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Topological properties and fractal analysis of a recurrence network constructed from fractional Brownian motions

Physical Review E 2014年第3期89卷 032814-032814页

作者： Jin-Long Liu Zu-Guo Yu Vo Anh 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 Xiangtan Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia

Many studies have shown that we can gain additional information on time series by investigating their accompanying complex networks. In this work, we investigate the fundamental topological and fractal properties of recurrence networks constructed from fractional Brownian motions (FBMs). First, our results indicate that the constructed recurrence networks have exponential degree distributions; the average degree exponent 〈λ〉 increases first and then decreases with the increase of Hurst index H of the associated FBMs; the relationship between H and 〈λ〉 can be represented by a cubic polynomial function. We next focus on the motif rank distribution of recurrence networks, so that we can better understand networks at the local structure level. We find the interesting superfamily phenomenon, i.e., the recurrence networks with the same motif rank pattern being grouped into two superfamilies. Last, we numerically analyze the fractal and multifractal properties of recurrence networks. We find that the average fractal dimension 〈dB〉 of recurrence networks decreases with the Hurst index H of the associated FBMs, and their dependence approximately satisfies the linear formula 〈dB〉≈2−H, which means that the fractal dimension of the associated recurrence network is close to that of the graph of the FBM. Moreover, our numerical results of multifractal analysis show that the multifractality exists in these recurrence networks, and the multifractality of these networks becomes stronger at first and then weaker when the Hurst index of the associated time series becomes larger from 0.4 to 0.95. In particular, the recurrence network with the Hurst index H=0.5 possesses the strongest multifractality. In addition, the dependence relationships of the average information dimension 〈D(1)〉 and the average correlation dimension 〈D(2)〉 on the Hurst index H can also be fitted well with linear functions. Our results strongly suggest that the recurrence network inherits the basic characteristic

关键词： TOPOLOGICAL property FRACTAL analysis BROWNIAN motion CORRELATION (Statistics) RECURSIVE sequences (Mathematics) COMPUTER networks

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Error Analysis of Virtual Element Method for the Poisson-Boltzmann Equation

arXiv

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arXiv 2023年

作者： Huang, Linghan Shu, Shi Yang, Ying Guangxi Guilin541004 China School of Mathematics and Computational Science Xiangtan University Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Hunan Xiangtan411105 China Guangxi541004 China

The Poisson-Boltzmann equation is a nonlinear elliptic equation with Dirac distribution sources, which has been widely applied to the prediction of electrostatics potential of biological biomolecular systems in solution. In this paper, we discuss and analysis the virtual element method for the Poisson-Boltzmann equation on general polyhedral meshes. Under the low regularity of the solution of the whole domain, nearly optimal error estimates in both L2-norm and H1-norm for the virtual element approximation are obtained. The numerical experiment on different polyhedral meshes shows the efficiency of the virtual element method and verifies the proposed theoretical prediction. Copyright © 2023, The Authors. All rights reserved.

关键词： Poisson equation

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Two-level overlapping Schwarz methods based on local generalized eigenproblems for hermitian variational problems

arXiv

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arXiv 2021年

作者： Lu, Qing Wang, Junxian Shu, Shi Peng, Jie School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan Xiangtan411105 China School of Mathematical Sciences South China Normal University Guangzhou510631 China

The research of two-level overlapping Schwarz (TL-OS) method based on constrained energy minimizing coarse space is still in its infancy, and there exist some defects, e.g. mainly for second order elliptic problem and too heavy computational cost of coarse space construction. In this paper, by introducing appropriate assumptions, we propose more concise coarse basis functions for general Hermitian positive and definite discrete systems, and establish the algorithmic and theoretical frameworks of the corresponding TL-OS methods. Furthermore, to enhance the practicability of the algorithm, we design two economical TL-OS preconditioners and prove the condition number estimate. As the first application of the frameworks, we prove that the assumptions hold for the linear finite element discretization of second order elliptic problem with high contrast and oscillatory coefficient and the condition number of the TL-OS preconditioned system is robust with respect to the model and mesh parameters. In particular, we also prove that the condition number of the economically preconditioned system is independent of the jump range under a certain jump distribution. Experimental results show that the first kind of economical preconditioner is more efficient and stable than the existed one. Secondly, we construct TL-OS and the economical TL-OS preconditioners for the plane wave least squares discrete system of Helmholtz equation by using the frameworks. The numerical results for homogeneous and non-homogeneous cases illustrate that the PCG method based on the proposed preconditioners have good stability in terms of the angular frequency, mesh parameters and the number of degrees of freedom in each element. Copyright © 2021, The Authors. All rights reserved.

关键词： Number theory

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The interior penalty virtual element method for fourth-order singular perturbation problems

arXiv

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arXiv 2023年

作者： Feng, Fang Yu, Yue School of Mathematics and Statistics Nanjing University of Science and Technology Nanjing China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Xiangtan University Hunan Xiangtan411105 China

This paper is dedicated to the numerical solution of a fourth-order singular perturbation problem using the interior penalty virtual element method (IPVEM) proposed in [42]. The study introduces modifications to the jumps and averages in the penalty term, as well as presents an automated mesh-dependent selection of the penalty parameter. Drawing inspiration from the modified Morley finite element methods, we leverage the conforming interpolation technique to handle the lower part of the bilinear form. Through our analysis, we establish optimal convergence in the energy norm and provide a rigorous proof of uniform convergence concerning the perturbation parameter in the lowest-order case. © 2023, CC BY-NC-ND.

关键词： Numerical methods

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Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles

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Molecular phylogenetics and evolution 2015年 89卷 37-45页

作者： Xian-Hua Xie Zu-Guo Yu Guo-Sheng Han Wei-Feng Yang Vo Anh 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 PR China School of Mathematics and Computer Science Gannan Normal University Jiangxi 341000 PR China. Electronic address: xxianhua@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: yuzuguo@***. 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 PR China. Electronic address: korea10282003@***. 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 PR China. Electronic address: yangweifeng09@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: v.anh@qut.edu.au.

There has been a growing interest in alignment-free methods for whole genome comparison and phylogenomic studies. In this study, we propose an alignment-free method for phylogenetic tree construction using whole-proteome sequences. Based on the inter-amino-acid distances, we first convert the whole-proteome sequences into inter-amino-acid distance vectors, which are called observed inter-amino-acid distance profiles. Then, we propose to use conditional geometric distribution profiles (the distributions of sequences where the amino acids are placed randomly and independently) as the reference distribution profiles. Last the relative deviation between the observed and reference distribution profiles is used to define a simple metric that reflects the phylogenetic relationships between whole-proteome sequences of different organisms. We name our method inter-amino-acid distances and conditional geometric distribution profiles (IAGDP). We evaluate our method on two data sets: the benchmark dataset including 29 genomes used in previous published papers, and another one including 67 mammal genomes. Our results demonstrate that the new method is useful and efficient.

关键词： Alignment-free whole-proteome comparison Conditional geometric distribution profile Inter-amino-acid distances Phylogenetic tree

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Exponentially Accurate Rayleigh–Ritz Method for Fractional Variational Problems

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Journal of computational and Nonlinear Dynamics 2015年第5期10卷 051009页

作者： Mao, Zhi Xiao, Aiguo Wang, Dongling Yu, Zuguo Shi, Long Hunan Key Laboratory for Computationand Simulation in Science and Engineering Xiangtan UniversityXiangtan Hunan 411105 China School of Mathematics Northwest UniversityXi’an Shaanxi 710127 China

A high accurate Rayleigh–Ritz method is developed for solving fractional variational problems (FVPs). The Jacobi poly-fractonomials proposed by Zayernouri and Karniadakis (2013, “Fractional Sturm–Liouville Eigen-Problems: Theory and Numerical Approximation,” J. Comput. Phys.,252(1), pp. 495–517.) are chosen as basis functions to approximate the true solutions, and the Rayleigh–Ritz technique is used to reduce FVPs to a system of algebraic equations. This method leads to exponential decay of the errors, which is superior to the existing methods in the literature. The fractional variational errors are discussed. Numerical examples are given to illustrate the exponential convergence of the method.

关键词： Errors Integration methods Algorithms Rayleigh-Ritz methods

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Hamiltonian Boundary Value Methods (HBVMs) for functional differential equations with piecewise continuous arguments

arXiv

引用

arXiv 2024年

作者： Gurioli, Gianmarco Wang, Weijie Yan, Xiaoqiang Università degli Studi di Firenze Florence Italy School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan411105 China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan411105 China

In this paper, a class of high-order methods to numerically solve Functional Differential Equations with Piecewise Continuous Arguments (FDEPCAs) is discussed. The framework stems from the expansion of the vector field associated with the reference differential equation along the shifted and scaled Legendre polynomial orthonormal basis, working on a suitable extension of Hamiltonian Boundary Value Methods. Within the design of the methods, a proper generalization of the perturbation results coming from the field of ordinary differential equations is considered, with the aim of handling the case of FDEPCAs. The error analysis of the devised family of methods is performed, while a few numerical tests on Hamiltonian FDEPCAs are provided, to give evidence to the theoretical findings and show the effectiveness of the obtained resolution *** Codes 65L05, 65L03, 65L06, 65P10 Copyright © 2024, The Authors. All rights reserved.

关键词： Ordinary differential equations

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Finite difference and sinc-collocation approximations to a class of fractional diffusion-wave equations

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Journal of Applied Mathematics 2014年第1期2014卷

作者： Mao, Zhi Xiao, Aiguo Yu, Zuguo Shi, Long Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan 411105 China Mathematics and Information Engineering Department Tongren University Tongren Guizhou 554300 China

We propose an efficient numerical method for a class of fractional diffusion-wave equations with the Caputo fractional derivative of order α. This approach is based on the finite difference in time and the global sinc collocation in space. By utilizing the collocation technique and some properties of the sinc functions, the problem is reduced to the solution of a system of linear algebraic equations at each time step. Stability and convergence of the proposed method are rigorously analyzed. The numerical solution is of 3 - α order accuracy in time and exponential rate of convergence in space. Numerical experiments demonstrate the validity of the obtained method and support the obtained theoretical results. © 2014 Zhi Mao et al.

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Cubic spline collocation method for fractional differential equations

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Journal of Applied Mathematics 2013年第1期2013卷

作者： Yang, Shui-Ping Xiao, Ai-Guo Department of Mathematics Huizhou University Guangdong 516007 China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan 411105 China

We discuss the cubic spline collocation method with two parameters for solving the initial value problems (IVPs) of fractional differential equations (FDEs). Some results of the local truncation error, the convergence, and the stability of this method for IVPs of FDEs are obtained. Some numerical examples verify our theoretical results. © 2013 Shui-Ping Yang and Ai-Guo Xiao.

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Synthesis of N-confused Porphyrin Derivatives with Substituted 3-C Position

Synthesis of N-confused Porphyrin Derivatives with Substitut...

引用

中国化学会第八届全国无机化学学术会议

作者： Bin Liu Xiaofang Li Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education Hunan Province College Key Laboratory of QSAR/QSPR School of Chemistry and Chemical Engineering Hunan University of Science and Technology Xiangtan Hunan 411201China Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education Hunan Province College Key Laboratory of QSAR/QSPR School of Chemistry and Chemical Engineering Hunan University of Science

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