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Gradient Recovery-Type a Posteriori Error Estimates for Steady-State Poisson-Nernst-Planck Equations

Advances in Applied Mathematics and Mechanics 2020年第6期12卷 1353-1383页

作者： Ruigang Shen Shi Shu Ying Yang Mingjuan Fang School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and EngineeringXiangtan UniversityXiangtanHunan 411105China School of Mathematics and Computational Science Guangxi Colleges and Universities Key Laboratory of Data Analysis and ComputationGuilin University of Electronic TechnologyGuilinGuangxi 541004China School of Mathematics and Computational Science Guilin University of Electronic TechnologyGuilinGuangxi 541004China

In this article,we derive the a posteriori error estimators for a class of steadystate Poisson-Nernst-Planck *** the gradient recovery operator,the upper and lower bounds of the a posteriori error estimators are established both for the electrostatic potential and *** is shown by theory and numerical experiments that the error estimators are reliable and the associated adaptive computation is efficient for the steady-state PNP systems.

关键词： Poisson-Nernst-Planck equations gradient recovery a posteriori error estimate

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Space-time finite element adaptive AMG for multi-term time fractional advection diffusion equations

Space-time finite element adaptive AMG for multi-term time f...

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作者： Yue, Xiaoqiang Liu, Menghuan Shu, Shi Bu, Weiping Xu, Yehong School of Mathematics and Computational Science Xiangtan University Hunan China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan China

In this study, we construct a space-time finite element (FE) scheme and furnish cost-efficient approximations for one-dimensional multi-term time fractional advection diffusion equations on a bounded domain Ω. Firstly, a fully discrete scheme is obtained by the linear FE method in both temporal and spatial directions, and many characterizations on the resulting matrix are established. Secondly, the associated condition number estimation (Formula presented.) is derived, where τn and h, respectively, are the current time and space step sizes. Next, we propose a lossless in robustness and adaptive algebraic multigrid (AMG) with (Formula presented.) computational cost and (Formula presented.) matrix-free storage, in contrast to classical AMG with (Formula presented.), where M is the number of spatial segments. Meanwhile, uniform convergence analyses on the two-level V(0,1)-cycle of classical and adaptive AMGs are provided. Finally, we demonstrate the optimal error order of space-time FE approximations in the L2(Ω) norm sense, present theoretical confirmations and predictable behaviors of the proposed algorithm in numerical experiments. © 2019 John Wiley & Sons, Ltd.

关键词： Matrix algebra

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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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IMPLICIT-EXPLICIT RUNGE-KUTTA-ROSENBROCK METHODS WITH ERROR ANALYSIS FOR NONLINEAR STIFF DIFFERENTIAL EQUATIONS

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Journal of computational Mathematics 2021年第4期39卷 599-620页

作者： Bin Huang Aiguo Xiao Gengen Zhang School of Mathematics and Computational Science&Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan UniversityXiangtan 411105China South China Research Center for Applied Mathematics and Interdisciplinary Studies South China Normal UniversityGuangzhou 510631China

Implicit-explicit Runge-Kutta-Rosenbrock methods are proposed to solve nonlinear sti ordinary di erential equations by combining linearly implicit Rosenbrock methods with explicit Runge-Kutta ***,the general order conditions up to order 3 are ***,for the nonlinear sti initial-value problems satisfying the one-sided Lipschitz condition and a class of singularly perturbed initial-value problems,the corresponding errors of the implicit-explicit methods are *** last,some numerical examples are given to verify the validity of the obtained theoretical results and the e ectiveness of the methods.

关键词： Sti di erential equations Implicit-explicit Runge-Kutta-Rosenbrock method Order conditions Convergence

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TWO-GRID ALGORITHM OF H^(1)-GALERKIN MIXED FINITE ELEMENT METHODS FOR SEMILINEAR PARABOLIC INTEGRO-DIFFERENTIAL EQUATIONS

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Journal of computational Mathematics 2022年第5期40卷 667-685页

作者： Tianliang Hou Chunmei Liu Chunlei Dai Luoping Chen Yin Yang School of Mathematics and Statistics Beihua UniversityJilin 132013China College of Science Hunan University of Science and EngineeringYongzhou 425199China School of Mathematics Southwest Jiaotong UniversityChengdu 611756China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing&Information Processing of Ministry of EducationSchool of Mathematics and Computational ScienceXiangtan UniversityXiangtan 411105China

In this paper,we present a two-grid discretization scheme for semilinear parabolic integro-differential equations by H1-Galerkin mixed finite element *** use the lowest order Raviart-Thomas mixed finite elements and continuous linear finite element for spatial discretization,and backward Euler scheme for temporal ***,a priori error estimates and some superclose properties are ***,a two-grid scheme is presented and its convergence is *** the proposed two-grid scheme,the solution of the nonlinear system on a fine grid is reduced to the solution of the nonlinear system on a much coarser grid and the solution of two symmetric and positive definite linear algebraic equations on the fine grid and the resulting solution still maintains optimal ***,a numerical experiment is implemented to verify theoretical results of the proposed *** theoretical and numerical results show that the two-grid method achieves the same convergence property as the one-grid method with the choice h=H^(2).

关键词： Semilinear parabolic integro-differential equations H^(1)-Galerkin mixed finite element method A priori error estimates Two-grid Superclose.

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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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Discovery of New Metastable Patterns in Diblock Copolymers

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Communications in computational Physics 2013年第7期14卷 443-460页

作者： Kai Jiang Chu Wang Yunqing Huang Pingwen Zhang LMAM and School of Mathematical Sciences Peking UniversityBeijing 100871P.R.China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan UniversityXiangtan 411105P.R.China

The ordered patterns formed bymicrophase-separated block copolymer systems demonstrate periodic symmetry,and all periodic structures belong to one of 230 space *** on this fact,a strategy of estimating the initial values of self-consistent field theory to discover ordered patterns of block copolymers is *** particular,the initial period of the computational box is estimated by the Landau-Brazovskii model as *** planting the strategy into the whole-space discrete method,several new metastable patterns are discovered in diblock copolymers.

关键词： Metastable patterns diblock copolymers self-consistent field theory(SCFT) space group theory initial values

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Some applications of nonlinear science methods and support vector machine methods to protein problems

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Mini-Reviews in Organic Chemistry 2015年第6期12卷 493-505页

作者： Hana, Guo Sheng Yu, Zu-Guo Zhao, Zhi-Qin Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University XiangtanHunan411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 BrisbaneQ4001 Australia

Protein folding, prediction of protein structure and functions are most important problems in bioinformatics. The protein fold process mainly reflects in the kinetic order of folding. Predicting the structural classes of low-homology protein is a difficult problem in the prediction of protein structure. In order to understanding the mechanism of programmed cell death, it is very necessary to obtain the information about subcellular locations and functions of apoptosis proteins. Predicting protein subnuclear localizations is a challenging problem which is harder than predicting protein subcellular locations. Predicting membrane protein types is related to the structure and function of proteins. In this review, we introduce some applications of nonlinear science methods and support vector machine methods to the above protein problems. The nonlinear science methods including the horizontal visibility network, kernel method, recurrence quantification analysis, global descriptor, Lempel-Ziv complexity, and Hilbert-Huang transform are used to extract features in these approaches. © 2015 Bentham science Publishers.

关键词： Support vector machines

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αSetup-PCTL:An Adaptive Setup-Based Two-Level Preconditioner for Sequence of Linear Systems of Three-Temperature Energy Equations

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Communications in computational Physics 2022年第10期32卷 1287-1309页

作者： Silu Huang Xiaoqiang Yue Xiaowen Xu Laboratory of Computational Physics Institute of Applied Physics and ComputationalMathematicsBeijing 100088China National Center for Applied Mathematics in Hunan Key Laboratory of Intelligent Computing and Information Processing of Ministry of EducationHunan Key Laboratory for Computation and Simulation in Science and EngineeringXiangtan UniversityXiangtan 411105China

The iterative solution of the sequence of linear systems arising from threetemperature(3-T)energy equations is an essential component in the numerical simulation of radiative hydrodynamic(RHD)***,due to the complicated application features of the RHD problems,solving 3-T linear systems with classical preconditioned iterative techniques is *** address this difficulty,a physicalvariable based coarsening two-level(PCTL)preconditioner has been proposed by dividing the fully coupled system into four individual easier-to-solve *** its nearly optimal complexity and robustness,the PCTL algorithm suffers from poor efficiency because of the overhead associatedwith the construction of setup phase and the solution of ***,the PCTL algorithm employs a fixed strategy for solving the sequence of 3-T linear systems,which completely ignores the dynamically and slowly changing features of these linear *** address these problems and to efficiently solve the sequence of 3-T linear systems,we propose an adaptive two-level preconditioner based on the PCTL algorithm,referred to as α*** adaptive strategies of the αSetup-PCTL algorithm are inspired by those of αSetup-AMG algorithm,which is an adaptive-setup-based AMG solver for sequence of sparse linear *** proposed αSetup-PCTL algorithm could adaptively employ the appropriate strategies for each linear system,and thus increase the overall *** results demonstrate that,for 36 linear systems,the αSetup-PCTL algorithm achieves an average speedup of 2.2,and a maximum speedup of 4.2 when compared to the PCTL algorithm.

关键词： Sequence of linear systems sparse linear solver preconditioning methods radiation hydrodynamics simulation

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Economical cascadic multigrid method (ECMG)

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science China Mathematics 2007年第12期50卷 1765-1780页

作者： Zhong-ci SHI~1 Xue-jun XU~(1+) Yun-qing HUANG~2 ~1 LSEC,Institute of computational Mathematics,Academy of Mathematics and Systems science,Chinese Academy of sciences,Beijing 100080,China ~2 hunan key laboratory for computation and simulation in science and engineering,Institute for computational and Applied Mathematics,Xiangtan University,Xiangtan 411105,China LSEC Institute of Computational Mathematics Academy of Mathematics Systems Science Chinese Academy of Sciences Beijing 100080 China Hunan Key Laboratory for Computation Simulation in Science Engineering Institute for Computational Applied Mathematics Xiangtan University Xiangtan 411105 China

In this paper, an economical cascadic multigrid method is proposed. Compared with the usual cascadic multigrid method developed by Bornemann and Deuflhard, the new one requires less iterations on each level, especially on the coarser grids. Many operations can be saved in the new cascadic multigrid algorithms. The main ingredient is the control of the iteration numbers on the each level to preserve the accuracy without over iterations. The theoretical justification is based on the observations that the error reduction rate of an iteration scheme in terms of the smoothing property is no longer accurate while the iteration number is big enough. A new formulae of the error reduction rate is employed in our new algorithm. Numerical experiments are reported to support our theory.

关键词： economical cascadic multigrid method (ECMG), cascadic multigrid method (CMG)

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