12th Project Access Call – Awarded Projects

Results of the 12th Call for Proposals for Project Access.

Projects from the following research areas:

Biochemistry, Bioinformatics and Life sciences (2)

DNA crystal simulations: a step towards the understanding of the crowded cellular environment.

Project Title: DNA crystal simulations: a step towards the understanding of the crowded cellular environment
Project Leader: Modesto Orozco, ES
Resource Awarded: 22000000 core hours on MareNostrum

Details

Team Members :
Pablo Dans, Institute for Research in Biomedicine (IRB-Barcelona), SPAIN
Antonija Kuzmanic, Institute for Research in Biomedicine (IRB-Barcelona), SPAIN

Abstract
Macromolecular crowding is an important factor that can influence the behavior of nucleic acids in cellular environments. In human cells, DNA of around one meter of length has to compress into a nucleus of less than 5 mm in diameter, suggesting that DNA is highly packed inside the nucleus leading to short DNA-DNA distances. Biomolecular simulations by means of atomistic Molecular Dynamics (MD), have proven to offer detailed complement to experiments like NMR or X-ray crystallography in elucidating at the molecular level the structure and dynamics of biomolecules. In particular, nucleic acids simulations in crystal environment have long been used to test simulation methods, since crystallographic structures has been historically used as the golden standard to compare and validate MD force-fields. A very interesting but yet unexplored facet of the DNA crystal environment, is that it can be considered as a surrogate of the real biological environment. In this sense, characteristics of the double helix measured in such crowded conditions can help to understand better the structure and dynamics of the DNA in the nucleus. More complex and long simulations are needed to begin to understand the behavior of B-DNA in “native” environment, and the simulations of DNA in crystal conditions are clearly an unavoidable step toward the full understanding of the real environment in the cell nucleus.

iHART – Characterization of genetic risk variants in ASD families using a reference-free approach

Project Title: iHART – Characterization of genetic risk variants in ASD families using a reference-free approach
Project Leader: Daniel Geschwind, USA
Resource Awarded: 7987200 core hours on MareNostrum

Details

Team Members :
Montserrat Puiggros, Barcelona Supercomputing Center, SPAIN
David Torrents, Barcelona Supercomputing Center, SPAIN
Laura Perez Cano, University of California Los Angeles (UCLA), UNITED STATES
Elizabeth K. Ruzzo, University of California Los Angeles (UCLA), UNITED STATES

Abstract
Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder that affects 1% of the population. In recent years, the analysis of next generation sequencing data has advanced our understanding of the genetics of the disease, which is essential in order to develop effective treatments. However, given its large heterogeneity, most of the genes involved in ASD remain still unknown and the development of large-scale studies is strongly required. In order to overcome this challenge, the Hartwell Foundation has launched the largest worldwide initiative to characterize the genetic basis of ASD: the Autism Research and Technology Initiative (iHART), which has generated open-source whole genome sequencing data for 1000 ASD families and will generate data for 900 more ASD families by early next year. In order to get a more accurate detection of de novo and inherited genetic ASD risk variants in these families, we will apply a novel strategy by using a reference-free approach, SMuFin, to directly compare the genome between all affected and unaffected children and their corresponding parents. Considering both, the use of a large-scale whole genome sequencing data set and the effectiveness of the method proposed for detecting genetic variants in ASD families, this PRACE project aims to characterize disease-associated genetic variants, identify novel risk genes and gain comprehension of the biological pathways affected in ASD.

SMOLER , Synaptic Mechanisms underlying Odor LEarning and Recognition

Project Title: SMOLER , Synaptic Mechanisms underlying Odor LEarning and Recognition
Project Leader: Michele Migliore, IT
Resource Awarded: 13000000 core hours on Fermi

Details

Team Members :
Rosanna Migliore, National Research Council, ITALY
Francesco Cavarretta, Yale University, UNITED STATES
Michael Hines, Yale University, UNITED STATES

Abstract
Understanding the neural basis of odor recognition may have a significant impact from many points of view, from providing a better explanation of physiological and behavioral processes at brain system level, to spin off industrial applications (in the setting of the development of odor-sensitive devices and the fragrance industry). While experimental findings have given important clues regarding the activation patterns of the cells involved in odor recognition, the underlying network mechanisms are, as with other brain systems, still unknown. This lack of information is due mainly to the fact that the circuits carrying out sensory processing in this system are usually investigated experimentally in single cells or in small, randomly selected sets of cells. The functional effects of network-wide processes, in relation to the patterns of glomeruli activated by different odors, thus remain relatively unknown. To aid in solving this problem, in a previous PRACE project we have constructed and used a large-scale 3-dimensional model of the olfactory bulb, with realistic 3D inputs, cell morphologies, and network connectivity. With this model, we started to reveal the mechanisms underlying the formation of glomerular-related synaptic clusters observed experimentally (Migliore et al., 2014). Building on these results, we have recently (Migliore et al., 2015) introduced a novel theoretical approach, and identified the dynamics of glomerular units formation in response to a given odor; how and to what extent the glomerular units interfere or interact with each other during learning; their computational role within the olfactory bulb microcircuit; and how their action can be formalized into a theoretical framework in which the olfactory bulb can be considered to contain “odor operators” unique to each individual. The findings provided new and specific theoretical and additional experimentally testable predictions. In this project, we plan to go one step further, extending the model to include additional, experimentally constrained, cell types. We believe this is particularly important for processing natural odorants, since complex natural odors activate a large portion of the olfactory bulb with a dense representation (Vincis et al., 2012). The major questions that we would like to investigate in this project are related to how and under what conditions the network self-organization occurring during odor learning can represent the different components in a mixture, helping to explain puzzling behavioral results on the emergence of synthetic or analytic perception of odor qualities. This would be the first implementation of the olfactory bulb at this scale and realism. We think it will have a major impact in the scientific community, promoting new experimental investigations, becoming a new framework to investigate the functions of a brain system, and guiding the development of a new generation of brain-inspired odor sensing devices. References: Migliore M, et al., (2015) Synaptic clusters function as odor operators in the olfactory bulb, Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8499-504. Migliore M, et al., (2014) Distributed organization of a brain microcircuit analyzed by three-dimensional modeling: the olfactory bulb, Front Comput Neurosci. 8:50.

Molecular Dynamics Simulations for Computing Kinetic Constants for Drug Discovery

Project Title: Molecular Dynamics Simulations for Computing Kinetic Constants for Drug Discovery
Project Leader: Marc Bianciotto, FR
Resource Awarded: 33000000 core hours on Fermi

Details

Team Members :
Daria Kokh, Heidelberg Institute for Theoretical Studies, GERMANY
Rebecca Wade, Heidelberg Institute for Theoretical Studies, GERMANY
Steffen Wolf, Ruhr-University Bochum, GERMANY

Abstract
There is now a growing body of evidence that the kinetic, and not only the thermodynamic, properties of binding and unbinding between a drug and its protein target are highly relevant for in vivo efficacy and clinical success. Our understanding of the molecular determinants of structure-kinetics relationships remains imperfect, especially because they rely on the relative stability of transient states. Contrarily to the stable bound and unbound states which are easier to observe, transient states are short-lived, thus the atomic description of these states remains challenging. Molecular dynamics simulations provide a valuable tool for such a description: unbiased simulations have been used on small ligands to describe the spontaneous ligand-protein association and the related kinetic constants have been calculated from Markov models. Currently, this procedure cannot be used for practical applications in Drug Discovery: the typical range of residence times for drug candidate-target interaction, which is from microsecond to hundreds of hours, is not affordable for a brute-force Molecular Dynamics simulation with state of the art hardware. In the framework of the IMI K4DD (Kinetics for Drug Discovery) consortium, a large set of experimantal structural, thermodynamic and kinetic data were generated on several series of ligands per target. This experimental data will allow us to investigate the applicability, performance and accuracy of several computational methodologies (Umbrella Sampling, Steered Molecular Dynamics, Targeted Molecular Dynamics and Metadynamics) for evaluating the thermodynamics and kinetics of protein-ligand binding. This study will lead us to elaborate a computationally efficient procedure for evaluation of ligand-protein binding rate constants, which can be used for rational design of drugs with specific kinetic properties.

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Chemical Sciences and Materials (7)

EyESPOT: Electronic states in pure and doped rutile and anatase TiO2

Project Title: EyESPOT: Electronic states in pure and doped rutile and anatase TiO2
Project Leader: Daniele Varsano, IT
Resource Awarded: 20000000 core hours on Fermi

Details

Team Members :
Andrea Ferretti, Italian Research Council,, ITALY
Elisa Molinari, Universita di Modena e Reggio Emilia, ITALY
Annabella Selloni, Princeton University, UNITED STATES

Abstract
Titanium dioxide (TiO2) is known as one of the best materials for photocatalysis and solar energy conversion. However, TiO2 can absorb only a small portion of the solar spectrum in the UV region. This is a serious drawback which severely limits the efficiency of TiO2 in photocatalysis. For this reason, over the last years intensive efforts have been devoted to the synthesis and characterization of doped TiO2 with the absorption edge shifted towards the visible light region,. In this context, an accurate theoretical description of the band gap and impurity levels of doped TiO2, as well as a study of the influence of doping on the optical absorption, would be extremely helpful by providing insights for the design of TiO2 materials with improved properties. The introduction of an impurity in the TiO2 lattice can affect the band edges and/or introduce impurity states in the band gap. The theoretical description of these effects is not straightforward and existing theoretical studies of the electronic and optical properties of doped TiO2 have typically focused on the Kohn Sham energy levels. It is well known however that these provide only a very rough description of one-particle levels and optical spectra. This also makes the comparison with experiments extremely uncertain. Our main goal is the accurate and quantitative investigation of the electronic structure and optical properties of doped TiO2, within a many body perturbation theory (MBPT) approach, namely using the GW approximation for the quasi particle energies and solving the Bethe Saltpeter equation for the optical spectra in order to allow for a direct comparison to available spectroscopic experiment (ARPES, STS, absorption) . We will consider both TiO2 main polymorphs, rutile and anatase and among relevant dopants, we will focus on H, Li, N, and Nb. Comparison of energy levels for a given dopants in rutile and anatase phase will be extremely useful for the design of materials with specific properties.

WASH ME – Water: Ab inito Siimulations to remove Heavy MEtals

Project Title: WASH ME – Water: Ab inito Siimulations to remove Heavy MEtals
Project Leader: Wanda Andreoni, CH
Resource Awarded: 63715334 core hours on Fermi

Details

Team Members :
Mauro Boero, CNRS Institut de Physique et Chimie des Materiaux – Uni Strasbourg, FRANCE
Burak Ozdamar, Université de Strasbourg et CNRS – IPCMS, FRANCE
Fabio Pietrucci, Université Pierre et Marie Curie (UPMC) – Paris 6, FRANCE

Abstract
The need of controlled and selective processes for the removal of all sorts of pollutants from water systems is outstanding and urgent. Recently, the performance of several solid biomaterials as trapping agents has been explored. Being cost effective and environment friendly, they provide unique advantages. In particular, numerous experiments have established that heavy metals – a tremendous threaten for human and animal health – can be captured in solutions containing common components not only of agricultural and industrial operations but also of our daily food, that we are used to discard, e.g. spent coffee grounds (SCG), tea leaves, lemon and orange peels. The possibility opens up, in principle, for a rational design of polymeric systems for the removal of specific pollutants, which are either extracted or inspired from natural materials. However, the lack of an understanding of the mechanisms responsible for metal uptake is a serious obstacle. We propose to exploit the power of advanced atomistic simulation methods combined with high-performance computing and start investigating questions like: How do such processes take place? Which are the characteristics of the complex natural material and of the solution that make it possible? How can we improve on it? In this one-year project we intend to explore and characterize the fundamental reactions leading to the binding of the metal ions to the polysaccharides (hemicellulose) mainly present in SCG solutions. We intend to use ab initio molecular dynamics preceded by larger-scale classical molecular dynamics and empowered by metadynamics and free-energy calculation techniques. Novel metadynamics and also analysis strategies will be adopted. Our research will benefit from collaboration with experimental activities at the Italian Institute of Technology (Genova). The results of this project are bound to extend also our knowledge of other cellulosic materials and their interactions with metal nanoparticles in water.

PCETHEMA – Modelling proton-coupled electron transfers in water oxidation on hematite

Project Title: PCETHEMA – Modelling proton-coupled electron transfers in water oxidation on hematite
Project Leader: Simone Piccinin, IT
Resource Awarded: 28000000 core hours on Fermi

Details

Team Members :
Nicola Seriani, Abdus Salam International Centre for Theoretical Physics, ITALY
Matteo Farnesi Camellone, CNR-IOM, ITALY

Abstract
Replacing fossil fuels with renewable energy sources like solar and wind requires developing a strategy to cope with the intrinsic variability of these sources. To this end, the strategy selected by Nature is photosynthesis, were sunlight promotes a series of electrochemical reactions starting from H2O and CO2, producing sugars and releasing O2 as a by-product. Mimicking this process with artificial devices would allow storing solar energy in the form of chemical fuels, the simplest fuel being H2 produced from water splitting. To this end we need materials that are able to absorb a good fraction of the solar spectrum and promote photo-catalytic reactions, namely the oxidation of water at the anode and the reduction of protons at the cathode. Hematite (alpha-Fe2O3) has raised considerable interest as a photo-anode material. Having a suitable band gap for solar light absorption, being cheap and stable, this material complies with several of the requirements for a water oxidation photocatalyst. However, the slow kinetics of the catalytic reaction is one of the most serious obstacles preventing its utilization in realistic devices. The goal of this project is to investigate at atomic level the mechanism of water oxidation promoted by hematite. We will achieve this goal modelling explicitly from first-principles the electrochemical interface between anode and electrolyte, and reconstructing the free energy surface for the photocatalytic WOX reaction, which involves a sequence of 4 proton-coupled electron transfers and the formation of O-O chemical bond. We will employ density functional theory calculations, using a combination of umbrella sampling and metadynamics to bias the dynamics of suitable collective variables that characterize separately both the electronic charge transfer and the proton transfer. Achieving this goal will enable us to better understand the origin of the slow kinetics of water oxidation on hematite. This will help us propose suitable modifications of the hematite surface that might improve the kinetics of the oxidation reaction.

COMPHOTOCAT – Computational design of TiO2 based nanoparticles for improved photocatalytic activity towards water splitting under visible sunlight

Project Title: COMPHOTOCAT – Computational design of TiO2 based nanoparticles for improved photocatalytic activity towards water splitting under visible sunlight
Project Leader: Francesc Illas, ES
Resource Awarded: 12000000 core hours on MareNostrum

Details

Team Members :
Stefan Bromley, Universitat de Barcelona, SPAIN
Kyong Chul Ko, Universitat de Barcelona, SPAIN
Oriol Lamiel Garcia, Universitat de Barcelona, SPAIN
Francesc Viñes, Universitat de Barcelona, SPAIN
Volker Blum, Duke University, UNITED STATES
Bjoern Lange, Duke University, UNITED STATES

Abstract
The seminal work of Fujishima and Honda (1972) on water photoelectrochemical photolysis opened new, interesting and technologically relevant opportunities in photocatalysis, in general, and in photocatalytic water splitting, in particular. The possible technological implications are enormous since it offers a direct way to take advantage of solar energy to obtain hydrogen just from water, thus providing a clean and sustainable fuel. This is even more the case since it has been shown that water splitting by TiO2 nanopowders spontaneously occurs under ultraviolet irradiation which is appealing since the whole process can be carried out without needing to rely on an electrochemical cell and expensive electrodes using scarce and expensive noble metals (Pt). The problem of this approach is that H2 and O2 are simultaneously produced but reactors have already been designed that allow for direct separation of these gases.
Unfortunately, over 40 years of research and thousands of papers have not been enough to find photocatalysts with activity in the visible region of sunlight higher than that of TiO2 under ultraviolet radiation which severely limits practical applications since sunlight at the Earth surface contains 2-3% of ultraviolet radiation only. Inspiration-driven, trial and error research is not efficient calling for new directions. This is clear when analyzing the impressive recent experimental advances showing that tailored TiO2 nanoparticles, stoichiometric or conveniently chemically modified, can be synthesized with predefined size and shape and exhibiting distinct photocatalytic activity in various reactions including water splitting. Unfortunately, the necessary link between the properties of a given type of nanoparticle and its photocatalytic activity has not yet been established.
A deep analysis of the electronic structure of these photocatalytic materials is necessary but going beyond the common solid state or surface chemistry paradigms, which often focus on ground state properties only and with little insight into the chemistry of the excited states involved in the photocatalytic reactions. The present proposal provides an alternative roadmap and a different strategy. It starts by building realistic TiO2 nanoparticle models with different sizes, shapes, compositions, and environments. From a systematic study of their electronic structure, a database will be constructed and candidate nanoparticles with appropriate absorption spectra in the visible light window selected, thus fulfilling a first necessary but not sufficient condition for photocatalysis. Excited states of interest on the candidate tailored nanoparticles will be investigated to select those with spatially well-separated electron-hole pairs (minimal recombination) and exhibiting long enough mean lifetimes (maximum photon efficiency). Further, effects of environment (solvent), on the electronic structure and nature of excited states will also accounted for. Finally, analysis of the reactivity of the nanoparticles towards photocatalytic reactions, mostly water splitting for hydrogen generation, in the appropriate electronic state will complete the picture. The task is huge, not exempt of risk, and requires enough computational resources to effectively deliver the necessary new knowledge for an efficient rational design.

CORNFLAKES – COmputational Renormalisation of Non-Fermi-Liquids: A ‘Kritischen Exponenten’ Study

Project Title: CORNFLAKES – COmputational Renormalisation of Non-Fermi-Liquids: A ‘Kritischen Exponenten’ Study
Project Leader: Chris Hooley, UK
Resource Awarded: 5921440 core hours on Fermi

Details

Team Members :

Abstract
In the 1960s, after several decades of work trying to describe the different phases of matter, interest turned to the description of the transitions between those phases. This led to important ideas such as universality, scaling, and critical exponents [1]. Those transitions occurred at finite temperature, and indeed were typically driven by changing the temperature itself. It can be shown that, sufficiently close to such transitions, quantum mechanics becomes unimportant, and a classical theory of the critical fluctuations suffices. By contrast, when the critical temperature is suppressed to zero by varying a control parameter (pressure, magnetic field, chemical doping, etc.), even near the transition the quantum-mechanical nature of the fluctuations can no longer be ignored. The region in which these fluctuations are dominant is called the quantum critical region, and it exhibits anomalous exponents in many physical observables [2]. The description of quantum criticality in metals is a particularly challenging topic, since in the metal one has two types of low-energy excitation: the critical fluctuations of the order parameter, plus the low-energy particle-hole excitations of the metal itself. Early attempts to guess the correct low-energy action [3] have been shown to be flawed [4], and the problem is peculiarly resistant to standard techniques [5]. One feature which is especially difficult to capture correctly is Landau damping: the alteration of the dynamics of the critical fluctuations due to their ability to decay into electron-hole pairs. Recent work using the functional renormalisation group [6] appears promising, but there is still no agreement in the community on how to handle such phenomena theoretically. Even apparently basic issues such as whether the phase transition becomes first-order at low enough temperatures [7] or not are still not settled. The aim of the proposed work is to obtain compelling and unbiased information about the order and nature of the ferromagnetic quantum phase transition in a two-dimensional model by computational means. To this end, we have formulated a model that (a) is expected to show such a quantum phase transition, and (b) does not suffer from the ‘sign problem,’ meaning that standard quantum Monte Carlo techniques can be deployed. The computational task involved in determining the critical exponents is still formidable, but if completed it promises to command community-wide attention by providing clear and unbiased information about one of the most significant open problems in modern condensed matter theory. [1] K.G. Wilson, Rev. Mod. Phys. 55, 583 (1983). [2] S. Chakravarty, B.I. Halperin, and D.R. Nelson, Phys. Rev. B 39, 2344 (1989). [3] J.A. Hertz, Phys. Rev. B 14, 1165 (1976). [4] S. Thier and W. Metzner, Phys. Rev. B 84, 155133 (2011). [5] Sung-Sik Lee, Phys. Rev. B 80, 165102 (2009). [6] S.P. Ridgway and C.A. Hooley, Phys. Rev. Lett. 114, 226404 (2015). [7] D. Belitz, T.R. Kirkpatrick, and T. Vojta, Phys. Rev. Lett. 82, 4707 (1999).

Computational study of redox reactions in a vanadium redox flow battery

Project Title: Computational study of redox reactions in a vanadium redox flow battery
Project Leader: Michele, Parrinello, CH
Resource Awarded: 44000000 core hours on Fermi

Details

Team Members :
Marta Bon, ETH Zurich, SWITZERLAND
Daniela Polino, ETH Zurich, SWITZERLAND

Abstract
Vanadium Redox Flow Batteries (VRFB) are promising electrical energy storage devices since are able to store large amount of energy and to resist to fluctuating power supplies. A VRFB consists of a sulfate solution containing V(II)/V(III) at the negative electrode and V(IV)/V(V) at the positive electrode. Similarly to most electrochemical processes, in these devices the core step to produce electricity is the electron transfer event, involving the reduction and the oxidation of various species close to the electrode. The typical electrodes used in a VRFB are carbon-based, due to their wide operating potential range, stability at both anode and cathode and availability at a reasonable cost. Despite several advantages, the carbon-based electrodes present also a few drawbacks, and, in particular, the slow kinetics of V(V) reduction near the surface. More specifically, it has been observed that the reaction at the cathode side is highly influenced by the type of electrode. Both the intrinsic structure of the surface and the presence of functional groups can affect the redox rate and the reversibility of the process. A comprehensive understanding of the factors that can influence the kinetics is a key element in the design of new and more efficient devices. Since the cathodic reaction is the most affected by the structure of electrode, we will study how the presence of different structures and different carbonyl groups affect the reduction kinetics. We will also provide an estimate of the reaction rates. To understand the impact of the carbon structure, we will use as a model system the edge and the basal planes of a graphite electrode, which are known to exhibit very different electrochemical properties. Both surfaces will be functionalized first with CO-groups and later with COH groups, following suggestions coming from experiment. We will pursue these objectives by means of ab-initio molecular dynamics simulations, employing Constrained DFT, Fragment Orbital DFT, Well-Tempered Metadynamics and Umbrella Sampling. Our calculations will profit from the collaboration and experimental data provided by the group of Prof. Schmidt, ETH Zürich. The synergistic comparison between our data and the experimental measurements will allow us to determine the effect of the functional groups on different structures and to shed light on the overall mechanism occurring at the electrode.

ProDyn/Q – Quantum proton dynamics in water charge defects by quantum Monte Carlo

Project Title: ProDyn/Q – Quantum proton dynamics in water charge defects by quantum Monte Carlo
Project Leader: Michele Casula, FR
Resource Awarded: 32400000 core hours on Fermi

Details

Team Members :
Rodolphe Vuilleumier, Ecole Normale Supérieure, France
Félix Mouhat, Université Pierre et Marie Curie, FRANCE
Marco Saitta, Université Pierre et Marie Curie, FRANCE
Sandro Sorella, SISSA, ITALY

Abstract
Simulating and understanding water properties is of paramount importance, as water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, a comprehensive description of its structure at different thermal conditions is still elusive, despite a large amount of theoretical work spent so far. The aim of this project is to shed light on the complex arrangement of the intermolecular network in water by studying the behavior of charge defects (hydronium H3O+ and hydroxide HO- ions) solvated in water clusters. The calculations will be carried out in the recently developed quantum Monte Carlo (QMC) based molecular dynamics (MD) framework, by including also quantum nuclear effects. Our approach is meant to combine three main theoretical ingredients: the accurate solution of the electronic problem from first principles provided by QMC, a Langevin-based molecular dynamics driven by the noisy QMC ionic forces, and the quantum description of nuclei via the path integral Langevin MD framework with a new solver which accelerates both the harmonic “quantum” part and the Langevin damped dynamics. The methodology developed in the project will open the way to more accurate and systematic studies of water properties. The importance of the theoretical development goes well beyond the specific application, as the proposed framework is very general and capable of dealing with electronic correlation, thermal and proton quantum effects playing together on equal footing.

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Earth System Sciences (1)

LSIHP – Land-Surface Initialization in High-resolution seasonal Prediction

Project Title: LSIHP – Land-Surface Initialization in High-resolution seasonal Prediction
Project Leader: Virginie Guemas, FR
Resource Awarded: 5000000 core hours on MareNostrum

Details

Team Members :
Muhammad Asif, Barcelona Supercomputing Center, SPAIN
Omar Bellprat, Barcelona Supercomputing Center, SPAIN
Miguel Castrillo Melguizo, Barcelona Supercomputing Center, SPAIN
Francisco Doblas-Reyes, Barcelona Supercomputing Center, SPAIN
Chloe Prodhomme, Barcelona Supercomputing Center, SPAIN
Oriol Tinto, Barcelona Supercomputing Center, SPAIN

Abstract
The seasonal forecasting science aims at producing reliable and actionable regional climate information at time scales ranging from two weeks to one year. Over the extra-tropics, the skill of current seasonal forecast systems is very limited. Recent results suggest however that initializing the land surface from observed soil moisture conditions could increase substantially the forecast quality over Europe for surface temperature and precipitation, in particular during heat waves, and that an increase of resolution in climate forecast systems is one of the necessary factors to reach a useful level of skill over Europe. LSIHP offers to investigate the land sources of climate predictability on seasonal timescales through sensitivity experiments run at the highest resolution ever used in seasonal forecasting. Seasonal forecasts will be run using the best possible estimate of observed land conditions as initial states and compared with seasonal forecasts initialized from land climatology. Their comparison will allow for the most robust identification performed up-to-date of the added-value from land-surface initialisation from observations on seasonal forecast quality, i.e., the role of land sources of predictability on seasonal forecast quality, thanks to seasonal forecasts ran at the highest resolution ever used in a seasonal forecasting context, and over an exceptionally long reforecasting period. LISHP will deliver crucial information about seasonal forecast quality and enhance our predictive capability over Europe, in particular for extreme events such as heat waves and droughts. LISHP will contribute to generating user-relevant climate information, in a wide range of sectors, such wind energy production or well as viticulture yield.

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Engineering (7)

Numerical experiments in a “virtual wind tunnel”: LES of the flow around a wing section at high Re

Project Title: Numerical experiments in a “virtual wind tunnel”: LES of the flow around a wing section at high Re
Project Leader: Philipp Schlatter, SE
Resource Awarded: 31000000 core hours on MareNostrum

Details

Team Members :
Ardeshir Hanifi, Linné Flow Centre, Swedish e-Science Research Centre, SWEDEN
Dan Henningson, Linné Flow Centre, Swedish e-Science Research Centre, SWEDEN
Prabal S. Negi, Linné Flow Centre, Swedish e-Science Research Centre, SWEDEN
Ricardo Vinuesa, Linné Flow Centre, Swedish e-Science Research Centre, SWEDEN

Abstract
A recent report by NASA discusses a number of findings and recommendations regarding the present and future role of CFD (computational fluid dynamics) in aircraft design. The main revelations point out the necessity of accurate predictions of turbulent flows with significantly separated regions for both analysis and optimization procedures. Industrial computations of aircraft components are mainly based on Reynolds-Averaged Navier-Stokes (RANS) simulations, where turbulence is modeled relying on empirical arguments. This approach only allows proper characterization of simple flow features (such as lift and drag) after proper tuning based on equivalent wind tunnel tests. It is only (temporally and spatially) resolved simulations that are able to properly characterize the mentioned flow features with the accuracy necessary for engineering design. The present proposal exactly addresses the proof of concept of performing such a simulation at relevant Reynolds number for industrial applications, which could significantly impact engineering optimization strategies. Available numerical studies of the flow around wing sections are limited to low Reynolds numbers up to around Rec=100,000. Our research group has recently finalized a fully resolved high-order DNS of the flow around a NACA4412 wing profile at Rec=400,000 with 5 degree angle of attack, using the massively-parallel spectral-element code Nek5000. The relevance of this flow case lies in the higher Reynolds number compared with other studies, and in the additional flow complexity introduced by the cambered airfoil. The scope of the proposed study is to perform a high-fidelity wall-resolved LES of the flow around a NACA4412 wing profile at an unprecedented Reynolds number Rec=1,000,000 with 5 degree angle of attack. These results would exceed by an order of magnitude other numerical databases available in the literature, and the generated database would be of great value to the study of complex wall-bounded turbulent flows, but also to the development of more sophisticated RANS models for industrial use. Our research group has already been able to successfully perform an LES validation in zero pressure gradient (ZPG) turbulent boundary layers. With this simulation we will provide a full description of the flow around the wing profile at a Reynolds typical of university wind tunnel experiments. The simulation proposed here is part of a larger effort to simulate flows around wings. Related projects where transition is not set at a specific location, but left free to move are done for oscillating or pitching airfoils. These are of high relevance for e.g. long endurance aircraft where the transition may move over large portions of the wings and influence the forces at the control surfaces. The motion of the transition line often experiences hysteresis and is therefore very difficult to predict, in particular with traditional CFD methods. The simulations performed in this project and the LES tested will be of paramount importance for the further development of such more complicated high-fidelity wing simulations.

SANDGRAIN – UnderStANDing the effects of wall-surface rouGhness on the flow past ciRculAr cylINders

Project Title: SANDGRAIN – UnderStANDing the effects of wall-surface rouGhness on the flow past ciRculAr cylINders
Project Leader: Assensio Oliva, ES
Resource Awarded: 31000000 core hours on Fermi

Details

Team Members :
Ugo Piomelli, Queen’s University, CANADA
Ricard Borrell, Technical University of Catalonia, SPAIN
Jorge Chiva, Technical University of Catalonia, SPAIN
Oriol Lehmkuhl, Technical University of Catalonia, SPAIN
Ivette Rodriguez, Technical University of Catalonia, SPAIN

Abstract
The objective of the present project proposal is to contribute to the understanding of the turbulent flow past rough bluff bodies, which is of importance in many engineering applications (e.g., flows past aircraft, buildings, submarines, automobiles, in turbo-machines, etc.). It is enclosed in a long term strategy devoted to the study of massive separated flows, which aims at shedding light into the underlying physics of these flows, for their application to flow control. In particular, the problem addressed here is the flow past a rough circular cylinder and the effects surface roughness has on the development of the boundary layer, the forces acting on the cylinder and the near-wake flow dynamics. This project will focus on highly resolved large-eddy simulations (LES) of the flow around a circular cylinder with a rough surface for Reynolds numbers ranging from the critical to the trans-critical regimes. The flow over smooth cylinders has been extensively studied; fewer investigations exist for the rough surfaces, and only experimental data is available: mainly global parameters such as drag coefficient, fluctuating lift and vortex shedding frequency are reported. Little is known about the development of the boundary layer and how roughness affects the flow dynamics inside and above the roughness sublayer. It is also important to understand how roughness generates turbulence on these flows, as this seems to be the main mechanism for triggering an early transition of the flow. Understanding the fundamental flow physics on these surfaces would have a direct impact on many engineering applications where this kind of interactions is commonly encountered.

Superfluid Turbulence under counterflows

Project Title: Superfluid Turbulence under counterflows
Project Leader: Luca Biferale, IT
Resource Awarded: 22000000 core hours on Fermi

Details

Team Members :
Dmytro Khomenko, Weizmann Institute of Science, ISRAEL
Victor L’vov, Weizmann Institute of Science, ISRAEL
Anna Pomyalov, Weizmann Institute of Science, ISRAEL
Fabio Bonaccorso, University of Rome ‘Tor Vergata’, ITALY

Abstract
Large scale turbulence in quantum fluids like 4He at low temperature is usually considered in the framework of the “two fluid” model of Landau and Tisza. Within this model the dynamics of the superfluid 4He is described in terms of a viscous normal component and an inviscid superfluid component. Due to the quantum mechanical restriction, the circulation around the superfluid vortices is quantized. The quantization of circulation results in the appearance of characteristic “quantum” length scale: the mean separation between vortex lines which is typically orders of magnitude smaller than the scale of the largest (energy containing) eddies. Experimental and numerical evidence indicates that superfluid turbulence at large scales is similar to classical turbulence if the mechanical forcing (e.g. a towed grid or a pressure drop) is similar. The reason for this similarity is due to the ‘mutual friction’ between the two components that tends to enhance their correlation. We propose here to investigate –for the first time– the superfluid turbulence developing under a counterflow set-up: with the two components moving with opposite mean velocities. This is a very relevant set-up for experiments using a heat current to force the flow. Recent experimental data suggest important difference in this case, because the counterflow tends to oppose the mutual friction. We propose to disentangle the statistical properties of the mutual correlation at all scales by highly resolved direct numerical simulations in order to provide a state-of-the-art data set for further understanding the physics of this novel scientific challenge.

SLIP – Salvinia-inspired surfaces in action: slip, cavitation, and drag reduction

Project Title: SLIP – Salvinia-inspired surfaces in action: slip, cavitation, and drag reduction
Project Leader: Alberto Giacomello, IT
Resource Awarded: 22000000 core hours on Fermi

Details

Team Members :
Matteo Amabili, Sapienza University of Rome, ITALY
Carlo Massimo Casciola, Sapienza University of Rome, ITALY
Emanuele Lisi, Sapienza University of Rome, ITALY
Antonio Tinti, Sapienza University of Rome, ITALY

Abstract
Superhydrophobic coatings show promise for underwater applications: surfaces with drag reducing, anti-fouling, and anti-corrosion properties can have a huge impact in naval and marine engineering. However, superhydrophobicity is fragile because it relies on the trapping of gas pockets inside surface roughness. In a previous PRACE project, we demonstrated that the special geometrical and chemical properties of the water fern Salvinia enhance the durability of entrapped gas pockets over a broad range of pressures. This biological example can inspire a new generation of superhydrophobic surfaces for submerged use, where the resistance to liquid penetration is guaranteed by engineering the geometry and chemistry of surface roughness. In view of this objective, we plan to quantify with advanced molecular dynamics techniques the following points:
1. The stability of gas pockets on different surfaces decorated with three-dimensional nanopatterns inspired to the Salvinia leaves. In particular, we are interested in clarifying whether interconnected gas domains are more stable than independent ones. In these simulations, the nanopatterned surfaces are subject to very low to large hydrostatic pressures and the stability of the gas pockets assessed in terms of free-energy barriers. At the end of this part, we will select the geometries that guarantee durable gas trapping to be tested in the second part.
2. The friction properties of Salvinia-inspired surfaces are characterized during the second part of the project in which the submerged surfaces are subject to shear (Couette flow). The presence of liquid-gas interfaces in this case reduces the wall friction as compared to the simple liquid-solid one. The drag-reducing properties of a given surface are usually characterized in terms of the effective slip length, which describes the virtual position of the flow boundary “inside” the wall.
The final outcome of the present project is the identification of engineering criteria to build durable superhydrophobic coatings for submerged applications. The two main properties we will target are the stability of gas pockets at changing pressure and the reduction of friction under shear flow (large slip length).

DIoNySUS – DIrect Numerical Simulation of Unstably Stratified channel flow

Project Title: DIoNySUS – DIrect Numerical Simulation of Unstably Stratified channel flow
Project Leader: Sergio Pirozzoli, IT
Resource Awarded: 22000000 core hours on Fermi

Details

Team Members :
Matteo Bernardini, Sapienza, University of Rome, ITALY
Paolo Orlandi, Sapienza, University of Rome, ITALY
George Carnevale, Scripps Institution of Oceanography, UNITED STATES

Abstract
This project is aimed at studying mixed heat transfer in turbulent flow arising from the combined action of convective transport and buoyancy. The subject dealt with is of great relevance in engineering as mixed convection plays a major role in heat exchanger pipelines, as well as in the dynamics of the atmosphere. More specifically, we are interested to study the behavior of a fluid flowing through a channel and heated from below, hence yielding a case of unstable stratification, whereby thermal plumes enhance turbulent motions, yielding an increase of friction and heat transfer. This flow is highly interesting from a basic physics standpoint as it involves the formation of large coherent structures in the form of quasi-streamwise rollers, which interact and modulate the near-wall structures observed in classical wall turbulence. Hence, we expect that the outcomes of the present study will have important consequences in terms of practical applications and increased physical insight. The study will be carried out by means of direct numerical simulation (DNS) of the Boussinesq system of equations, with the goal of covering a wide spectrum of Reynolds numbers and stratification parameter (Richardson number), in a sufficiently large box that the large-scale eddies are adequately described.

Geometrical and Statistical Properties of Turbulent Flows with Varying Viscosity

Project Title: Geometrical and Statistical Properties of Turbulent Flows with Varying Viscosity
Project Leader: Luminita Danaila, FR
Resource Awarded: 25400000 core hours on Fermi

Details

Team Members :
Michael Gauding, TU Freiberg, GERMANY
Emilien Varea, Université de Rouen, FRANCE

Abstract
Turbulent mixing of species with varying viscosity is of both fundamental and practical interest. In many applications, like combustion systems, more than one species is involved and the molecular viscosity of the species may vary by more than a factor of 20. The viscosity is the most important quantity of real flows, and its variation has a significant impact on the dynamics of the flow. For example, local viscosity gradients may result in local relaminarization affecting the efficiency of turbulent mixing. In combustion engines an efficient mixing between fuel and oxidizer is important to reduce fuel consumption and pollutant formation. It is to be expected that a better understanding of the dynamics of turbulent flows with varying viscosity will lead to a better prediction of the mixing efficiency in combustion systems. The physical mechanisms behind turbulent flows with varying viscosity are still not fully understood. Until now, most understanding of turbulent flows has been gained from Kolmogorov’s scaling theory. Kolmogorov’s theory postulates that, under the condition of sufficiently high Reynolds numbers, the small scales of the flow decouple from the large scales. In a statistical sense, the small scales reveal universal properties, and depend only on the viscosity and on the energy dissipation rate. As the viscosity is a small scale quantity, variations of it should mainly affect the small scales of the flow. However, it has been shown that Kolmogorov’s traditional view of universality is a crude assumption and that large and small scale quantities are strongly coupled. To move forward in the understanding of turbulent flows we will analyze turbulent flows by a novel approach based on higher order statistics and intrinsic geometrical properties. This comprises examination of the inter-scale transport by two-point statistics, the dissipation mechanism of turbulent energy by exact equations for higher order moments, and an analysis based on the method of dissipation elements. Dissipation element analysis take the geometrical structure of the turbulent field into account and will provide new information about the local structure and the length scale distribution of the underlying turbulent field. The analysis requires highly resolved direct numerical simulations (DNS) of turbulent flows at high Reynolds numbers. The present work aims at performing those simulations, namely homogeneous isotropic turbulence and, additionally, plane turbulent shear layers. DNS does not rely on models and provides highly resolved three-dimensional fields from which all relevant statistics can be computed. Summarizing, we will address the following questions by means of direct numerical simulations: – How will locally varying viscosity affect the transport through the turbulent cascade and what will be the impact on the dissipation mechanism? – How will locally varying viscosity change the mixing efficiency of turbulent flows? – What is the impact of the Reynolds number on statistics and how will these statistics scale in the limit of large Reynolds numbers? – What is the impact of varying viscosity on the large scales?

Roughness and bubbles in highly turbulent Taylor-Couette turbulence

Project Title: Roughness and bubbles in highly turbulent Taylor-Couette turbulence
Project Leader: Detlef Lohse, NL
Resource Awarded: 31070000 core hours on Fermi

Details

Team Members :
Vamsi Spandan Arza, University of Twente, NETHERLANDS
Richard Stevens, University of Twente, NETHERLANDS
Roberto Verzicco, University of Twente, NETHERLANDS
Yantao Yang, University of Twente, NETHERLANDS
Xiaojue Zhu, University of Twente, NETHERLANDS

Abstract:
Taylor-Couette (TC) flow, i.e. the flow between two coaxial, independently rotating cylinders, is one of the paradigmatic systems in fluid dynamics research and is therefore used to test various new concepts in the field [1-4]. In this project we propose the use of state of the art high resolution direct numerical simulations (DNS) to study the effect of surface roughness and bubbles on very turbulent TC flow and compare results with experiments performed in our group [5-7]. Turbulent flows over rough surfaces are very common in nature and industrial applications. Rough surfaces can enhance heat transfer at the expense of an increase in drag [8]. On the other hand carefully designed roughness elements like riblets that are properly aligned with the mean flow direction can lead to drag reduction [9]. While TC flow with smooth walls has been thoroughly investigated over the last years [1-8,10-16] the effect of roughness on global transport properties like the drag and the flow structure is still mostly unknown [1]. Therefore, as turbulent flows over rough surfaces are very common, it is important to study the effect of surface roughness on turbulent flows in more detail. In this project we want to study the effect of different surface roughness configurations on the Nusselt number scaling in TC turbulence, which is of prime importance because the scaling shows the relationship between the global transport properties and the driving force (indicated by the Taylor number). We hope that with the right roughness configuration we can trigger the transition to ultimate TC turbulence at a lower driving than for TC flow with smooth walls. Frictional losses in the form of drag in turbulent flows are a major energy drain in applications related to process technology, naval transportation, and transport of liquefied natural gas in pipelines. It has been known for a long time that the injection of a small concentration of dispersed phase into a carrier fluid (4%) can result in significant drag reduction (40%) [18-22] making it of interest for fundamental scientific research in order to understand the mechanism and optimize the effect for engineering applications. The exact mechanism however is largely unknown. Various theories have been suggested, among them theories based on an effective compressibility introduced through the (micro)-bubbles [8] and in particular theories based on bubble deformability [22]. In this project we want to use high resolution DNS to increase our understanding of bubbly drag reduction. We will study the influence of the spatial bubble distribution and its connection with the overall global drag, for various bubble sizes, concentrations, and Reynolds numbers. The aim is to unravel the mechanism of bubbly drag reduction and to understand how the flow and bubbles organize. The simulations will be compared with experimental drag reduction measurements [22-24] to validate the simulations and will then be analyzed to get a better understanding of bubbly drag reduction. With these simulations we hope to have a one-to-one comparison with the experiments that are conducted in our group [5-7].

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Fundamental Constituents of Matter (4)

Charge and Spin Hall Kubo Conductivity by Order N Real Space Methods

Project Title: Charge and Spin Hall Kubo Conductivity by Order N Real Space Methods
Project Leader: Stephan Roche, FR
Resource Awarded: 5000000 core hours on MareNostrum

Details

Team Members :
Aron Cummings, Catalan Institute of Nanotechnology, SPAIN
Jeil Jung, University of Seoul, KOREA, REPUBLIC OF
Nicolas Leconte, University of Seoul, KOREA, REPUBLIC OF

Abstract
This project addresses the computational study of quantum transport in disordered graphene in two different fascinating situations which are out of reach of current numerical tools. The first one is the formation of a fractal spectrum when graphene is weakly interacting with a boron-nitride layer and an external magnetic field is applied. This induces the Hofstadter butterfly, a fractal electronic spectrum that has been for the first time experimentally revealed in graphene in 2013 for graphene deposited on boron-nitride substrate and under high magnetic fields. The Quantum Hall Effect (QHE) is one of the most intriguing phenomena in physics since its discovery 30 years ago. It has been of great importance in experiments in the field of condensed matter physics, exemplified for instance by its pivotal role in the discovery of graphene. Despite the recent experimental observations of the Hofstadter butterfly in the QHE regime, a lot of fundamental issues and questions remain fiercely debated in the community, such as the nature of Hall conductance plateaus quantization in presence of a fractal spectrum, its possible dependence on disorder, temperature and the strength of the external magnetic field. We expect to clarify some complex unexplained features reported experimentally and also predict completely new properties, such as the values of Hall conductance plateaus at crossing points of replica Landau levels (a long-standing date issue dating back to previous century) that become increasingly complex (because of the fractal nature of the electronic spectrum) when higher energy resolution is accessed numerically. The second research direction is the study of the Spin Hall Effect (SHE) in complex forms of chemically functionalized (and disordered) graphene-based materials, in the frame of spin-based information processing technologies. SHE is a fundamental spin transport phenomenon that emerges in materials with strong spin-orbit interaction (SOI) and can be used to induce magnetization reversal of small magnets (spin torque effect). Recent experiments have reported on colossal SHE signals in chemically disordered graphene, but the precise origin of such spectacular spin transport phenomenon remains puzzling and controversial. The scientific project here aims to study the conditions for SHE in experimentally realistic sized samples of chemically functionalized graphene (hydrogenated or metal ad-atoms functionalized graphene) by using a generalized version of the Spin Hall Kubo conductivity and order-N real space implementation (N being the number of atoms). The measure of the figure of merit of the SHE (spin Hall angle) as well as the possibility to further enhance the signal will be explored in the project for several types of adatoms (heavy atoms such as induium and thallium) as well as metallic atoms such as gold and copper. Hydrogenated graphene also plays an important role in recent predictions of a giant enhancement of spin-orbit coupling due to sp3 hybridization but requires a better assessment of the physics at play in the framework of the SHE. We will study how SHE is generated and possibly enhanced by the hydrogenation, and compare our simulations with existing experimental data.

Charge and Spin Hall Kubo Conductivity by Order N Real Space Methods

Project Title: Charge and Spin Hall Kubo Conductivity by Order N Real Space Methods
Project Leader: Chris Allton, UK
Resource Awarded: 23000000 core hours on Fermi

Details

Team Members :
Pietro Giudice, University of Muenster, GERMANY
Jon-Ivar Skullerud, National University of Ireland, Maynooth, IRELAND
Michael Peardon, Trinity College, Dublin, IRELAND
Sinead Ryan, Trinity College, Dublin, IRELAND
Maria-Paola Lombardo, INFN Frascati, ITALY
Gert Aarts, Swansea University, UNITED KINGDOM
Simon Hands, Swansea University, UNITED KINGDOM
Benjamin Jaeger, Swansea University, UNITED KINGDOM

Abstract
There are four fundamental forces that describe all known interactions in the universe: gravity; electromagnetism; the weak interaction (which powers the sun and describes most radioactivity); and, finally the strong interaction – which is the topic of this research. The strong interaction causes quarks to be bound together in triplets into protons and neutrons, which in turn form the nucleus of atoms, and therefore make up more than 99% of all the known matter in the universe. If there were no strong interaction, these quarks would fly apart and there’d be no nuclei, and therefore no atoms, molecules, DNA, humans, planets, etc. Although the strong interaction is normally an incredibly strongly binding force (the force between quarks inside protons is the weight of three elephants!), in extreme conditions it undergoes a substantial change in character. Instead of holding quarks together, it becomes considerably weaker, and quarks can fly apart and become “free”. This new phase of matter is called the “quark-gluon” plasma. This occurs at extreme temperatures: hotter than 10 billion Celsius. These conditions obviously do not normally occur – even the core of the sun is one thousand times cooler! However, this temperature does occur naturally just after the Big Bang when the universe was a much hotter, smaller and denser place than it is today. As well as in these situations in nature, physicists can re-create a mini-version of the quark-gluon plasma by colliding large nuclei (like gold) together in a particle accelerator at virtually the speed of light. This experiment is being performed at the Large Hadron Collider in CERN. Because each nucleus is incredibly small (100 billion of them side- by-side would span a distance of 1mm) the region of quark-gluon plasma created is correspondingly small. The plasma “fireball” also expands and cools incredibly rapidly, so it quickly returns to the normal state of matter where quarks are tightly bound. For these reasons, it is incredibly difficult to get any information about the plasma phase of matter. To understand the processes occurring inside the fireball, physicists need to know its properties such as viscosity, pressure and energy density. It is also important to know at which temperature the quarks inside protons and other particles become unbound and free. With this information, it is possible to calculate how fast the fireball expands and cools, and what mixture of particles will fly out of the fireball and be observed by detectors in the experiment. This research project will use supercomputers to simulate the strong interaction in the quark-gluon phase. We will find the temperature that quarks become unbound, and calculate some of the fundamental physical properties of the plasma such as its conductivity, symmetry properties of baryons and response of hadronic excitations to the chemical potential. These quantities can then be used as inputs into the theoretical models which will enable us to understand the quark-gluon plasma, i.e. the strong interaction past its breaking point.

HEliOS — Hall Effects in Organic Semiconductors

Project Title: HEliOS — Hall Effects in Organic Semiconductors
Project Leader: Frank Ortmann, DE
Resource Awarded: 69451776 core hours on Fermi

Details

Team Members :
Amedeo Molnar, Technische Universitait Dresden, GERMANY
Michel Panhans, Technische Universitait Dresden, GERMANY

Abstract
The objective of HEliOS is to investigate possible Hall conductance quantization in Organic Semiconductors (OS), which has not been observed so far. In addition, the project aims at getting deep insight in the influence of magnetic fields on charge carrier localization and for the transport of electrons in OS. We will simulate the Hall effect, which today is the method of choice for determining the charge carrier concentration in semiconductors, and allows studying directly the carrier mobility one of the key quantities in electronic devices. Beyond this ‘conventional’ Hall Effect, sufficiently high magnetic fields may localize electrons such that a quantization of the Hall conductivity can be observed. This effect, known as Quantum Hall Effect (QHE), has been subject to intense research efforts worldwide with outstanding importance. For instance, it has led to the proof of the existence of monolayer graphene and in total led to three Nobel prizes. The present proposal is searching for signatures of quantization of the Hall conductance in completely new systems namely in crystalline molecular semiconductors, which so far has not been observed. Organic crystals are materials that have been studied for many decades to understand the fundamentals of charge transport of electrons and holes in organic semiconductors in general. In addition to having great technological relevance in Organic Electronics, several compounds exhibit exciting phenomena such as superconductivity. Given such amazing properties already observed in molecular systems, the question if Hall conductance quantization could be observed in organic materials is of great interest, but the conditions for its observation are unknown. Here we will focus on the low-temperature limit as the most likely region for the discovery of Hall-conductance quantization, while disorder is described microscopically. HEliOS aims at studying the emergence of the QHE under experimentally relevant conditions of crystalline organic materials by using an order-N scaling method. The project is based on an efficient algorithm for the Hall conductivity, which I have developed and which can tackle with models including several millions of molecules and micron-sized samples. The developed algorithms are highly parallelized and runs optimally on massively parallel machines such as the present generation of tier-0 HPC machines. Still the employed algorithm is more demanding than similar approaches to compute the standard longitudinal conductivity, which makes the use of PRACE infrastructure indispensable. We mention that our activity will be carried out in parallel to experimental work which so far could not draw a global phase diagram for the Hall effects, calling for guidance from theory. HEliOS will allow us to provide guidance for such intriguing experimental activity.

High pressure structural, optical and superconducting propertis of hydrides

Project Title: HEliOS — Hall Effects in Organic Semiconductors
Project Leader: Matteo Calandra, FR
Resource Awarded: 9000000 core hours on MareNostrum

Details

Team Members :
Raffaello Bianco, CNRS, FRANCE
Maria Hellgren, CNRS, FRANCE
Betul Pamuk, CNRS, FRANCE
Lorenzo Paulatto, CNRS, FRANCE
Guilherme Ribeiro, Université P. et M. Curie, FRANCE
Xabier Zubizarreta, Université P. et M. Curie, FRANCE
Ion Errea Lopez, University of the Basque Country (UPV/EHU), FRANCE
Francesco Mauri, Università di Roma la Sapienza, ITALY

Abstract
In December 2014, the group of Prof. Eremets in Meinz discovered high Tc superconductivity with a record breaking Tc=205 K in H2S at 200 GPa pressure. Soon after superconductivity with Tc>100 K was discovered in phosphine at pressures above 200 GPa. Due to the light mass of hydrogen, the structural properties of high pressure sulfides cannot be studied in the framework of the harmonic approximation and neglecting the quantum motion of the ions. In particular, it is know that in systems like ice at high pressure, the contribution to the free energy to to the quantum motion of the proton is large. Furthermore, correlation effects are important in describing the hydrogen bond and, more in general, the excitation spectrum of superconducting hydrides. Finally, in order to describe the superconducting gap structure the Migdal Eliashberg equations need to be solved by fully taking into account the anisotropy and multiband features of the electronic structure. Thus, A correct description of superconductivity in hydrides needs to treat anharmonicity, correlation and the electron-phonon interaction on equal footing. This is what we plan to do in the present project by tackling the problem over three different angles. Anharmonicity and the quantum motion of the proton will be handled via the stochastic self consistent harmonic approximation. Correlation effects on the total energy will be studied by using the RPA approximation together with hybrid functionals. Finally the superconducting gap properties and raman response in the superconducting state will be handled by solving the Migdal Eliashberg equations by using the Wannier interpolation technique developed by the authors. Our project will lead to a complete understanding of superconducting and normal state properties of Sulfur hydrides and phosphine.

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Mathematics and Computer Sciences (1)

B3DNSE- Blow-upr for 3D Navier-Stokes equations

Project Title: B3DNSE- Blow-upr for 3D Navier-Stokes equations
Project Leader: Sandra Frigio, IT
Resource Awarded: 10000000 core hours on Fermi

Details

Team Members :
Dong Li, University of British Columbia, CANADA
Carlo Boldrighini, Istituto Nazionale di Alta Matematica, ITALY
Pierluigi Maponi, University of Camerino (italy), ITALY
Yakov Grigorevich Sinai, Princeton University, UNITED STATES

Abstract
We propose a numerical study of the three-dimensional incompressible Navier-Stokes (NS) equations, both complex-valued and real-valued. Our project is inspired by the theoretical work of two of the proponents (D. Li and Ya.G. Sinai, [1]), and by the results of our previous computer simulations. The NS equations are the main mathematical model for viscous fluid motion and have been intensively studied both theoretically and numerically. The question of possible finite-time singularities (blow-up’s) for smooth initial data is the main open problem and is in the list of the Millennium Prize problems of the Clay Institute. Some recent theoretical results for modified NS equations indicate that a finite-time blow-up may occur [2]. The same indication comes from the results of Li and Sinai [1] who proved that there are complex solutions of the 3-d NS equations that blow up. The result is based on the convolution structure of the equation in Fourier k-space. The proofs are obtained by controlling the iterated convolutions for a set of initial data with support (in k-space) in a finite region far from the origin. The solutions are rather easy to follow on the computer, mainly because their support is concentrated in a thin cone and their behavior near the blow up is determined by a function (“fixed point” of the theory) which is determined by the initial data. The complex solutions of [1] are unphysical, as the energy diverges. They show however interesting features, such as the sudden concentration of energy in a small space region (“tornado effect” ), which makes them worth of detailed study. Moreover there are related real solutions, which share some of the properties of the complex ones, in particular a rapid increase for some period of time of the large k modes and of the enstrophy. Previous work. Results of simulations for the blow-up of solutions of the two-dimensional complex Burgers equations in the plane (predicted in [3] were reported in the paper [4] of some of the proponents. Some preliminary results on the 3-d NS equations, both complex- and real-valued, have been presented by one of us (C.B.) as an invited lecture at the Abel Symposium in Stockholm, celebrating the decision to award the 2014 Abel Prize to Prof. Ya. G. Sinai. A detailed study of some complex solutions of the 3-d NS equations corresponding to a single fixed point, is reported in the recent paper [5]. The simulations reveal important facts, not (as yet) predicted by the theory, such as the existence of two types of blow-up for the same fixed point, and convergence of the solution at the critical time everywhere in physical space, except for a few points of divergence (spikes)., the location of which depends on the initial data. Aims of our proposal. The expected results of our proposal may be summarized as follows. i) A deeper understanding of the blow-up mechanism for the complex equations, and its relation to the choice of the fixed point. ii) For the related real solutions, a better understanding of the phenomenon of concentration of energy and enstrophy, also in relation to a possible blow-up. More computational resources are needed in order to study the behavior of the solutions for different fixed points. Concluding remarks. Simulation of the 3-d NS equations is onerous and reliable evidence on a blow-up is difficult to obtain if one does not know its structure (see, e.g., [6]). We simulate solutions which are relatively easy to follow in k-space, as explained above, and for which (in the complex case) there is some general guideline which works, in part, also for the real case. Our team is also working on the theoretical aspects of the problem.

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Universe Sciences (3)

SMPI: Simulations of Magnetoconvection in Partially Ionized solar atmosphere

Project Title: SMPI: Simulations of Magnetoconvection in Partially Ionized solar atmosphere
Project Leader: Elena Khomenko
Resource Awarded: 6050000 core hours on MareNostrum

Details

Team Members :
Angel de Vicente, Instituto de Astrofí­sica de Canarias, SPAIN
Manuel Luna, Instituto de Astrofí­sica de Canarias, SPAIN
Nikola Vitas, Instituto de Astrofí­sica de Canarias, SPAIN

Abstract
Understanding solar magnetism and establishing connections between magnetic activity in sub-surface layers and its manifestation in the outer atmosphere is central to solar physics and extremely relevant to stellar astrophysics in general. By means of this project, we challenge to understand the questions of basic physics: how the magnetic energy propagates through the layer of almost neutral gas in the photosphere and chromosphere of the Sun, and how this energy is released in its upper atmosphere. In the recent years, it is gradually becoming accepted in the solar community that the presence of neutrals in the solar plasma plays extremely important role in the propagation of waves, and in the development of instabilities, including convective instability. It facilitates the energy release for both processes, which is, possibly, one of the key ingredients that allow maintaining solar upper atmosphere hot. Our group has been working on the modelling of partially ionized solar plasma already for several years. It is now time to use this accumulated experience and understanding of idealized processes to increase the complexity of our modeling. The aim of this project is to perform simulations of magneto-convective instability, where the flows, waves and currents will be generated self-consistently by fluid motions and dissipated by non-ideal effect, allowing the plasma, magnetic field, and radiation to interact. We will be going beyond the classical magnetohydrodynamical (MHD) description of solar plasma to take into account non-ideal effects due to the presence of neutral atoms and weak collisional coupling of different species. Many stars are similar to the Sun in their magnetic activity cycles, presence of starspots on their surface, or active phenomena such as jets. Understanding the magnetic activity of such a cool star as the Sun is directly extendable to other stars, and will help guiding theories of stellar structure and evolution.

Modeling gravitational-wave signals from black-hole binaries

Project Title: Modeling gravitational-wave signals from black-hole binaries
Project Leader: Sascha Husa, ES
Resource Awarded: 8400000 core hours on MareNostrum

Details

Team Members :

Alejandro Bohe, Max Planck Institute for Gravitational Physics (Albert Einstein Institute), GERMANY
Michael Pürrer, Max Planck Institute for Gravitational Physics (Albert Einstein Institute), GERMANY
Alfred Castro, University of the Balearic Islands, SPAIN
Francisco Jimenez Forteza, University of the Balearic Islands, SPAIN
David Keitel, University of the Balearic Islands, SPAIN
Miquel Oliver Almiñana, University of the Balearic Islands, SPAIN
Alicia Sintes, University of the Balearic Islands, SPAIN
Parameswaran Ajith, International Centre for Theoretical Physics, INDIA
Edward Fauchon-Jones, Cardiff University, UNITED KINGDOM
Mark Hannam, Cardiff University, UNITED KINGDOM
Gernot Heissel, Cardiff University, UNITED KINGDOM
Sebastian Khan, Cardiff University, UNITED KINGDOM
Lionel London, Cardiff University, UNITED KINGDOM
Frank Ohme, Cardiff University, UNITED KINGDOM
Francesco Pannarale, Cardiff University, UNITED KINGDOM
Alex Vaño Viñuales, Cardiff University, UNITED KINGDOM

Abstract
One century after Einstein’s general theory of relativity revealed space and time to be dynamical entities, gravitational research is about to be transformed once again. The first detection of gravitational waves (GW) will push open a new window on to the universe, comparable to the revolution brought about by the development of radio astronomy. Prime candidates for the first detection are catastrophic events involving compact relativistic objects and their strongly nonlinear gravitational fields, in particular the coalescence of compact binaries of black holes (BHs). In this project, we model these events and their GWs by solving the full nonlinear Einstein equations. Our results will help to identify the first such signals to be observed by advanced gravitational-wave detectors, and contribute to answering important open questions in astrophysics and fundamental physics, where BHs have taken center stage. The experimental challenge to meet the tremendous sensitivity requirements of gravitational-wave detectors is paralleled by a computational modelling challenge: the detection, identification, and accurate determination of the physical parameters of the sources relies on the availability of reliable waveform template banks, which are used to filter the detector signals. For some sources, such as the slow inspiral of widely separated BHs, good analytical approximations for the gravitational waveforms are provided by perturbative post-Newtonian expansion techniques. For the last orbits and merger, however, where the fields are particularly strong, and where one has the best chances of discovering entirely new physics, the Einstein equations have to be solved numerically. This is what we do. Over the last few years, we have developed the techniques that render possible large-scale parameter studies of black-hole binaries, and to synthesize the results into analytical template banks that describe the complete inspiral, merger and ringdown of BH binaries. This project will make it possible to combine all these techniques with large-scale parameter studies, in time to establish data analysis strategies for the advanced GW detectors. With the aim of establishing an efficient model for GW searches and source identification (parameter estimation), we have previously pioneered the construction of analytical template banks that “interpolate” numerical simulations in the subspace of non-precessing binaries, and which are already used for analyzing the data of the LIGO and Virgo detectors. We have recently produced the most accurate and complete aligned-spin model to date, which is expected to play an important role in gravitational-wave astronomy over the next few years. In this PRACE project we aim to extend this model to fill a key gap in the parameter space, highly spinning black-hole binaries. We will also begin to explore the precessing-binary parameter space, as a first step to extending our breakthrough precessing-binary model.

Particle acceleration by magnetic reconnection in turbulence

Project Title: Particle acceleration by magnetic reconnection in turbulence
Project Leader: Giovanni Lapenta, BE
Resource Awarded: 45000000 core hours on Fermi

Details

Team Members :
Jorge Amaya, KU Leuven, BELGIUM
Fabio Bacchini, KU Leuven, BELGIUM
Emanuele Cazzola, KU Leuven, BELGIUM
Maria Elena Innoccenti, KU Leuven, BELGIUM
Wei Jiang, KU Leuven, BELGIUM
Vyacheslav Olshevsky, KU Leuven, BELGIUM
Lorenzo Siddi, KU Leuven, BELGIUM

Abstract
High-energy particles are ubiquitous in space. They are detected by ground and satellite-based instruments, and observed by secondary radiation at all wavelengths: from radio to gamma-rays. To spacecraft and astronauts, such particles pose immediate danger; only the Earth’s magnetic field protects us from their influence on the ground. However these particles are extremely useful for astrophysicists, they are a precious source of information about most distant objects (through emitted radiation). The physical mechanism of magnetic reconnection is capable of accelerating particles to very high, supra-thermal speeds. It is also believed to be the primary source of energy release in solar flares, coronal mass ejections, Earth’s magnetotail and interplanetary medium. During magnetic reconnection, the topology of the magnetic field abruptly changes within seconds or minutes, much faster in comparison with the evolution time scales of solar and space weather events: the process is of an “explosive” nature. However, the very nature of magnetic reconnection in collisionless space plasmas has not been revealed yet, it is still among the biggest mysteries of present-day astrophysics and plasma physics. The reason behind it is the multi-scale nature of magnetic reconnection: reconnection is triggered on the scales of individual plasma particles where the kinetic effects shall be considered, and acts on the fluid scales, order of magnitude larger than kinetic ones. We aim to perform kinetic particle-in-cell simulations of large three-dimensional volumes of plasma to answer the specific questions regarding particle acceleration in magnetic reconnection. First, is it reconnection itself, or some associated phenomena, that produces particle acceleration? Second, are these acceleration mechanisms efficient enough to explain all observations? Finally, are our current models for magnetic reconnection complete enough to take into account all sources of particle acceleration? Achievement of our goals is possible thanks to a unique kinetic electromagnetic particle-in-cell code iPic3D, that, due to its implicit formulation of field equations, allows to consider plasma in physically relevant large volumes, and at relevant time scales. We address the space plasma, which is a ready laboratory for magnetic reconnection. However, our results are relevant in much broader fields of research. In particular, they will be useful in interpretation of astronomical radio and short-wavelength observations, such as solar radio bursts or gamma ray bursts. Our simulations are challenging due to the analysis of huge amounts of particle data, and we will need to improve the algorithms of particle data analysis which will provide added value to the scientific computing knowledge. Finally, our simulations will be used to develop and test the spacecraft data analysis techniques, which is especially timely due to the launch of the NASA’s new Magnitospheric Multiscale (MMS) mission.

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