9th Project Access Call – Awarded Projects

Results of the 9th Call for Proposals for Project Access.

Nucleon structure using lattice QCD simulations with physical pion mass

Project leader: Constantia Alexandrou, University of Cyprus and The Cyprus Institute, Cyprus

Research field: Fundamental Physics

Resource Awarded: 65 000 core hours on Curie H, 25 300 000 core hours on FERMI, 13 800 000 core hours on SuperMUC

Collaborators: Giannis Koutsou, The Cyprus Institute- Cyprus, Karl Jansen, DESY- Germany,  Marc Wagner, Goethe University Frankfurt am Main- Germany, Vincent Drach, Odense University- Denmark, Roberto Frezzotti, Universita di Roma Tor Vergata- Italy,  Giancarlo Rossi, Universita di Roma Tor Vergata- Italy, Chris Micahel, University of Liverpool – Untied Kingdom

Abstract: Fundamental properties of the nucleon, which makes the bulk of the visible matter in our universe are computed with focus on quantities that probe physics beyond the standard model. We use ab initio simulations of the fundamental theory of the strong interactions Quantum Chromodynamics (QCD) formulated in terms of quarks and gluons. The novelty of this project is that it uses simulations with physical values of the quark masses and recently developed methods to compute disconnected quark loop contributions. Using noise reduction techniques we aim at reaching unprecedented accuracy in the calculation of fundamental quantities such as the nucleon axial charge, the spin carried by the quarks in the proton and the charge radius as well as observables that probe beyond the standard model such as the neutron electric dipole moment, the nucleon sigma-terms and the charge and tensor charges. The project is part of the European Twisted Mass Collaboration, a consortium of more than 50 physicists from eight European countries. Approximately 20 PhD students and postdoctoral fellows are involved in these complex computations at the forefront of scientific computing.

Large-scale radiation damage cascades from first principles

Project leader: Emilio Artacho, CIC nanoGUNE, Spain

Research field: Chemistry

Resource Awarded: 36 000 000 core hours on Hermit

Collaborators: Fabiano Corsetti, CIC nanoGUNE- Spain,  Kai Nordlund, University of Helsinki-Finland

Abstract: Cascade dynamics in bulk materials from ion irradiation give rise to complex processes that disrupt the crystalline structure over large regions. Characterising and understanding such processes has long been recognized as a significant challenge in materials science, as well as being of great practical importance, especially in the nuclear industry. Although collision cascades have until now been studied with empirical classical potentials, due to the large length and time scales involved, electronic structure methods offer the possibility of much greater accuracy and true ab initio predictive power. To this end, we use density-functional theory with the SIESTA code to simulate a number of collision cascades in silicon entirely from first principles, using a large system size of more than four thousand atoms and a total simulation time of forty picoseconds.

EXCOMM — EXtreme scale domain decomposition solvers for COMputational Mechanics

Project leader: Santiago Badia, CIMNE (Universitat Politecnica de Catalunya), Spain

Research field: Mathematics and Computer Sciences

Resource Awarded: 10 000 000 core hours on FERMI

Collaborators: Oriol Colomés, CIMNE (Universitat Politecnica de Catalunya)-Spain, Alberto F. Martín, CIMNE (Universitat Politecnica de Catalunya)-Spain, Ramon Planas, CIMNE (Universitat Politecnica de Catalunya)-Spain, Javier Principe, CIMNE (Universitat Politecnica de Catalunya)-Spain

Abstract: In this project we want to demonstrate, via comprehensive experimentation, the high suitability of Multilevel Balancing Domain Decomposition by Constraints (BDDC) preconditioners for the efficient/scalable solution of huge sparse linear systems arising from the Finite Element (FE) discretization of Partial Differential Equations (PDEs) on current state-of-the-art petascale massively parallel processors. The ever increasing demand of accuracy in computer simulations of physical phenomena carried out nowadays often leads to such huge sparse linear systems, on the order of billions (if not tens of billions) of unknowns. On the other hand, current state-of-the-art massively parallel computers, such as the IBM BlueGene/Q, are equipped with thousands of hundreds of computational cores. Despite their high appeal for the efficient exploitation of such vast amount of computational power, as far as we know, it has not been proven such degree of scalability for parallel computer simulation codes based on Multilevel BDDC preconditioners. Their high appeal is mainly provided by their ability to aggressively coarsen the global linear system. We will explore both a new algorithmic variant of the Multilevel BDDC preconditioner and a package of novel implementation techniques in order to prove their potential as successful candidates for the development of solver codes on the road to the exascale era. The investigation of algorithms and techniques suitable for the future exascale computers is a highly challenging timeliness topic of strategic importance for the EU, as evidenced by the significant increase in EC’s investment during the past few years. Indeed, this proposal is framed within the EU-FP7 NUMEXAS project towards the next generation of numerical methods for exascale computing. The computational kernel to be explored in this proposal is part of a much larger and ambitious scientific software project, which includes efficient mesh generation, automatic parallel mesh partitioners, data visualization for postprocessing, and physical modules for the discretization of many different physical phenomena (fluid dynamics, structural mechanics, electromagnetism, transport, etc.), including complex multiphysics phenomena (magnetohydrodynamics, fluid-structure interaction, thermally coupled fluids/solids/MHD). We are focused on the application of cutting-edge numerical techniques (solvers and discretization techniques) for emerging fusion technology applications (in collaboration with the Fusion National Lab in Spain), mainly MHD simulations, since they involve extremely challenging multiphysics phenomena that require a high level of resolution due to the multiscale nature of the problem.

LASUO2 – Investigation of the formation of defects, incorporation of rare gases and oxidized phases of UO2 using large supercells

Project leader: Marjorie Bertolus, CEA, DEN, France

Research field: Chemistry

Resource Awarded: 38 000 000 core hours on FERMI

Collaborators: Jean-Paul Crocombette, CEA, DEN- France, Michel Freyss, CEA, DEN, FRANCE Lei Shi, CEA, DEN- France

Abstract: Uranium dioxide attracts much interest due to its technological value as the standard nuclear fuel for pressurized water reactors. Obtaining precise data on the formation and migration of point defects and on the atomic incorporation and migration of fission products at the atomic scale is essential to shed light on the atomic transport properties of nuclear fuels, interpret experiments and feed rate theory models used for the description of the microstructure evolution. The use of electronic structure calculations to obtain this type of data is a very active field of research in the nuclear materials community. Open questions include the elementary mechanisms involved in the nucleation of rare gas bubbles. Small vacancy clusters, which can act as traps for fission gas atoms, especially krypton and xenon, are of paramount interest to get further insight into this issue. Our aim is therefore to investigate the formation of these clusters, and in particular calculate their formation energies and structure, as well as the incorporation of rare gases in them. The results can then be coupled to experimental characterisations using X-ray absorption spectroscopy or positron annihilation spectroscopy to identify the defects induced by irradiation. In addition, oxidation of UO2 is an extremely important phenomenon for nuclear fuel fabrication and handling processes, as well as for understanding fuel evolution during reactor operation and predicting the chemistry of spent fuels. Hyperstoichiometric uranium dioxide is one of the most complex binary materials, with a very large domain of overstoichiometry beyond UO2. The U-O phase diagram exhibits large homogeneity fields at high temperature, as well as several long-range ordered compounds, among which the most stable ones are U4O9 and U3O7. Both compositions exhibit very large unit cells and multiple polymorphs as a function of composition and temperature. The exact structures of these polymorphs are quite complex and still under debate. Experimental observations indicate the presence of particular cuboctahedral oxygen interstitial clusters. Defined compositions are built by regular arrangements of such clusters. The structure and energy of the oxygen interstitial clusters have already been studied using DFT calculations. They were, however, always considered as isolated and no calculation exists on their interactions or ordering. The objective is therefore to investigate various cluster configurations to determine their interactions, as well as the transition from disordered arrangements of clusters to ordered compounds as a function of composition and temperature. Calculations in UO2, as most solid state calculations, are performed using the supercell approach. Because of computational limitations, supercells consisting of 96 atoms plus or minus interstitials or vacancies, are currently commonly used. The objective of this proposal is to improve the state of the art of electronic calculations on uranium dioxide by going to larger supercells containing 324 atoms and above all 768 atoms. This is absolutely necessary to study on the one hand the vacancy clusters we are interested in while minimizing the spurious interactions between the defect and its image in the periodic boundary condition formalism and on the other hand more realistic oxidized phases, ordered and disordered.

NewTURB – Effect of Helicity and Rotation in Turbulent flows: Eulerian and Lagrangian statistics

Project leader: Luca Biferale, University of Rome ’Tor Vergata’, Italy

Research field: Engineering

Resource Awarded: 55 000 000 core hours on FERMI

Collaborators: Stefano Musacchio, Centre national de la recherche scientifique- France,  Prasad Perlekar, TIFR Hydebarad- India, Alessandra Lanotte, Consiglio Nazionale delle Ricerche- Italy,  Fabio Bonaccorso, University of Rome ’Tor Vergata’- Italy,  Federico Toschi, Eindhoven University of Technology- The Netherlands

Abstract: This is a project about fundamental and applied problems in turbulent flows under different symmetry breaking mechanisms, concerning both Eulerian and Lagrangian statistics. We propose to perform a series of state-of-the-art Direct Numerical Simulations of homogeneous turbulence under mirror symmetry breaking (with direct input of helicity) and with different rotation rates. In such a set-up we expect the presence of a split-cascade regime: energy goes to large scales, helicity to small scales. In order to disentangle such huge bi-directional range of scales it is mandatory to achieve a world-record spatial resolution. Moreover, we propose for the first time for this set-up to combine Eulerian and Lagrangian measurements by seeding the fluid with millions of tracers and inertial particles, in order to study both single and multi-particle statistics in presence of direct helicity and inverse energy cascade for different values of the control parameters, the Reynolds number, the Rossby number and with different mirror-symmetry breaking mechanisms. The project aims to ask fundamental questions concerning all flows under rotation, about the interactions between slow (large-scale) tornado-like structures and the sea of small-scales tangled filaments, about the isotropic and anisotropic components of the Eulerian statistics and about relative dispersions for both fluid particles and inertial particles. Only a Tier-0 machines offer the computational resources for such challenging resolution and challenging physical set-up.

From local to global models of accretion discs: beyond the alpha prescription

Project leader: Gianluigi Bodo, INAF, Italy

Research field: Universe Sciences

Resource Awarded: 29 000 000 core hours on FERMI

Collaborators: Paola Rossi, INAF- Italy, Andrea Mignone, Universita di Torino- Italy

Abstract: The process of accretion is of great importance in astrophysics. Many compact objects like planets, stars and massive black holes are formed by the infall of material into a central gravitational well. The release of gravitational energy by the accreting material can be extremely efficient and can power some of the most energetic phenomena in the universe. The accreting material, in general, forms a disc around the central object and, despite many years of effort, a full understanding of accretion discs is still lacking and global models are still based on the forty year old phenomenological approach. In the theory of accretion discs, angular momentum transport is the crucial quantity that determines the accretion rate and therefore the entire disc structure. There is a general consensus that angular momentum transport is mainly due to turbulence driven by the magnetorotational instability (MRI). This instability requires the combined action of rotation, shear and magnetic field, whose presence is essential, because otherwise the disc would be stable. Turbulent motions must also be able to regenerate through a dynamo process the very magnetic field that is necessary for the MRI to develop. Up to now numerical simulations have been restricted to solutions in which the temperature is kept constant and therefore the heat generated by turbulence dissipation is neglected. However if we want to fully determine the disc structure we have to take into account this heat and how it is transported to the surface layers of the disc to be irradiated. Following this approach, we have demonstrated the existence of a novel solution in which the dissipated energy is carried outward by convection, an efficient large scale dynamo action is present and angular momentum transport is much more efficient than in the isothermal state. The simulations were performed, following a common practice, by using a local approach in which we consider a patch of the disc of small radial extent but covering the full vertical disc thickness . With this project we aim at better understanding the properties of this fully convective solution. In particular, by patching together different local simulations that can thought as performed at different radial position, we will be able to build a global model of the disc and this will represent the first attempt to go beyond the forty year old phenomenological alpha disc model by Shakura and Sunyaev (1973). In addition we will try to better model the surface layers of the disc to show the robustness of our novel fully convective solution.


Project leader: Matteo Calandra, CNRS, France

Research field: Chemistry

Resource Awarded: 9 000 000 core hours on Curie TN

Collaborators: Ion Errea, Donostia International Physics Center- Spain, Raffaello Bianco, CNRS- France,  Francesco Mauri, CNRS- France, Lorenzo Paulatto, CNRS- France, Guilherme Almeida Silva Ribeiro, Université P. et M. Curie- France

Abstract: State of the art calculations of vibrational properties from first principles rely on the harmonic approximation. However, in many superconductors, in all CDW materials, in ferroelectrics, and in thermoelectrics the harmonic approximation completely breaks down, imaginary phonon frequencies are present and the perturbative approaches fail. The aim of this project is to push the current knowledge of vibrational spectra in materials one step forward by applying the stochastic self-consistent harmonic approximation (SSCHA), a non-perturbative approach developed by ourself, to materials of great technological interest (superconductors, ferroelectrics, CDW materials and thermoelectrics). The results of the current proposal will be relevant for a wide scientific community far beyond that of condensed matter physics. As an example approximately 90% of the world’s electricity is generated by heat energy, typically operating at 30–40% efficiency, losing roughly 15 terawatts of power in the form of heat to the environment. Understanding and devising high ZT thermoelectrics devices would mean converting some of this waste heat into useful electricity, with evident consequences for everyday life. Similarly ferroelectric materials allow for capacitors with tunable capacitance that are used in ferroelectric RAM in modern computer.

SMOC – Submesoscale ocean MOdeling for Climate

Project leader: Xavier Capet, CNRS, France

Research field: Earth System Sciences

Resource Awarded: 11 000 000 core hours on Hermit

Collaborators: Marina Levy, CNRS- France, Gurvan Madec, CNRS-France, Julien Jouanno, Institute for research and development-France, Guillaume Roullet, Universite de Bretagne Occidentale- France

Abstract: Climate modeling has reached a point where biases in the ocean state and circulation are a primary concern. Some of its current deficiencies may only be resolved by explicit resolution of or improved parameterizations for meso- and submeso-scale (MSS) ocean turbulence. MSS processes are related to the ubiquitous presence of coherent mesoscale vortices (typical radii 30-100 km) and of cohorts of submesoscale fronts in their vicinity (typical transverse scale in the range 1-10 km). Because its typical time scales match those of atmospheric synoptic variability (hours to days) MSS is thought to impact ocean-atmosphere interactions and the mediation of atmospheric energy inputs into the ocean interior, with implications in terms of mixing and overall ocean functioning. The Southern Ocean is a region where MSS processes are important at leading order, eg. for tracer budgets and momentum balances. Yet, there have been no studies where they are fully resolved so that their long-term effects can be accurately quantified. Our project proposes to remedy this by computing and analyzing state-of-the-art Southern Ocean numerical solutions at kilometer-scale horizontal resolution. Some simplifications of the domain geometry will allow us to take the most advantage of Tier-0 computer resources and compute decade-long solutions that will provide robust statistics on MSS turbulence and their impacts on the ocean functioning.

Selective inhibition of the PI3Ka E545K mutant through MD simulations, in vitro assays and SPR experiments

Project leader: Zoe Cournia, Biomedical Research Foundation, Academy of Athens, Greece

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 15 247 000 core hours on Curie TN

Collaborators: Paraskevi Gkeka, Biomedical Research Foundation, Academy of Athens- Greece,  Hari Leontiadou, Biomedical Research Foundation, Academy of Athens- Greece, Pavlos Agianian, Democritus University of Thrace-Greece, Savvas Christoforidis, University of Ioannina-Greece, Francesco Gervasio, University College London- United Kingdom

Abstract: The kinase PI3Ka is involved in fundamental cellular processes such as cell proliferation and differentiation. PI3Ka is frequently mutated in human malignancies. One of the most common mutations is located in exon 9 (E545K), where a glutamic acid is replaced by lysine. The E545K mutation results in an amino acid of opposite charge, where the glutamic acid (negative charge) is replaced by lysine (positive charge). It has been recently proposed that in this oncogenic charge-reversal mutation, the interactions of the protein catalytic subunit with the protein regulatory subunit are abrogated, resulting in loss of regulation and constitutive PI3Ka activation, which can lead to oncogenesis. To test the mechanism of protein overactivation, MD simulations will be used here to examine conformational changes differing among the WT and mutant as they occur in microsecond simulations. Understanding how the E545K mutation leads to the increased PI3Ka activity will help us design new candidate drugs for cancer patients who carry this mutation. How? The dynamics and structural evolution of this E545K oncogenic protein, as described by our simulations, might reveal possible binding pockets, which will be then exploited in order to design small molecules that will target only the oncogenic mutant protein. Therefore, our simulation results will be used to identify putative allosteric pockets on the cancerous protein and perform computer-aided drug design for the identification of selective E545K inhibitors. These inhibitors will be further validated by in vitro assays and SPR experiments with the aim to discover novel candidate cancer drugs.

SAMC – Symmetry-Adapted Monte Carlo for ab initio modeling of disordered crystalline materials

Project leader: Philippe D’Arco, Universite Pierre et Marie Curie, France

Research field: Chemistry

Resource Awarded: 20 000 000 core hours on Hermit

Collaborators: Raffaella Demichelis, Curtin University- Australia, Valentina Lacivita, Universite Pierre et Marie Curie- France, Sami Mustapha, Universite Pierre et Marie Curie- France, Yves Noel, Universite Pierre et Marie Curie- France, Marco De La Pierre, Universita degli Studi di Torino-Italy

Abstract: The theoretical study of the properties of solid solutions and disordered crystalline systems is addressed. These materials are of major importance in both Earth and Material Sciences, as they are extremely common in nature and play a key role in a number of technological applications, e.g. solid-state lasers, solid oxide fuel cells, semi-conductors, pigments, ceramics, metallic alloys and many others. A theoretical approach to such systems implies dealing with large low-symmetry supercells where atom substitutions correspond to multitudes of different structure configurations. This tremendous computational challenge has seriously hindered ab initio quantum-mechanical simulations so far. A recent remarkable progress has been the fine-tuning of a new symmetry-adapted Monte Carlo (SA-MC) sampling method by D’Arco, Mustapha and co-workers [J. Phys.: Condens. Matter (2013) 25:105401 & 25:355401], and its pioneering implementation in the CRYSTAL code for ab initio periodic calculations. This is a novel theoretical approach that maximizes efficiency and representativeness of the configuration space sampling by full-exploitation of the system symmetry. On the one hand, symmetry is used to identify equivalent (i.e. degenerate) configurations in order to avoid redundancies, which greatly reduces the size of the configuration space to be sampled. On the other hand, symmetry is used to determine the Bayesian probability of any configuration to be found during the sampling and thus to guarantee statistic equilibrium. Our purpose for the present project is to apply this new method to calculate the average properties of two melilite mineral structures, i.e. soda-melilite (Na,Ca)AlSi2O7 (Sm) and gehlenite Ca2Al(Si,Al)2O7 (Geh). The melilite structure is characterized by corner sharing tetrahedral layers separated by interlayer cations. Both Sm and Geh display cation (dis)order: Sm is characterized by (dis)order of the interlayer cations Na and Ca; Geh is characterized by Al/Si disorder in the tetrahedral layers. Energy calculations will be performed using the CRYSTAL code. This will constitute the first full ab initio modelling of disorder in melilites, and will be a reference for simulations carried out at less accurate theoretical levels. We believe that the results obtained will show that the proposed method offers new opportunities for theoretical approaches to disordered or non-ideal solids. A strong methodology impact is envisaged with influences to material science, geology, but also Monte Carlo methodologies and molecular modelling.

MitoComp: Large-Scale molecular-dynamics simulations of the entire Mitochondrial Complex I

Project leader: François Dehez, CNRS – Université de Lorraine, France

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 7 458 000 core hours on Hermit , 5 850 000 core hours on SuperMUC

Collaborators: Chipot Christophe, CNRS – Université de Lorraine-France, Comer Jeffrey, CNRS – Université de Lorraine-France

Abstract: The mitochondrion, the powering unit of the cell, is where the last steps of the respiratory cycle occur, transforming the energy contained in nutriments (glucose) into energy directly usable by the cell (ATP). The successive steps of the oxydative phophorylation cycle are achieved by a series of complexes embedded in the inner membrane of mitochondria. The NADH-quinone oxidoreductase, also called Complex I, is the first and major entry point of electrons in the mitochondrial respiratory chain. This enzyme first catalyses the oxidation of NADH (reduced Nicotinamide Adenine Dinucleotide) by flavin mononucleotide, leading the transfer of two electrons to ubiquinone (Q) trough a chain of iron-sulfur clusters. This electron transport is coupled to the translocation of four protons across the inner membrane of the mitochondrion. Functional defects of Complex I have proven to be responsible for many human mitochondrial diseases (about one third of the disorders observed in the respiratory chain is linked to this complex) for which no cure currently exists. A three-dimensional structure of an entire bacterial Complex I was released only very recently, describing for the first time the complete molecular organization underlying the proton transport function of this enzyme. Our goal here is to complete the static view provided by X-ray crystallography using long-time scale molecular-dynamics simulations together with state-of-the-art free-energy approaches. We plan to gain insight into the mechanism by which half-channels composing the membrane domains open and close, to decipher the recognition process of the quinone and to understand how the quinone binding site is functionally coupled to the proton pathways. This work will pave the way toward the characterization of Complex I dysfunctions involved in human pathologies.

SISMAF – Strong Interactions in Strong Magnetic Fields

Project leader: Massimo D’Elia, University of Pisa, Italy

Research field: Fundamental Physics

Resource Awarded: 34 000 000 core hours on FERMI

Collaborators: Claudio Bonati, Istituto Nazionale di Fisica Nucleare-Italy,  Francesco Negro, Istituto Nazionale di Fisica Nucleare- Italy, Marco Mariti, University of Pisa- Italy, Michele Mesiti, University of Pisa-Italy, Francesco Sanfilippo, University of Southampton- United Kingdom

Abstract: Strong interactions are described by QCD, the theory of quarks and gluons. Quarks are also subject to electroweak interactions, which in general induce small corrections to strong interaction dynamics, but exceptions are expected in the presence of electromagnetic backgrounds, strong enough to directly affect the QCD scale, a situation relevant to many contexts. Large magnetic fields are expected in non-central heavy ion collisions [1-4] and may have been produced at the cosmological electroweak phase transition [5-6], with possible values of eB reaching around 0.1 GeV^2 in the first case and possibly going above 1 GeV^2 in the second case. How strong interactions get modified by such magnetic fields has been the subject of many recent theoretical studies (see Ref. [7] for a collection of reviews). Lattice QCD simulations, in particular, represent the best available tool for a non-perturbative study of such properties [8-28]. One important feature is that gluon fields, even if not directly coupled to electromagnetic fields, may undergo significant modifications, through effective QED-QCD interactions induced by quark loops. A very recent and interesting result [27, arXive:1403.6094] is that even the static quark-antiquark potential, which being related to Wilson loop expectations values is a property of gauge fields only, can undergo significant modifications, as predicted also by some model computations [28]. In particular, in our exploratory numerical study, we have shown the emergence of anisotropies both in the linear part and in the Coulomb part of the potential. That may have relevant phenomenological consequences, especially in the context of heavy ion collisions, and opens the way to a number of further investigations, that we would like to pursue in the present project: 1) Results of arXiv:1403.6094 will be checked on a finer 48^3 x 96 lattice, with a lattice spacing a = 0.1 fm and different values of the magnetic field, in order to: i) perform, by means of results obtained at the various lattice spacings, a proper continuum extrapolation; ii) investigate the detailed angular dependence of the quark-antiquark potential. 2) Extend our study to three finite temperature lattices, 48^3 x Nt, with Nt = 12, 14, 16, and the same lattice spacing as in point 1), corresponding to two temperature below and one temperature slghtly above the phase transition, in order to obtain information about quark-antiquark interactions in the presence of a magnetic field which might be useful for heavy ion collisions phenomenology. 3) Perform, exploiting the ensemble of configurations generated in point 1) and 2), a first study of the modifications of the flux tube profile in the presence of a magnetic background and of the modifications in the heavy meson spectrum. As in arXive:1403.6094, we will consider a state-of-the-art discretization of QCD with 2+1 flavors and physical quark masses, namely staggered fermions with three levels of stout smearing improvement [29] and a tree level improved Symanzyk action for the gauge sector. The expected outcome could be highly relevant to heavy ion phenomenology and to our understanding of the non-perturbative properties of strong interactions.

Noise radiation from a high-Reynolds-number turbulent boundary layer

Project leader: Xavier GLOERFELT, ENSAM, France

Research field: Engineering

Resource Awarded: 16 000 000 core hours on Curie TN

Collaborators: Miloud ALAOUI, ENSAM- France Elie COHEN, ENSAM- France

Abstract: Reduction of internal noise: an issue for transportation vehicles. An important part of aerodynamic noise for passengers of cars, trains, or airplanes comes from pressure fluctuations generated by the external flow over its walls. This source of noise dominates the other sources and is seen to be the main contribution to cockpit noise for recent long-haul aircraft. The reduction of this source of noise (often referred to as internal noise, or cabin noise) becomes a matter of concern for car or train manufacturers, in order to increase the comfort of passengers during cruising trip. The turbulent boundary layers developing over a plane wall can provide an indirect contribution to the noise by exciting the structure, and a direct noise contribution. The latter part can play a significant role even if its intensity is very low, explaining why it is hardly measured unambiguously. In the present project, the aerodynamic noise generated by a spatially developing turbulent boundary layer is computed directly by solving the compressible Navier-Stokes equations. These numerical experiments aim at giving some insight into the noise radiation characteristics. The main objectives are the investigation of the contribution of the acoustic part of the pressure fluctuations, and the improvement of the reliability of existing semi-empirical models, notably for a high-Reynolds-number boundary layers. PRACE HPC capabilities will be used to reach a Reynolds number representative of experiments, allowing new comparisons for wall pressure under a turbulent boundary layer. Several theoretical issues concern the effect of Reynolds number, notably on the acoustic contribution from wall turbulence.

NACRE – Micromechanics of Biocomposite Materials

Project leader: Frauke Graeter, Heidelberg Institute for Theoretical Studies, Germany

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 11 570 000 core hours on Hermit

Collaborators: Konstantinos Gkagkas, Toyota Motor Europe NV/SA- Belgium, Monika Fritz, University of Bremen- Germany

Abstract: During the past decades, there has been a continuous research effort to understand and develop composites of inorganic and biological matter. In particular, the European scientific community has played a key role and, through its funding agencies, has provided support for studying diverse systems with bio-inorganic interfaces, such as microchips for medical diagnosis or nanopores for fast DNA sequencing. The purpose of this PRACE proposal is to study nacre, which is one of the most fascinating bio-inorganic systems in nature. Nacre is a biocomposite located at the inner layer of seashells, with exceptional mechanical properties, such as fracture resistance, toughness and strength. Due to these properties, artificial nacre-like composites are among the most promising materials for novel applications. It is known that nacre’s stability relies on the integration of inorganic and organic layers through elaborate hierarchical nanostructures. However, it is not clear how those layers interplay with each other. This proposal presents a plan to study nacre stability using computer simulations. This project is part of a large collaboration with academic and industrial partners; namely the Research & Development Division of Toyota Motor Europe in Belgium and the Institute for Biophysics at the University of Bremen in Germany. The collaboration is focused on studying synthetic and biological materials for novel applications. Our group, the Molecular Biomechanics Group at the Heidelberg Institute for Theoretical Studies, develops computational and theoretical tools for molecular simulations. We will use all-atom molecular dynamics to study nacre. The simulations will employ realistic nanometer size models, including flaw details, inorganic crystals and organic layers under different stress conditions. We expect that our results will link the macroscopic stability with the atomic structure of the material, unraveling the atomic mechanisms behind the mechanical stability of nacre. We will employ the software GROMACS, which assures great scalability for the Hermit supercomputer system. Simulations require access to large partitions, 2048 cores, with an annual total request of 12 million CPU hours.

Pair-dominated plasmas in ultra intense fields: from the laboratory to extreme astrophysical conditions

Project leader: Thomas Grismayer, GoLP/IPFN – Instituto Superior Tecnico, Portugal

Research field: Fundamental Physics

Resource Awarded: 25 000 000 core hours on SuperMUC

Collaborators: Ricardo Fonseca, GoLP/IPFN – Instituto Superior Tecnico-Portugal, Joana Martins, GoLP/IPFN – Instituto Superior Tecnico-Portugal, Luis Silva, GoLP/IPFN – Instituto Superior Tecnico-Portugal, Marija Vranic, GoLP/IPFN – Instituto Superior Tecnico-Portugal, Mattias Marklund, Chalmers Univeristy- Sweden, Warren Mori, UCLA- United States

Abstract: Can we generate relativistic electron-positron (e-e+) pair plasmas in the laboratory using intense lasers, that mimick extreme astrophysical scenario? What is the role of collective effects in relativistic pair plasmas and what are their radiation signatures? These are prominent scientific questions where the physics of plasmas is intrinsically connected with quantum electrodynamics effects. This proposal aims to exploit the unique computing facilities provided by PRACE to address these exciting challenges by leveraging on the recently pioneered advances on ab initio simulations of quantum electrodynamics (QED) effects in plasmas with particle-in-cell (PIC) simulations. The main scientific route to address some of these outstanding challenges consists in exploring in the laboratory pair-dominated plasmas under the presence of ultra-intense fields and mimicking astrophysical scenarios resorting to the unprecedented power of future laser facilities. The intensity of the ultra-intense lasers of the Extreme Light Infrastructure (ELI) now under construction will provide transient fields whose magnitudes approach those assumed to be present in pulsars. This unique combination of parameters opened by the interaction of ultra-intense lasers provides a platform to study the dynamics of pair-dominated plasmas and promises too unveil some mysteries associated to a physics that is yet to be explored. The first goal of this research project is to predict the optimal laser parameters and configurations for the design of future experiments related to pair creation. The interaction of multiple lasers of ultra-high intensity leads to the development of pair cascades, forming eventually a pair-plasma approaching the critical density with large number of hard photons. The second objective is to investigate astrophysical scenarios such as the magnetosphere of pulsars where pair creation is believed to play a crucial role. For instance the pair plasma density inferred from the radiation of pulsars is found to be 1000 time bigger than the one given by standard force-free models that do not take into account pair creation. It is necessary to include such effects in a self-consistent manner in order to recover the observational results in simulations. Another key goal of this proposal is to investigate the radiation signatures in the Compton Regime, a regime not accessible with standard electromagnetic methods. We are here taking advantage from the fact that the QED-PIC code emits photons corresponding to the radiation of the particles in the presence of intense fields. The relevant temporal and spatial scales associated with these scenarios are very disparate. In addition, the microphysics that rules pair-dominated plasmas and photon emission is non-linear and stochastic and the associated collective phenomena very complex. Thus, full-scale, massively parallel kinetic particle-in-cell simulations are critical to address the challenges outlined in this proposal. This research proposal will take advantage of the available outstanding numerical and visualization frameworks in our group, and from the use of new advanced QED-PIC algorithms in order to model quantum regime of pair-plasma physics in various scenarios. The unique computational infrastructures provided by PRACE will be critical to explore some of the most fundamental physics questions at the forefront of science identified in this proposal.

BIOCHROMO – Ground state structures and electronic excitations of biological chromophores at Quantum Monte Carlo / Many Body Green’s Function Theory level

Project leader: Leonardo Guidoni, University of L’Aquila, Italy

Research field: BBiochemistry, Bioinformatics and Life sciences

Resource Awarded: 100 000 core hours on Curie FN, 45 416 379 core hours on JUQUEEN

Collaborators: Daniele Bovi, La Sapienza, Universit di Roma-Italy, Caterina De Franco, La Sapienza, Universit di Roma-Italy, Pietro De Gaetano, La Sapienza, Universit di Roma-Italy, Daniele Narzi, La Sapienza, Universit di Roma-Italy, Andrea Zen, La Sapienza, Universit di Roma-Italy, Ye Luo, SISSA-Italy, Guglielmo Mazzola, SISSA-Italy,Sandro Sorella, SISSA-Italy, Matteo Barborini, University of L’Aquila-Italy, Emanuele Coccia, University of L’Aquila-Italy, Emanuele Coccia, University of L’Aquila-Italy

Abstract: The accurate calculation of electronic excited states of large and electronically correlated biological chromophores in their complex protein environment still represents a challenge for quantum chemistry. Two ab initio techniques are recently emerging as candidates to correctly tackle this issue: Quantum Monte Carlo (QMC) calculations for the ground state geometry optimization, and Many Body Green’s Function Theory (MBGFT) for excited state energies. In the present work we use the Variational Monte Carlo (VMC) to carry out structural optimizations of different biological chromophores in gas phase and in protein environment within a Quantum Mechanics / Molecular Mechanics framework. Optical spectra will be calculated on these structures using Bethe-Salpeter equation. Two classes of biological systems will be approached. Firstly, we will study different forms of the Green Fluorescent Protein, which is a well characterized and widely used fluorescent marker in molecular biology. The bathochromic shifts ot the GFP chromophore still represent a challenge for ab initio computational chemistry methods. Our gas phase and QM/MM calculations using the QMC/MGFT scheme will be able to unravel this, providing us with a predicting tool for the color tuning of GFP mutants. As second target we will investigate several models of the class of the luciferin molecules, involved in the bioluminescence process occurring in several living organisms, like fishes, insects (fireflies, for instance), algae and bacteria. Our (gas phase) results will help us to shed the light on the relative stability of the various forms of oxyluciferin, for which several different hypothesis have been proposed so far. The proposed VMC/MBGFT methodologies will be able to provide a fully ab initio answer to open issues in the photochemistry and the optical properties of biological chromophores and can be applied in the future to other biological cases.

Study of shock/boundary layer interaction in supersonic nozzles using high-fidelity numerical simulations

Project leader: Abdellah HADJADJ, CORIA UMR 6614 CNRS, France

Research field: Engineering

Resource Awarded: 13 000 000 core hours on Curie FN

Collaborators: Arthur Piquet, CORIA UMR 6614 CNRS- France,  Anne-Sophie Mouronval, Ecole Centrale Paris- France,  Guy MOEBS, Laboratoire de Mathematiques Jean Leray UMR 6629 CNRS-France

Abstract: The project aims to contribute to the development of high-fidelity numerical simulations integrated in a massively parallel computer code, to study the dynamics and topological properties of shock induced flow separation in over-expanded nozzles and helps provide a basis for future work in this area. In terms of academic research, the project is expected to bring: 1) advances in both computational and theoretical fluid dynamics; 2) large scale data post-processing and the flow visualization; 3) DNS and LES for computations of shock-turbulence interaction; 4) best practice guidelines for numerical simulations of shock induced unsteady flow separation in supersonic nozzles.

COMFLOW — Colloids in multiphase flow

Project leader: Jens Harting, Eindhoven University of Technology, The Netherlands

Research field: Chemistry

Resource Awarded: 26 000 000 core hours on JUQUEEN

Collaborators: Gianluca Di Staso, Eindhoven University of Technology-The Netherlands, Stefan Frijters, Eindhoven University of Technology-The Netherlands, Florian Günther, Eindhoven University of Technology-The Netherlands,Dennis Hessling, Eindhoven University of Technology-The Netherlands, Riccardo Scatamacchia, Eindhoven University of Technology-The Netherlands,Federico Toschi, Eindhoven University of Technology-The Netherlands,Qingguang Xie, Eindhoven University of Technology-The Netherlands,Timm Krueger, University of Edinburgh-The Netherlands

Abstract: Particles as stabilizers for emulsions are attractive in the food and cosmetic industry, for crude oil recovery, or waste water treatment. However, the properties of such systems are only poorly understood. The main challenges are the complex particle-particle and particle-fluid interactions. We will investigate the behaviour of individual particle-covered droplets, as well as the influence of the particle properties on the stability of emulsions. Such systems are too complicated to be treated with theoretical models and experimental “trial and error” searches for the best stabilisation method are not only expensive, but also time consuming. Our large scale simulations utilizing combined lattice Boltzmann and molecular dynamics simulations are able to cover the relevant parameters of such systems and will not only lead to a better fundamental knowledge, but may also directly lead to improved production or spark the interest of companies in using particle stabilized multiphase systems for their own products.

Multi-scale simulations of Cosmic Reionization

Project leader: Ilian Iliev, University of Sussex, United Kingdom

Research field: Universe Sciences

Resource Awarded: 500 000 core hours on Curie FN, 150 000 core hours on Curie H, 13 000 000 core hours on Curie TN, 8 000 000 core hours on MareNostrum

Collaborators: Romain Teyssier, University of Zurich- Switzerland, Dominique Aubert, Observatoire Astronomique de Strasbourg- France, Pierre Ocvirk, Observatoire Astronomique de Strasbourg- France, Kyungjin Ahn, Chosun University- South Korea,  Karl Joakim Rosdahl, Leiden University,-The Netherlands, Garrelt Mellema, Stockholm University- Sweden, Keri Dixon, University of Sussex- United Kingdom,  David Sullivan, University of Sussex- United Kingdom, Peter Thomas, University of Sussex- United Kingdom, Jun-Hwan Choi, The University of Texas at Austin- United States, Anson D’Aloisio, The University of Texas at Austin- United States, Hyunbae Park, The University of Texas at Austin- United States,  Paul Shapiro, The University of Texas at Austin- United States

Abstract: The first billion years of cosmic evolution are one of the last largely uncharted territories in astrophysics. During this key period the cosmic web of structures we see today first started taking shape and the very first stars and galaxies formed. The radiation from these first galaxies started the process of cosmic reionization, which eventually ionized and heated the entire universe, in which state it remains today. This process had profound effects on the formation of cosmic structures and has left a lasting impression on them. This reionization process is inherently multi-scale. It is generally believed to be driven by stellar radiation from low-mass galaxies, which cluster on large scales and collectively create very large ionized patches whose eventual overlap completes the process. The star formation inside such galaxies is strongly affected by complex radiative and hydrodynamic feedback effects, including ionizing and non-ionizing UV radiation, shock waves, gas cooling and heating, stellar winds and enrichment by heavy elements. Understanding the nature of the first galaxies and how they affect the progress, properties and duration of the cosmic reionization requires detailed modelling of these complex interactions.The aim of this project is to combine a unique set of simulations of cosmic reionization covering the full range of relevant scales, from very small, sub-galactic scales, for studying the detailed physics of radiative feedback, all the way to very large cosmological volumes at which the direct observations will be done. These simulations will be bases on several state-of-the-art numerical tools, discussed in the sections below, including Adaptive Mesh Refinement (AMR) techniques for achieving very large dynamic range in radiative hydrodynamics calculations (RAMSES-RT code), GPU-based acceleration for radiative hydrodynamics (RAMSES-CUDATON), and a massively-parallel, highly numerically efficient radiative transfer method for accurate modelling at large scales (C2-Ray). We will complement the numerical simulations with semi-analytical galaxy formation modelling to explore the large parameter space available, to improve the treatment of reionizing sources in large-scale radiative transfer simulations as well as to derive detailed observational features of the first galaxies in different observational bands. The questions we will address are: 1) how do the radiative feedback from the First Stars hosted in cosmological minihaloes and dwarf galaxies affect the formation of early structures and subsequent star formation?; 2) how much does high-redshift galaxy formation differ from the one at the present day? What are the observational signatures of the first galaxies? 3) how important is the recently pointed out effect of local modulation of the star formation in minihaloes due to differential supersonic drift velocities between baryons and dark matter?; 4) how does the metal enrichment and the transition from Pop III (metal-free) to Pop II stars occur locally and how is this reflected in the metallicity distribution of the observed dwarf galaxies and globular clusters? and 5) How are these feedback effects imprinted on large-scale observational features?

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

Project leader: Hans-Thomas Janka, Max-Planck-Institut fuer Astrophysik, Germany

Research field: Universe Sciences

Resource Awarded: 5 120 000 core hours on MareNostrum , 92 160 000 core hours on SuperMUC

Collaborators: Tobias Melson, Max-Planck-Institut fuer Astrophysik-Germany, Alexander Summa, Max-Planck-Institut fuer Astrophysik-Germany,Andreas Marek, Rechenzentrum der Max-Planck-Gesellschaft-Germany

Abstract: Supernovae are gigantic stellar explosions that terminate the lives of massive stars and give birth to neutron stars and black holes. They belong to the most spectacular and brilliant cosmic events, produce potentially measurable neutrino and gravitational-wave signals, and are among the prime candidates for the still mysterious sources of roughly half of the heavy, neutron-rich chemical elements beyond iron. The exact processes that lead to the explosive disruption of a star are not satisfactorily understood yet, but deeper theoretical insight is indispensable to better define the role of supernovae in the evolution of stars and galaxies and as celestial laboratories of nuclear and particle physics at extreme conditions. Neutrinos are thought to play a central role in the solution of this important problem. They are produced in gigantic numbers when the degenerate core of a massive star ultimately reaches its stable mass limit and collapses catastrophically within less than a second to an extremely hot and dense neutron star. The neutrinos carry away the huge gravitational binding energy released in the collapse, but some of them are absorbed in the cooler, infalling stellar material around the nascent neutron star. If this neutrino heating deposits enough energy, a shock wave can be accelerated to expel the outer stellar layer in the supernova blast. But is the energy transfer by neutrinos sufficiently efficient? An answer to this question heavily rests on computer simulations, and the complexity of the involved processes poses a grand challenge for numerical modeling. The transport and reactions of neutrinos in the dense stellar medium are highly complicated and computationally extremely demanding, and hydrodynamical instabilities lead to vigorous nonradial flows and turbulence, which require multi-dimensional modeling. With the most sophisticated computations performed in two dimensions (2D) so far, we could confirm the viability of the neutrino-driven mechanism in a growing number of stellar models over the past years. However, three-dimensional (3D) simulations are needed to overcome the artificial constraint of axisymmetry of the 2D geometry. In previous PRACE projects we succeeded in simulating stellar core collapse in 3D with the same level of sophistication as in 2D. We could confirm the presence of spiral SASI (“Standing Accretion-Shock Instability”) modes for the first time in full-scale supernova models, have discovered a novel instability leading to a self-sustained dipolar lepton-emission asymmetry (“LESA”), and in one case observe a first hint of a neutrino-driven explosion with greater energy in 3D than in 2D. Nevertheless, the ingredients for a robust explosion mechanism have not been identified yet. With an improved numerical treatment due to a new, axis-free Yin-Yang computational mesh, we now plan to test the influence of higher resolution to reduce the worrisome influence of numerical viscosity. We will also explore the influence of stellar core rotation, whose presence even on a low level can have a large impact on the growth of SASI spiral modes. Moreover, we intend to study newly developed, state-of-the-art equations of state for neutron-star matter, which are compatible with all recent experimental, theoretical, and astrophysical constraints.

Direct Numerical Simulation of Equilibrium Adverse Pressure Gradient Turbulent Boundary Layers

Project leader: Javier Jiménez, Universidad Polytécnica de Madrid, Spain

Research field: Engineering

Resource Awarded: 17 040 000 core hours on SuperMUC

Collaborators: Omid Amili, Monash University- Australia, Callum Atkinson, Monash University- Australia, Vassili Kitsios, Monash University- Australia, Julio Soria, Monash University- Australia,Paul Stegeman, Monash University- Australia,Guillem Borrell, Universidad Polytécnica de Madrid- Spain,  Javier Jiménez, Universidad Polytécnica de Madrid- Spain, Juan Sillero, Universidad Polytécnica de Madrid- Spain, Ayse Gungor, Istanbul Technical University- Turkey

Abstract: This research project will investigate the structure and dynamics of wall-bounded turbulence in adverse pressure gradient (APG) environments using Direct Numerical Simulation (DNS). An APG is a pressure gradient that decelerates the flow leading to potential flow separation from the aerodynamic surface. The DNS program will be complimented by both theoretical studies, and by experiments in the water tunnel at the Laboratory for Turbulence Research in Aerospace and Combustion water tunnel at Monash University. The target Reynolds numbers based on the momentum thickness is 12000. The long term objectives of this research are to revolutionize the design of energy generation and transport platforms that operate in APG environments, and to develop active flow control systems that increase the operational envelope. This will improve the energy efficiency over a wide range of operating conditions. Real world examples include the flow over aircraft wings, wind turbine blades, and any form of turbo-machinery. Improvements in the performance of such systems will lead to more efficient and cleaner power generation, a reduction in fuel consumption, and minimization of CO2 emissions. In the present study our efforts are focussed on the canonical flow configuration of a flat plate turbulent boundary layer (TBL) subjected to an APG. The results of the DNS of the APG TBL will be post-processed and analysed to extract the energy and dissipation characteristics of the coherent structures, and study their evolution. Particular attention will be applied to the dynamics in the middle to outer regions and how these structures interact with structures in the near wall region. This analysis will allow us to address the following questions: 1) How are the middle and outer regions influenced by the structures of the inner region in APG wall bounded flows? This is important in the framework of APG wall-bounded flow control as sensors and control actuators would be located at the wall. 2) If there is an influence of the middle and outer flow by the structures of the inner region, what is the nature and mechanics of the interaction? If there is a strong influence then it may be possible for wall mounted actuators to dictate the behaviour of the middle and outer region to control boundary layer separation and drag. 3) What is the origin, structure and spatio-temporal evolution of coherent structures in the APG equilibrium TBL at the verge of separation? Are local instabilities due to inflectional mean velocity profiles present and if so what is their role? It may be possible to exploit these instabilities to amplify the actuated perturbations required for the control of separation in APG TBLs.

IMAGINE_IT — 3D full-wave tomographic IMAGINg of the Entire ITalian lithosphere

Project leader: Dimitri Komatitsch, CNRS, France

Research field: Earth System Sciences

Resource Awarded: 40 000 000 core hours on Curie TN

Collaborators: Emanuele Casarotti, INGV- Italy, Federica Magnoni, INGV- Italy, Daniele Melini, INGVp- Italy, Alberto Michelini, INGV- Italy, Antonio Piersanti, INGV- Italy, Jeroen Tromp, Princeton University- United Stated, Carl Tape, University of Alaska Fairbanks- United States

Abstract: Protecting our society from the effects of earthquakes is a crucial societal goal that requires improving our knowledge of geophysical processes and of the structure of the interior of the Earth. Analysing ground motion scenarios for potential seismic events or understanding the crucial mechanisms that can lead to earthquakes is a difficult task that must rely both on the capability of accurately imaging the geological structure of the interior of the Earth at multiple scales and on the use of information buried in seismic “big data” records. Our IMAGINE_IT project focuses on this universal societal need, and aims in particular at gaining extensive and detailed knowledge of the highly heterogeneous structure of the lithosphere below the whole country of Italy, based on highly-accurate seismic wave imaging. The recent seismic events that deadly struck Italy (L’Aquila in 2009, Emilia-Romagna in 2012) have highlighted its complex geodynamical behaviour and unsolved issues such as the shape of the roots of the Alpine chain, the characteristics of the main alluvial basins, as well as multiple subducting slabs or intrusions. The main accomplishment of IMAGINE_IT will therefore be to build a reference 3D seismic velocity model for Italy at unprecedented high resolution, constrained by a large number of observed full seismic waveforms. This paramount task has never been done nor even been feasible before because it requires simultaneously using the recorded data of dense seismological networks, extremely efficient numerical techniques, and an enormous computational power even by the standards of current Tier-0 systems. In order to achieve this goal, we have assembled an international team with exceptional experience in computational seismology and seismic data analysis, and we will use the powerful combination of a Spectral-Element Method (SEM, code SPECFEM3D) for the numerical simulation of seismic wave fields and adjoint methods for tomographic inversion and imaging. The SEM is a well-established approach, originally developed (by us) for high-resolution seismology, for accurately modelling seismic wave propagation in realistic 3D heterogeneous media. The adjoint technique is an inversion strategy that uses the differences between observed and synthetic full waveforms in order to illuminate model perturbations and iteratively improve initial models. In terms of timeliness, IMAGINE_IT will strongly benefit from the involvement of several of its team members in the ongoing FP7 projects “VERCE – Virtual Earthquake and seismology Research Community in Europe e-science environment” and “EPOS European Plate Observatory System” and of a strong connection with the Computational Infrastructure for Geodynamic in the USA. In terms of impact, IMAGINE_IT will help increase geophysical knowledge and address societal issues. Creating an accurate geological model of the lithosphere in Italy will enhance the capability of analysing seismic effects. This has paramount consequences for the assessment of seismic hazard, for engineering purposes and for planning preventive measures based on rapid scenarios. In addition, IMAGINE_IT will contribute to strengthen the adjoint inversion methodology, which has relevant applications in other disciplines besides Earth Sciences, for instance in industrial acoustic non-destructive testing and in medical imaging.

Direct Numerical Simulations of Cloud Cavitation Collapse in Turbulent Flows

Project leader: Petros Koumoutsakos, ETH Zurich, Switzerland

Research field: Engineering

Resource Awarded: 29 127 111 core hours on FERMI, 23 301 689 core hours on JUQUEEN

Collaborators: Panagiotis Hadjidoukas, ETH Zurich-Switzerland, Babak Hejazialhosseini, ETH Zurich-Switzerland, Jonas Sukys, ETH Zurich-Switzerland, Fabian Wermelinger, ETH Zurich-Switzerland, Nikolaus Adams, Technical University Munich- Germany, Steffen Schmidt, Technical University Munich- Germany

Abstract: Cloud cavitation collapse is detrimental to the lifetime of high pressure injection engines and ship propellers and instrumental to kidney lithotripsy and ultrasonic drug delivery. Despite its importance, we have limited understanding of its governing mechanisms to design effective strategies for its prevention and control. The study of cloud cavitation collapse presents a formidable challenge to experimental and computational studies due to its geometric complexity and the multitude of its spatiotemporal scales. Its simulation requires two phase flow solvers capable of capturing interactions between multiple deforming bubbles, traveling pressure waves, formation of shocks and their interaction with turbulent vortical flows. Turbulent cavitating flows pose two modeling problems for predictive simulations in practical applications. Turbulent subgrid-scales occur due to momentum fluctuations, due to density fluctuations and due to phase interfaces with phase transfer. In typical applications neither small turbulent structures nor individual cavitation bubbles can be resolved. For predictive engineering simulations the thermodynamic equilibrium model has proven itself as delivering the best predictions of cavitation events and providing the most reliable data for prediction of cavitation erosion. If the cavitating flow is turbulent, statistical or Large-Eddy Simulation models can be invoked. In these models subgrid-scale terms due to mass transfer are neglected. Finite-volume averaging gives a consistent approach to representing vapor-liquid mixture in a cell as a coarse-grained thermodynamic-equilibrium state and turbulent subgrid-scales as corresponding momentum fluctuations. This approach is supported by a priori data for immiscible two-phase fluids and is supported by experimental evidence, but so far has not been analyzed by direct numerical simulation of cavitating turbulent flow. Our goal is to perform simulations of cloud cavitation collapse of unprecedented resolution and performance in order to provide a Direct Numerical Simulation (DNS) database for turbulent cavitation bubble clouds that can be used to extract relevant models for Large Eddy Simulations (LES) simulations. We propose unprecedented large-scale simulation of cloud cavitation collapse including more than 50’000 bubbles and their interaction with turbulent flow fields. The results of these simulations will revolutionize the development of engineering models to predict the cavitation damage potential. The results will be used to drastically improve engineering models of cloud cavitation collapse.

iTesla – Innovative Tools for Electrical System Security within Large Areas

Project leader: Christian Lemaître, RTE Réseau de Transport d’électricité, France

Research field: Mathematics and Computer Sciences

Resource Awarded: 9 699 328 core hours on Curie TN

Collaborators: Olivier Bretteville, RTE Réseau de Transport d’électricité- France,  Jean-Baptiste Heyberger, RTE Réseau de Transport d’électricité- France, Geoffroy Jamgotchian, RTE Réseau de Transport d’électricité- France

Abstract: iTesla is a collaborative research project carried out by a consortium of 20 European partners and supported in large part by EU funding. The consortium members are the following: • 6 Transmission System Operators (TSO): RTE (France), Elia (Belgium), National Grid (UK), REN (Portugal), Statnett (Norway) and IPTO (Greece), • 1 regional coordination service centre: Coreso (Belgium), • 6 universities and research centers: Imperial College (UK), INESC Porto (Portugal), KTH (Sweden), KU Leuven (Belgium), RSE (Italy), DTU (Denmark), • 7 industrial R&D providers: AIA (Spain), Artelys (France), Bull (France), Pepite (Belgium), Quinary (Italy), Tractebel (Belgium), Technofi (France). Security issues of the pan-European electricity transmission system will become more and more challenging in the coming years due to factors such as: i) the growing contribution of less predictable and intermittent renewable energy sources, i.e. wind and photovoltaic generation ii) the introduction of new controllable devices such as HVDC lines iii) a partially controllable electricity demand iv) the increasing difficulty to build new overhead transmission lines v) the progressive construction of a single European electricity market. These new constraints but also new opportunities will result in more complex system operations, a grid operated closer to its operational limits and therefore a need for a major revision of operational procedures. In this context, currently available tools for security assessment will no longer be suitable for network operators to take the right decisions. Thus a new generation of tools is strongly awaited by European TSOs. Moreover, these tools are expected to foster the coordination among TSOs. Indeed, different coordination centers have recently been set up within different regions of the pan-European system (Coreso is one of them) and need tools able to provide the necessary scalability to address power systems of very large dimension (more than 10 000 electrical nodes). The main goal of the iTesla project is to develop the next generation tools that will be needed by TSOs to operate the European power system in the coming years. These tools address the three main following challenges: i) performing accurate security assessment taking into account the complex dynamics of the system ii) providing a risk-based assessment taking into account the different sources of uncertainties iii) providing operators with relevant proposals for remedial actions to keep the system in a secure state. To take into account the different sources of uncertainties as well as the different contingencies that could affect the transmission system, it is necessary to simulate a very large number of system operating conditions and to check for each one of them that no operational constraint is violated. However, there is a limit to the number of simulations that can be run in real time, severely limiting the analysis scope and forcing TSOs to operate nowadays in a conservative manner. The iTesla partners have developed an innovative methodology that allows splitting the simulations into two complementary computation platforms. An ‘offline’ platform is aimed at running massive dynamic simulations in order to elaborate criteria defining stability domains for an ‘online’ platform.

INFLUM2 – Effects of selective mutations on the ligand binding and unbinding to the M2 proton channel of influenza virus

Project leader: F. Javier Luque, University of Barcelona, Spain

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 22 069 248 core hours on MareNostrum

Collaborators: Axel Bidon-Chanal, University of Barcelona-Spian, Jordi Juarez-Jimenez, University of Barcelona- Spain, Salome Llabres, University of Barcelona- Spain, Andrea Cavalli, University of Bologna – Italy

Abstract: The M2 channel of the influenza virus is a transmembrane integral homotetramer protein involved in the viral pathogenicity, as it functions as a proton channel and mediates the transfer of protons to the interior of the viral capside. During virus endocytosis, the proton transfer into the vision interior triggers the acid-induced dissociation of the matrix protein from the ribonucleoprotein, which is required for the entry of the latter into the nucleus to initiate replication. Due to its essential functional role, it has been the target of drug discovery projects against influenza. In particular, the M2 proton channel is the target of amantadine and rimantadine, which have proven to be the most successful drugs to figth the influenza virus. The use of amantadine and rimantadine, however, is increasingly challenged by the occurrence of prominent resistance-conferring mutations, making then necessary to develop novel compounds able to inhibit the mutated channels. In this project, we plan to use a mixed computational strategy that combines atomistic molecular dynamics simulations and enhanced sampling techniques to determine the free energy profiles for ligand binding/unbinding processes in the membrane-anchored channel environment. These simulations will be performed with a twofold purpose: i) to derive structural and energetic information useful to understand the differences in inhibitory potency of amantadine against the wild type channel and its mutated variants, and ii) to explore novel scaffolds for the design of promising inhibitors of amantadine-resistant variants of the wild type M2 channel, specifically V27A and S31N mutants. This information will provide valuable guidelines to assist the design of novel size-expanded and size-contracted amantadine-like compounds with improved binding properties toward the mutated forms of the M2 channel.

PULSATION: Peta scale mULti-gridS ocean-ATmosphere coupled simulatIONs

Project leader: Sebastien Masson, Pierre and Marie Curie University, France

Research field: Earth System Sciences

Resource Awarded: 13 800 000 core hours on Curie FN

Collaborators: Sarah Berthet, CNRS – France, Julien Cretat, CNRS- France, Pinsard Francoise, CNRS- France, Christophe Hourdin, CNRS- France, Swen Jullien, CNRS- France,Gurvan Madec, CNRS- France, Fracois Colas, IRD- France, Vincent Echevin, IRD- France, Pascal Terray, IRD- France, fabien durand, IRD LEGOS- France, Vera Oerder, Pierre and Marie Curie University- France,Nicholas Hall, UPS, Univ. Toulouse- France, Severin Thibaut, UPS, Univ. Toulouse- France, cindy bruyere, NCAR Earth System Laboratory- United States,  james done, NCAR Earth System Laboratory – United States

Abstract: Climate modeling has become one of the major technical and scientific challenges of the century. One of the major caveats of climate simulations, which consist of coupling global ocean and atmospheric models, is the limitation in spatial resolution ( 100 km or 1°) imposed by the high computing cost. This constraint greatly limits the realism of the physical processes parameterized in the model. Small-scale processes can indeed play a key role in the variability of the climate at the global scale through the intrinsic nonlinearity of the system and the positive feedbacks associated with the ocean-atmosphere interactions. It is then essential to identify and quantify these mechanisms, referred here as “upscaling” processes, by which small-scale localized errors have a knock-on effect onto global climate. We propose to take up this scientific challenge in this project. However, instead of choosing the crude solution of a massive increase of the models resolution, we plan to explore new pathways toward a better representation of the multi-scale physics that drive climate variability and therefore to limit the use of the highest resolutions in limited areas. Our efforts will concentrate on key upscaling processes taking place in coastal areas characterized by cold surface waters (upwelling), which hold the models strongest biases in the Tropics at local but also at basin scales. This proposal is thus following the main objective initiated during our previous PRACE projects: Quantify to which extent and by which physical processes, increasing the resolution only in limited areas can upscale and reduce large scale, systematic biases in climate models. However, if the general questions are unchanged, the current project is exploring this subject following two paths: causes and consequences of the upscaling. The first part pursues our ongoing work on upscaling through a “process study” viewpoint by testing the robustness of mechanisms driving the upscaling processes. We will focus on the sensitivity of the intensity of the coastal upwelling to oceanic and/or atmospheric resolution and parameterisations. The second research axis has more a “climate study” viewpoint and focuses on the consequences of the upscaling and the robustness of these results. Does a model with high resolution in limited extent but key areas achieve the same quality of results than a model with high resolution everywhere? What are the impacts of upscaling on diverse phenomena of the tropical climate such as ENSO, the Asian and African Monsoon, the intraseasonal variability and the dynamics of cyclones. Our approach remains unchanged and we plan to use of the first multi-scale ocean-atmosphere coupled modeling platform developed and implemented in our previous PRACE projects. We will therefore directly benefit from the work achieved during the last 2.5 years, which succeeded in introducing embedded high–resolution oceanic and atmospheric zooms in key regions of a global climate model such as the coastal upwelling with a first application to the Peru/Chilli upwelling system. This proposal will not require any new technical development and targets to maximize the scientific exploitation of our simulations by performing numerous sensitivity experiments.


Project leader: Garrelt Mellema, Stockholm University, Sweden

Research field: Universe Sciences

Resource Awarded: 19 000 000 core hours on Curie TN

Collaborators: Kyungjin Ahn, Chosun University- South Korea, Fabian Krause, University of Groningen- The Netherlands, Saleem Zaroubi, University of Groningen- The Netherlands, Hannes Jensen, Stockholm University- Sweden, Kai Yan Lee, Stockholm University- Sweden, Suman Majumdar, Stockholm University- Sweden, Keri Dixon, University of Sussex- United Kingdom,  Ilian Iliev, University of Sussex- United Kingdom, Chaichalit Srisawat, University of Sussex- United Kingdom, David Sullivan, University of Sussex- United Kingdom,

Abstract: Cosmic reionization is the process that took place 12 billion years ago when the first generations of stars and galaxies formed in the Universe. Ionizing radiation produced by stars and more extreme objects such as black holes, escaped from the galaxies and spread through the medium in between the galaxies. This process transformed this medium from entirely neutral to entirely ionized, which it has remained ever since. Reionization is at the forefront of modern cosmological research. Within the next few years we expect to transform our knowledge about this period through the detection of the redshifted 21cm radio signal from neutral hydrogen during reionization. The European radio interferometer array LOFAR is best placed to make this discovery. However, the discovery of the signal alone will need interpretation in terms of the properties and distribution of the galaxies that caused reionization. This PRACE proposal forms part of the efforts of the LOFAR-EoR Key Science Project and will provide the basic data needed to interpret the observations. We will perform several simulations with the main goal to simulate, for the very first time the full, very large volume of the Epoch of Reionization (EoR) survey of LOFAR, while at the same time including all essential types of ionizing sources, first stars, normal galaxies and QSOs. The structure formation data will be provided by an N-body simulation of early structure formation with 6912^3 (330 billion) particles and 500/h Mpc volume. This combination of large volume and high resolution will allow us to study the multi-scale reionization process, including effects which are either spatially very rare (e.g. luminous QSO sources) or for which the characteristic length scales are large (e.g. X-ray sources of photoionization and heating; the soft UV that radiatively pumps the 21-cm line by Lyman-alpha scattering; the H_2-dissociating UV background). We will complement the results from this simulation with results of smaller volumes which allow us to include the effects of structures not resolved in this very large volume. This structure formation simulation will be used in the LOFAR Epoch of Reionization Key Science Project to construct a large library of reionization simulations on non-PRACE facilities on which the interpretation of the LOFAR observations will be based. As part of this proposal we will use the structure formation results to perform reionization simulations which will address the likely stochastic nature of the sources of reionization, an aspect that to date has not been explored. We will also study the effects from the early rise of the inhomogeneous X-ray background and how much of this background is due to the first stars. The forming early galaxies, and the stars and accreting black holes within them emit copious amounts of radiation in all spectral bands, which in turn affects future star and galaxy formation. There are multiple channels for such feedback which need to be taken into account, an important one of which are the subtle, but far-reaching effects of X-rays which strongly modulate the redshifted 21-cm emission and absorption signals at early times..

OLA – Ocean LAyering

Project leader: Claire Ménesguen, UMR CNRS-IFREMER, France

Research field: Earth System Sciences

Resource Awarded: 6 000 000 core hours on Curie TN

Collaborators: Patrice Klein, UMR CNRS-IFREMER- France, Sylvie Le Gentil, UMR CNRS-IFREMER-France

Abstract: Recent seismic observations have revealed the existence of thin layers in a number of oceanic regions, especially in the vicinity of meso-scale eddies such as Meddies. The typical thickness of these layers is of the order of 10-100m with horizontal extensions reaching length scales exceeding tens of kilometers. Such layers have been also observed in high resolution direct numerical simulations of meso-scale eddies. These structures are observed in an intermediate range of scales that are still not well understood. For larger scales,the combined effects of Earth rotation and stable stratification impose a 2D-like balanced dynamics (geostrophic turbulence). For smaller scales, these two effects are negligible and motions are nearly 3D isotropic. In the intermediate regime where the layering is observed, motions become 3D but affected by both stratification and rotation, constraints that are still not well understood. The goal of this project is to understand this intermediate regime, its role in transferring energy to large and small scales and its energy dissipation. Overall, the aim of this project is to determine whether the ’layering’ is the physical manifestation of an interior route (far away from boundaries) to dissipation of the energy injected at the planetary scales in the Ocean. Comparison of the importance of such a route with other alternative possibilities will be worked out: the inertia-gravity route involving the scattering of inertia-gravity waves and the frictional dissipative bottom and coastal boundary route. The long term evolution of the ocean, relevant for climate predictions, critically depends on the dominant energy dissipation mechanism.

ASOLRC – Advanced simulation of loaded reverberation chambers

Project leader: Franco Moglie, Universita` Politecnica delle Marche, Italy

Research field: Engineering

Resource Awarded: 34 000 000 core hours on FERMI

Collaborators: Mathias Magdowski, Otto-von-Guericke-University- Germany,  Hans Georg Krauthäuser, Technical University Dresden- Germany, Stephan Pfennig, Technical University Dresden- Germany, Andrea Cozza, Supelec- France, Florian Monsef, Supelec,- France, Guillaume Andrieu, XLIM Laboratory – University of Limoges- France, Giuseppe Ferrara, Universita` degli Studi di Napoli Parthenope- Italy, Angelo Gifuni, Universita` degli Studi di Napoli Parthenope- Italy, Maurizio Migliaccio, Universita` degli Studi di Napoli Parthenope- Italy,Antonio Sorrentino, Universita` degli Studi di Napoli Parthenope- Italy, Valter Mariani Primiani, Universita` Politecnica delle Marche- Italy, Pierpaolo Belardinelli, Università Politecnica delle Marche- Italy,Stefano Lenci, Università Politecnica delle Marche,- Italy,Lucio Demeio, Università Politecnica delle Marche- Italy, Alistair Duffy, De Montfort University-United Kingdom, David Chappell, Nottingham Trent University-United Kingdom, Gabriele Gradoni, University of Nottingham-United Kingdom, Steven Anlage, University of Maryland- United States, Tyler Grover, University of Maryland- United States, Scott Roman, University of Maryland- United States, Liangcheng Tao, University of Maryland- United States,

Abstract: The reverberation chamber is a structure for generating chaotic electromagnetic fields with collective properties suitable for performing robust, repeatable and realistic measurements in the radio-frequency and microwave ranges. This project is the continuation of the project entitled “CSSRC – Complete statistical simulation of reverberation chamber”, approved during the PRACE 7th Regular Call for the year 2013-2014. The code we are using in the current project and we plan to use in the continuation project is mainly divided in three modules: 1) an electromagnetic time domain solver based on finite difference time domain (FDTD) method; 2) a fast Fourier transform module to obtain the frequency domain behavior; 3) a statistical module to obtain the reverberation chamber proprieties like uncorrelated stirrer positions, field uniformity and statistics. All the modules was previous optimized for high-performance parallel computers using hybrid method (MPI and OpenMP) and they was used successfully in the previous Prace project. During the first 7 months of this project we found promising results about the statistics of reverberation chambers. In particular, the availability of a code that in a unique job solves the electromagnetic analysis in the time domain, performs the Fast Fourier Transform and evaluates the statistical behavior of a reverberation chamber makes the simulations very appealing. Moreover, the availability of an optimized simulation code will give the results in short time avoiding long measurement campaigns. For this reason, other EMC researcher are interested to participate to this project and now they are included. During the simulations and measurements of the current project we discovered that not only the stirrers but also other object like tripods or field probes can significantly affects the reverberation chamber statistic. As a consequence we want to investigate how the device under test that is inserted in the reverberation chamber during the measurements change the statistics as function of its dimension, its shape and its absorption characteristic. Another point that will be investigated in this new project is the possibility to excite the reverberation chamber with every signal in the time domain and not only with a pulse or a sinusoidal waveform. This allows us to apply the time reversal technique in a reverberation chamber, also including non-linear elements in the simulations. Not all the new participants to this project are working in the EMC topics, they are mathematicians and physicists working on the more general topic of chaotic systems. With respect to the current project, the multidisciplinarity of the new project is emphasized and its results will be useful to a large number of researchers.

Understanding the oligomerization of dynamin on the atomistic level

Project leader: Frank Noe, Free University Berlin, Germany

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 44 000 000 core hours on Curie

Collaborators: Nuria Plattner, Free University Berlin – Germany

Abstract: Dynamin is an enzyme essential for endocytosis in eucariotic cells. Dynamin oligomerizes into helical structures around the neck of budding vesicles and mediates the vesicle scission from the cell membrane. Understanding the oligomerization of dynamin is crucial in order to assess the dynamin function and the role of disease-related dynamin mutants. We propose to study the oligomerization of dynamin on the atomistic level with molecular dynamics simulation and Markov state models. The sampling problem caused by the large dynamin system and the long timescales of the oligomerization process will be addressed by adaptive sampling based on Markov state model, a recently developed enhanced sampling method. Based on this method and an overall simulation time of one millisecond distributed to several dynamin subsystem an atomistic model for the dynamin oligomerization will be constructed.

Protein-DNA binding allostery

Project leader: Modesto Orozco, Institute for Research in Biomedicine (IRB-Barcelona), Spain

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 29 200 000 core hours on MareNostrum

Collaborators: Alexandra Balaceanu, Institute for Research in Biomedicine (IRB-Barcelona),- Spain,  Pablo D. Dans Puiggròs, Institute for Research in Biomedicine (IRB-Barcelona)- Spain

Abstract: The accessibility of the genetic information stored in DNA regulates transcription and replication events and depends on the flexibility and conformational constraints of the macromolecule as well as on its energy landscape. Partial understanding of the processes involved in protein-DNA recognition has led to the classical view that DNA acts as an inert template onto which proteins assemble to replicate or transcribe genes. This view has been challenged and has evolved to acknowledge an active role of the DNA in its own replication and transcription through its capacity to undergo conformational changes in response to protein binding. Novel evidence regarding collaborative effects of specific protein binding on different DNA sites has consequently reopened the issue of DNA allostery, a property thought to have meaningful influence on regulatory functions, but virtually ignored until now because of the intrinsic complexity of an in-depth study of the problem. We aim to investigate the allosteric effect produced by the binding of chosen human transcription factors (TF) to real DNA promoters by all-atom molecular dynamics simulations. The study of such systems will allow us to address multiple questions: – What is the spatial and temporal extend of the information transfer along DNA? – Which are the effects of different binders? How is the perturbation induced? – Which are the underlying operating mechanisms behind the propagation of information along DNA? – Do differences in the binding pattern affect the nature of information transfer (in space and time)? – What is the role of allostery in the regulation of transcription initiation? – To which extend is it possible to employ DNA intrisic physical properties together with protein binding modes in order to predict allosteric effects?

NuMass – neutrino masses in cosmological large scale structures

Project leader: Nathalie Palanque-Delabrouille, CEA, France

Research field: Universe Sciences

Resource Awarded: 100 000 core hours on Curie, 7 900 000 core hours on Curie TN

Collaborators: Arnaud Borde, CEA, FRANCE Laurent Chevalier, CEA- France,  Christophe Magneville, CEA- France,  Christophe Yeche, CEA- France,  Matteo Viel, INAF/OATS- Italy, Graziano Rossi, Sejong University- South Korea

Abstract: Neutrino science has a received a boost of attention recently in cosmology, since the breakthrough discovery that neutrinos are massive. Cosmology offers a unique opportunity to pinpoint the long-sought neutrino masses with excellent sensitivity to neurtino mass since primordial neutrinos comprise a small portion of the dark matter and are known to significantly impact structure formation in the Universe. In this proposal, we propose to exploit the 5-year BOSS data in combination with the recently published Planck results to constrain to unprecedented levels the neutrino mass thanks to an extended grid of hydrodynamical simulations that reproduce the effect of changes in cosmological or astrophysical parameters on the power spectrum measured in the Lyman-alpha forest. We will also produce the largest simulations including massive neutrinos and reliably reproducing the matter and the flux power spectrum on scales ranging from a few Mpc to several tens of Mpc according to our best current knowledge of cosmology and astrophysics.

MCH – Minimal Composite Higgs

Project leader: Claudio Pica, CP3-Origins, University of Southern Denmark,Denmark

Research field: Fundamental Physics

Resource Awarded: 7 500 000 core hours on MareNostrum

Collaborators: Rudy Arthur, CP3-Origins, University of Southern Denmark-Denmark,Michele Della Morte, CP3-Origins, University of Southern Denmark-Denmark, Vincent Drach, CP3-Origins, University of Southern Denmark-Denmark,Martin Hansen, CP3-Origins, University of Southern Denmark-Denmark, Ari Hietanen, CP3-Origins, University of Southern Denmark-Denmark,Tuomas Karavirta, CP3-Origins, University of Southern Denmark-Denmark, Francesco Sannino, CP3-Origins, University of Southern Denmark-Denmark

Abstract: The historical discovery of a new boson by the Large Hadron Collider (LHC) experiments at CERN, which has very rapidly led to the Nobel price in physics to F. Englert and P. Higgs, has been the culmination of a journey lasted more than fifty years and it has opened a new era for high-energy physics. We are now left with the crucial question of the nature of the new boson: is this newly discovered particle the Standard Model “Higgs boson” or it is something different? Is the new boson a fundamental particle or it is a composite state? Several extension of the Standard Model exist in which the new boson is not elementary but instead made of something else. In this project we will investigate this possibility. Our project focus on the minimal realisation of two popular proposals in which the Higgs boson is a composite state: Technicolor and the so-called “composite Higgs” models. In Technicolor, the Higgs is a (light) scalar state, equivalent to the f0(500) — also known as the sigma resonance — in QCD. The Higgs-like state can be light due to the non-perturbative dynamics of the model and, in addition, because of the back-reaction of the Electroweak sector on the new Technicolor sector. In the second class of theories, the “composite Higgs” models, the Higgs-like state is the equivalent of pions in QCD, and it is light due to spontaneous breaking of a global symmetry. Recently the simplest realisation of a model which can be used for both the above proposal has been explicitly constructed. This model is based on the SU(2) gauge theory with 2 Dirac fermions in the fundamental representation. This model in isolation features spontaneous chiral symmetry breaking with 5 Goldstone bosons, 3 of which are needed to give mass to the Electroweak gauge bosons. An Higgs-like state is present in the model which, depending on how the model is embedded in the SM Electroweak sector, can be either the Technicolor scalar state or the extra Goldstone bosons or a mix of these two possibilities.

KETHYON – Kinetic model of ETHYlene epoxidatiON on Ag surfaces

Project leader: Simone Piccinin, CNR-IOM, Italy

Research field: Chemistry

Resource Awarded: 11 000 000 core hours on Hermit

Collaborators: Travis Jones, CNR-IOM- Italy

Abstract: Every year millions of tonnes of ethylene oxide are produced over silver catalysts. Improving the selectivity of this process by as little as 1% is estimated to save the chemical industry more than 10 million USD per year. This fact has long made identifying the mechanism by which ethylene oxide is formed over silver a major scientific goal. Despite decades of effort and broad acceptance of mechanisms in which atomic oxygen reacts with ethylene to form ethylene oxide, there have been few rational improvements made to silver catalysts. In fact, nearly every known method of increasing selectivity was determined through empirical means. This failure is widely attributed to the fact that the accepted picture of the atomic structure of the catalyst and the nature of the active species under catalytic conditions is incomplete. Recently, however, through a close collaboration with experimentalists in the Department of Inorganic Chemistry at the Fritz-Haber Institute in Berlin (Germany), we achieved a breakthrough in the field: We found that large concentrations of molecular oxygen are present on the surface of the working catalyst, and the concentration of this species correlates with the catalyst’s ability to selectively oxidize ethylene to ethylene oxide. Here we propose a timely computational study designed to exploit these new findings, with the goal of establishing a full dynamic model of this catalytic process through first-principles based kinetic Monte Carlo simulations. We will begin by using DFT calculations to compute the activation energies for the formation of ethylene oxide and for the competing reactions that lead to undesirable the total combustion side product, CO2. Once these barriers are identified we will construct a Cluster Expansion for the Ag/O/ethylene system by fitting lateral interactions among surface adsorbates on the basis of DFT total energies. With these information in our hands, we will set up a kMC model of the full catalytic process, in which the rates of each elementary step will depend on the spatial arrangement of adsorbates around the reactants. On metal surfaces, this is a key ingredient to obtain quantitative agreement with experimentally determined kinetic parameters. Having an accurate model of kinetics of the system will enable us to identify the reaction mechanism and the rate limiting step/steps, understand how external parameters like temperature and pressure influence the kinetics, and ultimately understand why Ag is the only known catalyst able to selectively oxidize ethylene to ethylene oxide.

MIMI – Modelling Interactions between Mesoscale, submesoscale and Internal tides for high resolution satellite altimetry

Project leader: Aurélien Ponte, Ifremer, France

Research field: Earth System Sciences

Resource Awarded: 30 000 000 core hours on FERMI

Collaborators: Patrice Klein, Ifremer- France,  Sylvie Le Gentil, Ifremer, FRANCE Nicolas Rascle, Ifremer- France, Gurvan Madec, IPSL- France

Abstract: Oceanic mesoscale eddies O(100-300km) and submesoscale structures (O(1-50km) are now well known to control exchanges between the interior and the surface of the ocean, to contribute to ocean mixing, and to play an important role for the physical, climatic and biochemical functioning of oceans (Capet et al. 2008, Klein and Lapeyre 2009; Ferrari 2011; Levy et al. 2012). Our group in Brest has much contributed to these results, in particular to highlight the significant dynamical impact of submesoscales, through their vertical velocity field, on larger oceanic scales (Klein et al. 2008, 2009). Our results were obtained from numerical simulations, with a resolution (1km, 200 vertical levels) never attained before, performed on the Earth Simulator in Japan (a machine more powerful than most Tier 1 machines). Some of these new numerical and theoretical results (Klein et al. 2009, Ponte et al. 2013, Ponte & Klein 2013) are presently used as one the main scientific arguments for the development of wide-swath altimeter satellite missions: the SWOT mission led by CNES (France) and NASA (US), and the COMPIRA mission led by JAXA (Japan). These missions should capture sea surface height (SSH) with a resolution ten times higher than conventional altimeters. This will provide an unprecented view of fine scale ocean dynamics and its impact on larger-scale dynamics (3000 km). However recent studies (Richman et al. 2012; Shriver et al. 2013) have revealed a major obstacle on the road to the full success of these missions: the existence of internal tides which are perturbations of ocean stratification by tidal currents. Internal tides are another class of motions whose range of spatial scales lies close to that of mesoscale and submesoscale turbulence. These studies suggest that internal tides contribution to the high resolution SSH observed by SWOT and COMPIRA in the Eastern part of oceanic basins will be stronger than expected and difficult to distinguish from that due to mesoscale/submesoscale motions because of the strong nonlinear interactions between the two classes of motions. The present MIMI project (Modelling Interactions between Mesoscale, submesoscale and Internal tides for high resolution altimetry) aims at better understanding these nonlinear interactions between internal tides and meso/submesoscale motions, which has never been investigated before. The resolution considered will be the same (1km) as in our previous studies and these simulations will therefore require to use one of Tier 0 class machines available in Europe. On a fundamental level, interactions between internal tides and mesoscale/submesoscale motions may have far reaching impacts on the dynamics of larger scales via inverse cascades of energy associated with oceanic turbulence. Another goal of this project is to provide testbeds to estimate the 3D ocean circulation from high resolution SSH (as what will be measured by SWOT and COMPIRA). To achieve these goals, high resolution numerical experiments need to consider large domains (O(1000km) and time integration of at least a couple of years.

EXCIST – Excited state charge transfer at the conjugated organic molecule – semiconductor interface

Project leader: Martti Puska, Aalto University School of Science, Finland

Research field: Chemistry

Resource Awarded: 92 160 core hours on Curie, 5 923 840 core hours Curie TN

Collaborators: Kari Laasonen, Aalto University-Finland, Olga Syzgantseva, Aalto University-Finland

Abstract: The current project aims the understanding of physical factors, governing the interfacial excited state charge transfer (CT) between conjugated organic molecules and a semiconductor surface. For this purpose, we follow the electron and coupled electron-ion dynamics via ab initio simulations. Recent efficient implementations of the Ehrenfest Dynamics (ED) approach and the Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) into the GPAW program have opened a way of such simulations for systems, containing hundreds of atoms. The objective of this project is to apply the above techniques to analyse the factors, affecting the electron injection rate at the organic dye – semiconductor interface. Among the factors to be investigated are: the role of the ionic dynamics in CT, the impact of the anchoring mode, the influence of surface characteristics and the initial excitation. The results of this work will help us to elucidate the CT-mechanisms on the molecular level and can be generalized and applied to a broader range of semiconductor – organic molecule interfaces, facilitating the optimal design of novel materials.

PeroCondution – Electron-Hole transport in Perovskites materials by non-equilibrium electron dynamics

Project leader: Ursula Roethlisberger, Swiss Federal Institute of Technology EPF Lausanne, Switzerland

Research field: Chemistry

Resource Awarded: 17 064 075 core hours on SuperMUC

Collaborators: Pablo Lopez, Swiss Federal Institute of Technology EPF Lausanne,-Switzerland, Simone Meloni, Swiss Federal Institute of Technology EPF Lausanne-Switzerland

Abstract: Halogen perovskites, ABX3 (A denotes an organic or inorganic cation, B a divalent metal – typically Sn or Pb, and X = Cl, Br, I), have attracted much attention as light-harvesting materials for high performance, meso/nanoporous solar cells. The role played by perovskites in these devices, whether only active in light harvesting or also in transport of carriers (electrons and holes), has been recently subject of intense research. Recent experimental work seems to suggest that perovskites can efficiently transport holes and electrons. This might open new avenues for the development of simpler and more efficient solar cell design. It is, therefore, important to identify the electron/hole transport mechanism in perovkite, so as to develop combined gap/conduction optimization strategies. The objective of this project is to use non-equilibrium excited state ab initio simulations to study this mechanism. We will employ state-of-the-art exited state dynamics, real time propagation time dependent Density Functional Theory (TDDFT) with Ehrenfest dynamics for the nuclei. We will also investigate the supposed anisotropy in the electron/hole transport by applying an external field in the direction parallel and orthogonal to the tetragonal axis.

NEMERTE – Numerical Experiment on the Mediterranean model response to Enhanced Resolution and TidE

Project leader: Gianmaria Sannino, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development), Italy

Research field: Earth System Sciences

Resource Awarded: 17 860 000 core hours on FERMI

Collaborators: Gabriel Jorda Sanchez, Mediterranean Institute for Advanced Studies (IMEDEA)- Spain,  Vincenzo Artale, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development)- Italy, Adriana Carillo, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development)- Italy,  Emanuele Lombardi, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development)-Italy, Giovanna Pisacane, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development)-Italy,  MariaVittoria Struglia, ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development),-Italy, Patrick Heimbach, Massachusetts Institute of Technology (MIT)-United States

Abstract: Over the last decades, research has demonstrated the necessity of a high resolution modeling approach to the description of the overall mechanism of the Mediterranean circulation (MTHC), which transforms the relatively fresher Atlantic inflow into the colder and saltier Mediterranean tongue that sinks into the adjacent ocean at intermediate depths. It has in fact been recognized that the Mediterranean Sea exhibits a variety of small scale features, and hosts numerous mesoscale eddies sometimes arranged in self organized systems. Moreover, it has been observed that the counter-flowing fluxes of Atlantic and Mediterranean waters are subject to tide-induced vigorous mixing within the Gibraltar Strait, where tidal forcing also affects the hydraulic control of volume fluxes, both processes determining larger heat, salt, and mass fluxes into the Mediterranean. A correct prescription of the lateral boundary condition at the Gibraltar inlet can therefore only be achieved by explicitly including the Gibraltar Strait in the numerical domain, at a spatial resolution sufficient to account for both the fast barotropic tidal signal propagating eastward from the Atlantic Ocean and the baroclinic mixing processes occurring within the strait. Despite the continuous progress in model credibility and the advancement in computational resources experienced by numerical modeling studies over the past decades, an explicit treatment of these potentially relevant processes has not yet been included in Mediterranean climate simulations, which are still in want of a comprehensive representation of the flow exchange through the Strait of Gibraltar, of the Mediterranean eddy-dominated flow field, and of the formation rates and transports of water masses involved in the Mediterranean Thermohaline Circulation. This project aims to evaluate the separate and joint long-term effects of increased resolution, SoG dynamics, and tides on the simulated MTHC by comparing results from three hindcast (30 years long) numerical simulations. First, results from a mesoscale-resolving Mediterranean model with a mesh refinement in the SoG will be compared to those from a mesoscale-permitting version (1/12° uniform resolution) of the same model that has already been run. Second, results from a mesoscale-resolving Mediterranean model (1/16°) including tides will be compared to those from the mesoscale-resolving experiment without tidal forcing. We will use the Massachusetts Institute of Technology general circulation model (MITgcm) over a domain including the entire Mediterranean Sea and the Gulf of Cadiz in the Atlantic Ocean. Tidal forcing will include both the internal and lateral tides. Simulations will cover the period 1974 -2004, surface atmospheric forcing being provided by the dynamical downscaling of the ECMWF-ERA40 air-sea fluxes reanalysis via a regional model (30 Km resolution). The planned experiments represent an absolute novelty for the Mediterranean ocean modeling community, as Mediterranean tides and thermohaline circulation have always been studied separately and in different contexts, tide effects having so far been considered relevant only for specific processes and events, over shorter time scales. To date only the leadership computing facilities offered by PRACE Tier-0 have the capability of managing such large-scale multi-decadal simulations.


Project leader: Yanick Sarazin, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), France

Research field: Fundamental Physics

Resource Awarded: 46 800 000 core hours on FERMI

Collaborators: Thomas Cartier-Michaud, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Guilhem Dif-Pradalier, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Rémi Dumont, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Damien Estève, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Xavier Garbet, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France,Philippe Ghendrih, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Jean-Baptiste Girardo, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Virginie Grandgirard, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Guillaume Latu, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Claudia Norscini, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Chantal Passeron, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France, Fabien Rozar, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)-France

Abstract: Using nuclear fusion as a promising energy source is a matter of international collaboration exemplified by the tokamak ITER presently built in Cadarache, France. In the foreseen burning plasmas, the energy amplification factor depends critically on the energy confinement time tE and is to diverge as t_E reaches the critical Lawson value (in the range of a few seconds for ITER). In low density controlled fusion devices such as the tokamaks, plasma confinement is ensured by strong magnetic fields and is mainly regulated by turbulent transport which usually dominates over collisional transport. The strongest dependence of the empirical scaling law for t_E, developed along the years with an international data base, is a nonlinear dependence on machine size. The device performance measured by t_E thus translates directly in the size of the reactor and consequently on its cost. Any means of controlling and reducing turbulent transport will lead to an appreciable gain in stored energy, and impact positively the ngineering and cost constraints. In that respect, plasma rotation shear appears as a key mechanism in turbulence regulation. This project aims at identifying key mechanisms by which ion turbulence can drive or affect plasma rotation, and, vice-versa, how plasma rotation can regulate plasma turbulence and transport. In tokamaks, plasma flows develop in both periodic directions of the torus, poloidal and toroidal. Both are considered in the project. The simulation effort is to be achieved with the 5D gyrokinetic code GYSELA. Because of the high temperature and low density of such fusion plasmas, the collision frequency is not large enough for legitimating the fluid description of the plasma medium. The 6-dimensional kinetic approach is then the appropriate escription. The small turbulence frequencies as compared to the cyclotron frequency allow one to perform a phase space reduction down to 5-dimensions. The originality of the GYSELA code is twofold: it models the entire ion distribution function, without any scale separation assumption between equilibrium and fluctuations, and prescribed sources allow one to drive the system out of thermo-dynamical equilibrium. Three main issues are considered in this project, within the global and flux driven approach allowing for turbulence self-organization. First, the generation mechanisms of large scale plasma flows are addressed. These are either extrinsic, such as the possible core penetration of edge flows via boundary conditions or oscillating modes driven unstable by fast particles, or intrinsic, due to turbulence self-generated flows. The latter mechanism requires symmetry breaking, and can lead to significant departures from neoclassical expectations. Second, the characteristics of momentum transport are explored and compared to theoretical predictions. Third, the impact of both poloidal and toroidal rotation on heat turbulent transport and on impurity transport is the ultimate focus of our study.

LEREC – Large-Eddy Simulation of a meso-scale rocket engine with self-sustained combustion instability

Project leader: Thomas Schmitt, EM2C laboratory, CNRS, Ecole Centrale Paris, France

Research field: Engineering

Resource Awarded: 80 000 000 core hours on FERMI

Collaborators: Benedicte Cuenot, CERFACS-France, Gabriel Staffelbach, CERFACS-France,Sebastien Candel, EM2C laboratory, CNRS, Ecole Centrale Paris-France, Sebastien Ducruix, EM2C laboratory, CNRS, Ecole Centrale Paris-France, Thomas Schmitt, EM2C laboratory, CNRS, Ecole Centrale Paris-France, Thierry Poinsot, IMFT, CNRS, FRANCE Laurent Selle, IMFT, CNRS-France, Annafederica Urbano, IMFT, CNRS-France

Abstract: The occurrence of combustion instabilities in high-performance engines, and in particular rocket engines is a major hurdle for industrial programs. Over some 70 years of development, most space programs have run into combustion instability problems resulting in reduced performance, increased costs and many failures. Thanks to high-speed visualization and numerical simulation, the under- standing of longitudinal and azimuthal combustion instabilities has seen great progress over the past 30 years. Nevertheless, combustion instabilities can still not be predicted before full-scale tests so that the development of fundamental knowledge as well as modeling and simulation strategies constitutes a major issue. The physical mechanisms leading to transverse instabilities are still not understood and there is vital need for fundamental research in this field. This research proposal will assess the capability of the Large-Eddy Simulation framework to predict transverse combustion instabilities in liquid-fuel rocket engines. Taking advantage of a unique experimental setup operated by DLR, we propose to conduct the first unsteady reactive simulation of a full engine-like configuration, from the injection manifold to the outlet of a choked nozzle.

Identification of somatic variations in PanCancer genomes using SMUFIN, a reference-free approach

Project leader: David Torrents, Barcelona Supercomputing Center, Spain

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 5 713 280 core hours on MareNostrum

Collaborators: Santi Gonzalez, Barcelona Supercomputing Center-Spain, Valenti Moncunill, Barcelona Supercomputing Center-Spain, Friman Sanchez, Barcelona Supercomputing Center-Spain

Abstract: Accurate identification and characterization of somatic structural variation from tumor genomes remains a big challenge. In particular, the definition of complex structural rearrangements and the resulting scenarios of tumor genomes involving chimeric chromosomes (as in chromothripsis or chromoplexia), still requires the combination of several experimental and complex computational approaches. This task is expected to be even more challenging in the context of the PanCancer project, where thousands of different tumor genomes sequenced at different sequencing centers must be described with different methods, as to their somatic variation. In the frame of a collaboration among several ICGC groups, we have recently developed a novel methodology, called SMUFIN (for Somatic MUtation FINder), for the identification of all types of somatic variation in cancer genomes. Our method takes FASTQ files as input and directly compares sequencing reads from normal and tumor genome samples, i.e. without the need of a reference genome, to identify SNV and SVs of all sizes in a single execution. Performance tests using in silico and real tumor data (at 60-­?fold depth of coverage), as well as orthogonal experimental approaches have shown average sensitivity and specificity values of 92% and 95% for SNVs, and 74% and 91% for SV respectively. SMUFIN was also able to identify, with a specificity of 92%, nearly all the breakpoints previously inferred using different experimental and computational approaches in aggressive forms of solid (Medulloblastoma) and blood (Mantle Cell Lymphoma) tumors. There, we were able to identify, at base pair resolution, hundreds of breakpoints that define chimeric forms of rearranged chromosomes that agree with the definitions of chromothripsis and chromoplexy. In addition, breakpoints corresponding to these large structural variants are provided by SMUFIN together with a reconstruction of the corresponding sequence in the tumor, including additional sequence shard or sequence not present in the reference genome. Since the original version of SMUFIN did not allow a massive and parallel processing of tumor genomes, we have developed, in collaboration with the group of Jesus Labarta (head of the Computer Science Department), a new optimized version of SMUFIN that is able to process several genomes in parallel in cluster-­?based computing (or HPC) environments. This improved version of SMUFIN is based on OmpSs (http://pm.bsc.es/ompss), a programming model that enables an enhanced parallelization of programs.

Lipid-modulation of the toll-like receptor TLR4

Project leader: Ilpo Vattulainen, Tampere University of Technology, Finland

Research field: Biochemistry, Bioinformatics and Life sciences

Resource Awarded: 21 000 000 core hours on Hermit

Collaborators: Moutusi Manna, Tampere University of Technology-Finland, Edouard Mobarak, Tampere University of Technology-Finland, Tomasz Rog, Tampere University of Technology-Finland

Abstract: Toll-like receptors (TLRs) constitute a class of membrane proteins that are part of the innate or non-specific immunological system. Meanwhile, ligands for TLRs are pathogens like bacterial lipids, lipoproteins, and bacterial fragments. After recognition of specific ligands, TLRs trigger signaling cascades resulting in the generation of pro-inflammatory and antimicrobial responses. As TLRs are involved in numerous illnesses and pathologies such as infectious and auto-immunological diseases, atherosclerosis, and cancer, TLRs are potential targets for drugs, highlighting their importance in health. This is also stressed by the fact that the ligands of TLRs are used in cancer therapy and often added to vaccines in order to increase their efficiency. Yet, the mechanistic understanding of their effects are not known. In this study, we will perform large-scale atomistic molecular dynamics simulations of the active dimer complex of TLR4 (encoded by the TLR4 gene) embedded in a lipid bilayer to understand how specific glycolipids affect the TLR4 conformation and dynamics. We further unravel the role of each component in these interactions resulting in the activation of the protein. The studies are bridged to experiments and have potential for a high impact on pharmacological applications of TLR4.

SODIFE – SOlute-Dislocation Interactions in FErritic steels

Project leader: Lisa Ventelon, CEA, France

Research field: Chemistry

Resource Awarded: 21 349 333 core hours on Curie TN

Collaborators: Lisa Ventelon, CEA-France, Francois Willaime, CEA-France, David Rodney, Universite Claude Bernard Lyon 1-France,

Abstract: The Service de Recherches de Metallurgie Physique (SRMP) of CEA/Saclay in France has developed an expertise on the application of ab initio electronic structure calculations of DFT type (Density Functional Theory) to large systems, in order to describe defects in materials, such as dislocations, which are line defects in the crystalline lattice governing plastic deformation. The present proposal is at the level of the predictive modelling of plasticity in body-centred cubic (bcc) iron in the presence of solutes that offers great promise to inform ferritic alloys design of considerable industrial interest. Quantitative modelling of the mechanical behaviour for these alloys above all requires describing interatomic bonding at the electronic structure level. This work will be performed in the framework of a basic science multiscale modelling approach to study the behaviour of steels starting from ab initio electronic structure calculations. As a starting point for the treatment of plasticity, the present proposal is focused on dislocation-impurity interactions at the atomic scale. These interactions are driving forces for solute strengthening/softening. The objective of this work is to provide a quantitative description from first principles of the effects of solutes on 1/2<111> screw dislocation properties in bcc iron. The effort will be placed on studying two solutes: (i) carbon, whose interaction with dislocations is known to play an important role in mechanical properties of ferritic steels and (ii) helium, which is present in reactor pressure vessel steels as fission product. The study of these complex systems requires large simulation cells particularly along the dislocation line because of the solute interactions with its periodic images, and also a high accuracy because the energy differences involved are rather small, typically 0.1-to-0.5 eV for supercells containing 300-to-600 atoms. This study therefore needs to be performed on massively parallel computers. After having successively studied straight dislocations in pure iron and the 2D energy landscape seen by these dislocations, the objective of this proposal is to introduce solute atoms in the vicinity of the dislocation core in order to investigate the subsequent changes induced on the dislocation core structure and on the glide mechanism. In these innovative calculations, the dislocation can not be considered solely as a straight line but will involve the possible nucleation of double-kinks around the solute. This project will be performed through interlinked atomic scale description levels (ab initio, line-tension model) and in relation with experimental observations at the macroscopic scale. This approach may serve as a guide to propose new ferritic alloy compositions, in order to improve materials performance.