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Nonconforming Multigrid Method for Eigenvalue problem

Nonconforming Multigrid Method for Eigenvalue problem

第一届重庆计算数学与应用数学研讨会(The 1st Chongqing Workshop on computational and Applied mathematics)(CQWCAM)

作者： Hehu Xie The Institute of Computational Mathematics and Scientific/Engineering Computing of Chinese Academy of Sciences

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LOD-MS for Gross-Pitaevskii Equation in Bose-Einstein Condensates

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Communications in computational Physics 2013年第6期14卷 219-241页

作者： Linghua Kong Jialin Hong Jingjing Zhang School of Mathematics and Information Science Jiangxi Normal UniversityNanchangJiangxi 330022P.R.China State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and System ScienceChinese Academy of SciencesP.O.Box 2719Beijing 100190P.R.China School of Mathematics and Information Science Henan Polytechnic UniversityJiaozuoHenan 454000P.R.China

The local one-dimensional multisymplectic scheme(LOD-MS)is developed for the three-dimensional(3D)Gross-Pitaevskii(GP)equation in Bose-Einstein *** idea is originated from the advantages of multisymplectic integrators and from the cheap computational cost of the local one-dimensional(LOD)*** 3D GP equation is split into three linear LOD Schrodinger equations and an exactly solvable nonlinear Hamiltonian *** three linear LOD Schrodinger equations are multisymplectic which can be approximated by multisymplectic integrator(MI).The conservative properties of the proposed scheme are *** is ***,the scheme preserves the discrete local energy conservation laws and global energy conservation law if the wave function is variable *** is impossible for conventional MIs in nonlinear Hamiltonian *** numerical results show that the LOD-MS can simulate the original problems very *** are consistent with the numerical analysis.

关键词： LOD-MS Gross-Pitaevskii equation local one-dimensional method midpoint method conservation laws

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One variant of a （2 ＋ 1）-dimensional Volterra system and its （1 ＋ 1）-dimensional reduction

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Frontiers of mathematics in China 2013年第5期8卷 1085-1097页

作者： Yingnan ZHANG Yi HE Hon-Wah TAM LSEC Institute of Computational Mathematics and Scientific Engineering ComputingAcademy of Mathematics and System Sciences Chinese Academy of SciencesBeijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 China Department of Computer Science Hong Kong Baptist University Hong Kong China

A new system is generated from a multi-linear form of a （2＋1）- dimensional Volterra system. Though the system is only partially integrable and needs additional conditions to possess two-soliton solutions, its （1＋1）- dimensional reduction gives an integrable equation which has been studied via reduction skills. Here, we give this （1＋1）-dimensional reduction a simple bilinear form, from which a Backlund transformation is derived and the corresponding nonlinear superposition formula is built.

关键词： Integrability soliton solution Bgcklund transformation （BT）,nonlinear superposition formula

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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ON THE QUASI-RANDOM CHOICE METHOD FOR THE LIOUVILLE EQUATION OF GEOMETRICAL OPTICS WITH DISCONTINUOUS WAVE SPEED

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Journal of computational mathematics 2013年第6期31卷 573-591页

作者： Jingwei Hu Shi Jin Institute for Computational Engineering and Sciences (ICES) The University of Texas at Austin 201 East 24th St Stop C0200 Austin TX 78712 USA Department of Mathematics University of Wisconsin-Madison 480 Lincoln Drive Madison WI 53706 USA Department of Mathematics Institute of Natural Sciences and MOE Key Lab in Scientific and Engineering Computing Shanghai Jiao Tong University Shanghai 200240 China

We study the quasi-random choice method （QRCM） for the Liouville equation of ge- ometrical optics with discontinuous locM wave speed. This equation arises in the phase space computation of high frequency waves through interfaces, where waves undergo partial transmissions and reflections. The numerical challenges include interface, contact discon- tinuities, and measure-valued solutions. The so-called QRCM is a random choice method based on quasi-random sampling （a deterministic alternative to random sampling）. The method not only is viscosity-free but also provides faster convergence rate. Therefore, it is appealing for the prob!em under study which is indeed a Hamiltonian flow. Our analy- sis and computational results show that the QRCM 1） is almost first-order accurate even with the aforementioned discontinuities; 2） gives sharp resolutions for all discontinuities encountered in the problem; and 3） for measure-valued solutions, does not need the level set decomposition for finite difference/volume methods with numerical viscosities.

关键词： Liouville equation High frequency wave Interface Measure-valued solution,Random choice method Quasi-random sequence.

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RETRACTED ARTICLE: Preface to the special issue on “Practical methods and rigorous theories in numerical algebra and scientific computing”

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Journal of engineering mathematics 2014年第1期91卷 211-211页

作者： Bai, Zhong-Zhi Duff, Iain S. State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing People’s Republic of China R18 Rutherford Appleton Laboratory Harwell Oxford Campus Didcot UK

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A Subspace Version of the Powell–Yuan Trust-Region Algorithm for Equality Constrained Optimization

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Journal of the Operations Research Society of China 2013年第4期1卷 425-451页

作者： Geovani Nunes Grapiglia Jinyun Yuan Ya-xiang Yuan Departamento de Matemática Universidade Federal do ParanáCentro PolitécnicoCx.postal 19.08181531-980CuritibaParanáBrazil The Capes Foundation Ministry of Education of BrazilCx.postal 25070.040-020BrasíliaDistrito FederalBrazil State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesZhongguancundonglu 55Beijing 100190P.R.China

This paper studied subspace properties of the Celis–Dennis–Tapia(CDT)subproblem that arises in some trust-region algorithms for equality constrained opti*** analysis is an extension of that presented by Wang and Yuan(***.104:241–269,2006)for the standard trust-region *** suitable conditions,it is shown that the trial step obtained from the CDT subproblem is in the subspace spanned by all the gradient vectors of the objective function and of the constraints computed until the current *** on this observation,a subspace version of the Powell–Yuan trust-region algorithm is proposed for equality constrained optimization problems where the number of constraints is much lower than the number of variables. The convergence analysis is given and numerical results arealso reported.

关键词： Constrained optimization Trust-region methods Subspace methods

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Multifractal computation for nuclear classification and hepatocellular carcinoma grading

Multifractal computation for nuclear classification and hepa...

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10th IASTED International Conference on Biomedical engineering, BioMed 2013

作者： Atupelage, Chamidu Nagahashi, Hiroshi Yamaguchi, Masahiro Kimura, Fumikazu Abe, Tokiya Hashiguchi, Akinori Sakamoto, Michiie Department of Computational Intelligence and Systems Science Tokyo Institute of Technology Japan Imaging Science and Engineering Laboratory Tokyo Institute of Technology Japan Global Scientific Information and Computing Center Tokyo Institute of Technology Japan Department of Pathology School of Medicine Keio University Japan

ISBN: (纸本)9780889869530

Hepatocellular carcinoma (HCC) is graded mainly based on the characteristics of liver cell nuclei. This paper proposes a textural feature descriptor and a novel computational method for classifying liver cell nuclei and grading the HCC histological images. The proposed textural feature descriptor observes local and spatial characteristics of the texture patterns by using multifractal computation. The textural features are utilized for nuclear segmentation, fiber region detection, and liver cell nuclei classification. Four categories of nuclear features are computed such as texture, geometry, spatial distribution, and surrounding texture, for HCC classification. Significance of liver cell nuclei classification method is evaluated by classifying non-neoplastic and tumor tissues. Furthermore, characteristics of the liver cell nuclei were utilized for grading a set of HCC images into four classes and obtained 97.77% classification accuracy.

关键词： Grading

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Accuracy of generalized gradient approximation functionals for density-functional perturbation theory calculations

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Physical Review B 2014年第6期89卷 064305-064305页

作者： Lianhua He Fang Liu Geoffroy Hautier Micael J. T. Oliveira Miguel A. L. Marques Fernando D. Vila J. J. Rehr G.-M. Rignanese Aihui Zhou LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China School of Applied Mathematics Central University of Finance and Economics Beijing 100081 China European Theoretical Spectroscopy Facility (ETSF) Institute of Condensed Matter and Nanosciences (IMCN) Université Catholique de Louvain Chemin des Étoiles 8 1348 Louvain-la-Neuve Belgium Center for Computational Physics University of Coimbra Rua Larga 3004-516 Coimbra Portugal Institut Lumière Matière UMR5306 Université Lyon 1-CNRS Université de Lyon F-69622 Villeurbanne Cedex France Department of Physics University of Washington Seattle Washington 98195 USA

We assess the validity of various exchange-correlation functionals for computing the structural, vibrational, dielectric, and thermodynamical properties of materials in the framework of density-functional perturbation theory (DFPT). We consider five generalized-gradient approximation (GGA) functionals (PBE, PBEsol, WC, AM05, and HTBS) as well as the local density approximation (LDA) functional. We investigate a wide variety of materials including a semiconductor (silicon), a metal (copper), and various insulators (SiO2 α-quartz and stishovite, ZrSiO4 zircon, and MgO periclase). For the structural properties, we find that PBEsol and WC are the closest to the experiments and AM05 performs only slightly worse. All three functionals actually improve over LDA and PBE in contrast with HTBS, which is shown to fail dramatically for α-quartz. For the vibrational and thermodynamical properties, LDA performs surprisingly very well. In the majority of the test cases, it outperforms PBE significantly and also the WC, PBEsol and AM05 functionals though by a smaller margin (and to the detriment of structural parameters). On the other hand, HTBS performs also poorly for vibrational quantities. For the dielectric properties, none of the functionals can be put forward. They all (i) fail to reproduce the electronic dielectric constant due to the well-known band gap problem and (ii) tend to overestimate the oscillator strengths (and hence the static dielectric constant).

关键词： PERTURBATION (Quantum dynamics) SILICON THERMODYNAMICS DIELECTRIC devices DIELECTRICS

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Finite-Difference Solution of the Helmholtz Equation Based on Two Domain Decomposition Algorithms

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Journal of Applied mathematics and Physics 2013年第4期1卷 18-24页

作者： Wensheng Zhang Yunyin Dai Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing China Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Beijing China

In this paper, wave simulation with the finite difference method for the Helmholtz equation based on the domain decomposition method is investigated. The method solves the problem by iteratively solving subproblems defined on smaller subdomains. Two domain decomposition algorithms both for nonoverlapping and overlapping methods are described. More numerical computations including the benchmark Marmousi model show the effectiveness of the proposed algorithms. This method can be expected to be used in the full-waveform inversion in the future.

关键词： Finite Difference Domain Decomposition Nonoverlapping Overlapping Helmholtz Equation Preconditioner

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