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arXiv 2018年

作者： Albrecht, Clelia Klaar, Constanze Pask, John Ernest Schweitzer, Marc Alexander Sukumar, N. Ziegenhagel, Albert Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin53757 Germany Physics Division Lawrence Livermore National Laboratory 7000 East Avenue LivermoreCA94550 United States Institute for Numerical Simulation Rheinische Friedrich-Wilhelms-Universität Wegelerstr. 6 Bonn53115 Germany Department of Civil and Environmental Engineering University of California DavisCA95616 United States

Quantum mechanical calculations require the repeated solution of a Schrödinger equation for the wavefunctions of the system, from which materials properties follow. Recent work has shown the effectiveness of enriched finite element type Galerkin methods at significantly reducing the degrees of freedom required to obtain accurate solutions. However, time to solution has been adversely affected by the need to solve a generalized rather than standard eigenvalue problem and the ill-conditioning of associated systems matrices. In this work, we address both issues by proposing a stable and efficient orbital-enriched partition of unity method to solve the Schrödinger boundary-value problem in a parallelepiped unit cell subject to Bloch-periodic boundary conditions. In the proposed partition of unity method, the three-dimensional domain is covered by overlapping patches, with a compactly-supported weight function associated with each patch. A key ingredient in our approach is the use of non-negative weight functions that possess the flat-top property, i.e., each weight function is identically equal to unity over some finite subset of its support. This flattop property provides a pathway to devise a stable approximation over the whole domain. On each patch, we use p-th degree orthogonal (Legendre) polynomials that ensure p-th order completeness, and in addition include eigenfunctions of the radial Schrödinger equation. Furthermore, we adopt a variational lumping approach to construct a (block-)diagonal overlap matrix that yields a standard eigenvalue problem for which there exist efficient eigensolvers. The accuracy, stability, and efficiency of the proposed method is demonstrated for the Schrödinger equation with a harmonic potential as well as a localized Gaussian potential. We show that the proposed approach delivers optimal rates of convergence in the energy, and the use of orbital enrichment significantly reduces the number of degrees of freedom for a given desired accu

关键词： Eigenvalues and eigenfunctions

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VERCE Delivers a Productive E-science Environment for Seismology Research

VERCE Delivers a Productive E-science Environment for Seismo...

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IEEE International Conference on e-Science and Grid computing

作者： Malcolm Atkinson Michele Carpené Emanuele Casarotti Steffen Claus Rosa Filgueira Anton Frank Michelle Galea Tom Garth André Gemünd Heiner Igel Iraklis Klampanos Amrey Krause Lion Krischer Siew Hoon Leong Federica Magnoni Jonas Matser Alberto Michelini Andreas Rietbrock Horst Schwichtenberg Alessandro Spinuso Jean-Pierre Vilotte University of Edinburgh UK Supercomputing Applications and Innovation Department (CINECA) Italy Istituto Nazionale di Geofisica e Vulcanologia (INGV) Italy Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Germany The University of Edinburgh Edinburgh Edinburgh GB Leibniz Supercomputing Centre Germany University of Liverpool UK Ludwig-Maximilians-University Germany Royal Netherlands Meteorological Institute (KNMI) The Netherlands Institut de Physique du Globe de Paris (IPGP) France

The VERCE project has pioneered an e-Infrastructure to support researchers using established simulation codes on high-performance computers in conjunction with multiple sources of observational data. This is accessed and organised via the VERCE science gateway that makes it convenient for seismologists to use these resources from any location via the Internet. Their data handling is made flexible and scalable by two Python libraries, ObsPy and dispel4py and by data services delivered by ORFEUS and EUDAT. Provenance driven tools enable rapid exploration of results and of the relationships between data, which accelerates understanding and method improvement. These powerful facilities are integrated and draw on many other e-Infrastructures. This paper presents the motivation for building such systems, it reviews how solid-Earth scientists can make significant research progress using them and explains the architecture and mechanisms that make their construction and operation achievable. We conclude with a summary of the achievements to date and identify the crucial steps needed to extend the capabilities for seismologists, for solid-Earth scientists and for similar disciplines.

关键词： Computational modeling Data models Logic gates Context Earthquakes Analytical models Libraries

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Trust Issues in Shibboleth-Enabled Federated Grid Authentication and Authorization Infrastructures Supporting Multiple Grid Middleware

Trust Issues in Shibboleth-Enabled Federated Grid Authentica...

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IEEE International Conference on e-Science and Grid computing

作者： Christian Grimm Ralf Groeper Siegfried Makedanz Hans Pfeiffenberger Peter Gietz Martin Haase Michael Schiffers Wolfgang Ziegler RRZN Leibniz Universität Hannover Hanover Germany Alfred Wegener Institute Bremerhaven Germany DAASI International GmbH Tubingen Germany Ludwig-Maximilians University of Munich Munich Germany Institute for Algorithms and Scientific Computing Fraunhofer Gesellschaft e. V. Sankt Augustin Germany

In Germany's D-Grid project numerous grid communities are working together to develop a common overarching grid. One major aim of D-Grid is thus to integrate the existing grid deployments and make them interoperable. The major challenge in this endeavor lies in the heterogeneity of the current implementations: three grid middleware and different VO management approaches have to be orchestrated to achieve the intended interoperability. This paper presents some of the findings of the IVOM project regarding VO management technologies. Furthermore, options are discussed for making Shibboleth federations and VO management systems interoperable so that attributes from both sources can be used for authentication and authorization in grids. Finally two approaches, one using a so called "trust proxy" and one without trust proxying, are presented and support by current grid middleware is discussed.

关键词： Authentication Authorization Middleware Project management Technology management Grid computing scientific computing Communities IP networks Web services

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A representer theorem for deep kernel learning

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2019年第1期20卷

作者： Bastian Bohn Christian Rieger Michael Griebel Institute for Numerical Simulation University of Bonn Bonn Germany Institute for Numerical Simulation University of Bonn Bonn Germany and Fraunhofer Center for Machine Learning Fraunhofer Institute for Algorithms and Scientific Computing SCAI Sankt Augustin Germany

In this paper we provide a finite-sample and an infinite-sample representer theorem for the concatenation of (linear combinations of) kernel functions of reproducing kernel Hilbert spaces. These results serve as mathematical foundation for the analysis of machine learning algorithms based on compositions of functions. As a direct consequence in the finite-sample case, the corresponding infinite-dimensional minimization problems can be recast into (nonlinear) finite-dimensional minimization problems, which can be tackled with nonlinear optimization algorithms. Moreover, we show how concatenated machine learning problems can be reformulated as neural networks and how our representer theorem applies to a broad class of state-of-the-art deep learning methods.

关键词： artificial neural networks deep kernel learning multilayer kernel regularized least-squares regression representer theorem

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CASP2 experiences with docking flexible ligands using FLEXX†

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Proteins: Structure, Function, and Bioinformatics 1998年第S1期29卷

作者： Bernd Kramer Matthias Rarey Thomas Lengauer German National Research Center for Information Technology (GMD) Institute for Algorithms and Scientific Computing (SCAI) Schloß Birlinghoven Germany

We have applied our docking program FLEXX to all eight CASP2 targets involving protein complexes with small ligands. Of the seven targets that were kept in the CASP2 experiment, we could solve two. We found important parts of the solution in four other examples, and were unsuccessful on the remaining example. This paper discusses all predictions in detail. Each of our prediction runs took just a few minutes of computer time on a standard workstation and could thus be demonstrated in real time at the CASP meeting. We believe that this speed is the prime strength of our program FLEXX. In quality, our predictions are competitive with those produced by other predictors. The experiment showed that possible objectives of improvement of the FLEXX program are to incorporate relevant aspects of receptor flexibility, deal with water molecules in the receptor pocket, allow for a postoptimization to refine favorable complexes, and improve the scoring function. Proteins, Suppl. 1:221–225, 1997. © 1998 Wiley-Liss, Inc.

关键词： molecular docking flexible docking protein–ligand interaction molecular flexibility conformational analysis drug design

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Mathematical modeling and visualization of topologically non-trivial solutions in general relativity

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Journal of Physics: Conference Series 2021年第1期1730卷

作者： Igor Nikitin Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven 53757 Sankt Augustin Germany

In general relativity, there is a class of solutions that currently do not have observed analogues, but on which the theory is shaped, giving an understanding what is fundamentally possible within its framework. Such solutions include wormholes, tunnels that connect distant regions in spacetime. Although not a single wormhole has yet been discovered, there is a large number of works devoted to their study, thanks to which wormholes as a class of solutions become firmly established in modern science. In this paper, we consider two topologically nontrivial types of solutions related to wormholes. First: wormholes that can open and close. In this relation, we will discuss topological censorship theorems, which under certain conditions prohibit changing topology. We will also discuss known ways to circumvent these theorems. Using analytical and numerical methods, as well as visualization, we will construct an example of an opening and closing wormhole with the dimensions of the central black hole in the Milky Way galaxy. Our construction continues the work by Kardashev, Novikov and Shatskiy, in which a static wormhole with the same parameters was considered. The second type is a modification of Visser's dihedral wormhole solution for a dynamic case.

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On dark matter, dark energy and Bose-Einstein condensate

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AIP Conference Proceedings 2023年第1期2872卷

作者： Igor Nikitin Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven 53757 Sankt Augustin Germany

Equation of state for Bose-Einstein condensate is evaluated in two cases: non-interacting particles and particles interacting via potential possessing a non-trivial minimum. In astrophysical context, the first case becomes equivalent to cold dark matter, while the second case – to dark energy. A particular cosmological scenario with dark matter injection from quasi-black holes to galactic halo, followed by Bose-Einstein condensation in the intergalactic medium is considered.

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On dark stars, galactic rotation curves and fast radio bursts

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Journal of Physics: Conference Series 2021年第1期1730卷

作者： Igor Nikitin Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven 53757 Sankt Augustin Germany

This paper is a continuation of our recent work on Radial Dark Matter stars (RDM-stars), black holes, coupled with radial flows of dark matter. As a galaxy model, it produces flat rotation curves, approximately valid for many galaxies far from the center. In this paper, more detailed modeling is carried out, including the vicinity of the galactic center. Assuming that the distribution of stellar black holes repeats the distribution of luminous matter, we get a perfect match between the model rotation curves and the observed ones. Further, using numerical integration, we examine the gravitational field of an individual RDM-star. The computation shows the event horizon being erased and rapidly increasing mass density arising instead (mass inflation). In this regime, we apply the previously constructed Planck star model, where at high densities a repulsive force occurs (quantum bounce). In our stationary model, the evolution of a Planck star has stopped under the pressure of dark matter flows. This system is considered as a possible source of Fast Radio Bursts (FRBs). In a scenario involving an asteroid falling onto an RDM-star, the model reproduces the correct frequency range of FRBs. Their total energy, coherence and short duration are explained as well.

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NFDI4Health workflow and service for synthetic data generation, assessment and risk management

arXiv

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arXiv 2024年

作者： Moazemi, Sobhan Adams, Tim Ng, Hwei Geok Kühnel, Lisa Schneider, Julian Näher, Anatol-Fiete Fluck, Juliane Fröhlich, Holger Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing SCAI Germany ZB MED – Information Centre for Life Sciences Germany Faculty of Technology Bielefeld University Germany Digital Global Public Health Hasso Plattner Institute for Digital Engineering University of Potsdam Germany Institute of Medical Informatics Charité–Universitätsmedizin Germany Method Development Research Infrastructure and Information Technology Robert Koch Institute Germany The Agricultural Faculty University of Bonn Germany Institute for Geodesy and Geoinformation University of Bonn Germany University of Bonn Germany

Individual health data is crucial for scientific advancements, particularly in developing Artificial Intelligence (AI);however, sharing real patient information is often restricted due to privacy concerns. A promising solution to this challenge is synthetic data generation. This technique creates entirely new datasets that mimic the statistical properties of real data, while preserving confidential patient information. In this paper, we present the workflow and different services developed in the context of Germany’s National Data Infrastructure project NFDI4Health. First, two state-of-the-art AI tools (namely, VAMBN and MultiNODEs) for generating synthetic health data are outlined. Further, we introduce SYNDAT (a public web-based tool) which allows users to visualize and assess the quality and risk of synthetic data provided by desired generative models. Additionally, the utility of the proposed methods and the web-based tool is showcased using data from Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Center for Cancer Registry Data of the Robert Koch institute (RKI). © 2024, CC BY-SA.

关键词： Electronic health record

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Ten new insights in climate science 2024

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One Earth 2025年

作者： Schaeffer, Roberto Schipper, E. Lisa F. Ospina, Daniel Mirazo, Paula Alencar, Ane Anvari, Mehrnaz Artaxo, Paulo Biresselioglu, Mehmet Efe Blome, Tanja Boeckmann, Melanie Brink, Ebba Broadgate, Wendy Bustamante, Mercedes Cai, Wenju Canadell, Josep G. Cardinale, Roberto Chidichimo, Maria Paz Ditlevsen, Peter Eicker, Ursula Feron, Sarah Fikru, Mahelet G. Fuss, Sabine Gaye, Amadou T. Gustafsson, Örjan Harring, Niklas He, Cheng Hebden, Sophie Heilemann, Adrian Hirota, Marina Janardhanan, Nandakumar Juhola, Sirkku Jung, Tae Yong Kejun, Jiang Kilkiș, Şiir Kumarasinghe, Nilushi Lapola, David Lee, June-Yi Levis, Carolina Lusambili, Adelaide Maasakkers, Joannes D. MacIntosh, Claire Mahmood, Jemilah Mankin, Justin S. Marchegiani, Pía Martin, Maria Mukherji, Aditi Muñoz-Erickson, Tischa A. Niazi, Zeenat Nyangon, Joseph Pandipati, Santosh Perera, Amarasinghage T.D. Persad, Geeta Persson, Åsa Redman, Aaron Riipinen, Ilona Rockström, Johan Roffe, Sarah Roy, Joyashree Sakschewski, Boris Samset, Bjørn H. Schlosser, Peter Sharifi, Ayyoob Shih, Wan-Yu Sioen, Giles B. Sokona, Youba Stammer, Detlef Suk, Sunhee Thiam, Djiby Thompson, Vikki Tullos, Erin van Westen, René M. Vargas Falla, Ana Maria Vecellio, Daniel J. Worden, John Wu, Henry C. Xu, Chi Yang, Yang Zachariah, Mariam Zhang, Zhen Ziervogel, Gina Federal University of Rio de Janeiro Rio de Janeiro Brazil University of Bonn Bonn Germany Future Earth Secretariat Stockholm Sweden Arizona State University Tempe AZ United States Amazon Environmental Research Institute (IPAM) Brasilia Brazil Fraunhofer Institute for Algorithms and Scientific Computing SCAI St. Augustin Germany Potsdam Institute for Climate Impact Research (PIK) Potsdam Germany University of São Paulo São Paulo Brazil İzmir University of Economics İzmir Turkey Climate Service Center Germany (GERICS) Helmholtz-Zentrum Hereon Hamburg Germany University of Bremen Bremen Germany Lund University Lund Sweden University of Brasilia Brasilia Brazil Ocean University of China Qingdao China Xiamen University Xiamen China Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment Canberra ACT Australia University College London London United Kingdom National Scientific and Technical Research Council (CONICET) Buenos Aires Argentina National University of San Martin Buenos Aires Argentina University of Copenhagen Copenhagen Denmark Concordia University Montreal QC Canada University of Groningen Groningen Netherlands Missouri University of Science and Technology Rolla MO United States Mercator Research Institute on Global Commons and Climate Change (MCC) Berlin Germany Humboldt-University of Berlin Berlin Germany Cheikh Anta Diop University Dakar Senegal Stockholm University Stockholm Sweden University of Gothenburg Gothenburg Sweden Institute of Epidemiology Helmholtz Zentrum München—German Research Center for Environmental Health (GmbH) Neuherberg Germany European Space Agency (ESA) - European Centre for Space Applications and Telecommunications (ECSAT) Oxford United Kingdom Federal University of Santa Catarina Florianopolis Brazil Institute for Global Environmental Strategies (IGES) Hayama Japan University of Helsinki Helsinki Finland Yonsei University Graduate Seoul South Korea Chinese Academy of Macroeconomic

The years 2023 and 2024 were characterized by unprecedented warming across the globe, underscoring the urgency of climate action. Robust science advice for decision makers on subjects as complex as climate change requires deep cross- and interdisciplinary understanding. However, navigating the ever-expanding and diverse peer-reviewed literature on climate change is enormously challenging for individual researchers. We elicited expert input through an online questionnaire (188 respondents from 45 countries) and prioritized 10 key advances in climate-change research with high policy relevance. The insights span a wide range of areas, from changes in methane and aerosol emissions to the factors shaping citizens’ acceptance of climate policies. This synthesis and communications effort forms the basis for a science-policy report distributed to party delegations ahead of the 29th session of the Conference of the Parties (COP29) to inform their positions and arguments on critical issues, including heat-adaptation planning, comprehensive mitigation strategies, and strengthened governance in energy-transition minerals value chains. © 2025 The Authors

关键词： adaptation climate policy climate science governance just transition mitigation resilience science policy

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