German Research School for Simulation science GmbH

Aachen, Germany

German Research School for Simulation science GmbH

Aachen, Germany

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Grant
Agency: European Commission | Branch: FP7 | Program: CPCSA | Phase: ICT-2013.9.9 | Award Amount: 72.73M | Year: 2013

Understanding the human brain is one of the greatest challenges facing 21st century science. If we can rise to the challenge, we can gain profound insights into what makes us human, develop new treatments for brain diseases and build revolutionary new computing technologies. Today, for the first time, modern ICT has brought these goals within sight. The goal of the Human Brain Project, part of the FET Flagship Programme, is to translate this vision into reality, using ICT as a catalyst for a global collaborative effort to understand the human brain and its diseases and ultimately to emulate its computational capabilities. The Human Brain Project will last ten years and will consist of a ramp-up phase (from month 1 to month 36) and subsequent operational phases.\nThis Grant Agreement covers the ramp-up phase. During this phase the strategic goals of the project will be to design, develop and deploy the first versions of six ICT platforms dedicated to Neuroinformatics, Brain Simulation, High Performance Computing, Medical Informatics, Neuromorphic Computing and Neurorobotics, and create a user community of research groups from within and outside the HBP, set up a European Institute for Theoretical Neuroscience, complete a set of pilot projects providing a first demonstration of the scientific value of the platforms and the Institute, develop the scientific and technological capabilities required by future versions of the platforms, implement a policy of Responsible Innovation, and a programme of transdisciplinary education, and develop a framework for collaboration that links the partners under strong scientific leadership and professional project management, providing a coherent European approach and ensuring effective alignment of regional, national and European research and programmes. The project work plan is organized in the form of thirteen subprojects, each dedicated to a specific area of activity.\nA significant part of the budget will be used for competitive calls to complement the collective skills of the Consortium with additional expertise.


Olubiyi O.O.,Jülich Research Center | Olubiyi O.O.,German Research School for Simulation science GmbH | Strodel B.,Jülich Research Center | Strodel B.,Heinrich Heine University Düsseldorf
Journal of Physical Chemistry B | Year: 2012

In this simulation study, we present a comparison of the secondary structure of the two major alloforms of the Alzheimer's peptide (Aβ1-40 and Aβ1-42) on the basis of molecular dynamics (MD) simulations on thea microsecond time scale using the two GROMOS96 force fields ffG43a2 and ffG53a6. We observe peptide and force-field related differences in the sampled conformations of Aβ1-40 and Aβ1-42, which we characterize in terms of NMR chemical shifts calculated from the MD trajectories and validate against the corresponding experimental NMR results. From this analysis, we can conclude that ffG53a6 is better able to model the structural propensities of Aβ1-40 and Aβ1-42 than ffG43a2. Furthermore, we provide a description of the influences of pH and binding of D3, a 12-residue d-enantiomeric peptide with demonstrated antiamyloid effects, on the structure of Aβ1-42. We demonstrate that, under slightly acidic conditions, protonation of the three histidine residues in Aβ1-42 promotes the formation of β-sheets via a reduction in electrostatic repulsion between the two terminal regions. Our studies further reveal that the binding between D3 and Aβ1-42 is driven by electrostatic interactions between negatively charged Aβ1-42 residues and the five positively charged arginine residues of D3. The binding of D3 was found to induce large conformational changes in the amyloid peptide, with a reduction in β-sheet units being the most significant effect recorded, possibly explaining the observed amyloid-inhibiting properties of the d-peptide. © 2012 American Chemical Society.


Kolar M.,Czech Institute of Organic Chemistry And Biochemistry | Kolar M.,German Research School for Simulation science GmbH | Kolar M.,Jülich Research Center | Hostas J.,Czech Institute of Organic Chemistry And Biochemistry | And 2 more authors.
Physical Chemistry Chemical Physics | Year: 2014

The σ-holes of halogen atoms on various aromatic scaffolds were described in terms of their size and magnitude. The electrostatic potential maps at the CAM-B3LYP-D3(bj)/def2-QZVP level were calculated and the σ-holes of more than 100 aromatic analogues were thoroughly analysed to relate the σ-holes to the binding preferences of the halogenated compounds. Both the size and magnitude of the σ-hole increase when passing from chlorinated to iodinated analogues. Also, the σ-hole properties were studied upon chemical substitution of the aromatic ring as well as in the aromatic ring. Further, the angular variations of the interactions were investigated on a selected set of halogenbenzene complexes with argon and hydrogen fluoride (HF). In order to analyse interaction energy components, DFT-SAPT angular scans were performed. The interaction energies of bromobenzene complexes were evaluated at the CCSD(T)/complete basis set level providing the benchmark energetic data. The strength of the halogen bond between halogenbenzenes and Ar atoms and HF molecules increases while its directionality decreases when passing from chlorine to iodine. The decrease of the directionality of the halogen bond is larger for a HF-containing complex and is caused by electrostatic and exchange-repulsion energies. These findings are especially valuable for protein-halogenated ligand-binding studies, applied in the realm of rational drug development and lead optimisation. © the Partner Organisations 2014.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: ICT-2011.9.13 | Award Amount: 16.30M | Year: 2011

DEEP proposes to develop a novel, Exascale-enabling supercomputing platform along with the optimisation of a set of grand-challenge codes simulating applications highly relevant for Europes science, industry and society. The DEEP System will realise a Cluster Booster Architecture that can cope with the limitations purported by Amdahls Law. It will serve as proof-of-concept for a next-generation 100 Petaflop/s PRACE production system, striving for independent provision of HPC technology, in particular general purpose Exascale performance supercomputers in Europe. The DEEP concept is based on the duality of an advanced multi-core Cluster system with InfiniBand interconnect complemented by a Booster of Intel many-core MIC processors connected through a Terabit EXTOLL network. A novel open source system software stack along with Cluster Booster adapted programming models, libraries, and performance tools will achieve high productivity and will enable unprecedented scalability on millions of cores. The DEEP hardware and software technology is developed in Europe while the new many-core processor is an essential component of international cooperation. The DEEP concept has the potential to improve the power efficiency of HPC systems by an order of magnitude. Its innovative cooling concept will allow approaching power usage effectiveness values very close to 1. Representative HPC codes from Health and Biology, Climatology, Seismic Imaging, Industrial Design, Space Weather, and Superconductivity will be optimised on DEEP and the extrapolation to millions of cores will be demonstrated. The pan-European DEEP consortium has proven competence to meet the projects massive technological and scientific challenges. DEEP aims at disseminating knowledge amongst major European industrial stakeholders and the entire PRACE consortium through its technical advisory group STRATOS and will contribute to the vision of the PROSPECT association for a European HPC technology platform.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA | Phase: INFRA-2012-3.3. | Award Amount: 1.68M | Year: 2012

The use of High Performance Computing (HPC) is commonly recognized a key strategic element both in research and industry for an improvement of the understanding of complex phenomena. The constant growth of generated data - Big Data - and computing capabilities of extreme systems lead to a new generation of computers composed of millions of heterogeneous cores which will provide Exaflop performances in 2020. Such hardware architectures lead to outstanding technological breakthrough possibilities in computations but also to outstanding software challenges. In front of this challenge, the international community has launched various programs and organizations. In US this has been done through some funding programs such as the Ubiquitous High Performance Computing program and the co-design centre call. The International Exascale Software Project (IESP) had the goal to built a US and international roadmap. In Europe the EU PRACE project which is preparing the tier-0 level of the European HPC ecosystem, has been implemented. The successful first European Exascale Software Initiative (EESI1) federated the European community, built a preliminary European cartography, vision and roadmap and stated as the European voice at international level. However, it is necessary to go one step further towards implementation, by establishing a European structure to gather the European community, by providing periodically cartography and roadmaps and dynamic synthesis and recommendations in (i) defining and following up concrete impacts of R&D projects, (ii) detecting disruptive technologies (iii) addressing cross cutting issues in numerical processing and software engineering, (iiii) developing gap analysis methodology towards Exascale roadmap implementation. Overall, to achieve Exascale targets, international collaboration need to be explored and a more dynamical structure must be implemented.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: ICT-2011.10.2 | Award Amount: 1.93M | Year: 2011

To maximise the scientific output of a high-performance computing system, different stakeholders pursue different strategies. While individual application developers are trying to shorten the time to solution by optimising their codes, system administrators are tuning the configuration of the overall system to increase its throughput. Yet, the complexity of todays machines with their strong interrelationship between application and system performance presents serious challenges to achieving these goals. The HOPSA project (HOListic Performance System Analysis) therefore sets out to create an integrated diagnostic infrastructure for combined application and system tuning - with the former being under EU and the latter being under Russian responsibility. Starting from system-wide basic performance screening of individual jobs, an automated workflow will route findings on potential bottlenecks either to application developers or system administrators with recommendations on how to identify their root cause using more powerful diagnostic tools. Developers can choose from a variety of mature performance-analysis tools developed by our consortium. Within this project, the tools will be further integrated and enhanced with respect to scalability, depth of analysis, and support for asynchronous tasking, a node-level paradigm playing an increasingly important role in hybrid programs on emerging hierarchical and heterogeneous systems. Using our infrastructure, the scientific output rate of a system will be increased in three ways: First, the enhanced tool suite will lead to better optimisation results, expanding the potential of the codes to which they are applied. Second, integrating the tools into an automated diagnostic workflow will ensure that they are used both (i) more frequently and (ii) more effectively, further multiplying their benefit. Finally, our holistic approach will lead to a more targeted optimisation of the interactions between application and system.

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