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arXiv 2021年

作者： Nikitin, Igor Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin53757 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, which can be considered as a model of a teleportation event. © 2021, CC BY.

关键词： Topology

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Cell-centred multigrid revisited

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computing and Visualization in Science 2004年第3期7卷 129-140页

作者： Marcus Mohr Roman Wienands Friedrich-Alexander-University of Erlangen-Nuremberg Erlangen Germany Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin Germany

In this paper we treat the cell-centred multigrid approach, which distinguishes itself from the classical vertex-centred multigrid by a non-nested hierarchy of grid nodes and the use of constant, problem-independent transfer operators even in complicated situations. We demonstrate, that the tool of Local Fourier Analysis can also be profitably applied in this setting. We consider in detail the standard transfer operators from literature and their respective polynomial and Fourier orders, paying special attention to the combination of piecewise constant interpolation and its adjoint. Furthermore, we give several numerical examples for model problems and an application from biomedical engineering.

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Computational Life Sciences 1

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丛书名： Studies in Big Data

1000年

作者： Jens Dörpinghaus Sebastian Schaaf Vera Weil Alexander Apke

ISBN: (数字)9783031084119

ISBN: (纸本)9783031084102;9783031084133

This book broadly covers the given spectrum of disciplines in Computational Life Sciences, transforming it into a strong helping hand for teachers, students, practitioners and researchers. In Life Sciences, problem-solving and data analysis often depend on biological expertise combined with technical skills in order to generate, manage and efficiently analyse big data. These technical skills can easily be enhanced by good theoretical foundations, developed from well-chosen practical examples and inspiring new strategies. This is the innovative approach of Computational Life Sciences-Data Engineering and Data Mining for Life Sciences: We present basic concepts, advanced topics and emerging technologies, introduce algorithm design and programming principles, address data mining and knowledge discovery as well as applications arising from real projects. Chapters are largely independent and often flanked by illustrative examples and practical advise.

关键词： Data Engineering Bioinformatics Big Data Computational Intelligence

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Large scale chemical patent mining with UIMA and UNICORE

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Journal of Cheminformatics 2012年第1期4卷 1-2页

作者： Alexander Klenner Marc Zimmermann Sandra Bergmann Mathilde Romberg Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin 53754 Germany Forschungszentrum Juelich GmbH Juelich 52425 Germany

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Iterative methods for reluctance based PEEC models

Iterative methods for reluctance based PEEC models

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International Zurich Symposium on Electromagnetic Compatibility (EMC Zurich)

作者： M.L. Zitzmann T. Clees R. Weigel Institute for Electronics Engineering University of Erlangen Nuremberg Erlangen Germany Algorithms and Scientific Computing Fraunhofer Institute Germany

This paper presents the application of iterative solution techniques to large sparse equation systems derived from PEEC modeling. The PEEC method (partial element equivalent circuit) is an approach to transform conducting objects into linear networks with basic electrical elements. Such equivalent circuit models can be simulated by conventional circuit solvers such as SPICE (simulation program for integrated circuit emphasis) based on the MNA (modified nodal analysis) approach. By applying appropriate sparsification techniques sparse system matrices can be obtained, adequate for iterative solvers. By using multilevel approaches linear complexity in time and memory requirements can be achieved in the best case. The suitability of different iterative methods as applied to such systems is compared by means of examples

关键词： Iterative methods Sparse matrices Circuit simulation Integrated circuit modeling Analytical models Iterative algorithms Equivalent circuits Transforms Integral equations Inductance

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A Graph-Theoretic Approach to the Train Marshalling Problem

A Graph-Theoretic Approach to the Train Marshalling Problem

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Federated Conference on Computer Science and Information Systems

作者： Jens Dorpinghaus Rainer Schrader Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Institut fur Informatik Universitat zu Koln

ISBN: (纸本)9781538623718

Rearranging cars of an incoming train in a hump yard is a widely discussed topic. We focus on the train marshalling problem where the incoming cars of a train are distributed to a certain number of sorting tracks. When pulled out again to build the outgoing train, cars sharing the same destination should appear consecutively. The goal is to minimize the number of sorting tracks. We suggest a graph-theoretic approach for this NP-complete problem. The idea is to partition an associated directed graph into what we call pseudochains of minimum length. We describe a greedy-type heuristic to solve the partitioning problem which, on random instances, performs better than the known heuristics for the train marshalling problem.

关键词： TRAIN Cars on-the-job training particle tracks Track tracks Tracks Heuristics REARRANGING grade Nondeterministic polynomial-time hard PULL-OUT

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Sparse tensor product approximation for a class of generalized method of moments estimators

arXiv

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arXiv 2020年

作者： Gilch, Alexandros Griebel, Michael Oettershagen, Jens Institute for Numerical Simulation Bonn Germany Fraunhofer Institute for Algorithms and Scientific Computing SCAI Sankt Augustin Germany

Generalized Method of Moments (GMM) estimators in their various forms, including the popular Maximum Likelihood (ML) estimator, are frequently applied for the evaluation of complex econometric models with not analytically computable moment or likelihood functions. As the objective functions of GMM-and ML-estimators themselves constitute the approximation of an integral, more precisely of the expected value over the real world data space, the question arises whether the approximation of the moment function and the simulation of the entire objective function can be combined. Motivated by the popular Probit and Mixed Logit models, we consider double integrals with a linking function which stems from the considered estimator, e.g. the logarithm for Maximum Likelihood, and apply a sparse tensor product quadrature to reduce the computational effort for the approximation of the combined integral. Given Hölder continuity of the linking function, we prove that this approach can improve the order of the convergence rate of the classical GMM-and ML-estimator by a factor of two, even for integrands of low regularity or high dimensionality. This result is illustrated by numerical simulations of Mixed Logit and Multinomial Probit integrals which are estimated by ML-and GMM-estimators, *** Codes 62P20, 65D30, 65D32 © 2020, CC BY.

关键词： Method of moments

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The octet rule in chemical space: generating virtual molecules

arXiv

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arXiv 2017年

作者： Hamaekers, Rafel Maaß, Astrid Hamaekers, Jan Fraunhofer Institute Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt AugustinD-53754 Germany

We present a generator of virtual molecules that selects valid chem- istry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated *** to existing approaches, our model is simpler and faster, generates new chemistry and avoids invalid chemistry. Its versatility is illustrated by the correct generation of molecules containing third-row elements and a surprisingly adept handling of complex boron chem- *** any empirical parameters, our model is designed to be valid also in unexplored regions of chemical space. One first unex- pected finding is the high prevalence of dipolar structures among gen- erated molecules. Copyright © 2017, The Authors. All rights reserved.

关键词： Molecules

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Grid-enabled virtual screening against malaria

Grid-enabled virtual screening against malaria

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作者： Jacq, N. Salzemann, J. Jacq, F. Legré, Y. Medernach, E. Montagnat, J. Maaß, A. Breton, V. Schwichtenberg, H. Sridhar, M. Kasam, V. Zimmermann, M. Hofmann, M. Breton, V. Laboratoire de Physique Corpusculaire Université Blaise Pascal IN2P3-CNRS UMR 6533 24 Avenue des Landais 63177 Aubière France Communication and Systèmes Grenoble France Informatique Signaux et Systèmes Université de Nice Sophia Antipolis CNRS UMR 6070 Sophia Antipolis France Department of Simulation Engineering Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

WISDOM is an international initiative to enable a virtual screening pipeline on a Grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public Grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to Grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to desktop Grids. The first large scale docking experiment ran on the EGEE Grid production service from 11 July 2005 to 19 August 2005 against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with Grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the Grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how Grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting avian flu neuraminidase N1. © Springer Science + Business Media B.V. 2007.

关键词： Grid computing

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A new optimization phase for scientific workflow management systems

A new optimization phase for scientific workflow management ...

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IEEE International Conference on e-Science and Grid computing

作者： Sonja Holl Olav Zimmermann Martin Hofmann-Apitius Juelich Supercomputing Centre (JSC) Juelich Germany Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin Germany

scientific workflows have emerged as an important tool for combining computational power with data analysis for all scientific domains in e-science. They help scientists to design and execute complex in silico experiments. However, with increasing complexity it becomes more and more infeasible to optimize scientific workflows by trial and error. To address this issue, this paper describes the design of a new optimization phase integrated in the established scientific workflow life cycle. We have also developed a flexible optimization application programming interface (API) and have integrated it into a scientific workflow management system. A sample plugin for parameter optimization based on genetic algorithms illustrates, how the API enables rapid implementation of concrete workflow optimization methods. Finally, a use case taken from the area of structural bioinformatics validates how the optimization approach facilitates setup, execution and monitoring of workflow parameter optimization in high performance computing e-science environments.

关键词： Optimization methods Planning Abstracts Engines Data analysis Genetic algorithms

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