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Advances in biomolecular surface meshing and its applications to mathematical modeling

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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A New Analysis on the Barzilai-Borwein Gradient Method

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Journal of the Operations Research Society of China 2013年第2期1卷 187-198页

作者： Yu-Hong Dai State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesP.O.Box 2719Beijing 100190P.R.China

Due to its simplicity and efficiency,the Barzilai and Borwein(BB)gradi-ent method has received various attentions in different *** paper presents a new analysis of the BB method for two-dimensional strictly convex quadratic *** analysis begins with the assumption that the gradient norms at the first two iterations are *** show that there is a superlinear convergence step in at most three consecutive ***,we provide a better convergence relation for the BB *** influence of the starting point and the condition number to the convergence rate is comprehensively addressed.

关键词： Unconstrained optimization Barzilai and Borwein gradient method Quadratic function R-superlinear convergence Condition number

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Reports of the AAAI 2014 conference workshops

Reports of the AAAI 2014 conference workshops

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作者： Albrecht, Stefano V. Barreto, André M. S. Braziunas, Darius Buckeridge, David L. Cuayáhuitl, Heriberto Dethlefs, Nina Endres, Markus Farahmand, Amir-Massoud Fox, Mark Frommberger, Lutz Ganzfried, Sam Guillet, Sébastien Gil, Yolanda Hunter, Lawrence E. Jhala, Arnav Kersting, Kristian Konidaris, George Lecue, Freddy McIlraith, Sheila Natarajan, Sriraam Noorian, Zeinab Poole, David Ronfard, Rémi Saffiotti, Alessandro Shaban-Nejad, Arash Srivastava, Biplav Tesauro, Gerald Uceda-Sosa, Rosario Van Den Broeck, Guy Van Otterlo, Martijn Wallace, Byron C. Weng, Paul Wiens, Jenna Zhang, Jie School of Informatics University of Edinburgh United Kingdom Department of Applied and Computational Mathematics Brazilian National Laboratory Brazil Big Data Group Kobo Inc. Brazil Department of Epidemiology and Biostatistics McGill University Canada School of Mathematical and Computer Sciences Heriot-Watt University in Edinburgh United Kingdom University of Augsburg Germany Carnegie Mellon University United States University of Toronto Canada Cognitive Systems Group University of Bremen Germany LIARA UQAC Chicoutimi Canada Information Sciences Institute University of Southern California Computer Science Department United States Center for Computational Pharmacology University of Colorado School of Medicine United States Department of Computational Media University of California Santa Cruz United States Computer Science Department Technical University of Dortmund Germany MIT Computer Science and Artificial Intelligence Laboratory CambridgeMA United States IBM Research - Smarter Cities Technology Centre Dubline Ireland School of Informatics and Computing Indiana University United States Department of Computer Science University of Saskatchewan Canada University of British Columbia Canada INRIA University of Grenoble France Orebro University Sweden McGill Clinical and Health Informatics Group McGill University Canada IBM Research United States Cognitive Computing Department IBM Research Yorktown HeightsNY United States Computer Science Department Katholieke Universiteit Leuven Belgium Cognitive Artificial Intelligence Department Radboud University Nijmegen Netherlands University of Texas Austin United States Pierre and Marie Curie University Paris France University of Michigan United States School of Computer Engineering Nanyang Technological University Singapore

The AAAI-14 Workshop program was held Sunday and Monday, July 27-28, 2014, at the Québec City Convention Centre in Québec, Canada. The AAAI-14 workshop program included 15 workshops covering a wide range of topics in artificial intelligence. The titles of the workshops were Artificial Intelligence and Robotics;Artificial Intelligence Applied to Assistive Technologies and Smart Environments;Cognitive computing for Augmented Human Intelligence;Computer Poker and Imperfect Information;Discovery Informatics;Incentives and Trust in Electronic Communities;Intelligent Cinematography and Editing;Machine Learning for Interactive Systems: Bridging the Gap Between Perception, Action, and Communication;Modern Artificial Intelligence for Health Analytics;Multiagent Interaction Without Prior Coordination;Multidisciplinary Workshop on Advances in Preference Handling;Semantic Cities - Beyond Open Data to Models, Standards, and Reasoning;Sequential Decision Making with Big Data;Statistical Relational AI;and the World Wide Web and Public Health Intelligence. This article presents short summaries of those events. © 2015, Association for the Advancement of Artificial Intelligence. All rights reserved.

关键词： Decision making

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Feasible Barzilai-Borwein-like methods for extreme symmetric eigenvalue problems

Feasible Barzilai-Borwein-like methods for extreme symmetric...

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作者： Jiang, Bo Dai, Yu-Hong State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences Beijing 100190 China

This paper aims to study feasible Barzilai-Borwein (BB)-like methods for extreme symmetric eigenvalue problems. For the two-dimensional case, we establish the local superlinear convergence result of FLBB, FSBB, FABB, and FADBB algorithms. A counter-example is also given, showing that the algorithms may cycle or stop at a non-stationary point. In order to circumvent the difficulty, we propose a safeguard in choosing the stepsize. We also adopt an adaptive non-monotone line search with an improved line search to ensure the global convergence of AFBB-like methods. Numerical experiments on a set of test problems from UF Sparse Matrix Collection demonstrate that, comparing several available codes including eigs, irbleigs and jdcg, AFBB-like methods are very useful for large-scale sparse extreme symmetric eigenvalue problems. © 2013 Copyright Taylor and Francis Group, LLC.

关键词： Eigenvalues and eigenfunctions

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Exa-dune: Flexible pde solvers, Numerical methods and applications

Exa-dune: Flexible pde solvers, Numerical methods and applic...

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International Workshop on Parallel Processing, Euro-Par 2014

作者： Bastian, Peter Müthing, Steffen Engwer, Christian Ohlberger, Mario Fahlke, Jorrit Kaulmann, Sven Göddeke, Dominik Ribbrock, Dirk Turek, Stefan Iliev, Oleg Ippisch, Olaf Interdisciplinary Center for Scientific Computing Heidelberg University Im Neuenheimer Feld 368 HeidelbergD-69120 Germany Institute for Computational and Applied Mathematics University of Münster Orleans-Ring 10 üunsterD-48149 Germany Department of Mathematics TU Dortmund Vogelpothsweg 87 DortmundD-44227 Germany Fraunhofer Institute for Industrial Mathematics ITWM TU Dortmund Fraunhofer-Platz 1 KaiserslauternD-67663 Germany Institut für Mathematik TU Clausthal-Zellerfeld Erzstr. 1 Clausthal-ZellerfeldD-38678 Germany

ISBN: (纸本)9783319143125

In the EXA-DUNE project we strive to (i) develop and implement numerical algorithms for solving PDE problems efficiently on heterogeneous architectures, (ii) provide corresponding domain-specific abstractions that allow application scientists to effectively use these methods, and (iii) demonstrate performance on porous media flow problems. In this paper, we present first results on the hybrid parallelisation of sparse linear algebra, system and RHS assembly, the implementation of multiscale finite element methods and the SIMD performance of highorder discontinuous Galerkin methods within an application scenario. ©Springer International Publishing Switzerland 2014.

关键词： Linear algebra

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An Error Analysis for the Finite Element Approximation to the Steady-State Poisson-Nernst-Planck Equations

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Advances in Applied mathematics and Mechanics 2013年第1期5卷 113-130页

作者： Ying Yang Benzhuo Lu Department of Computational Science and Mathematics Guilin University of Electronic TechnologyGuilin 541004GuangxiChina LSEC Institute of Computational Mathematics and Scientific/Engineering Computingthe National Center for Mathematics and Interdisciplinary SciencesAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China

Poisson-Nernst-Planck equations are a coupled system of nonlinear partial differential equations consisting of the Nernst-Planck equation and the electrostatic Poisson equation with delta distribution sources,which describe the electrodiffusion of ions in a solvated biomolecular *** this paper,some error bounds for a piecewise finite element approximation to this problem are *** numerical examples including biomolecular problems are shown to support our analysis.

关键词： Poisson-Nernst-Planck equations finite element method error bounds

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A trust region method based on a new affine scaling technique for simple bounded optimization

A trust region method based on a new affine scaling techniqu...

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作者： Wang, Xiao Yuan, Ya-Xiang State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering Computing Chinese Academy of Sciences PO Box 2719 Beijing 100190 China

In this paper, we propose a new trust region affine scaling method for nonlinear programming with simple bounds. Our new method is an interior-point trust region method with a new scaling technique. The scaling matrix depends on the distances of the current iterate to the boundaries, the gradient of the objective function and the trust region radius. This scaling technique is different from the existing ones. It is motivated by our analysis of the linear programming case. The trial step is obtained by minimizing the quadratic approximation to the objective function in the scaled trust region. It is proved that our algorithm guarantees that at least one accumulation point of the iterates is a stationary point. Preliminary numerical experience on problems with simple bounds from the CUTEr collection is also reported. The numerical performance reveals that our method is effective and competitive with the famous algorithm LANCELOT. It also indicates that the new scaling technique is very effective and might be a good alternative to that used in the subroutine fmincon from Matlab optimization toolbox. © 2013 Copyright Taylor and Francis Group, LLC.

关键词： Nonlinear programming

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Some progress in spectral methods Dedicated to Professor Shi Zhong-Ci on the Occasion of his 80th Birthday

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Science China mathematics 2013年第12期56卷 2411-2438页

作者： GUO BenYu Department of Mathematics Shanghai Normal University Scientific Computing Key Laboratory of Shanghai Universities Division of Computational Science E-institute of Shanghai Universities

In this paper, we review some results on the spectral methods. We first consider the Jacobi spectral method and the generalized Jacobi spectral method for various problems, including degenerated and singular differential equations. Then we present the generalized Jacobi quasi-orthogonal approximation and its applica- tions to the spectral element methods for high order problems with mixed inhomogeneous boundary conditions. We also discuss the related spectral methods for non-rectangular domains and the irrational spectral methods for unbounded domains. Next, we consider the Hermite spectral method and the generalized Hermite spec- tral method with their applications. Finally, we consider the Laguerre spectral method and the generalized Laguerre spectral method for many problems defined on unbounded domains. We also present the generalized Laguerre quasi-orthogonal approximation and its applications to certain problems of non-standard type and exterior problems.

关键词： Jacobi Hermite and Laguerre spectral approximations Jacobi and Laguerre quasi-orthogonalapproximations spectral and spectral element methods degenerated and singular problems problems on non-rectangular and unbounded domains problems of non-standard type exterior problems

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Nonlocal Diffusion Tensor for Visual Saliency Detection

Nonlocal Diffusion Tensor for Visual Saliency Detection

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International Conference on computational Intelligence and Security

作者： Xiujun Zhang Chen Xu Min Li College of Information and Engineering Shenzhen University Shenzhen China Institute of Intelligent Computing Science Shenzhen University Shenzhen China College of Mathematics and Computational Science Shenzhen University Shenzhen China

ISBN: (纸本)9781479974351

In this paper, visual attention transfer is formulated as a nonlocal diffusion equation. Different from the other diffusion based method, a nonlocal diffusion tensor is introduced to consider both the diffusion strength and direction. Along with the principle direction, the diffusion should be suppressed to preserve the dissimilarity between the foreground and background, and in other directions, the diffusion should be boosted to combine the similar regions and highlight the saliency object as a whole. Through a two-stages diffusion, the final saliency map is obtained and quantitative and visual comparisons are executed on two large benchmark databases. Experimental results demonstrate the superior performance of our method.

关键词： Visualization Tensile stress Databases Image color analysis Mathematical model Equations Vectors

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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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