DECI 14th Call

Find below the results of DECI-14 (Distributed European Computing Initiative) call.

Projects from the following research areas:

Applied Mathematics (1) Astro Sciences (3) Bio Sciences (12) Earth Sciences (1)
Engineering (7) Materials Science (14) Plasma & Particle Physics (2)

Descriptions of projects follow.

Applied Mathematics (1)


Project Title: Massively Parallel Quadratic Programming Algorithms Employing Total-FETI
Project Leader: Dr. David Horak, Vysoka Skola Banska – Technical University of Ostrava, Centre of Excellence IT4Innovations, Ostrava, Czech Republic
Resource Awarded: 4,550,000 standard core hours

Vaclav Hapla, Vysoka Skola Banska – Technical University of Ostrava, Centre of Excellence IT4Innovations, Ostrava, Czech Republic
Jakub Kruzik, Vysoka Skola Banska – Technical University of Ostrava, Centre of Excellence IT4Innovations, Ostrava, Czech Republic
Radim Sojka, Vysoka Skola Banska – Technical University of Ostrava, Centre of Excellence IT4Innovations, Ostrava, Czech Republic
Jiri Tomcala, Vysoka Skola Banska – Technical University of Ostrava, Centre of Excellence IT4Innovations, Ostrava, Czech Republic
PERMON (Parallel, Efficient, Robust, Modular, Object-oriented, Numerical) [] is a newly emerging collection of software libraries developed at IT4Innovations, uniquely combining quadratic programming (QP) and Domain Decomposition Methods (DDMs). There are two core modules in PERMON: PermonQP and PermonFLLOP. They are built on top of PETSc, mainly its linear algebra part.

They extend PETSc with new specific functionality, large sparse QP problem solvers and FETI-type DDMs. The same coding style is used so that users familiar with PETSc can utilize them with minimal effort.

PermonQP provides a base for solution of quadratic programming (QP) problems. It includes data structures, transforms, algorithms, and supporting functions for QP. It can be used in many applications such as data fitting, support vector machines, operations research, and others. PermonQP is available for free under the FreeBSD open source license on GitHub.

PermonFLLOP (FETI Light Layer on Top of PETSc) is an extension of PermonQP that adds support for DDM of the FETI type. This combination can be used to solve very large contact problems of mechanics. PermonFLLOP is currently under preparation for publishing.

A lot of work has been done since the start of PERMON development in 2011 and the algorithms and methods have been tuned and optimized. Ingredients ensuring high numerical and parallel scalability have been implemented, so that we can solve QPs with billions of unknowns. The main goal of this project is to test PERMON on various architectures and push its limits. Associated objectives are following:
a. For FE matrices and vectors assembling, we would like to optimize parallel meshing and assembling tools to generate large-scale model benchmarks for scalability testing with sizes up to billions of unknowns.
b. Coarse problem (CP) is the main bottleneck in FETI methods. Both assembling and solving of CP gets very complicated for tens or hundreds of thousands of subdomains. Several CP solving techniques will be evaluated using suitable parallel direct solvers as well as iterative methods. In particular, we would like to use communication hiding and avoiding techniques in combination with suitable deflation, so called Pipelined Deflated Conjugate Gradient method (PipeDCG).
c. Testing multiple subdomains per process and finding their optimal number, taking into account increased CP complexity.
d. FETI-1 and TFETI methods become numerically scalable after introducing the projector to the natural coarse space. Application of this projector includes CP solution. We are going to implement modification of the TFETI method eliminating projector application by means of the Moore-Penrose pseudoinverse of the stiffness matrix, obtained in a purely local and cheap way.
e. The implementation of several strategies for adaptive step length computation for the MPRGP expansion step.
f. The implementation of an efficient reconstruction formula for the rigid body modes amplitudes computation and testing of its effect for contact problems.
g. Massively parallel benchmarking with linear and contact problems of elasticity and elasto-plasticity, and scalability testing on various architectures. The performance and scalability results of our libraries will be demonstrated on model and engineering benchmarks with up to billions of unknowns.


Astro Sciences (3)


Project Title: AGN radiation and the cold interstellar medium
Project Leader: Dr. Tiago Costa, Leiden University, Leiden Observatory, Leiden, The Netherlands
Resource Awarded: 19,775,488 standard core hours

Dr. Alex Richting, Northwestern University, Centre of Interdisciplinary Exploration and Research in Astrophysics CIERA, Evanston, USA
Dr. Joakim Rosdahl, Centre de Recherche Astronomique de Lyon, France
Prof. Joop Schaye, Leiden University, Leiden Observatory, Leiden, The Netherlands
Over their lifetime, supermassive black holes release an amount of energy which is by many times higher than sufficient to completely unbind the galaxies at the centre of which they reside.
One the key potential consequences of this process, known as `AGN feedback’, is the complete shut-down of star formation in massive galaxies.

Among other observations, this mechanism might explain why massive galaxies in the present day Universe appear red in colour and why they seem to undergo little or no star formation.
Though crucial to our understanding of galaxy evolution, the physical processes governing the interaction between rapidly growing supermassive black holes (active galactic nuclei, or AGN) and the cold interstellar medium remain poorly constrained.
Important limitations in previous theoretical efforts that have hampered progress include the absence of a treatment for both the AGN radiation field and for the thermo-chemical processes that govern the properties of the cold interstellar medium.

Our aim is to overcome these technical limitations by performing a suite of fully radiation-hydrodynamic simulations combining two state-of-the-art tools: RAMSES-RT, a fast and robust radiation-hydrodynamic code, and CHIMES, a powerful new model for non-equilibrium cooling and chemistry of cold interstellar gas.
Our scientific goals are to explore the effect of AGN radiation on the properties of the galactic cold interstellar medium and, specifically, to (i) test the ability of radiation pressure to launch large-scale outflows, (ii) to unravel new mechanisms for the suppression of star formation in massive galaxies and (iii) to develop observational diagnostics to test AGN feedback.

In addition to simulations of galactic discs, which will allow us to probe the physics of the AGN-ISM interaction in controlled experiments, we will perform realistic cosmological simulations that will enable us to probe radiative AGN feedback in great detail across cosmological time down to the present day Universe.


Project Title: Numerical relativity beyond astrophysics
Project Leader: Dr. Pau Figueras, Queen Mary University of London, School of Mathematical Sciences, London, UK
Resource Awarded: 20,650,000 standard core hours

The detection of gravitational waves by the LIGO scientific collaboration is probably going to be one of the greatest discoveries of the 21st century. This discovery also led to the first direct observations of black holes. Therefore, black hole physics has left the realm of speculation and mathematical abstraction to become frontline physics.

Black holes play a fundamental role in our understanding of general relativity (i.e., Einstein’s theory of gravity) for essentially two reasons: 1) we have a complete mathematical description of these within the theory itself in terms of a handful of parameters, and hence no approximation are needed to study them. 2) In spite of their simplicity, black holes capture some of the key aspects of the theory, such as the non-trivial causal structure of the Universe and the presence of singularities in their interior where the theory breaks down.

In four spacetime dimensions and in vacuum, equilibrium black holes are well-understandood. In particular, it is thought that black holes are stable under small gravitational perturbations, and this is why they are relevant to describe the compact dark objects that we observe in the Universe. In recent years, motivated by string theory, there has been a growing interest in studying gravity (and black holes in particular) in dimensions greater than four and/or with different boundary conditions. It turns out that black holes in these new settings can be unstable under small perturbations. Understanding the endpoints of such instabilities is paramount in general relativity because it is directly related to the formation of singularities and the potential breakdown of Einstein’s theory of gravity. However, in order to determine the endpoints of these instabilities, one has to solve the Einstein equation in the fully non-linear regime, and to do so, numerical methods are needed.

Recently we found evidence that the instabilities of certain asymptotically flat doughnut-shaped black holes in five spacetime dimensions can lead to the formation of singularities in finite time. However, the lack of computational resources did not allow us to understand the details of such instabilities. Doing so is the goal of this project. Similarly, we have found that the evolution of certain rotationally symmetric instabilities of spherical black holes in six (and higher) dimensions also leads to the formation of singularities. The second goal of this project is study the endpoint of the generic (i.e., no symmetry assumptions) instabilities, since only in this case one is really addressing the fundamental question of the generic formation of singularities in general relativity.

The successful completion of this project will lead to a better understanding the structure of general relativity, and in particular, about the formation of singularities. Understanding the latter in higher dimensions and/or different boundary conditions will lead to insights about how to make progress in the astrophysically relevant settings.


Project Title: The effects of small-scale structure and halo stochasticity on Cosmic Reionization
Project Leader: Dr. Ilian Iliev, University of Sussex, Physics and Astronomy, Sussex, UK
Resource Awarded: 20,160,000 standard core hours

This proposal focuses on investigating the effects of small-scale structures and halo distribution stochasticity on the progress and observational signatures of the Epoch of Reionization (EoR). The first generations of baryonic structures, which formed before the Universe was a billion years old, released sufficient numbers of hydrogen ionizing photons into the intergalactic medium to completely ionize it. This process of cosmic reionization is generally assumed to be driven by ionizing photons produced by stellar sources, most of them with energies at or slightly above the Lyman limit. Furthermore, a variety of photon sinks (i.e. absorbers) affected the propagation of the ionizing photons and modified how many were required to complete this process. As a consequence, reionization was a very patchy process with ionized (H II) regions expanding around the positions of photon sources. The size, spatial distribution and evolution of the ionized and neutral patches is then reflected in the various observable EoR signatures.

We propose to study in detail and combine all these different effects into series of EoR radiative transfer simulations. We will evaluate their relative effects and derive any specific observational signatures, particularly at the redshifted 21-cm radiation signals for the LOFAR and SKA radio interferometers.


Bio Sciences (12)


Project Title: Classical and Ab Initio Molecular Dynamic Probes for Photosystem II Light Harvesting Complexes
Project Leader: Assistant Professor Evangelos Daskalakis, Cyprus University Of Technology, Department of Environmental Science and Technology, Limassol, Cyprus
Resource Awarded: 1,787,004 standard core hours

The elucidation of the conformational changes in LHCII upon Non-Photochemical Quenching (NPQ) are vital in understanding the main photoprotective mechanism in plants. The identification of key components of a central mechanism that regulates the balance between photochemistry and photoprotection can provide a basis for biochemistry that increase our understanding regarding plant sensitivity to stress and photosynthesis with optimal yield. On this line, we will employ methods like ab-initio Molecular Dynamics (AIMD), and the Time-Dependent Density Functional Theory (TD-DFT) for the electronic structures and absorption spectra of the major LHCII from spinach and pea at the two extremes modes (non-/dissipative).


Project Title: Benchmark data for structural biology in the gas-phase
Project Leader: Dr. Alexander Kulesza, Université Lyon 1 and CNRS, Institut Lumière Matière, Villeurbanne, France
Resource Awarded: 8,000,000 standard core hours

Ion mobility emerges as important method to deliver 3D structural information, especially about non-crystallizable proteins. Unfortunately, basic relationships between structure and the measured cross-section still are not clear. For example, if combinations of simpler descriptors (like the molecule’s gyration radius) can be used to represent the cross-section, and in which cases such correlations hold, is still to be determined. With an ambitious determination of benchmark data for a hot-topic in structural biology, we will lay the foundations to render ion mobility more routinely applicable. For a realistic Amyloid-β fibril model, we will determine charge-dependent structure and flexibility by state-of-the-art metadynamics simulations with parallel tempering and will explicitly and accurate calculate cross-sections. With this effort we are able to analyse the correlations of structural descriptors with the latter and can set up generalizations for analysis and refinement tools. While the gained knowledge will boost the field of Alzheimer Amyloid-β aggregation research, the delivered generalized methods contribute to modelling-supported ion mobility measurements for structural biology.


Project Title: Exploration of binding routes of a potent inhibitor blebbistatin by dynamic mapping of its multiple binding sites on the surface of a myosin target
Project Leader: Dr. Csaba Hetényi, Hungarian Academy of Sciences, Molecular Biophysics Research Group, Budapest, Hungary
Resource Awarded: 16,000,000 standard core hours

In the human body, forces and motion are generated in muscle tissues. Here, proteinsactin and myosin build up filaments which produce contraction changing the length and shape of the muscle cell (Murell 2015). Heart failure is a common human disease with a significant lifetime risk that increases with age (Lloyd-Jones 2010). In its most common manifestation, heart failure is marked by a decrease in cardiac contractility culminating in systolic heart failure. Directly targeting the contractile mechanism of cardiac myosin could improve heart performance without altering intracellular cAMP or calcium transients. Besides their physiological role, the actomyosin network (cytoskeleton) is of central importance in the deisgn of active gels (Linsmeier 2016), as well. In a previous study (Kovacs 2004), we published a small molecule inhibitor blebbistatin, which blocks myosin II in an actin-detached state making the compound useful both in muscle physiology and in exploring the cellular function of cytoplasmic myosin II isoforms. As blebbistatin stabilizes the ATPase intermediate with ADP and phosphate bound at the active site, our results have been used extensively in other structural investigations, and hundreds of studies have cited our paper. Although the final binding mode of blebbistatin has already been found, elucidation of the complete binding pathway of blebbistatin would be also beneficial for the design of other, similar compounds, and test if allosteric modulation is possible in the binding channel of blebbistatin similarly to a recently published compound (Winkelmann 2015).

Thus, in the present proposal we aim at further investigation of the binding route of blebbistatin leading to its binding pocket. For this, the possible binding sites of blebbistatin will be mapped using a modified version of our previously published blind docking method (Hetényi & van der Spoel, 2011, 2006, 2002). An advantage of the blind docking approach is that it does not require previous knowledge of the possible binding sites, and also that it can scan the entire surface of the target molecule. Subsequent real time molecular dynamics calculations will be performed for the representative bound complexes using the GROMACS (Abraham 2015) program package. In this way, the structural information can be analysed along a time dimension, and a full picture of the binding process can be obtained. With this approach molecular dynamics-based changes such as allosteric effects of the ligand can be precisely assigned at atomic resolution.


Project Title: Molecular mechanisms of a novel pro-apoptotic BH3-like protein in cancer
Project Leader: Elena Papaleo, Danish Cancer Society Research Center, Copenhagen, Denmark
Resource Awarded: 16,000,000 standard core hours

Francesco Cecconi, Danish Cancer Society Research Center, Copenhagen, Denmark
Daniela De Zio, Danish Cancer Society Research Center, Copenhagen, Denmark
Birthe Kragelund, University of Copenhagen, Denmark
Matteo Lambrughi, Danish Cancer Society Research Center, Copenhagen, Denmark
Mads Nygaard, Danish Cancer Society Research Center, Copenhagen, Denmark
Valentina Sora, Danish Cancer Society Research Center, Copenhagen, Denmark
Flavie Strappazzon, IRCCS Santa Lucia Foundation, Rome, Italy


Project Title: Simultaneous determination of protein structure and dynamics using cryo-electron microscopy data
Project Leader: Prof. Michele Vendruscolo, University of Cambridge, Department of Chemistry, UK
Resource Awarded: 6,160,000 standard core hours

Cryo-electron microscopy is emerging as a very powerful approach to enable the determination of the structures of biological systems that were not accessible through traditional techniques, such as X-ray crystallography or nuclear magnetic resonance spectroscopy. However, as biological protein functions and architectures are often intertwined with dynamics, single-structure pictures may not be sufficient to understand fully how a system works. In this highly innovative project, we propose to apply a integrative modelling approach, called metainference, to simultaneously determine structure and dynamics of membrane proteins from cryo-electron microscopy data. Matainference models conformational ensembles by integrating prior information with experimental data. By quantifying the level of noise in the data as well as dealing with its ensemble-averaged nature, metainference makes it possible to integrate multiple sources of information to model ensembles of states and infer their populations. This project will provide a proof-of principle of this approach in the case of membrane protein complexes as they present a high degree of flexibility and conformational variability. Metainference will allow the characterization of their heterogeneity and dynamics, thus shedding light into the crucial role of these complexes in the transport of small molecules and peptides through the membrane.


Project Title: High-throughput strategy to calculate rate constants for drug/membrane systems
Project Leader: Dr. Hugo Filipe, Universidade de Coimbra, Center for Computational Physics, Coimbra, Portugal
Resource Awarded: 9,800,000 standard core hours

Dr. Luís Loura, Universidade de Coimbra, Center for Computational Physics, Coimbra, Portugal
Dr. Maria Joao Moreno Silvestre, Universidade de Coimbra, Center for Computational Physics, Coimbra, Portugal
Failure to cross the Blood-Brain Barrier (BBB) is an important attrition factor in the development of drugs for brain disorders, and in this context, passive transport across cell membranes is a significant route for the permeation. Since in vivo experiments are time-consuming and expensive, high-throughput predictive tools for the passive permeation through the BBB are very important.

The major barrier for permeation through tight endothelia, such as the BBB, is the lipid bilayer that constitutes the plasma membrane of their cells, which has a polar region on both sides in contact with the aqueous media, and a central region with very low polarity. Permeation through the lipid bilayer involves several steps, namely association with the membrane leaflet in contact with the aqueous media, translocation into the opposite leaflet, and dissociation from the membrane into the aqueous compartment on the opposite side. Due to aqueous solubility requirements in the aqueous media, most drugs are relatively polar , and therefore translocation through the lipid membrane leaflets is usually the rate limiting step in the overall permeation process. However, as the hydrophobicity of the molecules increases, desorption from the lipid bilayer may become the rate limiting process. In recent years, our lab produced detailed studies on the interaction of amphiphilic molecules with lipid bilayers. Using that information we developed a mechanistic model for the permeation through tight endothelia, such as the BBB. The results show that the interaction of drugs with the various compartments considered in the model, including the translocation between membrane leaflets, strongly affects their permeation across the BBB. This approach is very promising, with potential to follow drug concentrations in physiologically relevant compartments, however, few experimental data exist in the literature regarding the individual steps involved in the permeation process. In this context, the current state of Molecular Dynamics (MD) simulations may be used to develop a strategy to obtain the required data. In addition, this data can be used to obtain Quantitative Structure Property Relationships (QSPRs), regarding the single steps on the permeation process, to guide the rational design of new drugs.

In this project MD simulations will be used to calculate the rate constants of molecules through lipid membranes. We will study an homologous series of amphiphilic molecules (NBD-Cn), with a common head group (NBD) and different alkyl chain sizes (n= 4, 8, 10). Using a coarse grained (CG) force field, long unrestrained simulations will be performed to obtain a significant number of events, which will be used to calculate the rate constants. In addition, Potential of Mean Force (PMF) profiles, which using a CG force field are much less computationally expensive, will be obtained and the applicability of several models to calculate rate constants from free energy barriers will be addressed. A high-throughput strategy to obtain rate constants for the interaction of drugs with lipid membrane will be developed and validated by comparison with experimental data.


Project Title: Molecular Dynamics study of ion permeation in wild-type and mutants of the human α7 nicotinic receptor
Project Leader: Dr Grazia Cottone, University of Palermo, Physics and Chemistry, Palermo, Italy
Resource Awarded: 4,158,336 standard core hours

Dr Luca Maragliano, Italian Institute of Technology (IIT), , Genova, Italy
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that regulate signal transmission at the neuromuscular junction. A detailed knowledge of the active and inactive structures, and of the gating transition between them in response to ligand binding, is of crucial importance. Structural information on human nAChRs is still lacking. In this respect, homology modeling and Molecular Dynamics (MD) simulations are valuable tools to predict and refine structures of unknown proteins, in particular transmembrane proteins. Using MD simulations we recently proposed an all-atom structural model of the human α7 nAChR in an open conformation complexed with the full agonist epibatidine. In the present project we will study the electrophysiological response of the open conformation to the agonist, both in native and mutant proteins. We plan to estimate the Potential of Mean Force (PMF) of single ion permeation through the channel pore and the kinetics of the ion translocation process by using the Milestoning with Voronoi Tessellation method. Given the single ion PMF, the maximum single channel conductance can be computed. The structural determinants of the ion translocation, i.e. the key residues responsible for the energy barrier, will be investigated and identified as well. This will help in understanding the basis of the ligand-receptor interactions, and in developing new pharmacological approaches to influence the receptor function. To further validate our model we will mutate selectivity filter residues known to affect ion permeation. Once the model is validated against these benchmarks, one could study other mutations associated to pathological phenotypes, and provide a molecular basis for the receptor malfunction.


Project Title: Molecular mechanisms of signal transduction through transmembrane receptors
Project Leader: Dr. Agnieszka Kaczor, Medical University of Lublin, Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Lublin, Poland
Resource Awarded: 35,000,000 standard core hours

Damian Bartuzi, Medical University of Lublin, Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Lublin, Poland
Katarzyna Targowska-Duda, Medical University of Lublin, Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Lublin, Poland
Transmembrane receptors, in particular rhodopsin-like G protein-coupled receptors (GPCRs), ion channels and receptor tyrosine kinases are the most important drug targets in current pharmaceutical industry. Recent reports about the new mechanisms of signal transduction through these receptors may lead to more efficient and safer drugs with fewer side effects. In particular allosteric modulation and oligomerization of transmembrane receptors are nowadays hot topics in medicinal chemistry. The aim of the project is to use molecular dynamics simulations to study signal transduction through selected transmembrane receptors on the molecular level. We will focus on opioid receptors, dopamine receptors, cannabinoid receptors, nicotinic receptors and receptor tyrosine kinases. The human µ opioid receptor is a drug target for the most potent antinociceptive medicines. Unfortunately, their usage bears a great risk of serious side effects, where some of them can even be lethal, e.g. respiratory center paralysis, while other make the prolonged usage problematic, e.g. tolerance, dependence or serious constipations. Moreover, the fact that most of the favorable and unvavorable effects of opiates involve activation of the same receptor was a source of the long-lasting impasse. The above-mentioned complications are a rationale for a search for novel, more sophisticated compounds, capable of separating the desired µopioid receptor activation pathways from the undesired ones.


Project Title: Conformational response of the super-complex of Niemann-Pick C proteins to cholesterol binding
Project Leader: Ilpo Vattulainen, University of Helsinki, Finland
Resource Awarded: 17,856,000 standard core hours

Elina Ikonen, University of Helsinki, Finland
Cholesterol has various essential structural and functional roles in the body and has been implicated in many disease conditions. To maintain healthy levels of cholesterol, cells tightly control its trafficking. One of the essential stages in cholesterol trafficking is its export out of the late endosomes/lysosomes, which process the endocytosed cholesterol derivatives. Niemann-Pick C proteins NPC1 and NPC2 are the key proteins that form a “tag-team duo” in shuttling the processed cholesterol out of the late endosomes/lysosomes. Mutations of NPC1 or NPC2 result in progressive neuronal degeneration and early death, called the Niemann Pick C disease. NPC2 is a small soluble protein that carries cholesterol between the internal membranes of the late endosomes/lysosomes and finally hands it down to its partner NPC1. As preliminary work we have recently performed an extensive computational investigation of NPC2-membrane interactions and its role in cholesterol transport.

As a large transmembrane protein, NPC1 is composed of many domains that coordinate the cholesterol transfer from the NPC2 to the limiting membrane and its subsequent export. Recently, multiple structures of individual domains of NPC1 and its complex with NPC2 have been discovered by crystallography and cryo-EM. These structures have now opened avenues in molecular investigation of the concerted mechanism of NPC1 and NPC2 and the super complex formed by them. The NPC1-NPC2 super complex has three cholesterol binding pockets, two on separate domains of NPC1 and one on NPC2. The occupancy of these pockets is associated with several functional conformational intermediates in the cholesterol transport cycle of NPC1. We have constructed models of the NPC1-NPC2 super-complex based on the available structures. To investigate the conformational response of the NPC1-NPC2 super complex to cholesterol binding, we will perform long time-scale simulations at various cholesterol bound states. These simulations will reveal key interactions and conformational changes, and will provide us with a dynamic picture of how cholesterol can allosterically modulate the organization of NPC1 domains and NPC2 in the transport cycle. Characterization of allosteric coupling and functional conformational intermediates can in turn help us understand the roles of mutations and other sources of malfunction that interfere with effective cholesterol transport and associated disorders.

The project benefits from excellent resources and will be performed in collaboration with the team of Academyprof. Elina Ikonen (CoE Director, Biomedicum, Uni. Helsinki). The Vattulainen team hosts an ERC Advanced Grant project and is a member of the Center of Excellence (CoE) in Biomembrane Research. Besides, the team with a large number of members from various fields has a long-standing experience in biomolecular simulations, taking advantage of high-performance computing resources.


Project Title: Studies of oxygen diffusion in prolyl hydroxylases by equilibrium and non-equilibrium molecular dynamics simulations
Project Leader: Carmen Domene, University of Oxford, UK
Resource Awarded: 6,300,000 standard core hours

The human body is able to sense changes in atmospheric oxygen levels and adjust its metabolic activities to suit the local environment. This is why we are able to live at a variety of altitudes ranging from below sea level to up on mountains high. How can cells detect and respond to oxygen levels? This project will lay the groundwork in order to exploit the basic science to artificially alter the activity of oxygenases, and to provide knowledge that will be useful for the pharmaceutical industry in targeting them for diseases.

Prolyl Hydroxylase Domain-2 (PHD2) is the most important of the human PHDs that enzymes involved in oxygen sensing. PHDs are a member of the 2OG-dependent dioxygenase family of enzymes that use dioxygen to catalyze a posttranslational hydroxylation reaction in the human oxygen sensing cycle. The mechanism of catalysis involves a slow diffusive entry of dioxygen into the active site of PHD2. Here, equilibrium classical molecular dynamics (MD) simulation, coupled with biased sampling methods, non-equilibrium steered MD (SMD) and adaptive biasing force (ABF) are proposed to study the mechanism of oxygen diffusion from the bulk solvent to the iron-coordinated active site. These results provide the first quantitative mechanism for oxygen-sensing properties of PHD 2OG-dependent dioxygenases.


Project Title: Protein-lipid interactions as a pharmacological target: Case of tyrosine kinase growth factor receptors
Project Leader: Tomasz Rog, University of Helsinki, Finland
Resource Awarded: 20,000,000 standard core hours

Protein tyrosine kinase is a family of 90 proteins in humans, among which 58 are receptors. Receptors belonging to this family are key players in development, immunological system, and numerous cellular and physiological processes. Not surprisingly, numerous pathologies are connected with these proteins, including the majority of cancers and the appearance of diabetes, degenerative diseases, and mental disorders. For this reason protein tyrosine kinase receptors are very common drug targets: for instance, the epidermal growth factor receptor (EGFR) inhibitors are used in non-small-cell lung cancer, pancreatic cancer, breast cancer, and colon cancer therapy. One of the common features of these receptors is the regulation of their function by lipids present in the extracellular leaflet of cell membranes—gangliosides. Gangliosides may either inhibit these receptors or facilitate their activation. In this project, we will perform a molecular dynamics simulation study of EGFR interacting with the ganglioside GM3, aiming to show the possibility of interfering these interactions with small molecular drugs—fluoxetine and tricyclic antidepressants. The ability of these drugs to interfere with lipid-modulated receptor activation may be used as a new mechanism for drug-controlled receptor action and as a source of drug-adverse effects.


Project Title: Molecular dynamics simulations on the sequence-structure- dynamics-function relationships of antithrombin
Project Leader: Istvan Komaromi, University of Debrecen, Faculty of Medicine, Debrecen, Hungary
Resource Awarded: 3,600,000 standard core hours

Haemostatic system is well regulated and finely tuned multiple component system. Its disorders can lead either to an increased risk of haemorrhage (bleeding) or to an unnecessary coagulation (thrombosis). In order to understand how this system is regulated one needs to understand the sequence-structure-function relationships of its components. Our department is also active on this field of research.1-4 While it is hard to overestimate the importance of the available X-ray structural data, such experiments reflects states in which the conformations are influenced by crystal forces and the dynamics nature of the structural elements can be studied only to a limited extent. One of the characteristic example for the significance of conformational flexibility in the activation and in the action of such proteins is the antithrombin, the main physiological inhibitor of blood coagulation factors IIa (thrombin), FXa and FIXa.

Antithrombin (AT, a member of the serpin family of proteins) circulates in the blood in relatively high concentration and in its “free” form it is a weak inhibitor 5-7 of proteinases. However, it has special mechanisms to attain its “full”, two or three order of magnitude larger inhibitory potential against its target proteinases where and when it is required, via formation of complex with heparins or heparin mimetic pentasaccharides (PSs). The inhibitory mechanism of antithrombin and its regulation is a subject of intensive studies. Several papers including reviews can be found in the literature on this topic.

On the other hand, molecular modeling and molecular simulation have been proven to be a valuable tool which can be applied to complement the “real” experiments. Our main goal is to reveal the sequence-structure-dynamics-function relationships at this protein by means of (biased and unbiased) molecular dynamics simulation. In our opinion it has both scientific and practical importance. From these simulations structural-functional consequences of pathogen mutations and/or polymorphisms can be revealed and these simulations can be used even for development of more efficient inhibitors or activators.


Earth Sciences (1)


Project Title: A Brief History of the Arctic Ocean
Project Leader: Dr. Laurent Bertino, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Resource Awarded: 11,404,800 standard core hours

Dr. Alfatih Ali, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Sylvain Bouillon, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Satoshi Kimura, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Einar Olason, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Pierre Rampal, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Abdoulaye Samake, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Annette Samuelsen, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Timothy Williams, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Jiping Xie, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
Dr. Caglar Yumruktepe, Nansen Environmental and Remote Sensing Center, Data Assimilation Group, Bergen, Norway
The general forecasting problem for nonlinear systems is a field where advanced statistical methods now are applied operationally in real-world applications. Indeed, making a decision based on a forecast requires probabilistic information about the forecast accuracy in order to quantify the risk of loss associated with a given decision. This information is a combination of the uncertainties in measurements of the system considered and uncertainties in the numerical model that processes the forecast. We therefore consider the data assimilation problem: the computation of the most likely system state and the associated uncertainties given a dynamical model and a set of observations. In the case of low dimensional linear dynamical systems, the data assimilation problem is solved by standard techniques like the Kalman filter and adjoint or inverse methods. However, in real geophysical applications the system is nonlinear and high-dimensional so the data assimilation problem becomes practically intractable. Multivariate three dimensional systems typically have ten to a hundred million unknown variables, constituting a huge state vector. There are therefore practical constraints on the usage of computer memory and especially on the processing time (an operational forecast has to be issued before the situation gets out of hand!). As shown for weather forecasts, the quality of a forecasting system relies on the use of advanced data assimilation techniques, but the computational demands of such techniques are high and the design of a forecasting system has become a pragmatic trade-off between the accuracy of the numerical model and the available computing resources. Both fundamental research and practical implementation work are therefore needed in order to progress in the field of data assimilation and to improve our forecasting capability. The project is multi-disciplinary an includes high-dimensional applications in climate and ocean modelling (physical and ecosystem modeling in Lagrangian vertical coordinates) sea ice modeling in the Marginal Ice Zone and in the ice pack (with the Elastic-Brittle rheology).

Engineering (7)


Project Title: Double Diffusive Convection in the Diffusive Regime
Project Leader: Prof. Dr. Roberto Verzicco, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Resource Awarded: 20,000,000 standard core hours

Dr. Vamsi Spandan Arza, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
M.Sc. Alexander Blass, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Prof.Dr. Detlef Lohse, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Dr. Richard Stevens, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Dr. Yantao Yang, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
MSc. Xiaojue Zhu, University of Twente, Faculty of Science and Technology, Enschede, The Netherlands
Double diffusive convection (DDC), i.e. the convection flow with fluid density depending on two scalars with very different molecular diffusivities, plays a crucial role in ocean mixing [1-3]. The density of seawater is mainly determined by temperature and salinity. The condition favouring DDC presents at more than 40% of the oceans [4]. In the tropic and sub-tropic oceans temperature and salinity often decreases as the depth increases, which is in the fingering regime [5-7]. While in the upper layer of the polar and sub-polar oceans, both temperature and salinity increases from the surface to bottom, and DDC occurs in the diffusive regime [8,9]. DDC can induce intense vertical mixing [10] and may even attenuate the ocean signatures of climate changes [11]. Thus it is of great interest to understand the dynamics of DDC flow and its mixing properties, such as scalar transfer rates and flow velocity.

Since the theoretical work by Stern in 1960 [12], numerous studies have been carried out experimentally, theoretically, and numerically in recent years. A thorough review on the field can be found in the recent book of Radko [13]. In the current proposal, we will focus on the DDC flow in the diffusive regime, which is widely observed in the high-latitude oceans such as Canadian Basin [9]. In this regime cold fresh water overlays warm salty water. Therefore, the fluid is unstably stratified by the temperature component and at the same time stably stratified by the salinity component. Diffusive DDC has profound importance for the vertical heat flux, which is critical to understand the evolution of the Artic sea-ice [14]. Early experiments resulted in models for the heat flux [15-17], which have been used to interpret observation data and to estimate the heat flux in the ocean [9]. Recently, numerical simulations prove to be another useful tool for studying diffusive DDC [18-20]. Numerical results can provide complete information of the flow and help to develop flux laws for heat flux. Still, more work is needed to fully understand the dynamics and flux laws of diffusive DDC.

During the past several years we has successfully conducted systematical simulations for the DDC flow in the fingering regime [21-24]. For this study we will extend our research to the diffusive regime. By utilizing the highly efficient in-house code developed by ourselves, we aim at exploring a wide range of control parameters that are directly relevant to the real ocean condition. With these numerical results we are planning to obtain detailed information about the flow dynamics and develop models for global responses of the flow, such as heat flux, salinity flux and flow velocity. All these results should be extremely useful for the community.


Project Title: Investigation of Installed Jets Noise Generation Mechanisms and Control
Project Leader: Prof. Paul Tucker, The University of Cambridge, Dept of Engineering, Cambridge, UK
Resource Awarded: 9,408,000 standard core hours

Jet noise is the dominant component when an aircraft is taking off. It is intensified when the jet is installed in the proximity of solid boundaries, i.e. the wing. Understanding of installed jet noise and its control is limited. The project is intended to perform the large-scale eddy-resolving simulations of installed jets from canonical jet flat-plate to industrially relevant ultra-high bypass-ratio engine jets. It combines computational methods with theoretical and experiment investigations to give more insight into the sound generation mechanisms in installed jets and develop an accurate physics-based acoustics model. Finally, effective and practical noise reduction strategies for installed jet noise is explored. The research bridges the gap on the research of isolated jets and realistic installed engine jets and shows how high-performance computing can be used to improve physical understanding and develop new engineering technologies.


Project Title: Direct Numerical Simulation of Non-equilibrium Adverse Pressure Gradient Turbulent Boundary Layer
Project Leader: Assistant Prof. Gungor Ayse, Istanbul Technical University, Faculty of Aeronautics and Astronautics, Istanbul, Turkey
Resource Awarded: 2,210,000 standard core hours

Taygun Gungor, Istanbul Technical University, Faculty of Aeronautics and Astronautics, Istanbul, Turkey
Prof. Yvan Maciel, Université Laval, Département de génie mécanique, Quebec, Canada
Dr. Mark Simens, Universidad Politécnica de Madrid, ETSI Aeronáuticos, Spain
Most real-world flows are subject to conditions that change rapidly over a short distance. Examples are flows around vehicles (terrestrial, aerial and marine) and inside gas or hydro turbines. In all these examples, one of the most important changing conditions is the pressure force acting on the flow. By accelerating or decelerating the flow near the wall, a flow region called a boundary layer, the pressure force modifies the properties of the boundary layer. These modifications may lead in turn to important global effects such as energy losses and stall of an airplane. The transposition of our knowledge acquired through the study of simple flows to more complex flows such as adverse pressure gradient turbulent boundary layers is not straightforward and raises several questions. For instance, how and to what extent can we apply the known similarity laws to complex flows? Are the self-sustaining and transport mechanisms of turbulence the same in these flows? Answering these questions is essential for the improvement of the turbulence models, which are the building blocks of practical flow simulation codes in industry, and for the design of effective methods of flow control in order to improve the aerodynamic performance of machines. The goal of this research project is to tackle these fundamental unsolved questions. They can only be answered with very detailed data and if the Reynolds number (ratio of inertia and viscous forces) is high. The only method that can provide accurate and very detailed data all the way down to the wall is direct numerical simulation (DNS) that is the full numerical resolution of the Navier-Stokes equations with no modeling of the physics. We will therefore obtain and analyse well-resolved numerical data by performing a direct numerical simulation of a carefully designed strongly decelerated non-equilibrium turbulent boundary layer at a sufficiently high Reynolds number.


Project Title: Hydrodynamics of fluidized non-spherical particles
Project Leader: Dr. Johan Padding, Delft University of Technology, The Netherlands
Resource Awarded: 8,000,000 standard core hours

Dr. Sathish Sanjeevi, Delft University of Technology, The Netherlands
The project is funded by the “European Research Council” for detailed investigation of non-spherical particles fluidization. The objective is to pioneer a novel multiscale simulation methodology for dense gas-solid flows of inelastic non-spherical particles, based on systematic coarse-graining of interactions from small to larger scales, backed up by validating in-house experiments. As a first step, fully resolved direct numerical simulations (DNS) are to be performed to obtain the drag, lift and torque closures of suspensions containing elongated axisymmetric particles. Such particles are relatively simple, yet many of the fundamental problems linked to anisotropic drag and collisions already appear. The closures would later be used to perform discrete particle model simulations, which are in-turn validated with experiments.

In the scope of requested compute time, we would perform detailed DNS of particle suspensions considering anisotropic gas-solid drag and effects of particles’ mutual alignment. The work will not only advance our scientific understanding of fluidized flow of elongated particles, but also be relevant to industrially important processes such as biomass-based fuel synthesis.


Project Title: Passive control on microswimmers’ trajectories via surface patterning
Project Leader: Dr Daniela Pimponi, Universita di Roma la Sapienza, Department of Physics, Italy
Resource Awarded: 6,237,088 standard core hours

Evolution had equipped microorganisms with a variety of strategy of locomotion such as Celia and flagella. A quite common strategy is represented by rotating or beating flagella. For instance, Escherichia coli and Pseudomonas aeruginosa, two widely diffused bacteria species that, in specific cases, can have a pathogenic action, employ one ore more rotating flagella to move across the surrounding liquid. The flagellum rotation exerts an action on the fluid that allows the bacteria to swim along a straight line when they are far from interfaces. However, in several relevant conditions, bacteria move in confined geometries, i.e. very close to interfaces. Examples are given by biomedical devices (such as catheters) or thin liquid films (e.g. the layer of liquid that wet the lung epithelium). In addition, bacteria typically accumulates close to the liquid interfaces forming microcolonies and biofilm precursors that can have a dramatic impact of their resistance to antibacterial and chemical disinfectant.

Understanding the swimming of the flagellated microorganism is hence, not only an interesting problem in fundamental fluid-dynamics, but can have also an impact on the development of new strategies to control the bacteria motion and, consequently, to reduce the propensity to form biofilms. Moreover, a clear understanding of microswimmer fluid dynamics, will also be beneficial for the design of artificial microswimmers that are though to be an enabling technology for several applications, such as targeted drug delivery and water purification.

In this project we aim at exploring, by means of hydrodynamics simulations, the possibility to passively control the motion of flagellated microswimmers using properly patterned super-hydrophobic surfaces.

Super-hydrophobic surfaces, the most celebrated example being the lotus leaves, are characterized by a rough structure where the air get trapped in the surface asperity, hence the liquid is in contact with a complex boundary where the usual solid-liquid (no-slip) boundary is intercalated by air-liquid (perfect-slip) patches. This non-homogeneous boundary condition induces interesting consequences on liquid motion, such as the presence of an effective drag reduction.

Our group already studied the motion of flagellated bacteria at homogeneous (solid-liquid and air-liquid) interfaces and the motion of passive tracers at SHS. Based on these acquired results, we expect that the super-hydrophobic structure can potentially control the motion of flagellated microswimmers hindering the formation of the typical circular trajectories that are thought to be a crucial ingredient for the boundary accumulation and consequently, the first stage for microcolonies formation.

In this project, we will employ a boundary element solver, named BeSwimmer, we developed in the past years. We already applied BeSwimmer to analyze E.coli motion at both solid-liquid and air-liquid interfaces and we are currently studying the E.coli motion under confinement. In both the cited case, the homogeneity of the planar surfaces drastically reduces the computational efforts, however, the extension to important case of super-hydrophobic surface, need a computational effort one-two orders of magnitude larger and can afforded only via Tier-1 resources.


Project Title: LES Aerodynamic characterization of swirling flames in combustors
Project Leader: Dr. Teresa Parra, University of Valladolid, Fluid Engineering, Valladolid, Spain
Resource Awarded: 15,435,000 standard core hours

MSc Victor Mendoza, University of Valladolid, Fluid Engineering, Valladolid, Spain
Diego Palomar, University of Valladolid, Fluid Engineering, Valladolid, Spain
PhD Student Ruben Perez, University of Valladolid, Fluid Engineering, Valladolid, Spain
This proposal is devoted to the development of high-resolution computational fluid dynamics (CFD) tools to be applied to turbulent reactive swirling flows. Methane is an interesting alternative fuel for gas engines due to low Ievels of emissions and high thermal efficiency. Also, the methane slip due to incomplete combustion is a common problem since methane is a harmful greenhouse gas. Lean flames produce less contaminant emissions and reduce fuel consume, however they are unstable.

The aim is to characterize premixed swirling flames. Swirling flows are suitable to stabilize lean flames near the limit of flamability. Previous studies have shown that the swirl generator has an enhanced ef fect on mixing of fuel and air in diffusive flames. It is the strong anisotropy of the swirling flows that prevents the accuracy of RANS models. Hence, Large Eddy Simulation (LES) allows accurate CFD simulations that shed light to the physics of the flow. A collateral challenging aim of this project is the implementation of a combustion model in an implicit LES.


Project Title: WAKE simulations in wind farms with MAPFlow solver using Large Eddy Simulations
Project Leader: Dr John Prospathopoulos, National Technical University of Athens, School of Mechanical Engineering, Athens, Greece
Resource Awarded: 14,700,000 standard core hours

Dr. Giorgos Papadakis, National Technical University of Athens, School of Mechanical Engineering, Athens, Greece
The proposed project aims at providing high fidelity simulations of the performance and loading of wind turbines operating under the combined effect of inflow (atmospheric) turbulence and of wakes that develop in wind farms. As wind turbines get larger in diameter, the range of the turbulence scales that act as unsteady excitation on the blades becomes wider. Therefore, conventional turbulence modelling of the eddy viscosity type is longer suitable. In the present proposal the LES approach is adopted allowing resolving the larger scales and model the smaller ones that affect the recovery of the flow. Inflow data to such simulations will correspond to a coherent turbulent flow field generated based on the wind velocity spectra and the spatial coherence as done for example by the Mann model.

In the case of a wind park composed of several wind turbines, including all of them in their exact geometry is at present not considered a mature enough option. One of the reasons is that in a multi-turbine context the development and the interactions of the wakes that are generated play an important and not well understood role. A valid option in this respect is to simulate the rotor blades as rotating actuator lines along which loading is distributed through a blade element approach. In this framework aeroelastic coupling based on beam structural modeling is well suited.

From a scientific point of view, the project is expected to provide new contributions to the following topics: a) Modeling of multiple scales in turbulent atmospheric flows near the ground, b) Modeling of the large scale eddies in the atmospheric boundary layer in the presence of obstacles (wind turbines), c) Modeling of the flow dynamics in vorticity dominated flows (wake induced turbulence) in response to disturbances from inflow turbulence. From a technological point of view, the project aims at providing high fidelity information about the complex problem of turbine operation in wind farms. This includes performance and loading estimations on blades of wind turbines located in large offshore wind farms due to the complex atmospheric inflow and the wake induced turbulence.

At present addressing the above problems otherwise is not possible. Downscaling at laboratory level will significantly violate Re similarity since the actual range is in between 10-20∙107. Also, conventional CFD of the URANS type is not suitable because eddy viscosity models integrate the complete turbulence spectrum and so there is no scale distinction. For the LES simulations proposed the foreseen grids are in the order of 100-200∙106 and therefore only HPC facilities in the scale PRACE provides can accommodate them.

The in-house developed compressible CFD solver MaPFlow will be used. MaPFlow is multi-block and MPI enabled. Its scalability has been verified for grids of up to 30 million cells on the national ARIS HPC.


Materials Science (14)


Project Title: 2D heterostructures for spintronics
Project Leader: Dr. Zeila Zanolli, RWTH Aachen University, Physics, Aachen, Germany
Resource Awarded: 27,200,000 standard core hours

M.Sc. Antoine Dewandre, University of Liege, Physics, Liege, Belgium
M.Sc. Farideh Hajiheidari, RWTH Aachen University, Physics, Aachen, Germany
Prof. Matthieu Verstraete, University of Liege, Physics, Liege, Belgium
This project will calculate the electron and spin transport properties of heterostructures of 2D materials. In particular, we will study combinations of graphene with transition metal dichalcogenides, taking into account van der Waals interactions, eventually with a spacing layer. Relaxed structures, both free standing and with a substrate, will be examined for their ground state properties (magnetic and electric) and equilibrium and non-equilibrium transport properties (NEGF). The results will be analysed in the light of spin-pseudospin coupling for the layer and valley degrees of freedom, to select favourable materials for spintronics applications.


Project Title: CHARge TransfER dynamics by time dependEnt Density functional theory
Project Leader: Dr. Biplab Sanyal, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
Resource Awarded: 29,904,000 standard core hours

Dr. Rudra Banerjee, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
Dr. Barbara Brena, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
Xin Chen, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
Raquel Esteban, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
Soumyajyoti Haldar, Uppsala University, Sweden
Dr. Heike Herper, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
In recent times, there has been a tremendous interest in the research community in developing suitable routes for realizing alternative energy sources for the need of human mankind in near future.

The vast abundance of sunlight gives us the opportunity to convert solar energy to electricity and chemical energy through hydrogen production by water splitting, photocatalysis and photosynthesis. In all these areas, ultrafast charge transfer process plays an important role. Though the experimental field has progressed quite significantly in the last decade in studying charge transfer dynamics by femtosecond pump probe techniques coupled with core-hole clock method in the realm of x-ray spectroscopy, femtosecond transient absorption spectroscopy, time dependent fluorescence spectroscopy etc., the theoretical understanding of the ultrafast charge transfer processes via quantum mechanics is still inadequate. The complexity lies in the time dependent description of coupled electron and ion dynamics that occurs non-adiabatically. The adiabatic charge transfer process is not suitable to describe photoactive systems where a transition between different electronic levels occurs due to photon absorption. In this proposal, we aim to study ultrafast charge transfer processes by time dependent density functional theory and non-adiabatic molecular dynamics simulations and apply in a variety of problems. Ab initio molecular dynamics simulations will be performed by VASP code followed by time dependent density functional theory calculations using OCTOPUS code. Finally, non-adiabatic molecular dynamics simulations will be carried out using PYXAID code.


Project Title: Ceria-Titania Composite Catalysts for Water and CO2 Activation
Project Leader: Dr. Michael Nolan, Tyndall National Institute, Cork, Ireland
Resource Awarded: 5,483,520 standard core hours

Mr Stephen Rhatigan, Tyndall National Institute, Cork, Ireland
We are presently facing into an uncertain energy future, with significant growth in the consumption of energy for transport and ICT devices, while at the same time, supplies of fossil fuels, which have been the mainstay of economic growth, are diminishing rapidly. Solutions based on new technologies and fuel sources are required to ensure a stable society and environment into the future and to meet the COP21 targets of limiting the average global temperature rise to less than 2oC. In this project we will work together with experimental collaborators, to apply state of the art Density Functional Theory simulations to develop new composite catalysts based on CeO2 nanoclusters supported on TiO2 and TiO2 nanocluster suppported on CeO2. We particularly aim for composites with high reducibility, activity towards water and CO2 activation. Our results will provide detailed characterisation of these composites, their reducibility, their ability to activate water and CO2. In addition, we will explore the oxidation of water to arrive at overpotentials and the key step in that process as well as CO2 hydrogenation to molecules such as HCOOH or CH3OH.


Project Title: First-principle Carrier Transport in semiconductors using the EPW code
Project Leader: Prof. Feliciano Giustino, University of Oxford, Department of Materials, Oxford, UK
Resource Awarded: 11,375,000 standard core hours

Understanding transport and carrier mobilities in semiconductors is crucial towards developing new electronics and optoelectronics devices for energy applications. Fully predictive first-principles calculations of mobilities have become possible only recently with the advance of ab-initio tools to compute electron-phonon interactions with high accuracy. In fact, engineering “in silico” new materials with tailored electronic properties would be a major step forward. Our Electron-Phonon Wannier (EPW) code allows computing those scattering rates on ultra-dense momentum grids (millions of sampling points), which are required for accurate predictions. We already studied the semiconductors Si, GaAs, GaN and bulk MoS2 to demonstrate the reliability of our EPW implementation; these four representative semiconductors cover the case of (i) direct/indirect bandgap; (ii) polar/non-polar interactions; (iii) strong/weak electron-phonon coupling; and (iv) wide/narrow bandgap. Within CTEPW, we are now aiming at using EPW on computationally more challenging materials such as 2D materials and hybrid perovskites. Our goal is to compute transport properties of a molybdenum disulphide (MoS2) monolayer and of the hybrid organic–inorganic methylammonium lead iodide (CH3NH3PbI3) perovskite. Both materials have attracted considerable attention recently: MoS2 belongs to the topical class of transition metal dichalcogenides and can be used as catalyst as well as in optoelectronic devices and for photovoltaic applications. Methylammonium lead iodide is one of the most promising materials for the next generation of solar cells.


Project Title: Tuning Photonics Properties of Doped Crystalline Silicon NanoParticles
Project Leader: Prof. Dr. Ivan Stich, Slovak Academy of Sciences, Institute of Physics, Department of Complex Physical Systems, Bratislava, Slovak Republic
Resource Awarded: 13,500,000 standard core hours

Dr. Jan Brndiar, Slovak Academy of Sciences, Institute of Physics, Department of Complex Physical Systems, Bratislava, Slovak Republic
Dr. Rene Derian, Slovak Academy of Sciences, Institute of Physics, Department of Complex Physical Systems, Bratislava, Slovak Republic
Prof. Adam Gali, Budapest University of Technology and Economics, Budapest, Hungary
Dr. Bálint Somogyi, Wigner Research Centre for Physics, Institute for Solid State Physics and Optics, Budapest, Hungary
Dr. Kamil Tokar, Slovak Academy of Sciences, Institute of Physics, Department of Complex Physical Systems, Bratislava, Slovak Republic
Dr. Robert Turansky, Slovak Academy of Sciences, Institute of Physics, Department of Complex Physical Systems, Bratislava, Slovak Republic
The DoCSiNaP project proposes to study and tune, using benchmark computational tools, the properties of heavily doped group-IV crystalline semiconductor nanoparticles (SiGe, heavy doping Si:B,P etc.) for photonic applications targeting the low absorption cross section and emission rate due to dominantly indirect transitions. The nanoparticle tuning is proposed via exciton – plasmon coupling, Purcell effect, and applied strain. An important ingredient in tuning opto-electronic properties of the nanoparticles is the access to computational modelling tools yielding accurate optical gaps, quasi-particle gaps, and exciton binding energies. Our target is sub-100meV (<5%) accuracy. We propose a 2-stage modelling procedure where first a benchmark method will be used to tune parameters entering a less accurate but more flexible method in terms of computational time required. To this end the key photonics parameters will first be calculated on smaller model systems with benchmark accuracy using the most accurate computational tools available for system sizes of relevance here, namely the Quantum Monte Carlo method with the quest to determine/tune the best xc-functionals to be used in the next step in advanced DFT techniques. In principle, QMC has the chemical accuracy (1kcal/mol, 0.04 eV) and hence, the gaps are expected to be of benchmark accuracy. This first stage is proposed for the 14DECI call for all qualitatively different systems and under applied strain. In the next stage, advanced DFT techniques (TDDFT) using the best available xc-functionals (most likely some form of a hybrid fuctional), determined in the previous step, will be used in calculations on our in-house HPC clusters on approx. 2nm nanoparticles, i.e. sizes more akin to those studied experimentally. The 2nm nanoparticles will also be studied experimentally by our project partners and hence, the 2 -> 4 nm limit important for the applications will be verified experimentally.


Project Title: On the combined effects of chemistry and temperature on planar fault energies
Project Leader: Dr. Alessandro Mottura, University of Birmingham, School of Metallurgy and Materials, Birmingham, UK
Resource Awarded: 3,528,000 standard core hours

In Ni-based superalloys, a fine distribution of intermetallic precipitates (the gamma prime phase, L12) provides high-temperature strength by reducing dislocation motion. At lower-to-intermediate temperatures, dislocations have to shear these precipitates and shearing modes affect the performance of the alloy. The shearing of the gamma prime precipitates is largely controlled by the planar fault energies in these intermetallics, which is itself affected by composition. As the proportion, shape and distribution of these precipitates has been optimised exhaustively of the past 60 years, attention has now been focussing on fine-tuning the composition of the gamma prime phase to ensure the best combination of planar fault energies to further improve performance of these alloys. This works aims to develop a complete understanding of how both chemistry and temperature affect planar fault energies.


Project Title: First-Principles Study of Complex Oxides
Project Leader: Dr. Julien Varignon, Unité Mixte de Physique CNRS/Thales, Oxitronics, Palaiseau, France
Resource Awarded: 6,615,000 standard core hours

Transition metal oxide perovskites display a wide range of properties and functionalities, coming from the intimate coupling between lattice, charge, orbital and magnetic degrees of freedom [1-4]. These materials are nowadays model systems in solid state physics, since they have shown their potential for devices and applications [5-7]. They have de facto already entered industry. However, novel phenomena are still discovered in perovskite oxides. For instance, a 2-dimensional electron gas has been observed at the interface between two band insulators such as SrTiO3 and LaAlO3 [8], or ferroelectricity, absent in the bulk parent compound, can emerge using strain engineering in SrTiO3 [9]. However, in order to further unlock the potential of perovskites and in the search of novel exotic phenomena, one requires to use or combine more complex systems involving strong electronic correlations and/or covalence effects and/or spin-orbit effects. In the project First-principles Study of Complex Oxides (FiPSCO), we aim to study three different typical systems in order to unveil novel properties that are absent from the bulk parent compound. We propose to use Density Functional Theory (DFT) calculations in order to get some insights on the possible new properties, and their microscopic origin, that can arise when applying strain or interface engineering on/between different oxides. Calculations will then be performed on bulk compounds, their film form (strained compounds) and their interface (combination of two or more materials). The study will be performed jointly with the experimental group of the “Unité Mixte de Physique CNRS Thales”.


Project Title: IN-SIlico DEsign of Transition Metal Dichalcogenide Lubricants
Project Leader: Dr. Benjamin Irving, Czech Technical University in Prague, Department of Control Engineering, Prague, Czech Republic
Resource Awarded: 15,400,000 standard core hours

Dr. Antonio Cammarata, Czech Technical University in Prague, Department of Control Engineering, Prague, Czech Republic
Dr. Paolo Nicolini, Czech Technical University in Prague, Department of Control Engineering, Prague, Czech Republic
The frictionless surface is a dream of mechanical engineers. Lower friction between mechanical components in contact diminishes energy consumption, contact temperature and wear. Transition metal dichalcogenides (TMDs) may be used as dry lubricants, permitting their use in a wide range of environments, making them ideal candidates for the next-generation of ultra-low friction materials.

Perhaps the most well-known TMD is molybdenum disulfide, MoS2, which was one of the first materials to exhibit superlubricity (a near-frictionless regime) under ultra-high vacuum. However, low hardness, high porosity and low adhesion to the substrate are still major drawbacks to understand and tackle.

Furthermore, although mechanisms explaining superlubricity were proposed as long ago as the early 1990s, a comprehensive understanding of the phenomena occurring during the sliding process (under load) is far from certain. Experimental discovery of new TMD-based materials with optimal characteristics is a time-consuming process, requiring development cycles that include candidate material identification, testing, and further structural optimisation. As such, we plan to use computational methods in order to expedite the material design process, by narrowing the composition-structure phase space for experimental exploration to only the most favourable compounds. Our state-of-the-art calculations will be used to establish a unique theory-driven approach for the expedited, property-oriented design of TMDs. Our results will guide the bottom-up approach to the nanofabrication of TMD-based materials of novel functional composition suitable for use as dry lubricants.


Project Title: Multiscale Modelling of Ionic Conductors – Structure, Conductivity and Thermodynamic Stability at Elevated Temperatures
Project Leader: Prof. Natalia Skorodumova, KTH, Sweden
Resource Awarded: 23,284,800 standard core hours

MSc Ana Dobrota, University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
PhD assistant Prof. Igor Pasti, University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
Prof. Andrei Ruban, KTH, Department of Materials Science and Engineering, Stockholm, Sweden
Pjotrs Zguns, Uppsala University, Department of Physics and Astronomy, Uppsala, Sweden
Ion conducting materials are in the heart of many modern clean energy technologies. Here we focus on rare earth doped ceria used for solid oxide fuel cells (SOFCs), various catalysts, etc. Better understanding of mechanisms operating in these materials starting from the atomic level is vital for future technological progress. In doped ceria oxide‑ion conductivity shows complex behaviour depending on dopant concentration, preparation method and sample history – factors influencing distribution of dopants, which largely determine conductivity on a microscopic level. This makes it difficult to draw reliable conclusions about mechanisms and decisive factors of optimal ionic conductivity based only on experimental data.
Even though rare earth doped ceria is widely used in technological applications, presently, there is little information about the 1) dopant & oxygen vacancy distribution and conductivity in bulk doped and co‑doped ceria and 2) thermodynamic stability towards phase separation or ordering at technologically relevant temperatures (T ≤ 1000 Cº). While the former is crucial for an educated improvement of oxygen conductivity, the letter is critical for prediction of long‑term stability of all rare earth ceria based applications.

It is well‑known that cation diffusion in ceria is slow, preventing full degradation. However, in some cases, e.g. as for La‑doped ceria, phase separation can occur during few weeks (S. Dikmen et al., Solid State Ionics, 1999, 126, 89–95) – a time‑scale relevant for industry. This motivates us to study rare earth doped ceria in search of dopants and co‑dopants: a) enhancing the stability of solid electrolytes at temperatures relevant for applications (T ≤ 1000 Cº) and b) improving the oxygen‑ion conductivity by studying structure–conductivity relation.
In order to achieve these goals we use multiscale approach: we combine Density Functional Theory calculations with cluster expansion method, allowing us to perform Monte Carlo modelling, paving the way for the study of i) distribution of dopants and vacancies at various temperatures and concentrations, and thus calculation of ii) phase diagrams, and iii) predicting thermodynamic stability towards phase separation / dopants’ ordering, as well as iv) modelling of oxygen ion diffusion at realistic distribution of dopants elucidating the relation between micro‑structure and conductivity.


Project Title: Rational catalyst design for making use of natural gas and for reducing greenhouse gases
Project Leader: Dr Ganduglia-Pirovano Maria, Centro Superior de Investigaciones Científicas (CSIC), Spain
Resource Awarded: 4,535,900 standard core hours

Dr. Pablo Lustemberg, Consejo Superior de Investigaciones Científicas, Instituto de Catálisis y Petroleoquímica, Madrid, Spain
Dr. Gustavo Murgida, Centro Superior de Investigaciones Científicas (CSIC), Structure Matter Institute, Madrid, Spain
Reforming technologies are gaining in importance because of the availability and price of natural gas, which is one of the cheapest sources of energy available on the planet. Methane can be used directly for combustion thus generating heat and/or power. However, it can be as well used for the production of longer chain alkanes through synthesis thus requiring a preliminary conversion to syngas, a fuel gas mixture consisting primarily of hydrogen and carbon monoxide. Among the different reforming techniques, dry reforming (CH4+CO2 -> 2CO+2H2) using heterogeneous catalysts could represent a very interesting approach both to valorize a cheap source or carbon (CO2) as well as to reduce the overall carbon footprint of the increasing worldwide fossil-based methane consumption. Efficient and and not too expensive catalysts for the dry reforming of methane (DRM) reaction are sought. Selective and stable conversion remains challenging due to the need to activate methane and CO2, unravel the mechanism that sustains good activity and selectivity, and mitigate deactivation through carbon deposition. The complexity of real (powder) catalysts hinders the knowledge of their structure, which is crucial to an understanding of the factors that affect activity and selectivity. However, understanding catalyst structure and reaction mechanism can be obtained by a reductionist approach consisting in creating and evaluating experimental and theoretical model catalysts that mimic the real ones in their complexity. The aim of this theoretical work based on state-of-the-art quantum chemical calculations is to elucidate the dry reforming of methane reaction mechanism on Ni and Cu nanoparticles on mixed oxide supports like Ce1-xZrxO2, as compared to the corresponding metal/CeO2 and metal/ZrO2 systems. The fundamental understanding of the reaction mechanisms, coupled to the detailed analysis of the configuration and properties of the active sites, is expected to help identify the key properties of a successful new catalytic system for the conversion of natural gas to usable chemical fuel. The expected intense interplay between theory and our experimental collaborators at the Brookhaven Natl. Lab. and the TU-Vienna will allow a great opportunity to explore implications of the results for applications.


Project Title: A study of the nano-ionics of yttria-stabilised zirconia using molecular dynamics
Project Leader: Prof. Graeme W. Watson, Trinity College Dublin, Dublin, Ireland
Resource Awarded: 17,000,000 standard core hours

Dr. Aoife Lucid, Trinity College Dublin, Dublin, Ireland
In recent years environmental concerns have driven research towards more efficient, less polluting and renewable energy sources. Solid oxide fuel cells (SOFCs) have emerged as a promising technology. They are believed to be the most efficient fuel cell and are highly fuel flexible. One component of fuel cells that are yet to be optimised are the interfaces in materials which the fuel cell is composed of. The electrolyte material in current generation fuel cells is yttria-stabilised zirconia (YSZ). This electrolyte material is polycrystalline; this multi-crystallinity becomes more pronounced with the move towards nano-materials. These interfaces are extended defects which govern many of the macroscopic properties of the electrolyte material, such as strength, thermal expansion and ionic conductivity. Despite the importance of these interfaces they are largely ignored in the optimisation of materials for SOFC electrolytes. It is generally believed that interfaces in electrolytes, such as grain boundaries, impede oxide ion conductivity across the boundary. An attempt to explain this effect is a macroscopic theory known as space charge layer (SCL) theory. However, there have been studies which have suggested that interfaces in nano-crystalline YSZ actually display in enhanced ionic conductivity which is in direct contradiction with the SCL theory. SCL theory attributes the impeded ionic conductivity at interfaces in nano-crystalline materials to oxygen vacancy depletion in the grain boundary region which is caused by unexplained “excess positive charge” in the grain boundary core repelling the vacancies. The use of a macroscopic theory to explain this atomistic mechanism has left the source of this positive charge a mystery as it is actually the oxygen vacancies which are responsible for positive charge in these materials. Computational studies of interfaces in YSZ are crucial to understanding the impact of interfaces in these materials on the atomic scale. Here, we aim to carry out long trajectory, highly accurate molecular dynamics calculations on bulk, surfaces and interfaces of YSZ in order to elucidate the effect of the interfaces on ionic conductivity in there materials which a view to optimising the performance of electrolytes in current generation SOFCs.


Project Title: Perovskite Interfaces from First-Principles
Project Leader: Prof. Feliciano Giustino, University of Oxford, Department of Materials, Oxford, UK
Resource Awarded: 8,750,000 standard core hours

Renewable energies, such as solar energy conversion, has become a crucial scientific and technological priority due to the environmental impact of fossil fuels and the increased energy demand. Over the last four years, halide perovskites have emerged as one of the most prominent materials for solution processable solar cells. These compounds have achieved power conversion efficiencies of more than 22%, have low materials costs, and are compatible with highly scalable manufacturing processes. Despite their remarkable performance, the fundamental physical phenomena that underlie charge extraction from the perovskite absorbers remain unclear. Within ‘Perovskite interfaces from first-principles’ (PerInt), we will employ a fully ab initio approach (i.e. based on the solution of the fundamental equations of quantum-mechanics) to explore the atomic-scale mechanisms that govern the interfaces of perovskite-based photovoltaic devices. We will explore interfaces between Pb- and Sn-based perovskite compounds and charge transport layers such as TiO2, graphene, graphene-oxide and MoS2. Within PerInt we will identify the structural details of the various interfaces and the related charge re-arrangement and finally, we will reveal the energy level alignment between the absorbers and the charge transport layers. Within PerInt, we will aim to achieve a detailed understanding of these layers, which is necessary for further optimization of perovskite-based solar cells.


Project Title: Computational modeling of the dealumination of rare earth loaded Y
Project Leader: Dr. Jaap Louwen, Albermarle Catalysts Company BV, ARQ, Amsterdam, The Netherlands
Resource Awarded: 4,800,000 standard core hours

Dr. Rosa Bulo, Utrecht University, Inorganic Chemistry and Catalysis, Utrecht, The Netherlands
Dr. Eelco Vogt, Albermarle Catalysts Company BV, ARQ, Amsterdam, The Netherlands
Prof.dr. Bert Weckhuysen, Utrecht University, Inorganic Chemistry and Catalysis, Utrecht, The Netherlands
We aim to model the dealumination process of a Y zeolite (a component of Fluidized Cracking Catalysts used in oil refinery) in the presence of Lanthanum ions within the sodalite cages of the zeolite. Acid strength of the intermediates will be gauged by computing the energy of ammonia sorption, mirroring a generic analytic method in the industry. This will provide an explanation for the observed retention of activity of Fluidized Cracking Catalysts and provide clues to develop more sustainable alternatives for the use of Rare Earths in FCC catalysts.

The CP2K code, optimized within PRACE, is well suited for this purpose given its good scaling properties, in particular for systems of lesser density. (Zeolites are micoporous solids and therefore qualify as such.)


Project Title: Designing artificial 2D crystals by engineering the domain walls
Project Leader: Dr. Jorge Iniguez, Luxembourg Institute of Science and Technology, Materials Research and Technology, Belvaux, Luxembourg
Resource Awarded: 12,773,376 standard core hours

WALLS2CRYST will apply first-principles simulation to design new 2D crystals, with tailor-made functional properties, by engineering the structural domain walls that are typical of ferroelastic and ferroelectric perovskite oxides. More specifically, we will identify optimum conditions to obtain long-range-ordered chemical substitutions at such domain walls, a possibility recently proven experimentally by B. Noheda (Groningen) in collaboration with WALL2CRYST’s P.I. J. Íñiguez (LIST) [FaroKhipoor et al., Nature 515, 379 (2014)]. We will work to obtain, e.g., ferroelectric walls in an otherwise paraelectric matrix, magnetic walls in a non-magnetic matrix, and conductive walls in an insulating matrix. We will thus explore a radically new route to the fabrication of nano-devices of application in next-generation data storage and computer logic architectures, among others.

Plasma & Particle Physics (2)


Project Title: Attoscale Dynamics: Absorption Spectroscopy and Arbitrarily Polarised Pulses of Light
Project Leader: Dr. Andrew Brown, Queen’s University Belfast, School of Maths & Physics, Belfast, UK
Resource Awarded: 6,440,000 standard core hours

The motion of electrons is key to understanding several fundamental processes in chemistry and even biology. Our ability to see, the mechanism of photosynthesis, and the manufacture and efficient operation of solar cells all depend on the underlying process of charge transfer— the transport of electrons across large molecules. Our understanding of this fundamental mechanism has been driven largely by the field of spectroscopy— the study of matter’s interaction with light—and has benefitted greatly from the age of the laser. As laser technology has advanced, it has allowed researchers to ‘view’ electronic motion on its own fundamental time scale: the so-called attosecond (1 as = 10(-18)s) scale. Investigating dynamics this fast requires ultra-short light pulses, and extremely high precision measurements which have only recently become available. With this advance in technology a corresponding advance in theory is required.

This is due to the fact that the motion of electrons in atoms and molecules is not simple. Even in simple atoms, there are several competing electrons, which interact with each other, their ‘parent’ nucleus and the driving laser field to the end of complex dynamics which cannot be captured by simplistic theoretical models. In order to resolve, understand and even predict these dynamics a comprehensive theory is required which can describe the time-dependent dynamics of general atoms, with a full inclusion of multi-electron interactions, and with the ability to describe multiphoton processes (i.e. those driven by long-wavelength laser pulses). While several methods exist which can boast some of these capabilities, none can offer all.

For this reason we have developed the R-matrix with time-dependence (RMT) method. Built on the R-matrix paradigm of dividing space into two regions— one close to the nucleus including all multi-electron interactions, and one far from the nucleus with a simplified description— RMT can describe general atoms in greater detail than any other method in a tractable way. RMT has been applied to resolve several open questions in ultrafast physics, and has recently been extended to treat interactions in the challenging mid-infrared laser regime, increasing its stock as a predictive and analytical tool for experimental attoscience.

In this project— Attoscale Dynamics: Absorption Spectroscopy and Arbitrarily Polarised Pulses of Light (or ADAmS APPLe) — we will apply the RMT code to two current hot topics in attosecond physics. Firstly we will employ the state-of-the-art technique of attosecond transient absorption spectroscopy to elucidate the ultrafast dynamics of ionised systems. This will allow the identification of the key pathways involved in photo-ionisation, one of the fundamental processes in nature. Secondly, we will use newly developed capability in the RMT code to describe so-called ‘circularly-polarised attosecond pulses’ (CPAP), a hugely important but as yet unrealised technological development in attoscience. The realisation of schemes to generate CPAP will be an landmark in the field, and here we will demonstrate RMT’s capability to assist with future experiments.


Project Title: Fast ions with a twist: confining energetic particles in W7-X and other challenging geometries
Project Leader: Taina Kurki-Suonio, Aalto University, Espoo, Finland
Resource Awarded: 16,000,000 standard core hours

Joona Kontula, Aalto University, Espoo, Finland
Patrik Ollus, Aalto University, Espoo, Finland
Seppo Sipilä, Aalto University, Espoo, Finland
Konsta Särkimäki, Aalto University, Espoo, Finland
Jari Varje, Aalto University, Espoo, Finland
Abstract:Stellarators could provide a fast track to fusion electricity via magnetic confinement. Their strengths and weaknesses are to a large extent orthogonal to those of tokamaks, which have so far been the most successful fusion concpet. The year 2015 witnessed the first plasmas in W7-X, the world´s largest stellarator, at the Max-Planck-Institut für Plasmaphysik in Greifswald, Germany. W7-X is expected to provide superior confinement compared to its predecessors thanks to the careful geometry optimization that was made possible only by the development of high-power supercomputers.

In the first operational phase only electrons were heated and the results exceeded all expectations. In 2016, also ion heating will be adopted, mainly in the form of high-energy neutral atom beams. The purpose of this proposal is to use our unique numerical tools to address critical fast ion issues for scenario optimization and wall protection.

The work is carried out using the ASCOT code, currently the most comprehensive fast ion simulation tool in the world. In 2015, ASCOT has been made compatible with stellarators. ASCOT follows particle trajectories in a static, true-to-life 3D magnetic field of tokamaks and stellarators. Interaction with a static plasma background is accomplished by Monte Carlo collision operators. The high-resolution 3D first wall consists of millions of elements. ASCOT has already been used to assess the ITER fast ion power loads in realistic 3D magnetic fields (EU project F4E-GRT-379).

The new, increasingly complex physics models have increased the computational cost of simulations. The high-resolution 3D first wall, the introduction of stellarator geometry, and the expanded test particle parameter space also require larger simulations to overcome the increased Monte Carlo noise. While the generation of test particles representing fusion alphas or NBI ions is quite straightforward, the recent introduction of ICRH operator called RFOF implies substantially longer simulation times for the ions representing ICRH-accelerated ones. In some cases the validity of the guiding-center formalism must be confirmed and expensive full-orbit simulations performed. The simulations of fast ions in W7-X plasmas are already running on the IFERC Helios (until it’s shutdown at the end of 2016), as is a new version of ASCOT, constructed to maximize the full power of Xeon Phi coprocessors.