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Current Bioinformatics 2014年第3期9卷 218-227页

作者： Chen, Xiao-Su Yu, Zu-Guo Zheng, Juan Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 BrisbaneQ 4001 Australia School of Information and Engineering Xiangtan University Hunan411105 China

Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The "distances" used in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view. © 2014 Bentham science Publishers.

关键词： Alignment

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An Iterative Discontinuous Galerkin Method for Solving the Nonlinear Poisson Boltzmann Equation

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Communications in computational Physics 2014年第7期16卷 491-515页

作者： Peimeng Yin Yunqing Huang Hailiang Liu Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational ScienceXiangtan UniversityXiangtan 411105P.R.China Iowa State University Mathematics DepartmentAmesIA 50011USA.

An iterative discontinuous Galerkin(DG)method is proposed to solve the nonlinear Poisson Boltzmann(PB)*** first identify a function space inwhich the solution of the nonlinear PB equation is iteratively approximated through a series of linear PB equations,while an appropriate initial guess and a suitable iterative parameter are selected so that the solutions of linear PB equations are monotone within the identified solution *** the spatial discretization we apply the direct discontinuous Galerkin method to those linear PB *** precisely,we use one initial guess when the Debye parameter l=O(1),and a special initial guess for l≪1 to ensure *** iterative parameter is carefully chosen to guarantee the existence,uniqueness,and convergence of the *** particular,iteration steps can be reduced for a variable iterative *** one and two-dimensional numerical results are carried out to demonstrate both accuracy and capacity of the iterative DG method for both cases of l=O(1)and l≪***(m+1)th order of accuracy for L2 and mth order of accuracy for H1 for Pm elements are numerically obtained.

关键词： Poisson-Boltzmann equation nonlinear existence uniqueness DDG methods numerical flux.

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Secondary structure element alignment kernel method for prediction of protein structural classes

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Current Bioinformatics 2014年第3期9卷 253-257页

作者： Han, Guo-Sheng Yu, Zu-Guo Anh, Vo Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q 4001 Australia

In this paper, we aim at predicting protein structural classes for low-homology data sets based on predicted secondary structures. We propose a new and simple kernel method, named as SSEAKSVM, to predict protein structural classes. The secondary structures of all protein sequences are obtained by using the tool PSIPRED and then a linear kernel on the basis of secondary structure element alignment scores is constructed for training a support vector machine classifier without parameter adjusting. Our method SSEAKSVM was evaluated on two low-homology datasets 25PDB and 1189 with sequence homology being 25% and 40%, respectively. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies on these two data sets are 86.3% and 84.5%, respectively, which are higher than those obtained by other existing methods. Especially, our method achieves higher accuracies (88.1% and 88.5%) for differentiating the α+ β class and the α/β class compared to other methods. This suggests that our method is valuable to predict protein structural classes particularly for low-homology protein sequences. The source code of the method in this paper can be downloaded at http://***/myphp/math/research/source/SSEAK_source_***. © 2014 Bentham science Publishers.

关键词： Support vector machines

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A Coupled Immersed Interface and Level Set Method for Three-Dimensional Interfacial Flows with Insoluble Surfactant

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Communications in computational Physics 2014年第2期15卷 451-469页

作者： Jian-Jun Xu Yunqing Huang Ming-Chih Lai Zhilin Li School of Mathematical and Computational Sciences Xiangtan UniversityHunan 410005China Department of Applied Mathematics National Chiao Tung UniversityHsinchu 30050Taiwan Department of Mathematics North Carolina State UniversityRaleighNC27695USA .4 Hunan Key Lab for Computation and Simulation in Science and Engineering Hunan 410005China School of Mathematical Sciences Nanjing Normal UniversityNanjingChina.

In this paper,a numerical method is presented for simulating the 3D interfacial flows with insoluble *** numerical scheme consists of a 3D immersed interface method(IIM)for solving Stokes equations with jumps across the interface and a 3D level-set method for solving the surfactant convection-diffusion equation along a moving and deforming *** 3D IIM Poisson solver modifies the one in the literature by assuming that the jump conditions of the solution and the flux are implicitly given at the grid points in a small neighborhood of the *** assumption is convenient in conjunction with the level-set *** allows standard Lagrangian interpolation for quantities at the projection points on the *** interface jump relations are re-derived accordingly.A novel rotational procedure is given to generate smooth local coordinate systems and make effective *** examples demonstrate that the IIM Poisson solver and the Stokes solver achieve second-order accuracy.A 3D drop with insoluble surfactant under shear flow is investigated numerically by studying the influences of different physical parameters on the drop deformation.

关键词： Multigrid method constrained Cauchy-Born elasticity nanoindentation CauchyBorn rule.

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Mathematical analysis of a PML model obtained with stretched coordinates and its application to backward wave propagation in metamaterials

Mathematical analysis of a PML model obtained with stretched...

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作者： Huang, Yunqing Li, Jichun Yang, Wei Hunan Key Laboratory for Computation and Simulation in Science Engineering Xiangtan University Hunan 411105 China Department of Mathematical Sciences University of Nevada Las Vegas Las Vegas NV 89154-4020 United States

We investigate the well-posedness of a perfectly matched layer model developed by Cohen and Monk [Comput Methods Appl Mech Eng 169 (1999), 197-217]. A new time-domain finite element method is proposed to solve the model. A novel feature of the scheme is that the number of unknowns is reduced to two from four in the original form. The scheme's effectiveness is demonstrated through numerical experiments. © 2013 Wiley Periodicals, Inc.

关键词： Maxwell equations

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Two classes of implicit–explicit multistep methods for nonlinear stiff initial-value problems

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Applied Mathematics and computation 2014年 247卷 47-60页

作者： Aiguo Xiao Gengen Zhang Xing Yi School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 China

The initial value problems of nonlinear ordinary differential equations which contain stiff and nonstiff terms often arise from many applications. In order to reduce the computation cost, implicit–explicit (IMEX) methods are often applied to these problems, i.e. the stiff and non-stiff terms are discretized by using implicit and explicit methods, respectively. In this paper, we mainly consider the nonlinear stiff initial-value problems satisfying the one-sided Lipschitz condition and a class of singularly perturbed initial-value problems, and present two classes of the IMEX multistep methods by combining implicit one-leg methods with explicit linear multistep methods and explicit one-leg methods, respectively. The order conditions and the convergence results of these methods are obtained. Some efficient methods are constructed. Some numerical examples are given to verify the validity of the obtained theoretical results.

关键词： Stiff problems Singular perturbation problems Implicit–explicit multistep methods One-leg methods Linear multistep methods Convergence

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Time-splitting finite difference method with the wavelet-adaptive grids for semiclassical Gross–Pitaevskii equation in supercritical case

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Journal of computational Physics 2014年 267卷 146-161页

作者： Xueyang Li Aiguo Xiao School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 PR China

The Gross–Pitaevskii equation is the model equation of the single-particle wave function in a Bose–Einstein condensation. A computation difficulty of the Gross–Pitaevskii equation comes from the semiclassical problem in supercritical case. In this paper, we apply a diffeomorphism to transform the original one-dimensional Gross–Pitaevskii equation into a modified equation. The adaptive grids are constructed through the interpolating wavelet method. Then, we use the time-splitting finite difference method with the wavelet-adaptive grids to solve the modified Gross–Pitaevskii equation, where the approximation to the second-order derivative is given by the Lagrange interpolation method. At last, the numerical results are given. It is shown that the obtained time-splitting finite difference method with the wavelet-adaptive grids is very efficient for solving the one-dimensional semiclassical Gross–Pitaevskii equation in supercritical case and it is suitable to deal with the local high oscillation of the solution.

关键词： Gross–Pitaevskii equation Wavelet-adaptive grids Time-splitting finite difference method Interpolating wavelet Lagrange interpolation method

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Underlying scaling relationships between solar activity and geomagnetic activity revealed by multifractal analyses

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Journal of Geophysical Research: Space Physics 2014年第9期119卷 7577-7586页

作者： Yu, Zu-Guo Anh, Vo Eastes, Richard Hunan Key Laboratory for Computation and Simulation in Science and Engineering Ministry of Education Xiangtan University Xiangtan Hunan China School of Mathematical Sciences Queensland University of Technology Brisbane QLD Australia Florida Space Institute University of Central Florida Orlando FL United States

This paper identifies some scaling relationships between solar activity and geomagnetic activity. We examine the scaling properties of hourly data for two geomagnetic indices (a_p and AE), two solar indices (solar X-rays X_l and solar flux F10.7), and two inner heliospheric indices (ion density Ni and flow speed Vs) over the period 1995-2001 by the universal multifractal approach and the traditional multifractal analysis. We found that the universal multifractal model (UMM) provides a good fit to the empirical K(q) and τ(q) curves of these time series. The estimated values of the Lévy index α in the UMM indicate that multifractality exists in the time series for a_p, AE, X_l, and Ni, while those for F10.7 and Vs are monofractal. The estimated values of the nonconservation parameter H of this model confirm that these time series are conservative which indicate that the mean value of the process is constant for varying resolution. Additionally, the multifractal K(q) and τ(q) curves, and the estimated values of the sparseness parameter C₁ of the UMM indicate that there are three pairs of indices displaying similar scaling properties, namely a_p and X_l, AE and Ni, and F10.7 and Vs. The similarity in the scaling properties of pairs (a_p,X_l) and (AE,Ni) suggests that a_p and X_l, AE and Ni are better correlated - in terms of scaling - than previous thought, respectively. But our results still cannot be used to advance forecasting of a_p and AE by X_l and Ni, respectively, due to some reasons. key Points The scaling properties of the geomagnetic and the solar indices are examinedThe results suggest that multifractality exists in a_p, AE, Xl, and ion densityThe scaling similarity of the a_p and Xl data suggests flare-storm dependence ©2014. American Geophysical Union. All Rights Reserved.

关键词： geomagnetic indices multifractal analysis scaling property solar indices universal multifractal model

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Parallelization of a DEM code based on CPU-GPU heterogeneous architecture

Parallelization of a DEM code based on CPU-GPU heterogeneous...

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26th International Conference on Parallel computational Fluid Dynamics, ParCFD 2013

作者： Yue, Xiaoqiang Zhang, Hao Luo, Congshu Shu, Shi Feng, Chunsheng School of Mathematics and Computational Science Xiangtan University 411105 Hunan China Heat and Mass Transfer Technological Center Technical University of Catalonia 08222 Terrassa Spain Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University 411105 Hunan China

ISBN: (纸本)9783642539619

Particulate flows are commonly encountered in both engineering and environmental applications. The discrete element method (DEM) has attracted plentiful attentions since it can predict the whole motion of the particulate flow by monitoring every single particle. However the computational capability of the method relies strongly on the numerical scheme as well as the hardware environment. In this study, a parallelization of a DEM based code titled Trubal was implemented. Numerical simulations were carried out to show the benefits of this research. It is shown that the final parallel code gave a substantial acceleration on the Trubal. By simulating 6,000 particles using a NVIDIA Tesla C2050 card together with Intel Core-Dual 2.93 GHz CPU, an average speedup of 4.69 in computational time was obtained. © Springer-Verlag Berlin Heidelberg 2014.

关键词： Finite difference method

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Firefly algorithm solving equal-task multiple traveling salesman problem

Communications in Computer and Information Science

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Communications in Computer and Information science 2014年 472卷 304-307页

作者： Ma, Jianhua Li, Mingfu Zhang, Yuyan Zhou, Houming School of Mechanical Engineering Xiangtan University Xiangtan China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan China

ISBN: (纸本)9783662450482

A kind of equal-task multiple traveling salesman problem (ET-mTSP) was proposed based on the mTSP and its corresponding mathematical model was constructed;Then, a series of discrete operations for firefly algorithm (FA) were conducted to solve this problem;Finally, the results and analysis of experiments showed that the improved algorithm was efficient and suitable for solving such ET-mTSP. © Springer-Verlag Berlin Heidelberg 2014.

关键词： Problem solving

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