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A Source Transfer Domain Decomposition Method For Helmholtz Equations in Unbounded Domain Part II: Extensions

Numerical mathematics(Theory,Methods and Applications) 2013年第3期6卷 538-555页

作者： Zhiming Chen Xueshuang Xiang LSEC Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China

In this paper we extend the source transfer domain decomposition method(STDDM)introduced by the authors to solve the Helmholtz problems in two-layered media,the Helmholtz scattering problems with bounded scatterer,and Helmholtz problems in 3D unbounded *** STDDM is based on the decomposition of the domain into non-overlapping layers and the idea of source transfer which transfers the sources equivalently layer by layer so that the solution in the final layer can be solved using a PML method defined locally outside the last two *** details of STDDM is given for each *** results are presented to demonstrate the efficiency of STDDM as a preconditioner for solving the discretization problem of the Helmholtz problems considered in the paper.

关键词： Helmholtz equation high frequency waves PML source transfer

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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Model reduction opportunities in detailed simulations of combustion dynamics 52

Model reduction opportunities in detailed simulations of com...

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52nd AIAA Aerospace sciences Meeting - AIAA science and Technology Forum and Exposition, SciTech 2014

作者： Munipalli, Ramakanth Liu, Zhining Zhu, Xueyu Menon, Suresh Hesthaven, Jan S. HyPerComp Inc Westlake Village CA 91361 United States Scientific Computing and Imaging Institute University of Utah United States Department of Aerospace Engineering Georgia Institute of Technology Computational Combustion Laboratory United States Division of Applied Mathematics Brown University United States EPFL-SB-MATHICSE-MCSS Lausanne Switzerland

ISBN: (数字)9781624102561

ISBN: (纸本)9781624102561

Rocket and gas turbine combustion dynamics involves a confluence of diverse physics and interaction across a number of system components. Any comprehensive, self-consistent numerical model is burdened by a very large computational mesh, stiff unsteady processes which limit the permissible time step, and the need to perform tedious, repeated calculations for a broad parametric range. Predictive CFD models rely on very large scale simulations and advanced hardware. Reduced Basis Methods (RBM) have grown in usage during the past decade, as promising new techniques in making large simulations more accessible. These methods create models with far fewer unknown quantities than the original system, by generating "proper" fundamental solutions and their Galerkin projections, while guaranteeing accuracy and computational efficiency. RBMs seek to reproduce full CFD solutions, rather than solutions to a simplified or linearized set of equations. We present here some recent work in this area, focusing on approaches to model large scale combustor systems. The maturation of methods leading to LES-based turbulent combustion modeling is discussed, and model reduction goals and strategies are explored from the perspective of applicability in real life problems in both gas turbine, and rocket engines.

关键词： Rockets

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Parallel Multicore CSB Format and Its Sparse Matrix Vector Multiplication

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Advances in Linear Algebra & Matrix Theory 2014年第1期4卷 1-8页

作者： Bing Yang Shuo Gu Tong-Xiang Gu Cong Zheng Xing-Ping Liu Graduate School of Chinese Academy of Engineering Physics Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics BeijingChina School of Electronic Engineering University of Electronic Science and Technology of China Chengdu China

Sparse Matrix Vector Multiplication (SpMV) is one of the most basic problems in scientific and engineering computations. It is the basic operation in many realms, such as solving linear systems or eigenvalue problems. Nowadays, more than 90 percent of the world’s highest performance parallel computers in the top 500 use multicore architecture. So it is important practically to design the efficient methods of computing SpMV on multicore parallel computers. Usually, algorithms based on compressed sparse row (CSR) format suffer from a number of nonzero elements on each row so hardly as to use the multicore structure efficiently. Compressed Sparse Block (CSB) format is an effective storage format which can compute SpMV efficiently in a multicore computer. This paper presents a parallel multicore CSB format and SpMV based on it. We carried out numerical experiments on a parallel multicore computer. The results show that our parallel multicore CSB format and SpMV algorithm can reach high speedup, and they are highly scalable for banded matrices.

关键词： SpMV Multicore Parallel Computers Parallel Multicore CSB Format

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New isomer found in Sb8951140: Sphericity and shell evolution between N=82 and N=90

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Physical Review C 2016年第1期93卷 014316-014316页

作者： R. Lozeva H. Naïdja F. Nowacki J. Dudek A. Odahara C.-B. Moon S. Nishimura P. Doornenbal J.-M. Daugas P.-A. Söderström T. Sumikama G. Lorusso J. Wu Z. Y. Xu H. Baba F. Browne R. Daido Y. Fang T. Isobe I. Kojouharov N. Kurz Z. Patel S. Rice H. Sakurai H. Schaffner L. Sinclair H. Watanabe A. Yagi R. Yokoyama T. Kubo N. Inabe H. Suzuki N. Fukuda D. Kameda H. Takeda D. S. Ahn D. Murai F. L. Bello Garrote F. Didierjean E. Ideguchi T. Ishigaki H. S. Jung T. Komatsubara Y. K. Kwon P. Lee C. S. Lee S. Morimoto M. Niikura H. Nishibata I. Nishizuka IPHC CNRS IN2P3 and University of Strasbourg F-67037 Strasbourg Cedex 2 France GSI Helmholtzzentrum für Schwerionenforschung GmbH D-64291 Darmstadt Germany University of Constantine 25000 Constantine Algeria Department of Physics Osaka University Osaka 560-0043 Toyonaka Japan Department of Display Engineering Hoseo University Chung-Nam 336-795 Republic of Korea RIKEN Nishina Center Wako-shi Saitama 351-0198 Japan CEA DAM DIF F-91297 Arpajon Cedex France Department of Physics Tohoku University Miyagi 980-8578 Japan School of Physics and State Key Laboratory of Nuclear Physics and Technology Peking University Beijing 100871 China Department of Physics University of Tokyo Tokyo 113-0033 Japan School of Computing Engineering and Mathematics University of Brighton Brighton BN2 4GJ United Kingdom Department of Physics University of Surrey Guildford GU2 7XH United Kingdom Department of Physics University of York Heslington York YO10 5DD United Kingdom School of Physics and Nuclear Energy Engineering Beihang University Beijing 100191 China CNS University of Tokyo Wako Saitama 351-0198 Japan Department of Physics Rikkyo University Toshima Tokyo 171-8501 Japan Department of Physics University of Oslo N-0316 Oslo Norway RCNP Osaka University Ibaraki Osaka 567-0047 Japan Department of Physics University of Notre Dame Notre Dame Indiana 46556 USA Rare Isotope Science Project Institute for Basic Science Daejeon 305-811 Republic of Korea Department of Physics Chung-Ang University Seoul Republic of Korea

In this article we report on the first spectroscopic information on Sb8951140 and the observation of an isomer in this nucleus with T1/2=41(8) μs. It is located in close proximity to Sn140 for N=90, where the νf7/2 orbit is completely filled. The possible origin of the isomeric state is a πg7/21×νf7/2−1 coupling configuration, resulting in a (6−) or (7−) spin-parity. This is likely caused by an inversion of the πg7/2 and πd5/2 orbitals at N=89. The existence of such an isomer far from stability is discussed extensively in the context of shell-model calculations and compared to results from mean-field calculations performed using a deformed Woods-Saxon potential. Both approaches suggest the observation of a single-particle excitation mode at an extreme neutron number.

关键词： Isomer decays Gamma ray spectroscopy Mean field theory Shell model

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Advances in biomolecular surface meshing and its applications to mathematical modeling

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Chinese science Bulletin 2013年第16期58卷 1843-1849页

作者： CHEN MinXin LU BenZhuo Center for System Biology Department of Mathematics Soochow University State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary Sciences Chinese Academy of Sciences

In the field of molecular modeling and simulation, molecular surface meshes are necessary for many problems, such as molecular structure visualization and analysis, docking problem and implicit solvent modeling and simulation. Recently, with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation, providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure. In this review, we summarize recent works on this issue. First, various definitions of molecular surfaces and corresponding meshing methods are introduced. Second, our recent meshing tool, TMSmesh, and its performances are presented. Finally, we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

关键词：数学建模分子表面应用啮合生物表面网格分子结构分子建模

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Parallel Mutual Information Based Construction of Whole-Genome Networks on the Intel (R) Xeon Phi (TM) Coprocessor

Parallel Mutual Information Based Construction of Whole-Geno...

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International Symposium on Parallel and Distributed Processing (IPDPS)

作者： Sanchit Misra Kiran Pamnany Srinivas Aluru Parallel Computing Lab Intel Corporation Bangalore India School of Computational Science and Engineering Georgia Institute of Technology Atlanta USA

Construction of whole-genome networks from large-scale gene expression data is an important problem in systems biology. While several techniques have been developed, most cannot handle network reconstruction at the whole-genome scale, and the few that can, require large clusters. In this paper, we present a solution on the Intel (R) Xeon Phi (TM) coprocessor, taking advantage of its multi-level parallelism including many x86-based cores, multiple threads per core, and vector processing units. We also present a solution on the Intel (R) Xeon (R) processor. Our solution is based on TINGe, a fast parallel network reconstruction technique that uses mutual information and permutation testing for assessing statistical significance. We demonstrate the first ever inference of a plant whole genome regulatory network on a single chip by constructing a 15,575 gene network of the plant Arabidopsis thaliana from 3,137 microarray experiments in only 22 minutes. In addition, our optimization for parallelizing mutual information computation on the Intel Xeon Phi coprocessor holds out lessons that are applicable to other domains.

关键词： Vectors Joints Coprocessors Mutual information Optimization Splines (mathematics) Arrays

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Hydrodynamic interaction between overlapping domains during recurrence of registration within planar lipid bilayer membranes

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Physical Review E 2014年第3期89卷 032717-032717页

作者： Tao Han Trevor P. Bailey Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Due to a thermodynamic coupling between the two leaflets comprising a lipid bilayer, compositional lipid domains residing within opposing leaflets are often found in registry. If the system is perturbed by displacing one domain relative to the other, diffusive and advective lipid fluxes are established to restore equilibrium and reestablish domain overlap. In this work, we focus on the advective part of the process, and first derive an analytical expression for the hydrodynamic drag coefficient associated with the advective flow for the special case of perfect domain overlap. The resulting expression identifies parameter regions where sliding friction between the leaflets dominates over viscous dissipation within the leaflets or vice versa. It is shown that in all practically relevant cases, sliding friction between the leaflets is the dominant factor. Finally, we investigate the domain separation dependence of the hydrodynamic drag coefficient via direct simulations of a continuum diffuse interface model, and provide useful empirical expressions for its behavior.

关键词： HYDRODYNAMICS BILAYER lipid membranes DRAG coefficient ENERGY dissipation SLIDING friction FLUX (Energy)

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Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT

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Journal of Structural and Functional Genomics 2015年第2期16卷 55-65页

作者： Tochio, Naoya Umehara, Takashi Nakabayashi, Kazuhiko Yoneyama, Misao Tsuda, Kengo Shirouzu, Mikako Koshiba, Seizo Watanabe, Satoru Kigawa, Takanori Sasazuki, Takehiko Shirasawa, Senji Yokoyama, Shigeyuki RIKEN Systems and Structural Biology Center 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Department of Mathematical and Life Sciences Research Center for the Mathematics on Chromatin Live Dynamics Graduate School of Science Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8530 Japan RIKEN Center for Life Science Technologies 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan PRESTO Japan Science and Technology Agency (JST) 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo 157-8535 Japan Department of Integrative Genomics Tohoku Medical Megabank Organization Tohoku University 2-1 Seiryo-machi Aoba-ku Sendai 980-8573 Japan RIKEN Quantitative Biology Center 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology 4259 Nagatsuta-cho Midori Yokohama 226-8502 Japan Institute for Advanced Studies Kyushu University 6-10-1 Hakozaki Higashi-ku Fukuoka 812-8582 Japan Department of Cell Biology Faculty of Medicine Fukuoka University Fukuoka 814-0180 Japan Center for Advanced Molecular Medicine Fukuoka University Fukuoka 814-0180 Japan RIKEN Structural Biology Laboratory 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan

ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structur... 详细信息

ZFAT is a transcriptional regulator, containing eighteen C₂H₂-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4–ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4–ZF5 interfinger linker in the regulation of ZFAT function. © 2015, The Author(s).

关键词： Gene expression NMR Transcription Zinc-finger

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Framework and modular infrastructure for automation of architectural adaptation and performance optimization for HPC systems

Framework and modular infrastructure for automation of archi...

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29th International Supercomputing Conference, ISC 2014

作者： Fialho, Leonardo Browne, James Institute for Computational Engineering and Sciences Austin TX 78712 United States Texas Advanced Computing Center Austin TX 78712 United States Department of Computer Science Austin TX 78712 United States University of Texas at Austin Austin TX 78712 United States

ISBN: (纸本)9783319075174

High performance systems have complex, diverse and rapidly evolving architectures. The span of applications, workloads, and resource use patterns is rapidly diversifying. Adapting applications for efficient execution on this spectrum of execution environments is effort intensive. There are many performance optimization tools which implement some or several aspects of the full performance optimization task but almost none are comprehensive across architectures, environments, applications, and workloads. This paper presents, illustrates, and applies a modular infrastructure which enables composition of multiple open-source tools and analyses into a set of workflows implementing comprehensive end-to-end optimization of a diverse spectrum of HPC applications on multiple architectures and for multiple resource types and parallel environments. It gives results from an implementation on the Stampede HPC system at the Texas Advanced computing Center where a user can submit an application for optimization using only a single command line and get back an at least, partially optimized program without manual program modification for two different chips. Currently, only a subset of the possible optimizations is completely automated but this subset is rapidly growing. Case studies of applications of the workflow are presented. The implementations currently available for download as the PerfExpert tool version 4.0 supports both Sandy Bridge and Intel Phi chips. © Springer International Publishing Switzerland 2014.

关键词： Application programs

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