DECI 7th Call

Find below the results of DECI-7 (Distributed European Computing Initiative) call.

Projects from the following research areas:

 

Astro Sciences (6)

ARTHUS-3

Project Title: Applying Radiation Hydrodynamics to understand Core Collapse supernovae (III)
Project Leader: Hans-Thomas Janka, Max Planck Institute for Astrophysics, Garching, Germany
Resource Awarded: 2 750 000 core hours on FZJ – JuRoPA
Details

Abstract:
Supernova explosions of massive stars are among the most powerful cosmic events. They give birth to neutron stars and stellar black holes, produce strong neutrino and gravitational wave signals, and are the prime source candidates of chemical elements from iron to plutonium. The details of the physical mechanism that leads to the final explosion of the star are not yet fully understood. In this project we take part in the competition for the currently most advanced simulations of the supernova evolution of massive stars and treat the neutrino-matter interactions in the supernova core with unprecedented accuracy. In this project we plan to move towards three-dimensional models of core collapse supernovae with detailed neutrino-transport, supplemented by faster two-dimensional simulations to explore variations in parameter space.

BlackHoles

Project Title: Black holes dynamics in metric theories of gravity
Project Leader: Vitor Cardoso, Instituto Superior Técnico, Portugal
Resource Awarded: 4 200 000 core hours on PSNC – SGI UV1000
Details

Abstract:
Formulated by Einstein in 1916, General Relativity (GR) passed many stringent tests, and is now accepted as the standard theory of gravity and one of mankind’s greatest scientific achievements. Nevertheless, most existing observations only probe the weak-field regime of gravity, whereas the strong-curvature regime, more specifically the small length scales and high energy domain, remains essentially unexplored. Exactly in this regime, quantum effects become non-negligable and GR is expected to break down, giving way to a more complete theory of gravitation. In fact, alternative theories of gravity are motivated by high energy scenarios and aim at completing GR in the quantum regime, but also at explaining astrophysical and cosmological observations in a more natural manner than GR, e.g., without invoking unknown forms of matter or energy. Viable alternative theories of gravity are basically indistinguishable from GR in the weak-field regime. However, new interesting effects are expected to appear at high curvature. One of the preferred testing grounds for new theories of gravitation are black holes (BHs). BHs are among the most exciting predictions of many theories of gravity and play a key role in fundamental physics. Because BHs are made of pure spacetime fabric, knowledge of the equation of state is not necessary, it is built in to the field equations; because BHs are the most compact objects one can conceive of and simultaneously extremely simple, described by only few parameter, they provide ideal testing ground for probing the strong-curvature regime of gravity and new theories of gravitation. BH motion is dominated by gravitational interactions and BH collisions are among the most violent scenarios in nature. Thus, the dynamics of BHs in alternative theories are expected to differ sensibly from GR, with dramatic and potentially observable effects. Indeed, observations of the highly dynamical strong-curvature regime of gravity might become available within the next decade, with advanced interferometric gravitational wave detectors, such as LIGO, GEO600, VIRGO and TAMA, being in place. A crucial input from numerical relativity is to provide theoretical waveforms of gravitational waves (GW) in modified theories of gravity to complement GR based template banks for these detectors. The modeling of BHs in non-standard background spacetimes has also attracted a great deal of attention in the context of high-energy physics. According to the gauge/gravity duality, gravitational physics in anti-de Sitter (AdS) backgrounds describes field theories on the boundary of that spacetime. Accordingly, BHs in AdS are dual to an equilibrium field theory and therefore interacting BHs off-equilibrium may represent interesting physics, as for example in the quark-gluon plasma formation in heavy-ion collisions. Numerical modeling of BHs in non-asymptotically flat spacetimes in metric theories of gravity, including GR, is still in its infancy and we here propose to extend our previous studies to BHs in spacetimes with a non-zero cosmological constant. Imprints of alternative theories are most likely carried by the GWs generated in highly dynamical processes involving black holes, and will become observable in the next decade by the several operating detectors worldwide.

MAESTRO

Project Title: Magnetized Accretion and Ejection phenomena in aSTROphysics
Project Leader: Dr Claudio Zanni, INAF Osservatorio Astronomico di Torino, Italy
Resource Awarded: 2 000 000 core hours on IDRIS – BABEL
Details

Collaborators:
Gianluigi Bodo – INAF Osservatorio Astronomico di Torino, Italy
Andrea Mignone – Università degli Studi di Torino, Italy
Dr Petros Tzeferacos – University of Torino, Dip. Fisica Generale, Italy
Abstract:
Collimated jets of ionized plasma are a common phenomenon observed in many astrophysical systems, from newly forming stars similar to our Sun, where Herbig-Haro (HH) jets take their origin, X-Ray binaries, in which galactic microquasars are produced, or Active Galactic Nuclei (AGN), where relativistic jets associated with extended radio-galaxies are accelerated. Despite being characterized by extremely different space, time, and energy scales, it is commonly accepted that all these systems derive their power from the gravitational energy liberated by material accreting onto a central compact object, most plausibly in the form of an accretion disk. Nowadays it is firmly accepted that accretion and ejection are deeply linked phenomena in many astrophysical systems: the gravitational and rotational energy of an accretion disks around compact objects represents a reservoir largely sufficient to power different classes of cosmic jets. We therefore propose to carry out three dimensional magneto-hydrodynamic (MHD) simulations of magnetized accretion disks launching supersonic jets. Analytical and numerical models of magnetized accretion-ejection structures have been often limited to axisymmetric studies. To date, 3D numerical experiments focused on the acceleration process and/or the large-scale propagation of the outflow, neglecting the dynamical connection with the underlying accretion disk. Our three dimensional simulations will therefore represent the first attempt to globally model the launching mechanism of jets from magnetized Keplerian disks. Our main aim is to study the stability of the accretion-ejection process and of the jet initial propagation to the onset of non-axisymmetric modes of instability.

PICKH

Project Title: PICKH
Project Leader: Post-doctoral Fellow Pierre Henri, Katholieke Universiteit Leuven, Belgium
Resource Awarded: 1 500 000 core hours on CINECA – CNE-SP8 and CINECA – PLX
Details

Collaborators:
Astr. Carine Briand – Observatoire de Paris, Meudon, France
Prof Francesco Califano – Universita di Pisa, Department of Physics, Italy
Postdoctoral Fellow Matteo Faganello – Universita di Pisa, Department of Physics, Italy
Professor Giovanni Lapenta – Katholieke Universiteit Leuven, Belgium
Postdoctoral Fellow Stefano Markidis – Katholieke Universiteit Leuven, Belgium
Dr. Francesco Valentini – Università della Calabria, Departement of Physics, Arcavacata di Rende, Italy
Abstract:
The interaction between the solar wind and the Earth’s magnetosphere is a rich and complex system. From a theoretical point of view, it is a natural laboratory for plasma physics for which in-situ observations are available. From a practical point of view, it is of primary importance for the understanding of Sun-Earth interactions and its implications in term of space weather. At low latitude, the velocity shear between the magnetosheath and magnetosphere plasma is unstable to the Kelvin-Helmholtz instability. This instability is at first order a fluid instability. However, (i) the magnetosheath and magnetosphere plasma are collisionless and (ii) the nonlinear evolution of the Kelvin-Helmholtz instability self-consistently generates gradients at kinetic scales (ion gyro-radius, ion skin depth). That is why a kinetic description of this instability is necessary to fully understand its nonlinear evolution. We thus plan to perform 2D-3V kinetic plasma simulations of the magnetized Kelvin- Helmholtz instability with application to the Earth magnetopause. Our goal is to understand the implications of a kinetic description of this instability. The Vlasov-Maxwell system is solved through the PIC implicit moment method, which allows to study plasma kinetic effects without the intrinsic limitations of the traditional (explicit) PIC method in terms of spatial resolution. Among the different phenomena of interest, collisionless magnetic reconnection spontaneously develops during the non linear evolution of a vortex chain generated by the development of the Kelvin-Helmholtz instability. This local mechanism leads to a global change in the magnetic topology at large scales which is of fundamental importance in understanding the transport properties of the low latitude magnetosphere system. The project represents today a major challenge in computational plasma physics to be tackled only by means of last generation computers. Goals: 1. Investigate optimization techniques for Particle-In-Cell implicit moment algorithm to create an high performant implicit PIC code 2. Production runs in 2D-3V configuration for a major cross-scale problem in space plasma research to better understand Sun-Earth interactions.

Planck-LFI

Project Title: Planck-LFI
Project Leader: Hannu Kurki-Suonio, University of Helsinki, Finland
Resource Awarded: 3 500 000 core hours on CSC – Louhi XT
Details

Collaborators:
Enrique Martinez-Gonzalez – Institute of Physics of Cantabria (CSIC-UC), Santander, Spain
Paolo Natoli – University of Ferrara, Italy
Jussi Väliviita – University of Helsinki, Finland
Abstract:
Planck is a European Space Agency satellite mission, whose task is to map the structure of the cosmic microwave background (CMB) in unprecedented detail, surpassing the accuracy of previous missions, like the NASA WMAP. The cosmic microwave background is radiation from the Big Bang, and it shows us the structure of the early universe.

Planck will constrain cosmological models and examine the birth of large-scale structure in the universe. It is thought that this structure originates from quantum fluctuations in the very early universe during a period of accelerated expansion called inflation, but Planck results are needed for a better understanding of this. The main scientific results expected from Planck are cosmological, but as a by-product, Planck will also yield all-sky maps of all the major sources of microwave to far-infrared emission, opening a broad expanse of other astrophysical topics to scrutiny. Planck was launched in May 2009, and the final results from the mission will be published in early 2014.

Planck carries two instruments, the Low-Frequency Instrument (LFI) and the High-Frequency Instrument (HFI), utilizing different technologies. It is important to map the sky at many frequencies to be able to separate the cosmic microwave background from the astrophysical foreground radiation. Two Planck data processing centres (DPCs) have been set up, one for each instrument, but the most resource-intensive tasks need to be done on supercomputers.

Because of the weakness of the signal and the high accuracy desired, Planck data analysis is a complicated task, requiring sophisticated statistical methods to separate out the signal from instrument noise and systematic effects.

Simulation work will dominate the computational load of Planck data analysis. Analysis pipelines will indeed be predominantly run on simulated rather than real data since Planck analysis codes either require simulations for self-calibration and validation of results, or depend critically on simulations for the results themselves.

The objective of this application is to carry out two resource-intensive tasks that are needed as part of Planck LFI data analysis:
– timeline-to-map Monte Carlo simulation of Planck data: thousands of realizations of instrument noise and hundreds of realizations of cosmic microwave background signal; also simulations of astrophysical foreground radiation signal; the analysis of this data in parallel to the analysis of the real data from the sky
– cosmological parameter estimation for a number of cosmological models, in particular those related to multi-field inflation.

SMARC

Project Title: Solar Magnetically Active Region Corona
Project Leader: Dr. Peter Hardi, Max Planck Institute for Solar System Research, Göttingen, Germany
Resource Awarded: 700 000 core hours on LRZ – SuperMig
Details

Collaborators:
Dr Sven Bingert – Max Planck Institute for Solar System Research, Göttingen, Germany
Philippe-André Bourdin – Max Planck Institute for Solar System Research, Göttingen, Germany
Abstract:
Cool stars are surrounded by hot coronae, which are heated to some million degrees Kelvin. The heating processes, widely proposed to be related to the stellar magnetic field, lead not only to temperatures in the outer atmosphere well in excess of the stellar surface, but result also in a highly dynamic response of the plasma, inducing flows and waves. To study these processes the Sun is of pivotal interest because here we can spatially resolve individual structures in the corona.

Utilizing increasing computing power, we plan to run new numerical experiments which will allow to study the structure and evolution of an active region in the solar corona. To this end we describe part of the solar corona, i.e. an active region, in a box using magneto-hydrodynamics. The system is driven by fluid motions on the solar surface driven by convection which carry around the magnetic fieldlines. This leads to currents in the upper layers which are dissipated, subsequently heat the atmosphere and thus create the corona.

So far this modelling has been possible only in simplified setups. The proposed simulation will allow for the first time to model the structure and evolution of a solar active region with a high spatial resolution (230 km) to resolve most of the driving motions on the surface and at the same time to describe the full extend of the active region (235×235 Mm).

The results from these simulations will be compared to real observations of the Sun by deriving synthesised observations, i.e. emission line spectra, from the numerical experiments (which is not part of this proposal, as it can be done on a “normal” computer).

top

Bio Sciences (7)

HELIXKINETICS

Project Title: HELIXKINETICS
Project Leader: Dr Robert Best, University of Cambridge, Department of Chemistry, UK
Resource Awarded: 2 713 190 core hours on FZJ – JuRoPA and ICHEC – Stokes
Details

Collaborators:
Dr David De Sancho – University of Cambridge, Department of Chemistry, UK
Abstract:
Proteins are biomolecules that are at the centre of the action in many biological processes, functioning as enzymes, regulatory molecules and structural components of the cell. In most cases proteins “fold” spontaneously – driven only by the physical interactions encoded by their sequences – to a unique three dimensional `native` structure1. We focus on the most common element of protein structure, the α-helix, whose formation (the helix-coil transition) is a classic sub-problem in protein folding. The kinetics of helix formation is of fundamental importance because it sets a basic “speed limit” for protein folding; yet these kinetics, on a nanosecondmicrosecond time scale, are usually difficult to interpret. We aim to use molecular simulations to shed new light on the microscopic events in helix formation. The first key aspect of our proposal is the accuracy of the energy function or “force field” we propose to use, since recent protein folding simulations have revealed shortcomings in the force fields employed, with many force fields overstabilizing either α and β structure2,3. The proposed energy function has been corrected to reproduce experimental observables in small peptides, resulting in parameter sets which were found to be transferable to a wide range of systems, from short helix-forming peptides4 to both α and β-peptides and small proteins5-8. The most recent improvement is the inclusion of an optimized water model, resulting in an improved temperature dependence of the transition.4 The second critical point is the method by which we will determine simultaneously both the equilibrium populations of different helical states, as well as their rates of interconversion. The replica exchange molecular dynamics (REMD)9 we propose to use for obtaining equilibrium populations is widely recognized for its effectiveness. However, extracting dynamical information on long time scales from such simulations is challenging due to the frequent coordinate exchange. Building on our recent work on a five residue helixforming peptide (W1H5), we will use a novel method of fitting a Markovian model to REMD data to determine the microscopic transition rates between stable states of the system.10. Here, we plan here to take our approach10,11 to longer helix-forming peptides – this is an important extension because the relaxation kinetics of longer peptides is more sensitive to helix elongation than the short W1H5 peptide, and a more critical test of the microscopic kinetic model. However, the larger system size makes the calculations very computationally demanding, motivating this application. We have identified a range of experimentally characterized peptides in the literature according to two criteria: (i) simple sequences, to allow sequence effects to be introduced systematically, and (ii) availability of multiple experimental probes. From this study we expect to obtain unprecedented detail about the microscopic mechanism of helix formation. We can both test the validity of the theoretical models of helix-coil equilibrium and kinetics and determine optimal parameters for such models. We will be able to analyse experimental data directly, without needing to invoke a phenomenological model; and we can investigate whether our simulations can explain the differences between the results of different experimental measurements.

LASIPROD

Project Title: LArge scale molecular SImulations of PROtein – DNA recognition in the combinatorial control of trnascription
Project Leader: Dr. Vlad Cojocaru, Max Planck Institute for Molecular Biomedicine, Cellular and Developmental Biology, Münster, Germany
Resource Awarded: 700 000 core hours on LRZ – SuperMig
Details

Collaborators:
Prof. Dr. Hans Schöler – Max Planck Institute for Molecular Biomedicine, Münster, Germany
Dr. Matthias Wilmanns – EMBL, Molecular Structural Biology, Hamburg, Germany
Abstract:
In eukaryotic cells, a complex gene expression network is controlled by a relatively small number of protein regulators. How does this limited set of factors regulate the expression of all genes in a complex spatio-temporal pattern is a challenging question. A subset of regulators, the transcription factors bind to regulatory DNA elements and interact either directly or indirectly with other transcription factors or protein regulators. Often, they adapt their conformation to the specific interaction partner and adopt different arrangements on different DNA elements, managing gene expression in a combinatorial fashion. In this project, we aim to reveal the molecular mechanisms of the combinatorial control of gene expression at atomic level of detail. This is essential for understanding a wide variety of biological phenomena. We will focus our study on factors relevant for the maintenance of stem cell ability to differentiate in different cell types and for the reprogramming of somatic cells into stem-like cells (induced pluripotent stem cells). We expect the results will contribute to the elucidation of the mechanisms by which somatic cells can be reprogrammed into pluripotent cells and, more generally, to the understanding of gene regulation. We aim to provide data that may be used in the development of novel stem cell based therapies for a wide range of diseases. To achieve our goals, we will calculate free energy profiles from atomistic molecular dynamics simulations for a set of representative protein-DNA and protein-protein interactions. These calculations are only attainable on large supercomputers due to the large number of degrees of freedom in the simulated system and the extensive sampling of the conformational space required. We will use the highly-parallel NAMD program for the calculations. This application is already available for production runs at several PRACE sites. This project will be performed in close collaboration with experimenters, thus giving us the opportunity to readily test the relevance of our findings.

LGICTAMD

Project Title: LGICTAMD
Project Leader: Dr. Grazia Cottone, University College Dublin, Dublin, Ireland
Resource Awarded: 3 024 000 core hours on ICHEC – Stokes
Details

Collaborators:
Prof. Giovanni Ciccotti – University College Dublin, Dublin, Ireland
Dr Luca Maragliano – University of Chicago, Chicago, USA
Abstract:
Nicotinic acetylcholine receptors are ligand-gated ion channels, i.e. transmembrane proteins that open or close in response to the binding of a chemical messenger. Some structural information on these proteins is available, but it only gives a fragmented vision of the conformational motions of the receptor during channel opening. Getting this information is of crucial importance to understand the basis of the ligand-receptor interactions, and to be able to develop new pharmacological approaches to influence the receptor’s biological function. Indeed, the interactions of nicotinic receptors with a variety of ligands and their different response on ligand binding is the basis of the pharmacological interest for these molecules, as these receptors were shown to play a crucial role in smoking addiction, Alzeihmer disease, schizophrenia.
In this project, we intend to characterize the mechanisms of channel opening/closure with full atomistic Molecular Dynamics simulations. To overcome sampling limitations due to the large time scale of the process, the recently developed Temperature Accelerated Molecular Dynamics (TAMD) will be used to efficiently explore the multi-dimensional conformational space of the receptor.
Results will give an insight into the transmission of the conformational changes from the binding pocket in the extra-membrane domain to the trans-membrane domain. A detailed description of the mechanism governing opening/closure will also allow the identification of mechanisms governing the binding of different ligands to receptors.

MUSIC

Project Title: Multi-Simulation Coordinator
Project Leader: Dr. Mikael Djurfeldt, KTH, Sweden
Resource Awarded: 231 000 core hours on IDRIS – BABEL
Details

Collaborators:
PhD Student Ekaterina Brocke – KTH, Sweden
Prof. Dr. Markus Diesmann – Forschungszentrum Jülich, Germany
Abstract:
MUSIC (http://software.incf.org/software/music) is an API specification that allows for run-time exchange of data between parallel applications in a cluster environment. A pilot implementation was released 2009. MUSIC is designed specifically for interconnecting large scale neuronal network simulators, either with each-other or with other tools. In this project, we will benchmark MUSIC and test its scalability up to hundreds of thousands of cores. The primary objective of MUSIC is to support multi-simulations where each participating application itself is a parallel simulator with the capacity to produce and/or consume massive amounts of data. Applications publish named MUSIC input and output ports. A specification file lists the applications participating in a multi-simulation and also specifies how ports are connected. The current version of the API supports transfer of time-stamped events, multi-dimensional time series and text messages. The API encourages modularity in that an application does not need to have knowledge about the multi-simulation in which it participates. Large scale neuronal network models and simulations have become important tools in the study of the brain and the mind. Such models work as platforms for integrating knowledge from many sources of data. They help to elucidate how information processing occurs in the healthy brain, while perturbations to the models can provide insights into the mechanistic causes of diseases such as Parkinson`s disease, drug addiction and epilepsy. A better understanding of neuronal processing may also contribute to computer science and engineering by suggesting novel algorithms and architectures for fault tolerant and energy efficient computing. Simulations of increasingly larger network models are rapidly developing. In principle, we have, already today, the computational capability to simulate significant fractions of the mammalian cortex. Neuronal network models have been formulated for a great diversity of different simulation tools. The reuse of such models is hampered by the lack of interoperability due to the multitude of languages and simulators used. Also, reimplementation of one model in other software is in practice both time consuming and error prone. Interoperability can be facilitated in several ways. One approach is to provide a model specification in some standardized format which can be understood by many simulation tools. Another approach is to allow different simulation tools to communicate data on-line. The MUSIC project was initiated by the INCF (International Neuroinformatics Coordinating Facility; http://www.incf.org) as a result of the 1st INCF Workshop on Large Scale Modeling of the Nervous System in order to support on-line communication between neuronal simulators and address the interoperability and reusability problems. In this PRACE project we will test the limits of MUSIC scalability and make the software ready for use in projects such as the Human Brain Project (candidate for the EU FET Flagship initiative).

SIVE-2

Project Title: All-atom Simulations of Influenza viral entry
Project Leader: Prof. Erik Lindahl, Stockholm University, CBR – The Stockholm Center for Biomembrane Research , Stockholm, Sweden
Resource Awarded: 6 250 000 core hours on EPCC – HeCToR XE8
Details

Collaborators:
Dr. Peter Kasson – Stockholm University, CBR – The Stockholm Center for Biomembrane Research , Stockholm, Sweden
Abstract:
Membrane fusion, the process by which neuronal exocytosis and infection by enveloped viruses occur, has been notoriously difficult to characterize at a molecular level. Part of the problem is that the underlying reaction that fusion proteins catalyze is not fully understood. The development of robust predictive models for the mechanism of lipid membrane fusion and its catalysis by viral fusion proteins will greatly aid in the understanding of the underlying physical process and how to effectively target it with antiviral agents. We have developing high-performance simulation methods to analyze membrane fusion. In our work thus far, we have simulated vesicle fusion at atomic resolution, yielding novel insight into structure and mechanism of fusion intermediates. We are now extending these simulations to generate high-fidelity models of fusion in a experimental model systems, and predict the catalytic mechanism of influenza fusion proteins. We particularly plan to examine how influenza-catalyzed fusion is similar to or differs from protein-free fusion. Simulations are performed using the Gromacs software package that we and our collaborators develop, one of the fastest in the world.

TanGrin

Project Title: TanGrin
Project Leader: Vesa Hytönen, University of Tampere, Finland
Resource Awarded: 3 500 000 core hours on EPCC – HeCToR XE9
Details

Collaborators:
Sampo Kukkurainen – University of Tampere, Finland
Ilpo Vattulainen – Tampere University of Technology, Finland
Bernhard Wehrle-Haller – University of Geneva, Switzerland
Abstract:
Cells are typically friendly and outgoing, meaning that they enjoy social situations and in particular communication. One of the means by which they do so is receptor molecules embedded in cell membranes. These receptors take part in communication between a cell and its outside world, thereby connecting the cell to its environment. One of the key proteins doing this is integrin. It mediates attachment between a cell and the tissues around it, and it also plays an important role in cell signaling by which it regulates functions and properties of cells such as their migration and shape. Meanwhile, integrins are also central components in cancer metastasis, and different tumor types have been reported to have altered numbers of their specific integrins. Understanding of the function as well as signaling pathways of the integrins would therefore pave way to finding better treatments for a number of diseases.

To understand proteins function, one has to clarify how it is activated. Here, we focus on two appealing aspects related to this matter. First, talin is known as a key protein that binds directly to integrin and is involved in its activation process. Second, experimental studies have reported that patches close to the integrin-binding site in talin appear to interact with acidic phospholipids in a cell membrane. Given the importance of talin in integrin activation and the possibly significant role of specific lipids in this process, it is exciting that the details of these lipid-protein interactions are not known.

In this project, we will use atomistic molecular dynamics simulations to consider the complex comprised of integrin and the integrin-bound talin interacting with lipids in a membrane. Our main objective is to unravel how the conformation of the integrin-bound talin depends on its interactions with lipids. More concretely, does talin interact with specific lipids, and what are the most central interaction mechanisms driving conformational changes of talin? Through these considerations our aim is to better understand the cellular adhesion process overall, and in this spirit contribute for future applications for better health.

VIRonSAMs

Project Title: VIRonSAMs
Project Leader: Prof. Michele Cascella, University of Bern, Bern, Switzerland
Resource Awarded: 4 480 000 core hours on CINECA – PLX and CINES – JADE-Nehalem
Details

Collaborators:
Dr. Greg Gannon – University of Bern, Bern, Switzerland
Prof. Tamar Kohn – École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
Dr. Michael Sander – ETH Zurich, Switzerland
Abstract:
Virus inactivation processes at water-solid interfaces are key factors determining the persistence of viruses in various aqueous environments. These include environmental systems such as surface and groundwater, various food products, and blood and other bodily fluids. Interactions with solid surfaces influence virus stability, and thus determine the spread and persistence of infective viruses. Despite the importance of interfacial inactivation processes, their underlying causes remain poorly understood. It is the overall aim of our project to identify the most important processes contributing to virus inactivation at interfaces, and to develop a comprehensive concept of the virus and surface parameters that dictate inactivation behavior. The simulations described herein will focus on a model system representative of one of the great challenges to public health, namely viral contamination of water resources. The main scientific question we wish to answer with this project is what happens to a virus when it is placed on a surface or alternatively what is the mechanism of virus inactivation on a surface. To this end we wish to perform all-atom molecular dynamics simulations of a water solvated virus capsid on a range of surfaces of self-assembled monolayers (SAMs) on gold(111). The virus to be studied will be the phage virus MS2. The advantages to selecting MS2 are manifold, 1) the availability of its crystallographic structure through the Protein Data Bank; 2) being a relatively small virus makes it amenable to fully atomistic molecular dynamics simulation while owning to the capsid symmetry, capsid fragments can be used rather than the entire capsid; 3) experimentally it is safe to work with unlike for example the polio virus which may revert to the live form thereby exposing researchers to the risk of infection; 4) culturing methods exist which allow infectivity to be assessed. SAMs offer a distinct advantage over other surfaces in their easily manipulable surface properties, for example hydrophilicity (water loving) and electrostatic properties are readily modified through changing the end group from -CH3 to -OH, -CO2- or -NH3+. Of great advantage to experimentalists is that a wide variety of SAM are readily commercially available. Finally the relative simplicity with which SAMs can be employed together with their availability and the advantages of MS2 outlined above means that the result generated from computational investigation can be readily confirmed by experiment using techniques such as Optical Waveguide Lightmode Spectroscopy (OWLS) or Quartz-Crystal Microbalance. Finally having understood binding at an atomistic level it may be possible to computationally design optimized SAMs for maximum virus binding.
top

Earth Sciences (3)

CASiMIR

Project Title: Chemistry of the Atmosphere Simulated with an Earth System Model for the Interpretation of Satellite based Remote sensing observations
Project Leader: Dr. Patrick Jöckel, DLR(German Aerospace Center), Institute for Atmospheric Physics, Oberpfaffenhofen, Germany
Resource Awarded: 3 263 148 core hours on SURFSARA – Huygens P6
Details

Collaborators:
Steffen Dörner – Max Planck Institute for Chemistry, Germany
Dr. Sven Kühl – Max Planck Institute for Chemistry, Germany
Abstract:
The project “Chemistry of the Atmosphere Simulated with an Earth System Model for the Interpretation of Satellite based Remote sensing observations (CASiMIR)” aims at an improved understanding of the physical and chemical processes, which determine the chemical state of the Earth atmosphere. Particular regions of interest are the polar upper troposphere and stratosphere. Here, the occurrence of polar stratospheric clouds (PSCs) and the heterogeneous chemistry (e.g., chlorine activation) on their particle surfaces are important processes responsible for the spring-time ozone depletion (Antarctic ozone-hole). Despite their importance, these processes are still not understood in detail. New data from satellite based remote sensing instruments promise additional insight in comparison to simulations with state-of-the-art atmospheric chemistry models, which represent the current knowledge about the underlying processes. A direct comparison of observations from satellite with results from model simulations, in particular of short-term and (in time and space) highly variable phenomena, such as PSCs, is, however, not straightforward. The ECHAM/MESSy Atmospheric Chemistry (EMAC) general circulation model has therefore been equipped with a new diagnostic capability: For instruments on sun-synchronous orbiters, the highest possible model data coverage, suitable for point-to-point comparison between satellite observations and model results, is achieved at the lowest possible output storage requirements. This new technique is applied in a series of EMAC model simulations for process studies revealing and assessing the gaps in the current understanding of the chemistry and dynamics in the polar upper troposphere and stratosphere. The simulations include sensitivity studies on the PSC forming process and a simulation with a finer model grid-resolution to optimally represent the horizontal gradients of short-lived, highly variable constituents. The results of the analyses will feed back to the further model development. The project, as detailed process study with a model of high complexity, is ambitious in terms of computational requirements and in particular in terms of data intensity, pushing the usage of resources, which are only available in a computational grid like PRACE, to the limits.

ElmerIce

Project Title: Ice-Sheet Contribution to Sea Level Rise
Project Leader: Dr. Olivier Gagliardini, Université Joseph Fourier, Laboratoire de Glaciologie et Géophysique de l’Environnment, Saint Martin d’Hères, France
Resource Awarded: 1 400 000 core hours on PDC – Lindgren
Details

Collaborators:
Dr. Thomas Zwinger – CSC-IT , Software and data solutions, Espoo, Finland
Abstract:
By gaining and loosing mass, glaciers and ice-sheets play a key role in the sea level evolution. This is obvious when considering the past 20000 years as the collapse of the large northern hemisphere ice-sheets after the Last Glacial Maximum contributed to a 120m rise in sea level. This is particularly worrying when the future is considered. Indeed, recent observations clearly indicate that important changes in the velocity structure of both Antarctic and Greenland ice-sheets are occurring, suggesting that large and irreversible changes may have been initiated. This has been clearly emphasised in the last report published by the Intergovernmental Panel on Climate Change (IPCC, 2007). IPCC has further insisted on the poor current knowledge of the key processes at the root of the observed accelerations and finally concluded that reliable projections of sea-level rise (SLR) are currently unavailable. The general aim of our research project is to (i) increase our understanding of englacial processes at the root of outlet glacier dynamics, (ii) develop numerical models which will allow massive parallel computing of ice-sheets flow and (iii) develop data assimilation methods related to ice flow modelling purpose, in order to provide accurate and reliable estimates on the future contribution of ice-sheets to SLR. These three directions of research are complementary. For the coming years, they are already well structured inside two important projects: the European FP7 project ice2sea which has the objective of improving projections of the contribution of continental ice to future sea- level rise and the French ANR ADAGe project, coordinated by O. Gagliardini, which has the objective to develop data assimilation methods dedicated to ice flow studies. Our research project, by its contribution to a better knowledge of the key processes that will lead to loss of continental ice and the development of data assimilation methods, will decrease the degree of uncertainty affecting SLR scenarii for the coming future and consequently feed up ongoing international debates surrounding coastal adaptation and sea- defence planning.

SPIESM

Project Title: Seasonal prediction improvement with an Earth System Model
Project Leader: Prof. Francisco Doblas-Reyes, Institut Català de Cienciès del Clima, Climate Forecasting Unit(CFU), Barcelona, Spain
Resource Awarded: 3 750 000 core hours on PDC – Lindgren
Details

Collaborators:
Dr. Laurent Brodeau – Stockolm University, Department of Meteorology (MISU), Stockholm, Sweden
Dr. Uwe Fladrich – Swedish Meteorological and Hydrological Institute (SMHI), Rossby Centre, Norrköping, Sweden
Dr. Virginie Guemas – Institut Català de Cienciès del Clima, Climate Forecasting Unit (CFU), Barcelona, Spain
Dr. Colin Jones – Swedish Meteorological and Hydrological Institute (SMHI), Rossby Centre, Norrköping, Sweden
Dr. Klaus Wyser – Swedish Meteorological and Hydrological Institute (SMHI), Rossby Centre, Norrköping, Sweden
Abstract:
This project contributes to the `Reducing Uncertainty in global Climate Simulations using a Seamless climate prediction system (RUCSS)` project funded by the Spanish Science and Investigation Ministry. In RUCSS we aim at testing the seamless approach (Palmer et al., 2008) for climate modelling with the EC-Earth Earth System Model (ESM) to constrain the sources of uncertainty in both short-term climate prediction and climate-change projections by increasing the understanding of the climate system. In this project, detailed analysis of climate simulations with different time horizons will be carried out using similar metrics to better understand the development of the systematic errors in EC-Earth with the hope of reducing the risk of overconfidence in both climate predictions and long-term projections. Among the processes that will be investigated are the water vapour feedback in the extratropics, the climate variability at the surface of the tropical Pacific and the extraordinary summer warming and drying observed and foreseen over Southern Europe. The basic premise of the seamless approach is that there are fundamental physical processes in common to both seasonal and decadal forecast, as well as climate-change time scales. If essentially the same ESM using a similar ensemble system can be validated both probabilistically and from a physical point of view on time scales where validation data exist, that is, on daily, seasonal and decadal time scales, then users will have the possibility of a) modifying the probabilistic estimates of regional climate-change, b) gaining insight into the ESM limitations to reduce the systematic error and c) improve the realism of the unavoidable physical parameterizations used in dynamical models. The seamless approach makes no distinctions about the relevance of particular processes in an ESM as a function of the time scale of the target problem, the correct representation of all physical processes affecting all types of climate simulations. This initiative is both innovative and ambitious. A limited number of seasonal forecasting research and operational groups already exists in Europe (EUROSIP, an operational system to which the UK Met Office, Météo-France and the European Centre for Medium-Range Weather Forecasts contribute; Stockdale et al., 2009), Canada (with the multi-model operational system run by Environment Canada; Derome et al., 2001), USA (the National Centers of Environmental Prediction, NCEP, with their Climate Forecast System; Saha et al., 2006), Australia (the Australian Bureau of Meteorology runs the POAMA system; Wang et al., 2008), and Korea (the Asia-Pacific Climate Community, APCC gathers quasioperational multi-model seasonal forecast information; Wang et al., 2008). At the same time, a great interest in climate modelling has risen in Europe and some skill in seasonal predictions of summer temperature has been found over Southern Europe, as well as for other regions where there are European interests (e.g. South America and areas of Africa).
top

Engineering (5)

HIFLY

Project Title: HIFLY
Project Leader: Dr Fehmi Cirak, The University of Cambridge, Dept of Engineering, Cambridge, UK
Resource Awarded: 2 100 000 core hours on EPCC – HeCToR XE6 and PSNC – HP
Details

Collaborators:
Dr Jakub Sistek – Institute of Mathematics of the AS CR, Constructive Methods of Mathmatical Analysis, Prague, Czech Republic
Abstract:
The aim of this project is the direct numerical simulation of flows occurring in insect and bio-inspired micro-air-vehicle flight. In such flows a very finely resolved computational mesh is crucial in order to capture the smallest features present in the flow. As the method of choice for discretization we use the finite element method (FEM). Since either fully implicit or semi-implicit time marching schemes are used, the method leads to a sequence of very large systems of equations, which are exceedingly difficult to solve with the available algorithms. Existing techniques either cannot tackle systems of sufficient size or need more time than we can afford for each step in unsteady computations. Thus, as an enabling building block of this project, we will develop parallel solvers for systems of linear algebraic equations based on multilevel domain decomposition techniques. To this end, we will optimize the publicly available implementation of multilevel BDDC method (BDDCML package) to perform well on thousands of processors and to extend its applicability to non-symmetric and advection dominated problems as they occur in computational fluid dynamics. At last, the solver will be applied to our flow computations and optimized with respect to experience gained on them.

HRPIPE

Project Title: HRPIPE
Project Leader: Prof.Dr. B.J. Boersma, Delft University of Technology, The Netherlands
Resource Awarded: 1 800 000 core hours on PDC – Lindgren
Details

Collaborators:
Dr. Geert Brethauer – KTH, Sweden
Abstract:
From an engineering point of view turbulent pipe flow is extremely important, because of its wide range of applications. In the past many fundamental studies on wall bounded flow have been performed in plane channel flow, see for instance (Kim et al. 1987), (Moser et al. 1999) and (Del Alamo et al. 2004). Although there is a clear similarity between both flow in the near wall region there are also considerable differences, especially in the core region of the flow. In the case of turbulent pipe flow only a limited number of numerical studies have been carried out, see for instance (Eggels et al. 1993), (Loulou et al. 1997) and (Wu & Moin 2008), while there is an enormous amount of experimental data for a large range of Reynolds numbers available, see for instance (McKeon et al. 2004), (Den Toonder & Niewstadt 1997), and (Morrison et al. 2004). There are still many unsolved questions, for instance it is argued by (Mochizuki & Nieuwstadt 1996) that the peak of the axial rms decreases with Reynolds number, while in the paper by (Morrison et al. 2004) it is argued that the peak should increase with Reynolds number. The goal of the present research is to develop a highly accurate numerical model that is able to simulate, by means of DNS, flow with Reynolds numbers in the range of the experiments carried out by (McKeon et al. 2004) and (Morrison et al. 2004).

MIXTUDI

Project Title: MIXTUDI
Project Leader: Alfredo Soldati, University of Udine, Italy
Resource Awarded: 3 750 000 core hours on CINECA – CNE-SP7 and FZJ – JuRoPA
Details

Collaborators:
Prof Sanjoy Banerjee – City College of New York, The Energy Institute, New York, USA
Abstract:
Mixing of two fluid phases is a physical process where one fluid is introduced, dispersed and finally mixed at molecular level into another fluid. This process is of extreme importance in many environmental and industrial applications such as blending of temperature and salinity fields in large-scale ocean currents or mixing of miscible polymers in stirred reactors. Its dynamics is deeply related to the flow field properties and the ability of turbulence to enhance microscale fluid mixing is vital to maximize mixing efficiencies. Turbulent mixing involves a wide range of spatial and temporal scales which must be taken into account to capture the underlying physics of the phenomena. Furthermore mass transport is deeply coupled with turbulent convection, making theoretical modeling non trivial. For these reasons experimental, theoretical and computational analyses of turbulent mixing still represent an open field of research where huge efforts are necessary to improve knowledge. Phase Field Models (PFM) offer a systematic physical approach for the investigation of complex multiphase systems such as near-critical interfacial phenomena, phase separation and mixing; some examples of these applications can be founded in Molin and Mauri [1]. This approach is based on the Cahn-Hilliard equation, where the interfaces between the two fluids are replaced by thin transition regions (Diffuse Interfaces) which require very high resolution to be numerically represented. The flow field behavior is described by the Navier-Stokes equation coupled with the Cahn-Hilliard equation (CHNS) yielding to the so-called Model H [2]. In this project we propose to study systematically the mixing of a fluid in a fully developed turbulent channel flow. Particularly the project will focus on the connection between mixing processes and turbulence structures with specific focus on the coupling between turbulence and mass transport properties. This task will be achieved by means of high resolution pseudo-spectral DNS ([3] – [4]) of the CHNS system ([5] – [6]) in turbulent channel flow. We will consider different values of the Reynolds number (Re), which measures turbulence intensity, of the Weber number (We) which measures the relative importance of fluid surface tension effects with respect to the inertial forces and of the Peclet number (Pe) which measures the relative importance of the fluid diffusivity properties. This study is expected to advance the state of the art in turbulent mixing simulations introducing an accurate and robust framework specifically tailored for this kind of analysis.

RBflow

Project Title: RBflow
Project Leader: Prof.Dr. Detlef Lohse, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Resource Awarded: 6 000 000 core hours on RZG – RZG P6 and SURFSARA – Huygens P9
Details

Collaborators:
Prof. Maurizio Quadrio – Politecnico di Milano, Dipartimento di Ingegneria Aerospaziale, Milano, Italy
MSc. Richard Stevens – University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Roberto Verzicco – University of Rome Tor Vergata, Italy
Abstract:
Rayleigh-Bénard (RB) convection – the buoyancy driven flow of a fluid heated from below and cooled from above – is a classical problem in fluid dynamics. From an applied viewpoint, thermally driven flows are of utmost importance. Examples are thermal convection in the atmosphere, ocean, and in process technology. The main control parameters are the Rayleigh number Ra (the dimensionless temperature difference) and the Prandtl number Pr (a fluid property). RB convection is studied in experiments and numerical simulations, since both methods are complementary. In experimental measurements of the heat transport, which require a completely isolated system, the flow field cannot be determined. In simulations, where one has full access to the complete flow field, this is possible. However, due to the fine mesh that is necessary to accurately resolve the flow, the Ra number and time averaging that can be obtained in simulations are more limited than in experiments. The agreement between experiments and properly resolved simulations is excellent and this has already allowed us to clarify important experimental issues. This holds up to Ra=1011. However, what happens beyond that Ra number is subject of a 15 years long controversy. The experiments by Chavanne et al. show that for Ra>1011 the heat transfer scales as Nu〜~Ra0.38, while Niemela et al. find a scaling of Nu〜~Ra0.31. The origin of this discrepancy is still unknown. Recently, Ahlers et al. have obtained these two scaling branches in one experiment, depending on experimental details. The group of Roche obtained similar results. However, it remains elusive why one or the other state is realized, and it is speculated that the existence of multiple turbulent states may be the origin of the observed behavior. As the difference in heat transport between the two turbulent states is a factor of 3 in the Ra number range that is relevant for various geophysical, astrophysical, and process-technological situations a better prediction of the heat transfer is necessary. The experiments of Ahlers et al. and Roche et al. show that differences in the physical properties of the sidewall and/or the temperature boundary condition at the sidewall are probably responsible for the different turbulent states that are observed. However, in high Ra number experiments there is no possibility to visualize the flow in order to verify this hypothesis and determining the influence of the physical properties of the sidewall is very hard in experiments. The goal of this project is to study the influence of the temperature boundary conditions at the sidewall on the heat transport. As we have information on the entire flow field we will be able to see whether changes in the heat transport are reflected in the flow dynamics. We emphasize that the Ra number regime in which the coexistence of different turbulent states is observed can only be achieved on state of the art computers and the simulations proposed here will break the current world record for high Ra number simulations.

WESF

Project Title: WEt & Strectched Flames
Project Leader: Prof. Yves D’Angelo, Université de Rouen – CNRS – INSA Rouen, CORIA, Rouen, France
Resource Awarded: 1 200 000 core hours on CSC – Louhi XT and RZG – Genius
Details

Collaborators:
Prof.Dr.-Ing. Eric Albin – Technische Universität Berlin, Berlin, Germany
Prof. Christian Oliver Paschereit – Technische Universität Berlin, Berlin, Germany
Abstract:
Humidified Gas Turbines promise a significant increase in efficiency compared to the conventional, dry gas turbine cycle. In single cycle applications, efficiencies up to 60% are possible with humidified turbines. Additionally, the steam effectively inhibits the formation of NOx emissions and also allows for operating the gas turbine on biofuels. In order to achieve the high efficiencies, large amounts of steam have to be injected into the combsution chamber. This poses a challenge to the combustor design, since the steam significantly affects the flame stability, and so far, humid gas turbines have usually been investigated with moderate degrees of humidity not higher than 15% to 20%. In the current study, the combustion process is investigated at ultra-wet conditions with steam levels up to 50%.
In this context, Direct Numerical Simulations of two dimensional premixed flames are computed at wet conditions with detailed chemistry. Fundamental combustion properties like turbulent flame speeds, flame stretch and emissions are extracted from these simulations for various temperatures, fuel compositions, degrees of humidity and overall equivalence ratios. The results are compared to new experimental data for prismatic flames. The measurements are conducted on a new rectangular slot burner, using advanced laser diagnostics to gain insight into the flow field, the species concentrations and the temperature distribution. Additional simulations of 2D and 3D stretched flames are also performed with a simplified chemistry model in order to assess the influence of local flame stretch and flame curvature on the measurement results.
This project is conducted in collaboration with the European Advanced Grant GREENEST at the Chair of Experimental Fluid Dynamics at the Technische Universität Berlin, in which a practicle combustor prototype for operation at ultra-wet conditions will be developed during the next 5 years. In the current study WESF, a fundamental understanding of the combustion process at high steam contents will be gained, which is of direct interest for future research on wet combustion. Additionaly, the results will provide the required knowledge for further CFD simulations of practical gas turbine combustors.
top

Materials Science (11)

CatDesign

Project Title: CatDesign
Project Leader: Dr Ganduglia-Pirovano Maria, Centro Superior de Investigaciones Científicas(CSIC), Spain
Resource Awarded: 1 292 181 core hours on LRZ – SuperMig and PSNC – SGI UV1001
Details

Abstract:
Hydrogen, used as fuel in electrochemical cells, could satisfy many of our energy needs in a clean and sustainable way. To be a suitable fuel in the currently used polymeric cells it has to be virtually free of CO, and to this aim two chemical processes play a key role: the water-gas shift (WGS) reaction (H2O + CO ↔ H2 + CO2) and the preferential CO oxidation. Noble-metal supported catalysts such as (Pt, Cu)/ceria-titania systems have significant activity for such processes, however, the high cost of these materials limits their application. Recent experimental insight has revealed that nickel-based catalysts can also be stable, inexpensive, and highly active for WGS and CO methanation reactions [Zhou, 2010; Senanayake, 2011]. In particular, Ni/CeO2 catalysts have shown an excellent potential for WGS reaction at small coverages of Ni, whilst catalyzing the production of methane from CO and H2 at medium and large coverages of Ni. These findings demonstrate the critical role played by metal-oxide interactions on perturbing the electronic properties of Ni and suppressing its activity for methanation at low coverages, which points out the importance of considering both the metal and the oxide phase when tailoring the catalyst in order to improve catalytic performance. The aim of our project is to elucidate the structure and functioning of Ni/CeO2 catalysts and to develop a molecular-level model for the WGS reaction on such promising systems, which are currently under investigation by our experimental collaborators at both the Institute of Catalysis and Petrochemistry-CSIC in Madrid and the Brookhaven National Laboratory in the US. To this end we propose to create computational models for these catalysts and to apply density functional theory (DFT) based approaches, as implemented in the VASP code, to investigate atomic structures as well as electronic and chemical properties. The binding of CO, H, and OH and the barriers for water dissociation and formation of key intermediates precursors of CO2 production will be calculated. The full mechanistic picture of the reaction will be investigated for the most promising model catalysts. By systematically examining a range of Nix/CeO2 systems with different Ni particle size (x<4), presence of oxygen vacancies, and adsorption sites we expect to establish in the clearest detail how factors such as cluster size, electronic structure, and metal/substrate interaction affect the catalysts performance for H2 production. This project is focus directly on obtaining such understanding and in providing answers from first principles to the question: what is likely to make Ni/CeO2 systems suitable candidates for the next generation catalysts for WGS and how their performance could be improved?, thus contributing to the rational design of catalysts for hydrogen production.

DIAVIB

Project Title: DIAVIB
Project Leader: Prof. Adam Gali, Budapest University of Technology and Economics, Budapest, Hungary
Resource Awarded: 1 080 000 core hours on CINECA – CNE-SP6 and SURFSARA – Huygens P7
Details

Collaborators:
Dr. Elena Cannuccia – Universidad del País Vasco, Donostia-San Sebastian, Spain
Tamás Demjén – Academy of Sciences, Budapest, Hungary
Dr. Andrea Marini – University of Rome Tor Vergata, Italy
Dr. Maurizia Palummo – University of Rome Tor Vergata, Italy
Márton Vörös – Budapest University of Technology and Economics, Budapest, Hungary
Abstract:
Low dimensional semiconductor systems exhibit several favourable properties that are not present in their bulk counterpart, eg. the optical gap of nanocrystals can be tuned with the charateristic size, however in many cases the size and composition is not exactly known. Recent developments allow the size and shape selected preparation of small diamond nanocrystals (diamondoids) [1]. These small diamondlike carbon cages can be considered as building blocks of larger nanodiamonds that have been extensively applied in biological studies where the optical properties are of crucial importance. Theoretical studies can significantly contribute to the underlying mechanisms of the excitation process. The structure of small diamondoids is known exactly and their absorption spectra have been measured in gas phase close to room temperature [2]. Recently, we have calculated the absorption spectrum by time-dependent density functional theory (TDDFT) with applying a hybrid density functional in the kernel where the hybrid functional was semi-empirical in nature [3]. Later, we also applied a parameter-free quasiparticle correction (GW-method) and the static electron-hole correlation was taken into account by Bethe-Salpeter equation (BSE-method). All these calculations were carried out with frozen coordinates. These results may not even be valid at 0 K due to intrinsic zero-point vibration of atoms. It is well known for example, that in bulk diamond, a zero point renormalization of 0.4 eV occurs for the band gap, thus a direct comparison with the experiment is not straightforward [4]. We found that optical gaps tended to be consequently larger both in TD-DFT and even more in GW+BSE calculations than the measured ones. Since C-C and C-H bonds have strong vibration modes a strong electron-phonon coupling [5-6] may shift the onset of absorption significantly that may explain the discrepancy between the experimental and simulation data. By taking into account the electron-phonon interaction, we will be able to calculate the temperature dependent absorption spectrum close to the optical gap of small nanodiamonds by a parameter-free BSE method [7]. These calculations would reveal how the absorption peaks can shift and broaden as function of the temperature where the spectra were recorded. In that way, direct comparison between the experiment and full ab-initio theory will be possible and it can be considered as a ‘horseshoe’ test of this methodology, which up to now has been applied mainly to periodic systems. The calculation of temperature dependent absorption spectra with the ab-initio BSE method is extremely demanding. Harnessing the computational capacity of supercomputers allows the usage of the very advanced many-body perturbation theory to real problems with the capability to compare results with experimental findings and previous theoretical results.

DiSMuN

Project Title: Diffusion and spectroscopical properties of multicomponent nitrides
Project Leader: Prof. Igor Abrikosov, Linköping University, Department of Physics, Chemistry and Biology(IFM), Linköping, Sweden
Resource Awarded: 3 750 000 core hours on PDC – Lindgren and SURFSARA – Huygens P8
Details

Collaborators:
Dr. Björn Alling – Linköping University, Department of Physics, Chemistry and Biology (IFM), Linköping, Sweden
Prof. Claudia Ambrosch-Draxl – University of Leoben, Atomistic Modelling and Design of Materials, Leoben, Austria
Dr. Weine Olovsson – Linköping University, Department of Physics, Chemistry and Biology (IFM), Linköping, Sweden
Abstract:
Hard protective coatings applied on the cutting tools are crucial for all types of metal cutting and drilling in contemporary industry. The better the coating, the more efficient is the industrial production process. Multicomponent nitrides, such as TiAlN and CrAlN, are the backbone materials used for these coatings and the fundamental understanding of their properties are crucial for a further materials development. In this project we aim at investigating the diffusion processes and spectroscopic properties of multicomponent nitrides using the most fundamental quantum mechanical equations of physics. Since the mixed systems form disordered solid solutions when grown as thin films the stochastic distribution of e. g. Ti and Al atoms in the crystals must be carefully considered which adds a huge complexity and computational challenge to our project. To investigate atomic diffusion in these materials we will use electronic structure codes to calculate the energy barriers needed to be overcome by diffusing species, both inside bulk materials and on top of crystal surfaces. The different local chemical environments in the solid solutions will be studied using a large number of parallel calculations of different paths inside, and on top of, alloy supercells. In order to accurately interpret experimental spectroscopical measurements of nanostructured multicomponent nitrides we will apply state-of-the-art modeling scheme for these properties: the Bethe- Salpeter equation. In this methodology the intricate quantum mechanics of the spectroscopical process is modelled far more accurate then with standard density fucntional theory methods. Using a clever parallel procedure these difficult equations will be solved to give a solid ground in the understanding of the nanostructure of multicomponent nitrides in collaboration with experimental work.

EC4aPDEs-2

Project Title: Extreme Computing for Advanced Methods of Solving PDEs
Project Leader: Dr Lee Margetts, University of Manchester, Manchester, UK
Resource Awarded: 2 500 000 core hours on BSC – MareNostrum, CSC – Louhi XT, HLRS – Laki and IDRIS – BABEL
Details

Collaborators:
Prof. Stephane Bordas – University of Cardiff, Cardiff, UK
Prof. Marc Duflot – Cenaero, CFD and mutiphysics group, Gosselies, Belgium
Prof Oubay Hassan – University of Swansea, Swansea, UK
Dr Cathy Hollis – University of Manchester, Manchester, UK
Prof. Guillaume Houzeaux – Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain
Dr Paul Mummery – University of Manchester, Manchester, UK
Prof. Timon Rabczuk – University of Weimar, Weimar, Germany
Abstract:
Today’s global challenges in the energy, aerospace and biotechnology sectors require extreme engineering approaches that take into account the complex interplay of different physical processes that operate at multiple length and time scales. The effective collaboration of domain scientists who have access to a European infrastructure for supercomputing applications is essential to accelerate research in these areas, providing the simulation tools that will enable European industry to be highly innovative and internationally competitive. The project has four broad aims: (I) To continue work started in the EC4aPDEs DECI-6 project, using the PRACE Tier 1 architecture. The DEISA project ran from Oct 2010 to March 2011. (II) To foster a network of European scientists who are researching advanced methods for solving partial differential equations. The methods include, but are not limited to, the finite element method, the extended finite element method, meshfree methods and molecular dynamics. (III) To implement and deploy a “Virtual Laboratory” for materials characterisation that will be used to evaluate the response of exemplar high performance engineering materials to a range of insilico tests. The materials will be scanned at a high resolution using a state of the art X-ray tomography scanning facility at the University of Manchester. The resulting 3D images will be converted into micro-structurally faithful computer models. Finally, stress, thermal, fluid flow, vibration and fracture mechanics tests will be carried out. (IV) To carry out benchmarking and performance optimisation in preparation for a future proposal that will request access to the PRACE Tier 0 architecture. This work is particularly exciting because extremes of temperature, pressure and vibration, which are experienced by materials in the energy, space and aerospace sectors, are difficult and costly to recreate in the laboratory. In contrast, with the necessary computing infrastructure, they are easier to simulate. After the PRACE funded project, the newly established EC4aPDEs network will continue to recruit new members, with the aim of developing and sharing a common application software infrastructure that will make use of future European extreme computing resources.

HYDROGEN-ILs

Project Title: HYDROGEN-ILs
Project Leader: Prof. Michael Bühl, University of St Andrews, St Andrews, UK
Resource Awarded: 1 314 000 core hours on EPCC – HeCToR X and PDC – LindgrenE7
Details

Collaborators:
Dr Nicolas Sieffert – Université Joseph Fourier, Department of Chemistry, St Martin D’Heres, France
Abstract:
This project aims at a microscopic-level understanding of a Ru-catalyzed reaction affording the production of H2 from formic acid in ionic liquids, which is of prime interest in the framework of sustainable energy supply. High-level molecular dynamics simulations will allow us to explain the key solvation effects occurring in this system and will provide detailed mechanistic information. The results will be of fundamental interest for the understanding of chemical reactivity in ionic solvents and will also be beneficial to experimentalists for optimizing catalytic systems.

NANOBIO-2

Project Title: NANOBIO-2
Project Leader: Niall English, University College Dublin, School of Chemical and Bioprocess Engineering, Dublin, Ireland
Resource Awarded: 2 000 000 core hours on CINES – JADE-Nehalem and HLRS – Laki
Details

Collaborators:
Gilles Civario – ICHEC, Dublin, Ireland
Prof. John Tse – University of Saskatchewan, Canada

NUWCLAY

Project Title: Safe and sustainable management of nuclear waste
Project Leader: Dr Andrey Kalinichev, Ecole des Mines de Nantes, SUBATECH UMR6457, Nantes, France
Resource Awarded: 1 500 000 core hours on CINECA – PLX
Details

Collaborators:
(Dr. Narasimhan Loganathan – Ecole des Mines de Nantes, SUBATECH UMR6457, Nantes, France
Brice Firmin Ngouana Wakou – Ecole des Mines de Nantes, SUBATECH UMR6457, Nantes, France
Abstract:
Safe and sustainable management of nuclear waste poses major scientific challenges to make the environmental footprint of nuclear energy as small as possible for a long period of time (up to 1 million years). This requires a detailed understanding of radionuclides interaction with natural and engineered barriers (consisting mostly of clay and cementitious materials used to protect the environment) and their behavior in the geosphere over time- and distance- scales spanning many orders of magnitude from the molecular-level chemical reactivity to the larger scale geochemical mobility of radionuclides in macroscopically heterogeneous systems. Computational molecular modeling of materials for nuclear waste disposal applications is the primary objective of our research in the framework of the industrial chair `Storage and Management of Nuclear Waste` recently created at the Ecole des Mines de Nantes with support from ANDRA, AREVA, and EDF. Clay rock formations of nuclear waste repositories contain significant amounts (up to ~1 mass %) of organic matter. The effects of natural and anthropogenic organic molecules on the mobility and toxicity of various elements in the context of nuclear waste storage are not yet well understood and are the priority topics of the present project. We address these problems on the fundamental molecular level by performing detailed quantitative studies of the energetic, structural, and dynamic aspects of different interaction mechanisms between radionuclides, organic matter, and clay particles using computational molecular modeling techniques. Free energies of adsorption and other thermodynamic and structural parameters obtained through the potentials of mean force calculations will then be utilized to significantly improve the predictive capabilities of the thermodynamic and geochemical models used for the performance assessment of nuclear waste repositories. From a more general perspective, similar clay-like hydrous inorganic interfaces are ubiquitous in many natural and technological environments. Thus, our research will also contribute to the development of viable carbon sequestration technologies, new membranes for water purification, and other research and engineering fields where detailed molecular scale understanding of materials and processes represents one of the most important cross-cutting fundamental problems of materials and environmental chemistry concerned with more efficient production and use of clean energy and clean water.

PETAHUB

Project Title: The Phase diagram of the Hubbard model by quantum Monte Carlo and Petaflop supercomputers
Project Leader: Sandro Sorella, SISSA/ISAS, Trieste, Italy
Resource Awarded: 1 800 000 core hours on NCSA – EA ECNIS and PDC – Lindgren
Details

Collaborators:
Dr Federico Becca – SISSA/ISAS, Trieste, Italy
Leonardo Guidoni – Università degli Studi de L’Aquila, Department of Chimistry, Chemical Engineering and Materials, Aquila, Italy
Mr Wenjun Hu – SISSA/ISAS, Trieste, Italy
Abstract:
In this project we propose to study the phase diagram of the Hubbard model in two dimensional lattices by using an highly developed quantum Monte Carlo method. Recently there is a renewed interest in this model, as ultracold atoms trapped in optical lattices, could be an ideal experimental realization of this simple but still unsolved model so important for condensed matter physics. The main purpose is to use the large computer power available by the PRACE call to obtain reliable simulations of the model on lattice sizes containing several hundred electrons. By using the established auxiliary field techniques, developed also by the project leader in the `90s, it was possible to obtain very accurate ground state properties of the Hubbard model for small lattice or at half filling, and the extension of the simulations to large clusters and finite doping was limited by the well known sign problem. At small and finite doping, in the most important region, the sign problem is particularly severe and, in such conditions, the reduction of the statistical errors is particularly difficult with conventional computers. The main idea here is that the reduction of the statistical errors, by direct sampling of the sign, is nowadays possible with massively parallel supercomputers, because this error is inversely proportional to the square root of the number of processors, and a machine like JuGene containing up to 300000 cores should allow to obtain exact ground state properties of the Hubbard model for a sufficiently large number of electrons and low enough temperatures. In our opinion this is not a prohibitive task if we consider that already in 1997 with a Megaflop machine, it was possible to obtain rather accurate ground state energy estimates in the t-t` model at U/t=4 and few hundred electrons. The main point is that, within the auxiliary field technique, the origin of the sign problem is not related to the fermion statistics and is much less severe than standard fermion Monte Carlo methods, affected by a much more severe instability of the signal/noise ratio as the temperature is lowered. This project should allow us to give robust answers to fundamental issues that have triggered all the scientific community for about half a century, and several questions could be eventually solved, such as, the stability of the Ferromagnetic phase at large U/t values, the role of strong correlation for High temperature superconductivity to the still unsolved question of the existence of stripes and/or non homogeneous phases in the verge of a Mott insulating phase.

PHOTMAT

Project Title: PHOTMAT
Project Leader: Dr. Manthos G. Papadopoulos, National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Athens, Greece
Resource Awarded: 5 062 500 core hours on CINES – JADE-Harpertown and PSNC – SGI UV1002
Details

Collaborators:
Dr. Aggelos Avramopoulos – National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Athens, Greece
Dr. Didier Bégué – Université de Pau et des Pays de l’Adour, Pau, France
Prof. Vladimir Kellö – Comenius University, Bratislava, Slovak Republic
Dr. Georgios Leonis – National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Athens, Greece
Dr. Jiabo Li – Accelrys Inc., San Diego, CA, USA
Dr. Josep Maria Luis – University of Girona, Department of Chemistry, Girona, Spain
Prof. Dr. Kristine Pierloot – Katholieke Universiteit Leuven, Belgium
Dr. Heribert Reis – National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Athens, Greece
Haralambos Tzoupis – National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Athens, Greece
Abstract:
The proposed project involves the design of fullerene and M- dithiolene-based materials, where M=Ni, Pd etc, for photonic applications. The key parameters for such a design are the nonlinear optical (NLO) properties. The increasing demand for faster data processing, storage and distribution can only be fulfilled by ongoing miniaturisation of the basic electronic devices. The traditional silicon-based technologies used nowadays are approaching intrinsic limits in this respect, and new approaches are needed. Photonic technology, where light is used as information carrier instead of electrons, is considered to offer the answer. An important step towards this goal is the development of new photonic materials with large NLO properties by employing nano-derivatives. Thus, the basic concept on which the proposed project is based, involves first, the design of novel derivatives for photonic applications, employing fullerenes and metal-dithiolenes as the main building blocks and second, the solution of several methodological problems, which are of current interest in this area and which are instrumental for the computation of reliable L&NLO properties of the proposed compounds. Specifically, we note that the first goal is to develop a protocol (that is a hierarchical set of methods), which will allow to compute in a reliable way the electronic structure and the L&NLO properties of the photonic derivatives which will be selected or designed. The first problem to be solved is the reasonable representation of the electronic structure of the derivatives which will selected or designed and, second, using this structure to compute their L&NLO properties. In addition the satisfactory understanding of the electronic structure will allow to interpret the computed properties. The second goal involves the design of: (i) A series of oligomers involving n units of C60 or M@C60, where M=metal, e.g. Li@C60, in various configurations, for example Li@C60 – Li@C60 – Li@C60. We have recently found that Li@C60 has impressive vibrational contributions to the L&NLO properties, thus we expect that the proposed oligomer, based on Li@C60 will have very interesting properties. (ii) A series of oligomers involving several units of Ni(SCH)4 (NiBDT), monomers composed of NiBDT-TTF (TTF: tetrathia-fulvalene), etc. (iii) Dyads and/or triads, involving fullerenes and metal-dithiolenes. These are just a few of the ideas we propose to explore and pilot studies have shown that they have a great potential as photonic materials. The scientific innovation potential of the proposed project is connected with the development of the proposed protocol, which will involve the appropriate methods for the satisfactory treatment of the electronic structure and the L&NLO properties of the photonic derivatives which will be selected or designed. The technical innovation potential is connected with the materials we propose to design and which are expected to have exceptionally large nonlinearities. Such materials are greatly needed by the photonic industry.

SCW

Project Title: SCW
Project Leader: Marco Masia, University of Sassari, Department of Chemistry, Italy
Resource Awarded: 1 410 000 core hours on LRZ – SuperMig
Details

Collaborators:
Dr Malay Rana – University of Michigan, Mechanical Engineering, Ann Arbor, USA
Abstract:
This project aims at studying the behaviour of supercritical water (SCW) as a function of the system density, by means of ab initio Molecular Dynamics simulations. Experiments have shown that the rotational relaxation of SCW does not follow a monotonic trend but rather show a turnover for intermediate densities. This finding has not been confirmed by classical Molecular Dynamics simulations, probably because the existing force fields (both polarizable and non-polarizable) are not accurate enough to properly model SCW. The reduced extent of force field validity is one of the main problems addressed in this project. The (short) dynamics obtained with ab initio Molecular Dynamics, in fact, will be used to parameterize a new polarizable force field for SCW, allowing to explore, with high accuracy, larger time and space scales with classical Molecular Dynamics. The proposers have just developed a new method to apply the force matching algorithm to polarizable models. The method yields electron cloud fluctuations in good agreement with ab initio ones, what is not possible with present empirical potentials. Eventually, we expect two major outcomes of our study: the first concerns the study of short time dynamics with first principles Molecular Dynamics (what, for itself, constitute an important novelty in the field) and the second concerns the possibility of producing a new force field targeting the properties of SCW.

SIMONA

Project Title: SIMONA
Project Leader: Prof. Dr. Grzegorz Kamieniarz, University Poznan, Department of Physics, Poznan, Poland
Resource Awarded: 600 000 core hours on IDRIS – BABEL, PSNC – SGI UV1003 and SURFSARA – Huygens P10
Details

Collaborators:

Abstract:
Molecular-based metallic clusters and chains behave like individual quantum nanomagnets, displaying quantum phenomena on macroscopic scale. In view of potential applications of such materials in magnetic storage devices or in envisaged quantum computer processor as well as in the low-temperature refrigerants, the accurate simulation of these complex objects becomes the key issue. The magneto-structural correlations, the role and mechanism of magnetic anisotropy and intrinsic quantum effects following from the geometrical frustration induced by the topological arrangement of spins or particular interactions count among the new challenges for computer simulations. The simulations planned in the SINA project address the quantum phenomenological models which are the most reliable theoretical representatives of the physical molecular-based nanomagnets investigated recently and their reliability from the fundamental microscopic point of view assessed by the well established first-principle electronic structure calculations. Exploiting a number of deterministic verified techniques (exact diagonalization, quantum transfer matrix , density-matrix renormalization group), the model calculations will be performed without any uncontrolled approximations and will be numerically accurate. The chromium-based rings which are outstanding materials for quantum information processing and for low-temperature cooling will be the principal objects of investigation. The real challenges appear for the molecules containing more than eight CrIII S=3/2 ions and/or are doped by magnetic NiII or CuII ions, nevertheless the exact energy spectra, S-mixing, the total spin oscillations essential for quantum coherence and frustration phenomena important for magnetic refrigeration will be accomplished. Interesting behaviour characteristic of single-chain magnets for canted MnIII antiferromagnetic chains with magneto-structural correlations and for rare-earth compounds with interaction-driven frustration will be addressed in the framework of quantum approach. Nevertheless, to be technological appealing, they must be organized on solid surfaces or wired to metal electrodes in a controlled way. This represents the nowadays challenge and a key achievement is represented by the functionalization of the magnetic “core” of the SMM with appropriate chemical groups with the aim to preserve both the uncommon magnetic properties and to make it suitable for being attached to a surface. We individuated as optimal SMM candidate in addition of the SMM mentioned above also the Fe4(C11H19O2)6[(OCH2)3C(CH2)5SCOCH3]2 grafted on Au(111). The program suited for handling such big systems is CP2K.

top

Plasma & Particle Physics (3)

EUTERPE-4

Project Title: Global electromagnetic gyrokinetic simulation in 3D equilibria
Project Leader: Dr. Ralf Kleiber, Max Planck Institute of Plasma Physics(IPP), Greifswald, Germany
Resource Awarded: 1 500 000 core hours on FZJ – JuRoPA
Details

Collaborators:
Dr. E. Sánchez Gonzáles – CIEMAT para Fusión, Spain
Abstract:
It is necessary to accompany stellarator experiments, as e.g. Wendelstein 7-X, by simulations of plasma microinstabilities and related turbulence. Especially important for the comparison of experiment and theory are full torus simulations for stellarator configurations since they need no approximations regarding the geometry. Gyrokinetics as a first principle based theory is well suited to describe the relevant physics. An established and flexible method for solving the gyrokinetic system of equations is the simulation via the particle-in-cell (PIC) Monte-Carlo method. For this purpose the EUTERPE code has been developed which solves the gyrokinetic equation globally in arbitrary stellarator geometry including kinetic electrons, and electromagnetic perturbations. The full kinetic treatment of the electrons allows the investigation of trapped electron effects (e.g. TEM) and the inclusion of electromagnetic effects establishes the connection to magnetohydrodynamics (MHD). By using a third species the destabilisation of MHD modes (e.g. TAE, HAE) can also be studied. These developments will make EUTERPE the first code worldwide that is able to simulate global gyrokinetic electromagnetic instabilities in three dimensions.

HIGHQ2FF

Project Title: HIGHQ2FF
Project Leader: Dr. Giannis Koutsou, The Cyprus Institute, Nicosia, Cyprus
Resource Awarded: 5 000 000 core hours on PDC – Lindgren
Details

Collaborators:
Prof. Constantia Alexandrou – University of Cyprus, Department of Physics, Nicosia, Cyprus
Kyriakos Hadjiyiannakou – University of Cyprus, Department of Physics, Nicosia, Cyprus
Dr. Stefan Krieg – Forschungszentrum Jülich, Germany
Dr. Theodoros Leontiou – Frederic Institute of Technology, General Department, Nicosia, Cyprus
Prof. Dr. Dr. Thomas Lippert – Forschungszentrum Jülich, Germany
Dr. Marcus Petschlies – The Cyprus Institute, Nicosia, Cyprus
Abstract:
The nucleon, the hadronic state which makes up most of the observable mass in the universe, has been extensively studied both theoretically as well as experimentally. The internal structure of hadrons is studied by measuring form factors and generalized parton distributions, which can be associated to the charge and magnetization distributions as well as the momentum distribution of quarks and gluons. Recently there have been many studies of these fundamental quantities using state-of-the-art simulations of Quantum Chromodynamics (QCD), the theory of the strong interactions. However, these calculations have been almost entirely restricted to momentum transfers (Q2) up to about 2 GeV2. This is due to the fact that one takes numerically the Fourier transform, which for large momenta becomes very noisy making calculations of the form factors at higher momentum transfers prohibitively expensive. In this project we propose applying a variational method which has been shown to improve the statistical accuracy of form factors at high Q2. We therefore propose to apply this method for extracting accurately nucleon form factors at Q2>2.5 GeV2 for which lattice data are currently scarce. Insight on the form factors in this region of momentum transfer will shed light on open issues such as whether the electric Sachs form factor GE crosses zero, and the question of whether the ratio of the electric to magnetic form factor is independent on Q2. The method shall be applied for a set of state-of-the-art lattice gauge configurations simulated with the Twisted Mass Fermion action at a pion mass of ~270 MeV and a lattice spacing of about 0.078 fm. The technique relies on the variational method which has been used to obtain excited states, but which has only recently been applied to form factor calculations. This variational method is used to define a Generalized Eigenvalue problem (GEV), which is solved to determine trial states with an optimal overlap to finite momentum nucleon states. These improved trial states subsequently allow for more reliable extractions of the form factors at higher momenta. Therefore this method can be quite generally applied to any hadron form factor calculation, irrespective of the hadronic states involved and the lattice formulation employed.

NR-NSNS-BHNS

Project Title: Accurate Gravitational Waves from Unequal Mass Compact Binaries and Their Tidal Signatures
Project Leader: Bernd Brügmann, Universität Jena, Germany
Resource Awarded: 3 000 000 core hours on CSC – Louhi XT
Details

Collaborators:
Dr. Sebastiano Bernuzzi – Universität Jena, Germany
Dr. David Hilditch – Universität Jena, Germany
Dr. Charalampos Markakis – Universität Jena, Germany
Marcus Thierfelder – Universität Jena, Germany
Abstract:
The goal of this project is to compute gravitational waves (GWs) from the inspiral and collision of binaries involving neutron stars in Einstein’s theory of General Relativity (GR). Recently it has become possible to simulate several inspiral orbits and the merger and post-merger phase of compact binaries using the methods of Numerical Relativity (NR) on high performance parallel computers. These simulations are of interest for the theoretical and technical challenges they represent but more importantly for their use in the larger context of GW detection. In support of the emerging field of GW astronomy, we intend to compute highly accurate waveforms to investigate specific aspects of the most relevant astrophysical sources. The scientific objective of this proposal is to characterize the GW emission from the quasi-circular inspiral and merger of two binary systems – mixed binary (black hole-neutron star) systems, – unequal-mass binary neutron stars.

top

Share: Share on LinkedInTweet about this on TwitterShare on FacebookShare on Google+Email this to someone