bacterial membranes”, planned for defence in April 2014

Talks:

  • CADMOS Workshop On Large Scale Computing, Lausanne, Switzerland
  • Biophysical Society Annual Meeting 2012, San Diego, USA

Massively-parallel molecular simulation studies of nano-scale crystal formation

Project leader: Niall English, UCD – Chemical & Bioprocess Engineering, Ireland
Research field: Chemistry and Material Sciences

Publications:

  • N.J. English, Massively-Parallel Molecular Dynamics Simulation of Clathrate Hydrates on Blue Gene Platforms, Energies, 6, 3072-3081; DOI 10.3390/en6063072 – invited to special issue in hydrates 2013 (20 Jun 2013)

Theses:

  • Marco Lauricella (UCD) – Molecular dynamics exploration of clathrate hydrate formation

Invited talks:

  • Experiences with PRACE, Research IT Briefing (7 Mar 2013, Univ. College Dublin,

Identification of redox competent species in biological processes

Project leader: Giovanni La Penna, National research council of Italy – Institute for chemistry of organo-metallic compounds, Italy
Research field: Chemistry and Material Sciences

Publications:

  • “Identifying redox competent forms in the amyloid cascade of Alzheimer’s disease by first-principles simulations”, P. Faller, C. Hureau, G. La Penna, O. Andreussi, in preparation

Quantum Monte Carlo simulation of hydrogen at high pressure

Project leader: Carlo Pierleoni, University of L’Aquila – Physics, Italy
Research field: Chemistry and Material Sciences

Publications:

  • M.A. Morales, J.M. McMahon, C. Pierleoni and D.M. Ceperley, “Nuclear Quantum Effects and Nonlocal Exchange-Correlation Functionals Applied to Liquid Hydrogen at High Pressure”. Phys. Rev. Lett., vol. 110 (6) pp. 065702 (2013).
  • M.A. Morales, J.M. McMahon, C. Pierleoni and D.M. Ceperley, “Toward
    s a predictive first-principles description of solid molecular hydrogen with density functional theory”. Physical Review B vol. 87 (18) pp. 184107 (2013).
  • J.M. McMahon, M.A. Morales, C. Pierleoni, D. M. Ceperley, “Atomic Hydrogen: a superconducting superfluid or a metallic solid?”. Submitted (2013).
  • M.A. Morales, R. Clay, C. Pierleoni, D.M. Ceperley. “First Principles Methods: A Perspective From Quantum Monte Carlo.” Submitted (2013).

Theses:

  • Guglielmo Mazzola. SISSA, PhD thesis ” Novel molecular dynamics with quantum Monte Carlo forces, application to hydrogen and water liquids”

Invited talks:

  • C. Pierleoni, “Properties of Hydrogen and Helium in the Warm-Dense matter regime”, 7th International Workshop on Warm Dense Matter, Saint-Malò June 2013.

Talks:

  • C. Pierleoni, “First Principle methods for High pressure hydrogen”, XXV IUPAP Conference on Computational Physics, August 20-24, 2013, Moscow, Russia, plenary talk.
  • M. A. Morales, “High Pressure Hydrogen: A First-Principles Perspective”, College of William & Mary, Physics Colloquium, December 2012.
  • M. A. Morales, “High Pressure Hydrogen: A First-Principles Perspective”, UC Berkeley Condensed Matter Seminar, Berkely CA, January 2013.
  • M. A. Morales, “High Pressure Hydrogen: A First-Principles Perspective”, UC Davis, Condensed Matter Seminar, Davis CA, April 2013.
  • M. A. Morales, “Quantum Monte Carlo Benchmark of Exchange-Correlation Functionals for Ab-Initio Simulations”, Institute of Nuclear Theory Program on “Advances in quantum Monte Carlo techniques for non-relativistic many-body systems”, University of Washington, Seattle Wa, June 2013
  • S. Sorella, “Recent progress in quantum Monte Carlo techniques”, Institute of Nuclear Theory Program on “Advances in quantum Monte Carlo techniques for non-relativistic many-body systems”, University of Washington, Seattle Wa, June 2013.
  • G. Mazzola, “Variational Monte Carlo for Hydrogen under high pressures”, “Summer School on Atomistic Simulation Techniques for Material Science, Nanotechnology and Biophysics”, July 2013, SISSA Trieste

Lattice Study of Baryon Resonances

Project leader: Paul Rakow, University of Liverpool – Mathematical Sciences, UK
Research field: Fundamental Physics

Publications:

  • M. Goeckeler, R. Horsley, M. Lage, U-G. Meissner, P. E. L. Rakow, A. Rusetsky, G. Schierholz and J. M. Zanotti, “Scattering phases for meson and baryon resonances on general moving-frame lattices,’’ Phys. Rev. D 86 (2012) 094513

The way to heating the solar corona: Finely-resolved twisting of magnetic loops

Project leader: Fabio Reale, University of Palermo – Department of Physics, Italy
Research field: Astrophysics

Talks:

  • F. Reale – MHD modeling of twisted coronal loops – ISSI (International Space Science Institute) working group “Coronal Heating – Using Observables to Settle the Question of Steady vs. Impulsive Heating”, Bern, Switzerland, 28 February 2013
  • S. Orlando – HPC projects in Astrophysics at INAF/OAPa: current challenges and future perspectives, PRACE-2IP WP8 Fifth Face to Face Meeting?CSCS, Lugano, Switzerland, 6-8 March 2013
  • F. Reale – Non linear processes in the solar corona – Physical Processes in Astrophysical Plasmas Inflow/outflow and stellar winds, Torino, Italy, March 12th – 14th 2013
  • F. Reale – Toward self-consistent 3D MHD modeling of the heating of a twisted coronal loop – 6th Coronal Loop Workshop, 25-28 June 2013, LaRoche, Belgium

Understanding the bacterial efflux systems: insights into structure-function relationship from all-atom simulations

Project leader: Paolo Ruggerone, University of Cagliari – Department of Physics, Italy
Research field: Medicine and Life Sciences

Theses:

  • Francesca Collu, Molecular dynamics simulations of large systems: the case of multidrug efflux pumps in Gram-negative bacteria (University of Bern)

Talks:

  • Miniworkshop in Molecular and Statistical Biophysics, Triest (Italy), October 11-12, 2012
  • Gordon Conference “Multi-drug efflux systems: Shared Molecular Mechanisms but Diverging Roles in Physiology and Medicine”, Ventura (USA), March 17-22, 2013
  • 541. WE Seminar “Transport through Nanopores: From Understanding to Engineering”, Bremen (Germany), July 28-August 3, 2013

GYSELA

Project leader: Yanick Sarazin, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) – Institut de Recherche sur la Fusion par confinement Magnétique (IRFM), France
Research field: Engineering and Energy

Publications:

  • Y. Sarazin, V. Grandgirard et A. Strugarek, “La Fusion bientôt sous Contrôle”, La Recherche – Supercalculateurs 469 (Nov. 2012)
  • A Strugarek, Y Sarazin, D Zarzoso, J Abiteboul, A S Brun, T Cartier-Michaud, G Dif-Pradalier, X Garbet, Ph Ghendrih, V Grandgirard, G Latu, C Passeron and O Thomine, “Ion transport barriers triggered by plasma polarization in gyrokinetic simulations”, Plasma Phys. Control. Fusion 55, 074013 (2013)
  • D Zarzoso, Y. Sarazin, X. Garbet, R. Dumont, A Strugarek, J Abiteboul, T Cartier-Michaud, G Dif-Pradalier, Ph Ghendrih, V Grandgirard, G Latu, C. Passeron and O Thomine, “Impact of energetic particle driven geodesic acoustic modes on turbulence”, Phys. Rev. Lett. 110, 125002 (2013)
  • J Abiteboul, Ph Ghendrih, V Grandgirard, T Cartier-Michaud, G Dif-Pradalier, X Garbet, G Latu, C Passeron, Y Sarazin, A Strugarek, O Thomine and D Zarzoso, “Turbulent momentum transport in core tokamak plasmas and penetration of scrape-off layer flows”, Plasma Phys. Control. Fusion 55, 074001 (2013)
  • A Strugarek, Y Sarazin, D Zarzoso, J Abiteboul, A S Brun, T Cartier-Michaud, G Dif-Pradalier, X Garbet, Ph Ghendrih, V Grandgirard, G Latu, C Passeron and O Thomine, “Unraveling quasi-periodic relaxations of transport barriers with gyrokinetic simulations”, Soumis à Phys. Rev. Lett. (2013)

Theses:

  • Jérémie Abiteboul (2009-2012): Transport turbulent et néoclassique de quantité de mouvement toroïdale dans les plasmas de tokamak”
  • Antoine Strugarek (2009-2012): ” Turbulence, transport et confinement: des tokamaks au magnétisme des étoiles”
  • David Zarzoso (2009-2012): “Kinetic description of the interaction between energe
    tic particles and waves in fusion plasmas”

Invited talks:

  • Sheared flows and transport barriers: from tokamaks to stars, A. Strugarek et al.Theory of fusion plasmas, Varenna, Italy, Sept. 2012,
  • Interplay between fast ions and turbulence in magnetic fusion plasmas, R. Dumont et al., European Physical Society conference, Espoo, Finland, July 2013,
  • Impact of energetic particles on turbulence: on the way from electrostatic to electromagnetic simulations, D. Zarzoso et al., Festival de Théorie, Aix-en-Provence, France, July 2013,
  • Energetic particles, EGAMs and turbulence: a complex interplay, D. Zarzoso et al., European Fusion Theory Conference, Oxford, UK, Oct. 2013,

Talks:

  • Turbulent momentum transport in core tokamak plasmas & penetration of scrape-off layer flows, J. Abiteboul et al., Theory of fusion plasmas, Varenna, Italy, Sept. 2012, Poster
  • Towards turbulence control via EGAM excitation and vorticity injection, Y. Sarazin et al., IAEA Fusion Energy Conference, San Diego, USA, Oct. 2012, Poster
  • Spatial Propagation of Turbulence & Formation of Mesoscopic Structures in Plasma Turbulence, G. Dif-Pradalier et al., US Transport Task Force workshop, Santa Rosa, USA, April 2013, Oral

First Lattice QCD study of B-physics with four flavors of dynamical quarks

Project leader: Silvano Simula, INFN – Sezione di Roma Tre, Italy
Research field: Fundamental Physics

Theses:

  • P. Lami: ” Study of quark mass and decay constant on the lattice” (Thesis, September 2012, supervisor: C. Tarantino);
  • E. Picca: “Determination of the b-quark mass on the lattice” (Thesis, Septmber 2012, supervisor: V. Lubicz).
  • Presently we have 3 PhD students (P. Lami, E. Picca and L. Riggio) and 2 post-docs (N. Carrasco Vela and P. Dimopoulos) involved in the analyses of the results.

Talks:

  • Oral contributions to the XXXI Int’l Conference on “Lattice Field Theory” (Mainz, July-August 2013), N. Carrasco Vela: “K and D oscillations in the Standard Model and its extensions from Nf=2+1+1 twisted mass lattice QCD”;
  • Oral contributions to the XXXI Int’l Conference on “Lattice Field Theory” (Mainz, July-August 2013), P. Lami: “A determination of the average up-down, strange and charm quark masses at Nf=2+1+1”
  • Oral contributions to the XXXI Int’l Conference on “Lattice Field Theory” (Mainz, July-August 2013), E. Picca: “A Nf=2+1+1 twisted determination of the b-quark mass”
  • Oral contributions to the XXXI Int’l Conference on “Lattice Field Theory” (Mainz, July-August 2013), L. Riggio: “Pseudoscalar decay constant fK/fPi, fD and fDs with Nf=2+1+1 ETMC configurations”

Numerical simulation of air flow in the human large airways

Project leader: Guillaume Houzeaux, Barcelona Supercomputing Center – Computer Applications in Science and Engineering, Spain.
Research field: Engineering and Energy

Publications:

  • Alister Bates, Hadrien Calmet, Raul Cetto, Denis J. Doorly, Guillaume Houzeaux, Raúl de la Cruz, Mariano Vázquez and Alberto M. Gambaruto, Modelling a Sniff in Extensive Human Airways: Aspects of Physiology and Fluid Mechanics, Congress on Numerical Methods in Engineering 2013 Bilbao (Spain), 2013.
  • Guillaume Houzeaux,Beatriz Eguzkitza, Bela Soni, Hadrien Calmet, Shahrouz Aliabadi, Alister Bates, Denis Doorly, Mariano Vázquez, A Gluing Method for Non-matching Meshes, ParCFD2013, Changsha (China) 2013.

Talks:

  • Mariano Vázquez, How do I compute the Body Electric?, TEDMED2013, April 16-19th, Washington DC.

Towards an atomistic understanding of the selective oxidation of alcohols at the Au/TiO2(110) solid-liquid interface

Project leader: Dominik Marx, RUHR-UNIVERSITAET BOCHUM – LEHRSTUHL FUER THEORETISCHE CHEMIE, Germany
Research field: Chemistry and Material Sciences

Publications:

  • Matteo Farnesi Camellone and Dominik Marx “On the Impact of Solvation on a Au/TiO2 Nanocatalyst in Contact with Water”, J. Phys. Chem. Lett. 4, (3), 514, 2013.
  • Matteo Farnesi Camellone, Jianli Zhao, Lanying Jin, Yuemin Wang,. Martin Muhler, and. Dominik Marx “Molecular Understanding of Reactivity and Selectivity for Methanol Oxidation at the Au/TiO2 Interface”, Angew. Chem. Int. Ed. doi: 10.1002/anie.201301868

Invited talks:

  • D. Marx, Advanced Ab Initio Simulation of Hard and Soft Materials, Opening Keynote Lecture at WATOC 2011 Satellite Meeting “Theoretical Modelling of Materials”, Barcelona, July 13-15 (2011)
  • D. Marx, On the Water/Gold/Titania Interface, CECAM Workshop “Functional Oxides for Emerging Technologies”, Bremen, October 14-18 (2013)

Talks:

  • M. Farnesi Camellone, Chemical Reactions at the Au/TiO2 Interface in the Gas and Liquid Phase, poster at “XVI International workshop on Computational Physics and Material Science: Total Energy and Force Methods”, Trieste, January 10-12 (2013)

3D-3V Vlasov simulations of plasma turbulence

Project leader: Francesco Valentini, Universita’ della Calabria – Physics, Italy
Research field: Fundamental Physics

Publications:

  • D. Perrone, R.O. Dendy, I. Furno, R. Sanchez, G. Zimbardo, A. Bovet, A. Fasoli, K. Gustafson, S. Perri, P. Ricci, F. Valentini, “Nonclassical Transport and Particle-Field Coupling: from Laboratory Plasmas to the SolarWind”, Space Sci .Rev. DOI 10.1007/s11214-013-9966-9, published online on March 2013 (in press)
  • F. Valentini, D. Perrone, F. Califano, F. Pegoraro, P. Veltri, P. J. Morrison, and T. M. O’Neil, “Response to “Comment on ‘Undamped electrostatic plasma waves’” [Phys. Plasmas 20, 034701 (2013)], Phys. Plasmas 20, 034702 (2013)
  • S. Donato, S. Servidio, P. Dmitruk, F. Valentini, A. Greco, P. Veltri, M.Wan, M.A. Shay, P.A. Cassak and W.H. Matthaeus, “Overview on numerical studies of reconnection and dissipation in the solar wind”, AIP Conf. Proc. 1539, 99 (2013); doi: 10.1063/1.4810999
  • S. Servidio , K.T. Osman , F. Valentini , D. Perrone , F. Califano , S. Chapman , W. H. Matthaeus , and P. Veltri, “Proton Kinetic Effects in Vlasov and SolarWind Turbulence”, submitted to Phys. Rev. Lett. (2013)
  • O. Pezzi, F. Valentini, D. Perrone and P. Veltri, “Eulerian simulations of collisional effects on electrostatic plasma waves”, submitted
    to Phys. of Plasmas (2013)
  • D. Perrone, S. Bourouaine, F. Valentini, E. Marsch and P. Veltri, “Generation of nongyrotropic velocity distributions of alpha particles in the solar wind: Vlasov simulations and HELIOS observations”, submitted to Astrophysical Journal (2013)
  • F. Valentini, A. Vecchio, S. Donato, V. Carbone, P. Veltri, C. Briand and J. Bougeret, “The long and winding road to the heating of the solar wind”, to be submitted to Nature Physics (2013)
  • D. Perrone, F. Valentini, S. Servidio, S. Dalena, P. Veltri, “Ion temperature anisotropy in the turbulent solar wind: Hybrid-Vlasov simulations”, to appear in the proceedings book of the 40th European Physical Society Conference on Plasma Physics (2013)

Theses:

  • Denise Perrone, PhD student at Università della Calabria (she graduated on 17th December 2012), “A kinetic multi-component numerical model for the solar wind smallscale turbulence”
  • Oreste Pezzi, undergraduate student at Università della Calabria (he is going to defend his master thesis on July 2013), “Collisional effects in plasmas: theoretical background and numerical approach”
  • Gaetano De Vita, PhD student at Università della Calabria (he is going to defend his PhD thesis on October 2013), “Turbulence and structures in plasmas: sign singularity and cancellation analysis.”
  • Christian Vasconez, PhD student at Università della Calabria (he is going to graduate in 2015), he just started to work on the numerical data from the simulations developed within the present PRACE project Pra04-771.

Invited talks:

  • F. Valentini,D. Perrone, F. Califano, F. Pegoraro, P. Veltri, P. J. Morrison, T. M. O’Neil, “XCVIII Congresso Nazionale della Società Italiana di Fisica”, Napoli, 17 – 21 Settembre, 2012, “Undamped electrostatic plasma waves: theory and Vlasov simulations”
  • D. Perrone, F. Valentini, S. Servidio, S. Dalena, P. Veltri, Observatory of Meudon, Paris, France, 3 Giugno 2013, ’Kinetic multi-component simulations for the solar wind small-scale turbulence: ion temperature anisotropy’
  • S. Servidio, F. Valentini, F. Califano, P. Veltri, “American Geophysical Union (AGU) Fall Meeting, 3-7 December 2012, San Francisco, California (USA), “Local kinetic effects in a turbulent plasma: numerical simulations”

Talks:

  • Regular talk: F. Valentini, D. Perrone, S. Servidio, S. Dalena, P. Veltri, “Arcetri 2012 Workshop on Plasma Astrophysics”, 5-8 Novembre 2012, Arcetri (Firenze), Italy, “Kinetic simulations of plasma turbulence in the solar wind: temperature anisotropy of the ion species”
  • Poster communication: F. Valentini, D. Perrone, F. Califano, F. Pegoraro, P. Veltri, P. J. Morrison, T. M. O’Neil, “54th Annual Meeting of the APS Division of Plasma Physics”, October 29–November 2 2012; Providence, Rhode Island (USA), “Undamped electrostatic plasma waves”
  • D. Perrone, F. Valentini, P. Veltri, S. Bourouaine, E. Marsch, ’Workshop on Plasma Astrophysics’, Arcetri, Italy, 5-8 Novembre 2012, ’Non-gyrotropic features of the alpha particle velocity distributions in the solar wind: Helios 2 observations and hybrid Vlasov simulations’
  • D. Perrone, F. Valentini, S. Servidio, S. Dalena, P. Veltri, ’40th European Physical Society Conference on Plasma Physics’, Espoo, Finland, 1-5 Luglio 2013, ’Ion temperature anisotropy in the turbulent solar wind: hybrid-Vlasov simulations’
  • D. Perrone, F. Valentini, S. Servidio, S. Dalena, P. Veltri, ’FitMat2013’, Milano, Italy, 9-13 settembre 2013, ’Temperature anisotropy of the solarwind heavy ions in hybrid-Vlasov simulations’
  • S. Servidio, F. Valentini, F. Califano, P. Veltri, “Arcetri 2012 Workshop on Plasma Astrophysics, November 5-8, 2012, Department of Physics & Astronomy, University of Florence, Florence, Italy. “Kinetic effects in two-dimensional plasma turbulence
  • P. Veltri, F. Valentini, F. Califano, D. Perrone, F. Pegoraro, A. Vecchio, A. Mangeney, “Arcetri 2012 Workshop on Plasma Astrophysics, November 5-8, 2012, Department of Physics & Astronomy, University of Florence, Florence, Italy. “Electrostatic turbulence generated by solar-wind nolnlinear energy cascade”

Electronic structure of wet systems

Project leader: Paolo Umari, Università degli studi di Padova – Dipartimento di Fisica ed Astronomia, Italy
Research field: Chemistry and Material Sciences

Publications:

  • P. Umari, L. Giacomazzi, F. De Angelis, M. Pastore, and Stefano BaroniJ. Chem. Phys. 139, 014709 (2013); doi: 10.1063/1.4809994

Theses:

  • Carla Verdi, final undergraduate thesis, University of Padova, Italy

Talks:

  • DPG conference in Regensburg, 11/3/2013, “Electronic properties of isolated and supported organic dyes modeled through the GW method”

Invited talks:

  • University of Perugia, Italy 18/2/2013, “Accurate quasi-particle GW energy levels with the GWL method: application to dye sensitized solar cells”

Fluid turbulence: self and passive scalar diffusion. Application to stably stratified flows

Project leader: Daniela Tordella, Politecnico di Torino – Ingegneria Meccanica e Aerospaziale, Italy
Research field: Earth Sciences & Environment

Publications:

  • Small-scale anisotropy in turbulent shearless mixing. Author(s): Tordella, Daniela; Iovieno, Michele; Source: Physical review letters Volume: 107 Issue: 19 Pages: 194501 Published: 2011-Nov-4 (Epub 2011 Oct 31)
  • S. Di Savino, L. Gallana, M. Iovieno, D. Tordella, “Turbulent interfaces as sites to measure the passive scalar–velocity intermittency relationship” report, accepted for ETC14 Lyon
  • S. Di Savino, L. Gallana, M. Iovieno, and D. Tordella, “Transient formation of the passive scalar spectrum at a turbulent interface”, accepted for the XXI AIMETA Conference, 17-20 September 2013, Torino, Italy
  • S. Di Savino, L. Gallana, M. Iovieno, D. Tordella “Transport across interfaces: the doubling of the intermittency regions in the case of a passive scalar and mass transport”, in preparation (2013)
  • D. Tordella, K.R. Sreenivasan, “Special Issue on Small Scale Turbulence Preface”, Phisica D – Nonlinear phenomena 241, 2012 D.
  • Tordella, M. Iovieno, “Decaing turbulence: What happens when the correlation length varies spatially in two adjacent zones” , Phisica D – Nonlinear phenomena 241, 2012
  • D. Tordella, M. Iovieno, “Small-scale anisotropy in turbulent shearless mixing” 107, 2011
  • M. Iovieno, L.Ducasse, D. Tordella, “Dimensionality influence on passive scalar transport”, Journal of Physics Conference Series (ETC13), 318, 2011
  • D. Tordella, M. Iovieno, L. Ducasse, “Intermittency layers associated to turbulent interfaces” 9th EFMC, Rome, September 2012
  • L. Gallana, M. Iovieno, S. Di Savino, F. De Santi, D. Tordella, “Turbulent mixing trough cloud/clear-air interface” in preparation 2013

Theses:

  • L. Gallana “High resolution
    numerical simulation of the turbulent transport of a passive scalar by using a new pencil parallelization method suitable for massive parallelized machines”, Jul 2012
  • L. Verso “Lagrangian analysis on turbulent transport in absence of mean flow through numerical and laboratory experiment”, Jul 2013
  • T.P. Parmentier “Study of temporal evolution of the cloud/clear-air interface considering various levels of stratification” , Sep 2013

Talks:

  • S. Di Savino, L. Gallana, M. Iovieno, and D. Tordella, “Transient formation of the passive scalar spectrum at a turbulent interface”, accepted for the XXI AIMETA Conference, 17-20 September 2013, Torino, Italy
  • D. Tordella, “Turbulence mixing and the study of clouds”, VentureFest 2012, Jun 2012, Said Business School
  • F. De Santi, Phd presentation, Politecnico di Torino, Turin
  • S. Di Savino, Phd presentation, Politecnico di Torino, Turin
  • L. Gallana, ME Diploma presentation, July 2012, Politecnico di Torino, Turin
  • L. Verso, “Seminar on Lagrangian statistics in shear-free mixings”, April 2013, Technical University, Tel Aviv
  • M. Iovieno, “Intermittency layers associated to turbulent interfaces” 9th EFMC, Rome, September 2012

LUCIDUS – Cosmological simulations of galaxy formation on a moving mesh

Project leader: Volker Springel, University of Heidelberg – Heidelberg Institute for Theoretical Studies, Germany
Research field: Astrophysics

Publications:

  • Vogelsberger M., Genel S., Sijacki D., Torrey P., Springel V., Hernquist L.: “A physical model for cosmological simulations of galaxy formation”, 2013, submitted to MNRAS, eprint arXiv:1305.2913
  • Torrey P., Vogelsberger M., Genel S., Sijacki D., Springel V., Hernquist L.: “A physical model for cosmological simulations of galaxy formation: multi-epoch validation”, 2013, submitted to MNRAS, eprint arXiv:1305.4931

Theses:

  • The following PhD students use the simulation data for ongoing thesis projects:Paul Torrey, Andreas Bauer, Dylan Nelson, Martin Sparre

Talks:

  • V. Springel and S. Genel delivered talks at the Conference “Mind the Gap: From microphysics to large-scale structure in the Universe” in Cambridge, UK, 8-12 July, 2013
  • M. Vogelsberger and D. Sijacki gave talks at the Conference “The Physical Link between Galaxies and their Halos” in Garching, Germany, 24-28 June, 2013

Strong interactions beyond QCD

Project leader: Claudio Pica, CP3-Origins, University of Southern Denmark – IMADA, Denmark
Research field: Fundamental Physics

Talks:

  • “Strongly interacting dynamics beyond the Standard Model and the Higgs boson” workshop, Higgs centre for Theoretical physics, Edinburgh, 24-26 April 2013. C. Pica

Ab Initio Modeling of Solar Active Regions

Project leader: Aake Nordlund, University of Copenhagen – Niels Bohr Institute, Denmark
Research field: Astrophysics

Publications:

  • Baumann, G., Haugbølle, T., Nordlund, Å.. “Kinetic Modeling of Particle Acceleration in a Solar Null-point Reconnection Region”. The Astrophysical Journal, 771, 93, July, 2013
  • Baumann, G., Galsgaard, K., Nordlund, Å.. “3D Solar Null Point Reconnection MHD Simulations”. Solar Physics, 284, 467, June, 2013
  • Stein, R. F., Nordlund, A.. “Ab Initio Active Region Formation”. American Astronomical Society Meeting Abstracts, 221, #415.02, January, 2013
  • Georgobiani, D., Stein, R., Nordlund, A.. “Realistic numerical simulations of solar convection: emerging flux, pores, and Stokes spectra”. IAU Special Session, 6, December, 2013
  • Stein, R. F., Nordlund, Å.. “Flux Emergence and Pore Formation: What ATST can See”. Second ATST-EAST Meeting: Magnetic Fields from the Photosphere to the Corona., 463, 83, December, 2012
  • Fabbian, D., Moreno-Insertis, F., Khomenko, E., Nordlund, Å.. “Solar Fe abundance and magnetic fields. Towards a consistent reference metallicity”. Astronomy and Astrophysics, 548, A35, December, 2012
  • Cargill, P. J., Vlahos, L., Baumann, G., Drake, J. F., Nordlund, Å.. “Current Fragmentation and Particle Acceleration in Solar Flares”. Space Science Reviews, 173, 223, November, 2012
  • Haugboelle, T., Trier Frederiksen, J., Nordlund, A.. “Photon-Plasma: a modern high-order particle-in-cell code”. ArXiv e-prints, arXiv:1211.4575, November, 2012
  • Baumann, G., Nordlund, Å.. “Particle-in-cell Simulation of Electron Acceleration in Solar Coronal Jets”. The Astrophysical Journal, 759, L9, November, 2012
  • Stein, R. F., Nordlund, Å.. “On the Formation of Active Regions”. The Astrophysical Journal, 753, L13, July, 2012
  • Stein, R. F., Lagerfjärd, A., Nordlund, &., Georgobiani, D.. “Emerging Flux Simulations and Proto-Active Regions”. 4th Hinode Science Meeting: Unsolved Problems and Recent Insights, 455, 133, June, 2012

Theses:

  • Gisela Baumann, “Particle dynamics in magnetic reconnection regions”, PhD thesis, joint between University of Copenhagen and Ruhr University Bochum, July 2012

Talks:

  • “Magnetic Energy: Transport and Dissipation”, SWIFF Summer School, Spineto (Italy), June 2012
  • “Ab Initio Solar Active Region Simulations”, NORDITA Computational Astrophysics Codes Workshop, August 7, 2012
  • “Scaling of Turbulent and Hierarchical Reconnection”, 5th Cambridge Workshop on Reconnection, Copenhagen (Denmark), August 28, 2012
  • “HPC User Requirements on the Danish e-Infrastructure Collaboration (DeIC)”, Middelfart (Denmark), November 13, 2012
  • “Coupling at the Solar Surface: Photosphere, Chromosphere & Corona”, SWIFF 2nd Annual Meeting, Torino (Italy), January 15, 2013
  • “Advanced Elements of Particle-in-Cell Codes”, SWIFF 2nd Annual Meeting, Torino (Italy), January 16, 2013

The Life-cycle of Energy in Space Weather

Project leader: Giovanni Lapenta, KU Leuven, Belgium
Research field: Astrophysics

Publications:

  • V. Olshevsky, G. Lapenta, S. Markidis “Energetics of kinetic reconnection in threedimensional null points cluster”. 2013, submitted to Phys. Rev. Lett.
  • S. Markidis, P. Henri, G. Lapenta, A. Divin, M. Goldman, D. Newman, E. Laurie, Kinetic Simulations of Plasmoid Chain Dynamics, submitted to Phys. Plasmas.
  • S. Markidis, P. Henri, G. Lapenta, K. Ronnmark, M. Hamrin, Z. Meliani,
    E. Laurie, A Fluid-Kinetic Particle-in-Cell Solver for Plasma Simulations, submitted to J. Computat. Phys.
  • V. Olshevsky, A. L. Restante, G. Lapenta, R. Keppens Coupling Solar Simulations with Space Weather: code Comparison within SWIFF Consortium, Workshop on Partially Ionized Plasmas in Astrophysics, Puerto de la Kruz, Tenerife, Spain, June 19 – 22, 2012.
  • M.E. Innocenti, G. Lapenta, S.Markidis, A. Beck, A. Vapirev A Multi Level Multi Domain method for Particle In Cell plasma simulations, 39th European Physical Society Conference on Plasma Physics, July 2-6 2012, Stockholm, Sweden.
  • K. Steed, D. M. Long, J. A. Davies, A. P. Walsh, G. Lapenta, The origins and heliospheric evolution of CMEs on 7 and 14 August 2010 originating from the same solar source region, Solar Orbiter 5 workshop, Bruges, Belgium, 10 – 14 September 2012.
  • D.L. Newman, M.V. Goldman, G. Lapenta, S. Markidis, Magnetospheric Reconnection in Modified Current-Sheet , 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • A. Divin, G. Lapenta, S. Markidis, D.L. Newman, M.V. Goldman, Numerical simulations of separatrix instabilities in collisionless magnetic reconnection, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • L. Bettarini, G. Lapenta, Spontaneous transition to a fast 3D turbulent reconnection regime , 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • M.V. Goldman, D.L. Newman, J.T. Gosling, G. Lapenta, L. Andersson, S. Eriksson, S. Markidis, Energy Transport during Magnetotail Reconnection, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • G. Lapenta, S. Markidis, D.L. Newman, M.V. Goldman, L. Andersson, S. Eriksson, Observations and Simulations of nonlionear energtic signatures in reconnection, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 -November 2, 2012.
  • P.P. Kronberg, R.V.E. Lovelace, G. Lapenta, SA Colgate, Measurement and Simulation of the Electric Current in a kpc-Scale Jet, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • G. Lapenta, S. Markidis, A.L. Restante, T. Intrator, Flux ropes in 3D kinetic reconnection: psontaneous generation and evolution, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • S. Markidis, G. Lapenta, P. Henri, H. Karimabadi, T. Intrator, E. Laure, Flux Rope Dynamics in 3D Kinetic Simulations, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • M.E. Innocenti, G. Lapenta, S. Markidis, M. Lazar, S. Poedts, Electron streams formation and secondary two stream instability onset in the postsaturation regime of the classical Weibel instability, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • S. Markidis, P. Henri, G. Lapenta, K. Ronnmark, M. Hamrin, E. Laure, A Fluid-Kinetic Particle-in-Cell Solver, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • A. Beck, M.E. Innocenti, G. Lapenta, S. Markidis, Multi-level multi-domain simulations: a new approach to multi-scale multi-physics descriptions, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • J. Deca, S. Markidis, G. Lapenta, E. Jarleberg, R. Apostolov, E. Laure, Rethinking Electrostatic Solvers in Particle Simulations for the Exascale Era, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November2, 2012.
  • L. Siddi, L. Guazzotto, G. Lapenta, R. Paccagnella, Computational Study of the Grad-Shafranov Equation with Flow in Helical Symmetry, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • G. Lapenta, S. Markidis, A. Vapirev, M.V. Goldman, D.L. Newman, Reconnection: where is the party?, 54th Annual Meeting of the Division of Plasma Physics of the American Physical Society, Providence, Rhode Island, USA, October 29 – November 2, 2012.
  • M.E. Innocenti, A. Beck, G. Lapenta, S. Markidis, A. Vapirev, Increasing the domain Size of kinetic Simulations: a Multi Level Multi Domain method for Plasma Simulations, 9th European Space Weather Week, November 13-17 2012, Brussels, Belgium.
  • S. Poedts, G. Lapenta, A. Lani, H. Deconinck, B. Fontaine, J. Depauw, N. Mihalache, D. Heyndrickx, Daniel, J. De Keyser, N. Crosby, L. Rodriguez,R. Van der Linden, The ESA Virtual Space Weather Modelling Centre – Phase 1, Ninth European Space Weather Week, Brussels, Belgium, November 5 -9, 2012.
  • J. Deca, S. Markidis, A. Divin, and G. Lapenta, 3D implicit PIC simulations of solar wind – body interactions, Ninth European Space Weather Week, Brussels, Belgium, November 5 – 9, 2012.
  • V. Olshevsky, A. L. Restante, G. Lapenta Kinetic modeling of magnetic reconnection in three dimensions Ninth European Space Weather Week, Brussels, Belgium, November 5 – 9, 2012.
  • A. Beck, M.-E. Innocenti, G. Lapenta Multi-Level Multi-Domain PIC simulations, 1st International Conference on Frontiers in Computational Physics: Modeling the Earth System, December 16-20 2012, Boulder, Colorado, USA.
  • S. Eriksson, S. Markidis, D.L. Newman; J.T. Gosling; T.D. Phan; C. M. Carr; I. Dandouras; G. Lapenta; M. V. Goldman, Evidence of Multiple X-lines in the Solar Wind from Overlapping Hall Magnetic Fields, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • L. Andersson; D. L. Newman; G. Lapenta; M. V. Goldman; S. Markidis, Particle motion in association with Reconnection in the Earth’s tail, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • M. E. Innocenti; A. Beck; G. Lapenta; S. Markidis, Simulations of magnetic reconnection with Parsek2D-MLMD, a new Multi Level Multi Domain (MLMD) Implicit Moment Method (IMM) Particle in Cell (PIC) code, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • D. L. Newman; M. V. Goldman; G. Lapenta; S. Markidis; L. Andersson; J. T. Gosling; J. P. Eastwood, Particle Velocity Distributions in the Magnetotail Reconnection Exhaust: Results from Implicit PIC Simulations, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • M. V. Goldman; D. L. Newman; G. Lapenta; S. Markidis; J. T. Gosling; L. Andersson; S. Eriksson, Particle and Wave Energy Transport During Magnetic Reconnection, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • G. Lapenta; S. Markidis; D. L. Newman; M. V. Goldman, Characteristic speeds of reconnection processes, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • J. Deca; G. Lapenta; S. Markidis, 3D Full Kinetic Modelling of the interaction of the Moon with the Magnetosphere and Solar Wind, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • G. Lapenta; K. Steed; V. Olshevsky; A.L. Restante, Homologous CME: a multispacecraft approach supported by simulations, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • A. E. Vapirev; G. Lapenta; A. V. Divin; S. Markidis; M. V. Goldman; D. L. Newman, Structure of Dipolariz
    ation Front at Reconnection Point in 3D PIC simulations, 2012 AGU Fall Meeting, San Francisco, California, USA, December 3-7, 2012.
  • P. Henri, F. Califano, S. Markidis, M. Faganello, G. Lapenta, F. Pegoraro, Fluid and Kinetic Modelling of the Magnetized Kelvin-Helmholtz Instability, 14th European Turbulence Conference, Lyon, France, 1-4 September 2013.
  • V. Olshevsky, G. Lapenta, S. Markidis “Kinetic simulations of magnetic reconnection in three-dimensional null points”, European Gesciences Union General Assembly, Vienna, Austris, 7-12 April 2013
  • V. Olshevsky, G. Lapenta, S. Markidis “Energetics of kinetic reconnection in three-dimensional null points cluster”, General Scientific Meeting of Belgian Physical Society, Louvain-la-Neuve, Belgium, 22 May 2013

Theses:

  • Maria Elena Innocenti – Simulating the heliosphere: from empirical models to a new numerical technique

Talks:

  • G. Lapenta, Relavistic reconnection, 3rd ISSI Meeting on “Collisionless shock physics: from non-relativistic to relativistic shocks”, Bern, Switzerland, 17-20 December, 2012.

Discrete Logarithms on Elliptic Curves over composite extension fields in characteristic 2

Project leader: Antoine JOUX, Univ. Versailles St-Quentin-en-Yvelines – PRISM, France
Research field: Maths & Computer Sciences

Publications:

  • Antoine Joux: A new index calculus algorithm with complexity $L(1/4+o(1))$ in small characteristic (Invited Talk). Selected Areas in Cryptography
  • Razvan Barbulescu, Pierrick Gaudry, Antoine Joux, Emmanuel Thomé : A quasipolynomial algorithm for discrete logarithm in finite fields of small characteristic, Preprint

Theses:

  • Razvan Barbulescu (Loria)

Invited talks:

  • Selected Areas in Cryptography 2013, Elliptic Curve Cryptography 2013, Algorithmic Number Theory Symposium 2014

Talks:

  • Discrete logarithms in small characteristic finite fields: A L(1/4+o(1)) algorithm, Antoine Joux (Séminaire ENS March 26th 2013, Séminaire Loria Nancy March 28th 2013, Séminaire IRMAR May 23rd 2013, Stanford security seminar June 5th 2013, Ecole Polytechnique June 20 2013, Séminaire CCA June 28th 2013).

High-accuracy quantum mechanic models for extended molecular systems.

Project leader: Branislav Jansik, Aarhus University – Institute of Chemistry, Denmark
Research field: Chemistry and Material Sciences

Publications:

  • J. J. Eriksen, P. Ettenhuber, K. Kristensen, T Kjærgaard, and P. Jørgensen, “A linear–scaling, embarrassingly parallel implementation of the coupled cluster CCSD(T) model” (to be submitted to J. Chem. Phys.)

Theses:

  • Patrick Ettenhuber, “The coupled cluster singles and doubles (CCSD) model in a divide expand consolidate (DEC) context” (midterm PhD progress report)

Talks:

  • Poul Jørgensen, “CCSD(T) Divide-Expand-Consolidate” at the Very Accurate and Large Computations and Applications (VALCA) 2013 conference in Fevik, Norway

Simulations of global accretion discs: turbulent transport and dynamo action

Project leader: Gianluigi Bodo, INAF – Osservatorio Astronomico di Torino, Italy
Research field: Astrophysics

Publications:

  • Bodo, G., Cattaneo, F., Mignone, A., Rossi, P., “Magnetorotational Turbulence in Stratified Shearing Boxes with Perfect Gas Equation of State and Finite Thermal Diffusivity”, ApJ, 761, 116, December 2012
  • Bodo, G., Cattaneo, F., Mignone, A., Rossi, P., “Fully Convective Magnetorotational Turbulence in Stratified Shearing Boxes” , ApJ, 771, L23, May 2013

Talks:

  • Gianluigi Bodo – International School of Space Science, Course on Astrophysical and Space Plasmas – L’Aquila September 2012
  • Fausto Cattaneo – Workshop on dynamical processes in astrophysical plasmas – Torino March 2013

High Performance Computing with Generic Solvers for Partial Differential Equations (HPC-PDE)

Project leader: Frederic Nataf, Universite Pierre et Marie Curie – Laboratoire Jacques-Louis Lions, France
Research field: Maths & Computer Sciences

Publications:

  • Jolivet, P., Hecht, F., Nataf, F., Prud’homme, C. A domain specific language for overlapping domain decomposition methods. To appear in Domain Decomposition Methods in Science and Engineering XXI.
  • Jolivet, P., Dolean, V., Hecht, F., Nataf, F., Prud’homme, C., Spillane, N. 2012. High performance domain decomposition methods on massively parallel architectures with FreeFem++. In Journal of Numerical Mathematics 20.4, pp. 287–302.
  • Nataf, F., Xiang, H., Dolean, V. 2010. A two level domain decomposition preconditioner based on local Dirichlet-to-Neumann maps. Comptes Rendus Mathematique, 348(21), 1163-1167.
  • Nataf, F., Xiang, H., Dolean, V., Spillane, N. 2011. A coarse space construction based on local Dirichlet to Neumann maps. SIAM Journal on Scientific Computing, 33(4), 1623-1642.
  • Spillane, N., Dolean, V., Hauret, P., Nataf, F., Pechstein, C., Scheichl, R. 2011. A robust two-level domain decomposition preconditioner for systems of PDEs. Comptes Rendus Mathematique.

Theses:

  • Jolivet Pierre, Domain decompositiong methods, Universite de Grenoble.

Talks:

  • Twelfth Copper Mountain conference on iterative methods, Copper Mountain, USA, March 25 – 30 March, 2012
  • SIAM Conference on Linear Algebra, Valencia, Spain, June 18 – 22, 2012
  • 21st International Conference on Domain Decomposition Methods, Rennes, France, June 25 – 29, 2012

Direct numerical simulation of reaction fronts in partially premixed charge compression ignition combustion: structures, dynamics

Project leader: Xue-Song Bai, Lund University, Sweden
Research field: Engineering and Energy

Publications:

  • Rixin Yu, Xue-Song Bai, “Direct numerical simulation of lean hydrogen/air autoignition in a constant volume enclosure”, Combustion and Flame, in press, 2013, Doi: http://dx.doi.org/10.1016/j.combust….
  • F. Zhang, R. Yu, X.S. Bai, “Direct numerical simulation of PRF70/air ignition in PPC engine conditions”, accepted by European Combustion Meeting, 2013.
  • F. Zhang, R. Yu, X.S. Bai, “DNS of Flame/spontaneous ignition interaction under SACI conditions”, Manuscript to be submitted for journal publication, 2013.
  • H. Carlsson, R. Yu, X.S. Bai, “DNS of flame/turbulence interaction at high Karlovitz numbers”, manuscript to be submitted for journal publication, 2013.

Theses:

  • Henning Carlsson
  • Fan Zhang

Invited talks:

  • Swedish national graduate school organized by the Swedish National Center for Combustion Science and Technology (CeCOST), within the course “Combustion Science”, May 8, 2013, by Xue-Song Bai
  • Federal University of Itajuba, Brazil, on “CFD modeling of biomass combustion”, April 15-18, 2013, by Xue-Song Bai

Eulerian and Lagrangian Turbulence over a reduced fractal skeleton

Project leader: Alessandra Sabina Lanotte, Consiglio Nazionale delle Ricerche – Istituto di Scienze dell’Atmosfera e del Clima, Italy.
Research field: Fundamental Physics

Publications:

  • Abstract at 2013 APS meeting ID: BAPS.2013.MAR.T16.8
  • Abstract: T16.00008 : Inverse Energy cascade in 3D Navier-Stokes eqsL. Biferale, S. Musacchio and F. Toschi
  • “The relation between degrees of freedom and intermittency in hydro-dynamical turbulence”, L. Biferale, A. S. Lanotte, S. Musacchio, P.Perlekar, and F. Toschi “Turbulent direct cascade of energy modified by fractal Fourier decimation”, L. Biferale, A. S. Lanotte, R. Scatamacchia, and F. Toschi

Theses:

  • Riccardo Scatamacchia, PhD student in cooperation between Dept. Physics, Univ.Tor Vergata, Rome Italy and the Technical Univ. of Eindhoven, Eindhoven, TheNetherlands.

Talks:

  • December 11, 2012. ENS Lyon, FranceL. Biferale “Inverse and Direct cascades in turbulence, revisited”
  • January 28, 2013. TUE Eindhoven, The NetherlandsL. Biferale, “Novel eddy simulations tools for turbulence”
  • September 23, 2013. At “Large Deviations and Rare Events in Physics andBiology” conference, Rome, Italy
  • A. Lanotte, “Turbulent direct cascade of energy modified by fractal Fourierdecimation”.

How strange is the nucleon?,

Project leader: Gunnar Bali, Universitaet Regensburg – Fakultaet fuer Physik, IT
Research field: Fundamental Physics

Publications:

  • G.S. Bali, S. Collins, B. Gläßle, M. Göckeler, J. Najjar, R. Rödl, A. Schäfer, R. Schiel, Wolfgang Soeldner, Andre Sternbeck and Philip Wein, “Nucleon generalized form factors and sigma term from lattice QCD near the physical quark mass”, PoS Lattice 2013, 291 (2013), arXiv:1312.0828 and in preparation.

Theses:

  • Johannes Najjar, “Nucleon structure from stochastic estimators”

Talks:

  • Sara Collins, “Nucleon strangeness from the lattice”, Workshop on Nucleon Matrix Elements for New-Physics Searches, ECT* Trento, 22 – 26 July, 2013.
  • Andre Sternbeck, “Nucleon generalized form factors and sigma term from lattice QCD near the physical quark mass”, 31st International Symposium on Lattice Field Theory – LATTICE 2013, Mainz, Germany, 29 July – 3 August, 2013.
  • Gunnar Bali, “The proton: where is its mass, where is its spin”, Conference on Scientific Computing 2013 (CSC 2013), Paphos, Cyprus, 3 – 6 December, 2013.

Direct Numerical Simulation of the Flow in an Internal Combustion Engine,

Project leader: Wolfgang Schröder, RWTH Aachen University – Institute of Aerodynamics, DE
Research field: Engineering and Energy

Publications:

  • M. Meinke, L. Schneiders, C. Günther, W. Schröder. “A cut-cell method for sharp moving boundaries in Cartesian grids”. Computers & Fluids, 85, pp. 135–142, 2012
  • C. Günther, M. Meinke, W. Schröder. “Application of a Cartesian-mesh immersed boundary method to 3D in-cylinder flow”. ASME paper, paper no. ICEF2012-92042, pp. 687-696, 2012
  • A. Lintermann, M. Meinke, W. Schröder. “Investigations of Human Nasal Cavity Flows Based on a Lattice-Boltzmann Method”. High Performance Computing on Vector Systems 2011, pp. 143-158, Springer Berlin/Heidelberg 2012
  • C. Günther, D. Hartmann, M. Meinke, W. Schröder. “A Level-Set Based Cartesian Grid Method to Simulate In-Cylinder Flow”. New Results in Numerical and Experimental Fluid Mechanics VIII, pp. 481-488, Springer, 2013
  • A. Lintermann, G. Eitel-Amor, M. Meinke, W. Schröder. “Lattice-Boltzmann Solutions with Local Grid Refinement for Nasal Cavity Flows”. New Results in Numerical and Experimental Fluid Mechanics VIII, pp. 583-590, Springer, 2013
  • N. Achilles, N. Pasch, A. Lintermann, W. Schröder, R. Mösges. “Computational fluid dynamics: a suitable assessment tool for demonstrating the antiobstructive effect of drugs in the therapy of allergic rhinitis”. Acta Otorhinolaryngologica Italica, 33, pp. 36-42, 2013
  • Lintermann, M. Meinke, W. Schröder. “Fluid Mechanics Based Classification of the Respiratory Efficiency of Several Nasal Cavities”. Computers in Biology and Medicine, accepted for publication, 2013 (doi:10.1016/j.compbiomed.2013.09.003)
  • C. Günther, M. Meinke, W. Schröder. “A flexible multiple level-set method for capturing and tracking moving embedded interfaces”. Computer & Fluids, under review, 2013

Theses:

  • Marcus Haas, Jan-Niklas Paprott, Dennis Schmechta: “Simulation von 3D Motorinnenströmungen für verschiedene Flow-Bench Konfigurationen mit einem kartesischen Cut-Cell Strömungslöser” (Project work)
  • Henning Krings: “Optimized representation and tracking of complex moving boundaries using a level-set method” (Bachelor thesis)
  • Gonzalo Brito Gadeschi: “A partitioned fluid-structure interaction method on solution-adaptive hierarchical Cartesian grids” (Diploma thesis)
  • Alexander Richter: “Implemenation and assessment of two methods for the efficient computation of distance functions on hierarchically refined Cartesian grids” (Bachelor thesis)
  • Jiechu Jiang: “Pulsatile Boundary Conditions for a Lattice-Boltzmann Method to Simulate the Unsteady Flow in the Lower Human Respiratory System” (Bachelor thesis)
  • Stephan Karth, Nils Köpke-Chappele: “Integration of thermal induced convection and thermal boundary
    conditions in a Lattice-Bolztmann flow solver to simulate natural convective flows” (Project work)
  • Andreas Langenfeld: “Simulation of particel transport coupled to flow solutions obtained by a Lattice-Boltzmann Method” (Bachelor thesis)
  • Simon Dieckmann: “Wall shear stress computation with a Lattice-Boltzmann Method” (Study thesis)

Talks:

  • C. Günther, M. Meinke, W. Schröder. “A multiple-level-set approach for the simulation of flows with moving immersed boundaries”. 6th European Congress on Computational Methods in Applied Sciences and Engineering (Eccomas 2012), 10.-14.09.2012
  • C. Günther, M. Meinke, W. Schröder. “Application of a Cartesian-mesh immersed boundary method to 3D in-cylinder flow”.ICEF 2012 – ASME Internal Combustion Engine Fall Conference, Vancouver, 23.-26.09.2013
  • C. Günther, W. Schröder, B. Kerschgens, P. Zeng, M. Gauding, N. Peters, H. Pitsch. “Multi-Scale Simulationsof TMFB in Internal Combustion Engines”. 5. TMFB International Workshop, Aachen, 13.-14.06.2012
  • M. Meinke, L. Schneiders, C. Günther, W. Schröder. “A Cut-Cell Method for Sharp Moving Boundaries in Cartesian Grids”. International Workshop on Future of CFD and Aerospace Sciences, Kobe, Japan, 23.-25.04.2012
  • A. Lintermann, M. Meinke, W. Schröder. “ZFS – Flow Solver AIA”. NVIDIA Application Lab at Jülich: 1st Annual Workshop, 08.-09.07.2013
  • A. Lintermann, M. Meinke, W. Schröder. “Parallel Mesh Generation for HPC Applications”. PRACE – WP 8 Workshop, Paris, 21.03.2012
  • A. Lintermann, C. Siewert, M. Meinke, W. Schröder. “Flow Solver ZFS – Expectations, Concerns, and Experiences with XE6”. CRAY Optimisation Workshop, HLRS Stuttgart, 07.02.2012

Shock Acceleration in the Laboratory with Ultraintense Lasers: from astrophysics to ion acceleration for medical applications,

Project leader: Luis Silva, Instituto Superior Técnico – Instituto de Plasmas e Fusão Nuclear – Laboratório Associado, PT
Research field: Fundamental Physics

Publications:

  • H. Nakamura et al. “Generation and guiding of narrow divergence electron beams in relativistically intensle laser-matter interactions”, in preparation
  • M. Vranic, J. Vieira, H. Nakamura, R. A. Fonseca, P. Norreys, L. O. Silva, “Simulations of ps-laser channeling and fast electron generation in realistic density gradients”, in preparation;
  • M. Vranic, J. Vieira, H. Nakamura, R. A. Fonseca, P. Norreys, L. O. Silva “Two-pulse channeling”, in preparation;
  • A. Stockem, F. Fiuza, R.A. Fonseca, and L.O. Silva, “Transition from electrostatic to electromagnetic collisionless shocks”, in preparation;
  • A. Stockem, T.A. Grismayer, R.A. Fonseca, and L.O. Silva, “Electromagnetic field generation in the downstream of electrostatic shocks due to electron trapping”, in preparation;
  • F. Fiuza, R. A. Fonseca, W. B. Mori, and L. O. Silva, “On the generation of collisionless shocks: from astrophysical settings to laboratory plasmas”, in preparation;
  • A. Stockem, F. Fiuza, E. Boella, R.A. Fonseca, L.O. Silva, C. Joshi, and W.B. Mori, “Theoretical studies of collisionless shocks for laser-acceleration of ions”, SPIE – Optics and Optoelectronics, 8779-10 (2013).
  • A. Bret, A. Stockem, F. Fiuza, C. Ruyer, L. Gremillet, R. Narayan, L. O. Silva, “Relativistic collisionless shocks formation in pair plasmas”, Journal of Plasma Physics, accepted (2013)
  • A. Stockem, E. Boella, F. Fiuza, L. O. Silva, “Relativistic generalization of formation and ion-reflection conditions in electrostatic shocks”, Physical Review E 87, 043116 (2013);
  • A. Bret, A. Stockem, F. Fiuza, C. Ruyer, L. Gremillet, R. Narayan, L. O. Silva, “Collisionless shock formation, spontaneous electromagnetic fluctuations, and streaming instabilities”, Physics of Plasmas 20, 042102 (2013);
  • F. Fiuza, A. Stockem, E. Boella, R. A. Fonseca, L. O. Silva, D. Haberberger, S. Tochitsky, W. B. Mori, C. Joshi, “Ion acceleration from laser-driven electrostatic shocks”, Physics of Plasmas 20, 056304 (2013);
  • F. Fiuza, A. Stockem, E. Boella, R. A. Fonseca, L. O. Silva, D. Haberberger, S. Tochitsky, C. Gong, W. B. Mori, C. Joshi, “Laser-driven shock acceleration of monoenergetic ion beams”, Physical Review Letters 109, 215001 (2012);
  • A. Stockem, F. Fiuza, R. A. Fonseca, L. O. Silva, “The impact of kinetic effects on the properties of electron-positron shocks”, Plasma Physics and Controlled Fusion 54, 125004 (2012);
  • A. Stockem, F. Fiuza, R. A. Fonseca, and L. O. Silva, “Acceleration in perpendicular relativistic shocks for plasmas consisting of leptons and hadrons”, The Astrophysical Journal 755, 68 (2012);
  • K. Singh, J. R. Davies, G. Sarri, F. Fiuza, and L. O. Silva, “Dynamics of intense laser propagation in underdense plasma: polarization dependence”, Physics of Plasmas 19, 073111 (2012);
  • F. Fiuza, R. A. Fonseca, J. Tonge, W. B. Mori, and L. O. Silva, “Weibel-instability-mediated collisionless shocks in laboratory with ultraintense lasers”, Physical Review Letters 108, 235004 (2012);

Theses:

  • Frederico Fiuza, “Multi-scale PIC modeling of high energy density scenarios: from laboratory to astrophysics”

Invited talks:

  • F. Fiuza, “Producing high-quality and high-energy ion beams from laser-driven electrostatic shocks”, 40th EPS Plasma Physics Division, Espoo (Finland), 2013;
  • A. Stockem, “Theoretical studies of collisionless shocks for laser-acceleration of ions”, SPIE – Optics and Optoelectronics, Prague (Czech Republic), 2013;
  • A. Stockem, “Theoretical studies of collisionless shocks and electromagnetic field generation for laser acceleration of ions”, Seminar at Helmholtz-Institut, Jena (Germany), 2013;
  • A. Stockem, “The importance of electromagnetic modes in electrostatic shocks”, ISSI meeting, Bern (Switzerland), 2012;
  • F. Fiuza, “Collisionless shocks and particle acceleration in laser-driven laboratory plasmas”, 54th APS Division of Plasma Physics, Providence (USA), 2012;

Talks:

  • A. Stockem, “Exploring the transition from electromagnetic shocks to electrostatic shocks”, ICHED, St. Malo (France), 2013
  • M. Vranic, “Simulations of laser channeling and fast electron generation in realistic density gradients”, 11th Direct Drive and Fast Ignition Workshop, Rome (Italy), 2013;
  • F. Fiuza, R. A. Fonseca, L. O. Silva, W. B. Mori, “Fully kinetic modeling of laser absorption and electron transport for fast ignition conditions”, 12th International Workshop on Fast Ignition of Fusion Targets, Napa Valley (USA), 2012;
  • F. Fiuza, R. A. Fonseca, L. O. Silva, W. B. Mori, “Integrated hybrid-PIC modeling of fast ignition”, 54th APS Division of Plasma Physics, Providence (USA), 2012;
  • A. Stockem, “On the transition from electromagnetic to electrostatic shocks”, 54th APS Division of Plasma Physics, Providence (USA), 2012;

Numerical Simulation of 3D Unsteady Reactive Dense Particle Laden Flows,

Project leader: Olivier Simonin, Institut National Polytechnique de Toulouse – Institut de Mécanique des Fluides de Toulouse, FR
Research field: Engineering and Energy

Publications:

  • Neau, H., Fede, P., Laviéville, J., Simonin, O., High Performance Computing (Hpc) For The Fluidization Of Particle-Laden Reactive Flows, Fluidization XIV, May 26-31, 2013, Netherlands

Theses:

  • Nicolas Nouyrigat, 2012, “Hydrodynamic modeling of poly-solid reactive circulating fluidized beds: Application to Chemical Looping Combustion”
  • Guillaume Moula, 2012, “Multi-scale analyze of gas-particle reactive flow in a dense fluidized bed”
  • Ali Ozel, 2011, “Development of Large Eddy Simulation Approach for Simulation of Circulating Fluidized Beds”
  • Jean-François Parmentier, 2010, “Extension of the Euler/Euler formalism for numerical simulations of fluidized beds of Geldart A particles

Talks:

  • The team has participated to the International Conference on Multiphase Flows (ICMF) 2013 in Jeju South Corea. Four talks have been done by the team. All talks was based on results obtained with NEPTUNE CFD.

Star formation in extreme conditions: Shock heating, thermal cooling and turbulent dissipation in Stephan’s Quintet,

Project leader: Frederic Bournaud, CEA Saclay – DSM/IRFU, FR
Research field: Astrophysics

Publications:

  • F. Renaud et al. Star cluster formation and evolution in interacting galaxies (in submission)
  • F. Bournaud et al. ISM turbulence and fragmentation in interacting galaxies (in submission)
  • K. Kraljic et al. Star formation scaling-laws in isolated and interacting galaxies (in submission)

Theses:

  • Ms. Katarina Kraljic (CEA Saclay, France) – On the link between galaxy evolution and star formation physics
  • Ms. Orianne Roos (CEA Saclay, France) – ionization of the galactic interstellar medium : stars, active nuclei, and feedback processes

Talks:

  • Star formation and AGN fueling by disk instabilities and galaxy mergers (F. Bournaud, Leiden University, July 2013)
  • Star formation in interacting systems (F. Bournaud, Naples Observatory, September 2013)
  • Star formation in isolated and interacting galaxies (F. Renaud, Santa Fe USA, October 2013)
  • ISM turbulence: internal and external triggers (F. Bournaud, Munchen Germany, June 2013)

High-fidelity simulations of multiscale-generated turbulence,

Project leader: John Christos Vassilicos, Imperial College London – Aeronautics, UK
Research field: Engineering and Energy

Publications:

  • Laizet S. & Vassilicos J.C., Stirring and mixing by grid-generated turbulence in the presence of a mean scalar gradient, 4th International Conference on Jets, Wakes and Separated Flows, Nagoya, Japan – 17/09-21/09 2013
  • Vassilicos J.C. & S. Laizet, What are the origins of -5/3 spectra and related dissipation scalings?, 4th International Conference on Jets, Wakes and Separated Flows, Nagoya, Japan – 17/09-21/09 2013
  • Vassilicos J.C. & Laizet S., Coexistence of regions of equilibrium and non equilibrium two-point turbulence dynamics in grid-generated turbulence, both with -5/3 spectra but different underlying physics, 8th International Symposium on Turbulence and Shear Flow Phenomena Poitiers, France – 28/08-30/08 2013
  • Laizet S. & Vassilicos J.C., Stirring and mixing by grid-generated turbulence in the presence of a mean scalar gradient, 8th International Symposium on Turbulence and Shear Flow Phenomena Poitiers, France – 28/08-30/08 2013
  • Laizet S., Fortune V., Lamballais E., Vassilicos J.C., Low Mach number prediction of the acoustic signature of fractal-generated turbulence, 65th Annual DFD Meeting American Physics Society, San Diego, California, USA, 18/11-20/11 2012

Full-f gyrokinetic simulation of edge pedestal in Textor,

Project leader: Timo Kiviniemi, Aalto University – School of Science, FI
Research field: Engineering and Energy

Publications:

  • S. Leerink, V. V. Bulanin, A. D. Gurchenko, E. Z. Gusakov, J. A. Heikkinen, S. J. Janhunen, S. I. Lashkul, A. B. Altukhov, L. A. Esipov, M. Yu. Kantor, T. P. Kiviniemi, T. Korpilo, D. V. Kuprienko, and A. V. Petrov,”Multiscale Investigations of Drift-Wave Turbulence and Plasma Flows: Measurements and Total-Distribution-Function Gyrokinetic Simulations” Phys. Rev. Lett. 109, 165001 (2012).
  • Korpilo, T., Heikkinen, J.A., Janhunen, S.J., Kiviniemi, T.P., Leerink, S., Ogando, F., Numerically stable method for kinetic electrons in gyrokinetic particle-in-cell simulation of toroidal plasmas, Journal of Computational Physics 239, pp. 22-29 (2013)
  • Gusakov, et al “Anomalous transport and multi-scale drift turbulence dynamics in tokamak ohmic discharge as measured by high resolution diagnostics and modeled by full-f gyrokinetic code”, submitted to plasma physics and controlled fusion
  • T.P. Kiviniemi et al, “Comparison of gyrokinetic simulation of parallel plasma conductivity to analytical models”, to be submitted to Plasma Physics and Controlled Fusion
  • T.P. Kiviniemi, P.Niskala, S.Leerink, J.Heikkinen, S.Janhunen and T.Korpilo, Gyrokinetic simulation of GAMs in Textor plasma edge, P2.187, in Proceedings of 40th EPS Conference on Plasma Physics 1 – 5 July 2013, Espoo, Finland.
  • J.A. Heikkinen, T. Korpilo, T. Pyy, S.J.Janhunen, T.P. Kiviniemi, S. Leerink, Gyrokinetic calculation of plasma transport with a material boundary, P1.109, T. Kurki-Suonio and the ASDEX Upgrade team, P5.101, in Proceedings of 40th EPS Conference on Plasma Physics 1 – 5 July 2013, Espoo, Finland.

Theses:

  • Doctoral Dissertation:Susan Leerink, “Gyrokinetic full-f transport simulations of ohmic FT-2 tokamak discharges”, Aalto University, 2012
  • Doctoral Dissertation: S. Janhunen, “Gyrokinetic particle simulation for thermonuclear plasma turbulence studies in magnetic confinement”, Aalto University, 2013.

Talks:

  • S.Leerink, “Multiscale transport in ohmic FT-2 tokamak discharges” EU-US TTF meeting in Santa Rosa, USA (9-12.4.2013)
  • S. Janhunen, “Multi-Scale Drift Turbulence Dynamics in Ohmic Discharge as Measured at the FT-2 Tokamak and Modeled by Full-f Gyrokinetic ELMFIRE-code”, 24th IAEA FEC in San Diego, 8-13.10.2012

Invited talks:

  • E.Gusakov, “Anomalous transport and multi-scale drift turbulence dynamics in tokamak ohmic discharge as measured by high resolution diagnostics and modeled by full-f gyrokinetic code”, 40th EPS Conference on Plasma Physics 1 – 5 July 2013, Espoo, Finland.

All-atom simulation of the Amyloid-beta peptide interacting with Gold nanoparticles (AmyGo),

Project leader: Stefano Corni, CNR Istituto Nanoscienze – Centro S3, IT
Research field: Chemistry and Material Sciences

Invited talks:

  • S. Corni -XI International Conference on Nanostructured Materials, NANO 2012, Rhodos (Greece), Aug. 2012
  • S.Corni-Workshop ADGLASS “Atomistic modelling for industrial product development”, Bremen (Germany), Nov. 2012
  • S. Corni -Workshop “Stat Phys of Bio-molecules”, Trieste (Italy), Dec. 2012
  • S. Corni – 142nd TMS annual meeting, San Antonio(USA), Mar. 2013

Talks:

  • IIT Center for Nanobiotecnology (Dr. P.P.Pompa), Lecce (Italy), Nov. 2012
  • ETH/USI (Prof. M. Parrinello), Lugano (Switzerland), Aug. 2013
  • L. Bellucci – Workshop on Neuro Degenerative Diseases, Udine (Italy), Jan. 2013
  • L. Bellucci – Workshop on nanoMedicine and Nanobiosystems (WoMeN), Lecce (Italy) Sept. 2012

Comprehensive ab initio simulations of turbulence in ITER-relevant fusion plasmas,

Project leader: Frank Jenko, Max Planck Institute for Plasma Physics (IPP) – Tokamak Physics, DE
Research field: Engineering and Energy

Publications:

  • D. Told, F. Jenko, T. Görler, F. J. Casson, E. Fable, and ASDEX Upgrade Team, “Characterizing Turbulent Transport in ASDEX Upgrade L-mode Plasmas via Nonlinear Gyrokinetic Simulations”, Physics of Plasmas 20, 122312 (2013)
  • T. Görler, D. Told, A. E. White, and F. Jenko, “A complementary and comparative gyrokinetic analysis of DIII-D L-mode turbulence”, to be submitted to Physics of Plasmas (2014)

Talks:

  • T. Görler, “Issues in local and nonlocal transport modeling”, 6th Gyrokinetic Working Group Meeting, Mar 18th – 29th, 2013, WPI, Vienna
  • F. Jenko, “Simulations of Turbulence in Fusion and Astrophysical Plasmas on Exascale Platforms”, International Supercomputing Conference, Leipzig, 19th June 2013
  • F. Jenko, “Does gyrokinetics predict a transport shortfall in the outer core of L-mode plasmas?”, 7th Festival de Théorie, Aix-en-Provence, France, 8 July 2013
  • T. Görler, “Gyrokinetic turbulence investigations with GENE – the numerics behind and some applications”, Numerical Methods for the Kinetic Equations of Plasma September 2nd-6th, 2013, Garching, Germany
  • F. Jenko, 11th ITPA Transport & Confinement Meeting, October 7th-9th, 2013, Kyushu University, Fukuoka, Japan
  • D. Told, “Characterizing Turbulent Transport in ASDEX Upgrade L-mode Plasmas via Nonlinear Gyrokinetic Simulations”, Theory Seminar, November 18th -22th, 2013, Usedom, Germany
  • T. Görler, “Can gyrokinetics describe outer-core DIII-D L-modes?”, Theory Seminar, November 18th -22th, 2013, Usedom, Germany

The domain interplay in protein kinases: free energy calculations on the allosteric effect of the SH2 domain on kinase activation,

Project leader: Francesco L. Gervasio, Spanish National Cancer Research Center (CNIO) – Structural Biology and Biocomputing, ES
Research field: Chemistry and Material Sciences

Publications:

  • C. Herbert, …, F.L. Gervasio* et al. Molecular mechanism of SSR128129E, an extracellularly acting small molecule allosteric inhibitor of FGF receptor signaling, Cancer Cell, 23, 489-501, 2013
  • J. Juraszek, G. Saladino, T. VanErp, F.L. Gervasio* Efficient numerical reconstruction of protein folding kinetics with partial path sampling and path-like variables. Phys Rev Lett, 110, 108106, 2013
  • L. Sutto & F L Gervasio* The effect of oncogenic mutations on the conformational free energy landscape of EGFR kinase Proc Natl Acad Sci USA, 110, 10616-10621, 2013.
  • N. Dölker, Maria. Górna, A. S. Torralba, F. L. Gervasio, and G. Superti-Furga. The SH2 domain regulates c-Abl kinase activity by a cyclin-like mechanism and impairment of the hinge motion submitted to PNAS.

Theses:

  • Silvia Lovera

Invited talks:

  • 7th International Conference Inhibitors of Protein Kinases Warsaw 24-27 Aug 2012
  • CECAM ” Machine learning in atomistic simulations”, Lugano, Sep 2012
  • Invited talk CPMD meeting 2013, Leipzig, Sept. 2-6, 2013
  • CECAM “Innovative Approaches to Computational Drug Discovery, Lausanne, Oct 2013

Extreme Star-Formation Modeling: From the Galactic Fountain to Single Stars in One Run,

Project leader: Paolo Padoan, Catalan Institute for Research and Advanced Studies (ICREA) and University of Barcelona – Institute of Cosmos Sciences (ICC), ES
Research field: Astrophysics

Publications:

  • Padoan, P., et al. 2013, “The Star Formation Rate of Molecular Clouds”, Protostars and Planet VI, invited review, submitted

Talks:

  • “The Star Formation Rate of Molecular Clouds”, Protostars and Planets VI, Heidelberg, Germany, 15/07/2013.
  • “The Star Formation Rate and the Stellar Initial Mass Function in Turbulent Clouds”, Ringberg workshop on Regulation of Star Formation in Molecular Gas, Ringberg, Germany, 23/06/2013.

Thousands of trees for 4 billion years of life evolution on Earth,

Project leader: Bastien Boussau, CNRS – Life sciences, FR
Research field: Medicine and Life Sciences

Publications:

  • Szollosi GJ, Rosikiewewicz W,Boussau B, Tannier E, Daubin V. “Efficient Exploration of the Space of Reconciled Gene Trees”. Systematic Biology, 2013.

Talks:

  • Phylogenetics session, Evolution 2013, Snowbird, USA
  • Tree of Life symposium, Evolution 2013, Snowbird, USA
  • MCEB 2013 seminar, Montpellier, France
  • MVZ lunch seminar, UC Berkeley, USA

NadiaSpectral DNS of boundary layer transition in channel flows,

Project leader: Marc BUFFAT, Université Lyon 1 – LMFA, FR
Research field: Engineering and Energy

Publications:

  • M. Buffat, L. Le Penven., A. Cadiou, and J. Montagnier. “DNS of bypass transition in entrance channel flow induced by boundary layer interaction”, European Journal of Mechanics-B/Fluids, doi:10.1016/j.euromechflu.2013.06.009, June, 2013.
  • J. Montagnier, A. Cadiou, M. Buffat, L. Le Penven, “Towards petascale spectral simulations for transition analysis in wall bounded flow”, Int. J. Numer. Methods Fluids, doi:10.1002/fld.3758, December, 2012.
  • L. Le Penven, M. Buffat, “On the spectral accuracy of a fictitious domain method for elliptic operators in multi-dimensions”. Journal of Computational Physics,231(23):7893-7906, October, 2012.
  • M. Buffat, L. Le Penven, “A spectral fictitious domain method with internal forcing for solving elliptic PDEs”, Journal of Computational Physics, 230, 2433-2450. doi:10.1016/j.jcp.2010.12.004, 2011.
  • M. Buffat, L. Le Penven, A. Cadiou, “An efficient spectral method based on an orthogonal decomposition of the velocity for transition analysis in wall bounded flow”, Comput. Fluids, 42, 62-72, doi:10.1016/j.compfluid.2010.11.003, 2011.

Talks:

  • A. Cadiou, M. Buffat, L. Le Penven, “Analyse et visualisation en temps-réel de calculs HPC pour l’étude de la transition turbulence en entrée de canal : vers la réalisation d’expériences numériques”, Colloque Equip@Meso : Journées MesoChallenge, Paris, France, September, 2013.
  • A. Cadiou, M. Buffat, L. Le Penven, “Vers la simulation sur les nouvelles architectures massivement parallèle : un retour d’expérience”, Séminaire au Laboratoire d’Hydrodynamique, Energétique et Environnement Atmosphérique, September, 2013.
  • A. Cadiou, M. Buffat, L. Le Penven, “HPC et Mécanique des Fluides”, Ecole découverte du calcul, Villeurbanne, France, September, 2013
  • M. Buffat, L. Le Penven, A. Cadiou, “Non modal subcritical transition of a channel entry flow”, 14th European turbulence conference, Lyon, France, September, 2013.
  • A. Cadiou, M. Buffat, L. Le Penven, J. Montagnier. “Passage à l’échelle Tier1 -> Tier0 d’une application de CFD par hybridation MPI / OpenMP”. Colloque Equip@Meso, Mécanique des fluides numérique intensive : méthodes et nouvelles applications, Rouen, France, May, 2013.
  • A. Cadiou, M. Buffat, L. Le Penven, and J. Montagnier. “Simulation sur les nouvelles architectures massivement parallèles : un exemple en mécanique des uides”. LyonCalcul, Lyon France, December, 2012.

Structural determination of complex organic/biological molecular assembly from ab-initio NMR,

Project leader: Stefano De Gironcoli, International School for Advanced Studies – SISSA – Condensed Matter Theory Sector, IT
Research field: Chemistry and Material Sciences

Publications:

  • N. Varini, D. Ceresoli, L. Martin-Samos, I. Girotto and C. Cavazzoni, “Towards Petascale DFT-calculations: a new parallelization approach for linear response and exact exchange”, Comput. Phys. Comm. 184, 1827 (2013)
  • R. Sabatini, E. Kucukbenli, B. Kolb, T. Thonhauser, S. de Gironcoli, “Structural evolution of amino acid crystals under stress from a non-empirical density functional”, Journal of Physics-Condensed Matter 24, 424209 (2012).
  • R. Sabatini, T. Gorni, S. de Gironcoli, “Nonlocal van der Waals density functional made simple and efficient”, Phys. Rev. B 87, 041108 (2013)
  • A.R. Ferreira, E. Kucukbenli, S. de Gironcoli, et. al., “Structural models of activated gamma-alumina surfaces revisited:Thermodynamics, NMR and IR spectroscopies from ab initio calculations”, Chemical Physics 423, 62 (2013).
  • C.H.Pham, E.Kucukbenli, X. Zhu, A. Oganov, S.de Gironcoli, “Prediction of Glycine polymorphism from first principles”, in preparation
  • C.H.Pham, E.Kucukbenli, S.de Gironcoli, “NMR spectra of Cholesterol polymorphs”, in preparation
  • M. Monni, X. Ge, B.I. Adetunj, E. Kucukbenli, S. de Gironcoli, A. Dal Corso, “Validation and Verification of pseudopotentials and PAW datasets across the periodic table”, in preparation

Theses:

  • Cong Huy Pham – PhD @ SISSA

Three-Dimensional Simulations of Core-Collapse-Supernova-Explosions of Massive Stars Applying Neutrino Hydrodynamics,

Project leader: Hans-Thomas Janka, Max-Planck-Institut fuer Astrophysik – Hydrodynamics Group, DE
Research field: Astrophysics

Publications:

  • Müller B., et al., “New Two-Dimensional Models of Supernova Explosions by the Neutrino-Heating Mechanism: Evidence for Different Instability Regimes in Collapsing Stellar Cores”, Astrophys.J. 761, 72, December 2012
  • Janka H.-Th., et al., “Core-collapse supernovae: Reflections and directions”, Prog. Theor. Exp. Phys., Vol. 2012, id. 01A309, December 2012
  • Müller B., et al., “A New Multi-Dimensional General Relativistic Neutrino Hydrodynamics Code of Core-Collapse Supernovae III. Gravitational Wave Signals from Supernova Explosion Models”, Astrophys.J. 766, 43, March 2013
  • Hanke F., et al., “SASI Activity in Three-Dimensional Neutrino-Hydrodynamics Simulations of Supernova Cores”, Astrophys.J., 770, 66, May 2013
  • Tamborra I., et al., “Neutrino signature of supernova hydrodynamical instabilities in three dimensions”, arXiv:1307.7936 (astro-ph), submitted to Physical Review Letters, July 2013

Theses:

  • F. Hanke, PhD thesis, Technical University Munich, in preparation

Invited talks:

  • H.-Th. Janka:• Connecting the Electromagnetic and Gravitational Wave Skies in the Era of Advanced LIGO (Princeton, New Jersey, 30.4.–4.5.2012)• CompStar: the Physics and Astrophysics of Compact Stars (Papeete, Tahiti, 4.6.–8.6.2012)• Outstanding Problems in Massive Star Research the Final Stages (St. Paul, MN, 30.9.–3.10.2012)• Quarks to Universe in Computational Science (QUCS 2012) (Nara, Japan, 13.12.–16.12.2012)• Death of Stars and Lives of Galaxies (Santiago, Chile, 8.4.–12.4.2013) • Fifty-One Ergs (Raleigh, North Carolina, 13.5.–17.5. 2013)• Nuclear Physics in Astrophysics VI (NPA-VI) (Lisbon, Portugal, 19.5.–24.5.2013)• University Thessaloniki, Greece (23.04.2013)• Universität Würzburg (6.6.2013)• MPI Astronomie, Heidelberg (11.6.2013)• Universität Gießen (13.6.2013)• Universität Dresden (25.6.2013)
  • B. Müller:• Formations of Compact Objects: From the Cradle to the Grave (Tokyo, 7.3.- 9.3.2012)• Supernovae Illuminating the Universe: from Individuals to Population (Garching, 10.9.-14.9.2012)• Outstanding Problems in Massive Star Research (St Paul, MN, 30.9.- 3.10.2012)• Technische Universität Darmstadt (28.6.2012)• Indiana University Bloomington (22.2.2013)• Monash University (23.7.2013)
  • F. Hanke:• TGCC/CEA

Talks:

  • F. Hanke:• Sixteenth Workshop on Nuclear Astrophysics (Ringberg Castle at Lake Tegernsee, 26.3-31.3.2012)• INT Program INT-12-2a Core-Collapse Supernovae: Models and Observable Signals (Seattle, Washington, 25.6-27.7.2012
  • H.-Th. Janka:• INT Program INT-12-2a Core-Collapse Supernovae: Models and Obs
    ervable Signals (Seattle, Washington, 25.6-27.7.2012)• International Workshop on Astrophysics and Nuclear Structure (Hirschegg, Austria, 27.1.–31.1. 2013)• International Workshop on Realtime Astroparticle Physics (Bonn, 4.2.– 6.2.2013)• 10-th Russbach School on Nuclear Astrophysics (Russbach, Austria, 10.3.– 15.3.2013)• International Workshop “Neutron Stars: Nuclear Physics, Gravitational Waves and Astronomy” (Surrey, England, 29.07.–30.7.2013)
  • B. Müller:• Sixteenth Workshop on Nuclear Astrophysics (Ringberg Castle at Lake Tegernsee, 26.3-31.3.2012)• INT Program INT-12-2a Core-Collapse Supernovae: Models and Observable Signals (Seattle, 25.6-27.7.2012)• Death of Stars and Lives of Galaxies (Santiago, Chile, 8.4.–12.4.2013)• Fifty-One Ergs (Raleigh, North Carolina, 13.5.–17.5. 2013)

Public understandings:

  • H.-Th. Janka:• Congress Center Hamburg (19.6.2012)• Lehrerakademie Dillingen (19.9.2012)• Universität Bochum (27.10.2012)• Planetarium Münster (5.3.2013)• Planetarium Stuttgart (21.3.2013)
  • B. Müller:• Volkssternwarte Winzer (24.3.2012)• Astronomie-Club Vilshofen (10.10.2012)• VHS Deggendorf (25.4.2013)

Mesoporous silica for drug delivery: a quantum mechanical simulation,

Project leader: Piero Ugliengo, Università di Torino – Dip. Chimica, IT
Research field: Chemistry and Material Sciences

Publications:

  • Delle Piane M., Corno M., Ugliengo P. “Does dispersion dominate over H-bonds in drug-surface interactions? The case of silica-based materials ad excipients and drug-delivery agents”, Journal of Chemical Theory and Computation, 9, 5, 2404-2415, March 2013.
  • Delle Piane M., Corno M., Pedone A., Dovesi R., Ugliengo P. “B3LYP and B3LYP-D* simulation of ibuprofen adsorbed in MCM-41: structural, energetic, vibrational and NMR spectroscopic features”, in preparation to be submitted to J. Am. Chem. Soc.

Theses:

  • Ms. Francesca Peccati – “Density functional static and dynamic study of carbonate apatite”
  • Mr. Stefano Vaccari – “Ab initio study of amorphous silica/ibuprofen system: the role of microsolvation”

Talks:

  • Delle Piane M., “Silica-Based Materials In Pharmaceutical Formulations: An Insight From Quantum-Mechanical Simulations” – National Congress of the Physical Chemistry Division of the Italian Chemical Society, Alessandria (IT), June, 23rd, 2013. (http://www.chimicafisica2013.unipmn…)
  • Ugliengo P., “Can dispersion overcome H-bond interactions? The case of drugs adsorbed on silicas modeled at DFT-D2 level” – IV Jornada IQTCUB, 4th IQTCUB Symposium, Universitat de Barcelona (ES), June, 21st 2013. (http://www.iqtc.ub.es/ca/news/60-4t…)
  • Ugliengo P., “Can dispersion overcome H-bond interactions? The case of drugs adsorbed on silicas modeled at DFT-D2 level” – QUITEL2013, XXXIX International Conference, Theoretical Chemists of Latin Expression, Granada (ES), June, 30th – July, 5th 2013. (http://granada.congresoseci.com/qui…)
  • Ugliengo P., “Quantum Mechanical Modeling of Molecular Recognition at the Surface of Inorganic Biomaterials” – Workshop in Solid State Quantum Chemistry in honour of Cesare Pisani, Torino (IT), September, 6-7th 2013. (http://www.theochem.unito.it/WSSQC-…)