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Numerical Analysis of Bacterial Meningitis Stochastic Delayed Epidemic Model through computational methods

Computer Modeling in Engineering & Sciences 2024年第10期141卷 311-329页

作者： Umar Shafique Mohamed Mahyoub Al-Shamiri Ali Raza Emad Fadhal Muhammad Rafiq Nauman Ahmed Department of Mathematics National College of Business Administration and EconomicsLahore54660Pakistan Department of Mathematics Applied CollegeMahayl AssirKing Khalid UniversityAbha62529Saudi Arabia Department of Physical Sciences The University of ChenabGujrat50700Pakistan Department of Mathematics&Statistics College of ScienceKing Faisal UniversityP.O.Box 400Al-Ahsa31982Saudi Arabia Department of Computer Science and Mathematics Lebanese American UniversityBeirut1102-2801Lebanon Department of Mathematics Faculty of Science and TechnologyUniversity of Central PunjabLahore54000Pakistan Department of Mathematics and Statistics University of LahoreLahore54000Pakistan

Based on theWorld Health Organization(WHO),Meningitis is a severe infection of the meninges,the membranes covering the brain and spinal *** is a devastating disease and remains a significant public health *** study investigates a bacterial meningitis model through deterministic and stochastic ***-compartment population dynamics explain the concept,particularly the susceptible population,carrier,infected,and *** model predicts the nonnegative equilibrium points and reproduction number,i.e.,the Meningitis-Free Equilibrium(MFE),and Meningitis-Existing Equilibrium(MEE).For the stochastic version of the existing deterministicmodel,the twomethodologies studied are transition probabilities and non-parametric ***,positivity,boundedness,extinction,and disease persistence are studiedrigorouslywiththe helpofwell-known *** and nonstandard techniques such as EulerMaruyama,stochastic Euler,stochastic Runge Kutta,and stochastic nonstandard finite difference in the sense of delay have been presented for computational analysis of the stochastic ***,standard methods fail to restore the biological properties of the model,so the stochastic nonstandard finite difference approximation is offered as an efficient,low-cost,and independent of time step *** addition,the convergence,local,and global stability around the equilibria of the nonstandard computational method is studied by assuming the perturbation effect is *** simulations and comparison of the methods are presented to support the theoretical results and for the best visualization of results.

关键词： Bacterial Meningitis disease stochastic delayed model stability analysis extinction and persistence computational methods

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computational methods in super-resolution microscopy

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Frontiers of Information Technology & Electronic Engineering 2017年第9期18卷 1222-1235页

作者： Zhi-ping ZENG Hao XIE Long CHEN Karl ZHANGHAO Kun ZHAO Xu-san YANG Peng XI College of Physics and Information Engineering Fuzhou University Fuzhou 350116 China Department of Biomedical Engineering Peldng University Beijing 100871 China MOE Key Laboratory of Bioinformatics Tsinghua University Beijing 100084 China Bioinformatics Division and Center for Synthetic & Systems Biology TNLIST Tsinghua University Beijing 100084 China Department of Automation Tsinghua University Beijing 100084 China

The broad applicability of super-resolution microscopy has been widely demonstrated in various areas and disciplines. The optimization and improvement of algorithms used in super-resolution microscopy are of great importance for achieving optimal quality of super-resolution imaging. In this review, we comprehensively discuss the computational methods in different types of super-resolution microscopy, including deconvolution microscopy, polarization-based super-resolution microscopy, structured illumination microscopy, image scanning microscopy, super-resolution optical fluctuation imaging microscopy, single-molecule localization microscopy, Bayesian super-resolution microscopy, stimulated emission depletion microscopy, and translation microscopy. The development of novel computational methods would greatly benefit super-resolution microscopy and lead to better resolution, improved accuracy, and faster image processing.

关键词： Super-resolution microscopy Deconvolution computational methods

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Bio-Inspired computational methods for the Polio Virus Epidemic Model

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Computers, Materials & Continua 2022年第8期72卷 2357-2374页

作者： Fatimah Abdulrahman Alrawajeh F.M.Allehiany Ali Raza Shaimaa A.M.Abdelmohsen Tahir Nawaz Cheema Muhammad Rafiq Muhammad Mohsin Department of Mathematics Faculty of Science CollegeImam Abdulrahman Bin Faisal University(IAU)Dammam31441Saudi Arabia Department of Mathematical Sciences College of Applied SciencesUmm Al-Qura UniversityP.O.Box 715Makkah21955Saudi Arabia Department of Mathematics Govt.Maulana Zafar Ali Khan Graduate College Wazirabad52000Punjab Higher Education Department(PHED)Lahore54000Pakistan Department of Physics College of SciencePrincess Nourah bint Abdulrahman UniversityRiyadh 11671Saudi Arabia Department of Mathematics University of GujratGujrat50700Pakistan Department of Mathematics Faculty of SciencesUniversity of Central PunjabLahore54600Pakistan Department of Mathematics Technische Universitat Chemnitz6209111Germany

In 2021,most of the developing countries are fighting polio,and parents are concerned with the disabling of their *** transmits from person to person,which can infect the spinal cord,and paralyzes the parts of the body within a matter of *** to the World Health Organization(WHO),18 million currently healthy people could have been paralyzed by the virus during 1988–*** all countries but Pakistan,Afghanistan,and a fewmore have been declared *** mathematical modeling of poliovirus is studied in the population by categorizing it as susceptible individuals(S),exposed individuals(E),infected individuals(I),and recovered individuals(R).In this study,we study the fundamental properties such as positivity and boundedness of the *** also rigorously study the model’s stability and equilibria with or without *** numerical study,we design the Euler,Runge–Kutta,and nonstandard finite difference ***,the standard techniques are time-dependent and fail to present the results for an extended *** nonstandard finite difference method works well to study disease dynamics for a long time without any ***,the results of different methods are compared to prove their effectiveness.

关键词： Poliovirus modeling stability results computational methods

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Recent Advances in computational methods for Nuclear Magnetic Resonance Data Processing

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Genomics, Proteomics & Bioinformatics 2013年第1期11卷 29-33页

作者： Xin Gao Computer Electrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)

Although three-dimensional protein structure determination using nuclear magnetic res- onance （NMR） spectroscopy is a computationally costly and tedious process that would benefit from advanced computational techniques, it has not garnered much research attention from special- ists in bioinformatics and computational biology. In this paper, we review recent advances in com- putational methods for NMR protein structure determination. We summarize the advantages of and bottlenecks in the existing methods and outline some open problems in the field. We also dis- cuss current trends in NMR technology development and suggest directions for research on future computational methods for NMR.

关键词： Nuclear magnetic resonance Protein structure computational methods Bioinformatics

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Comprehensive evaluation of computational methods for predicting cancer driver genes

Comprehensive evaluation of computational methods for predic...

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2021年中国肿瘤标志物学术大会暨第十五届肿瘤标志物青年科学家论坛

作者： Xiaohui Shi Fengbiao Mao Zhongsheng Sun University of Chinese Academy of Sciences Peking University Third Hospital Beijing Institutes of Life Science Chinese Academy of Sciences

Objective:Some studies have evaluated performance in some of algorithms for predicting pathogenic or driver mutations and genes. However, for the identification methods of tumor driver genes, several methods proved to have the best performance in the corresponding researches. Moreover, recently developed methods such as Moonlight, nCOP, OncoIMPACT, MutPanning, driverMAPS, WITER,and DriverML have not been compared with each other until now, and the comparison of network datasets for network-based approaches is still lack. Furthermore, the lack of accepted gold standard of driver genes and appropriate measurements limited the research on assessment of methods for predicting cancer driver genes. Thus, it is urgently needed to perform a comprehensive and systematic evaluation of computational methods for predicting cancer driver ***:Herein, considering the novelty and practicality, we independently assessed the performance of12 recently published approaches of driver gene prediction without our participation, including eight network-based, one functional-based, and three frequency-based methods. Then we integrated the gene driver scores which represent the possibility of cancer driver predicted by different tools into a website of cancer driver catalog. In total, we performed eight measurements of 12 methods with six network datasets based on eight benchmark ***:Given that the importance of drivers in pan-cancer analysis have been highlighted, we obtained the AUC scores calculated from the pan-cancer dataset of PCAWG using different algorithms based on aforementioned eight reference gene sets. Performance evaluations based on somatic mutations of pan-cancer dataset showed that a frequency-based method of driverMAPS outperformed other algorithms under most of reference *** further evaluate the ability of different algorithms for predicting cancer drivers in specific cancer types,we employed somatic mutation data from each of the 36 cancer t

关键词： cancer driver genes computational methods predicting algorithms method assessments TCGA

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Preliminary Investigation of Copper(II) Ion Binding or Complex Coordination in Lysozeme Molecules

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Journal of Materials Science and Chemical Engineering 2024年第4期12卷 98-103页

作者： Kou Takahashi Ryotaro Miyazaki Daisuke Nakane Temitayo O. Aiyelabola Takashiro Akitsu Department of Chemistry Faculty of Science Tokyo University of Science Tokyo Japan Department of Chemistry Faculty of Science Obafemi Awolowo University Ile-Ife Nigeria

Hydrophobic Val derivative Schiff base copper(II) complexes and dipeptide (AlaAla, GlyGly) derivative Schiff base copper(II) complexes were introduced into egg white lysozyme. X-ray crystal structure analysis revealed amino acid derivative Schiff base copper(II) complexes were obtained. Herein we discuss primarily on the binding mode of copper(II) of the complexes obtained with egg white lysozyme. The electron density of copper(II) ions was confirmed by X-ray crystal structure analysis. The Val derivative Schiff base copper(II) complex was weakly bound at Arg114 of egg white lysozyme. In other copper(II) complexes, binding of copper(II) ions with dissociated ligands to various residues was observed. The binding sites of copper(II) ions were compared with computational scientific predictions.

关键词： Copper Schiff Base Lysozyme Metal-Protein Binding computational methods

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基于神经网络势能函数实现多组分金属液体玻璃化转变过程的精确高效模拟（英文）

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Science China Materials 2024年第10期67卷 3298-3308页

作者：苏锐余洁意管鹏飞汪卫华 College of Materials&Environmental Engineering Hangzhou Dianzi University Beijing computational Science Research Center Songshan Lake Materials Laboratory

多组元金属液体中玻璃化转变的计算模拟面临精确势能函数构建及玻璃转变温度附近指数增长的结构弛豫时间这两大关键问题.通过高效的神经网络势训练算法和程序实现,以及基于原子交换的杂化蒙特卡洛方法,我们提出了一套高效且精确的处理... 详细信息

多组元金属液体中玻璃化转变的计算模拟面临精确势能函数构建及玻璃转变温度附近指数增长的结构弛豫时间这两大关键问题.通过高效的神经网络势训练算法和程序实现,以及基于原子交换的杂化蒙特卡洛方法,我们提出了一套高效且精确的处理多组元金属液体玻璃化转变模拟问题的通用算法并在Zr-Cu-Al三元金属玻璃体系中进行了验证.验证结果表明,该算法可以准确地再现第一性原理计算和实验中所获得的合金相稳定性和结构关联函数,并将深过冷温度下的结构弛豫时间缩短至少五个数量级同时得到了接近实验冷却速率范围的玻璃结构样品.该研究为进一步研究多组元金属液体中的玻璃化过程特别是成分依赖的玻璃形成能力和物理性能奠定了理论基础.

关键词： metallic glass computational methods glass transition

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一类组合KdV方程的数值方法

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高等学校计算数学学报 2007年第3期29卷 236-244页

作者：左进明张天德山东理工大学数学与信息科学学院山东大学数学与系统科学学院

1引言从Scott-Russell[1]提出在平静的水面上孤波运动的情形以后,大量的目光开始关注它的存在性、其中的性质和动态的交互情形[2],这是因为许多非线性动态的物理现象可以被描述成一个孤立子的模型[2,3].诸如,Korteweg-de Vries(KdV)方程... 详细信息

1引言从Scott-Russell[1]提出在平静的水面上孤波运动的情形以后,大量的目光开始关注它的存在性、其中的性质和动态的交互情形[2],这是因为许多非线性动态的物理现象可以被描述成一个孤立子的模型[2,3].诸如,Korteweg-de Vries(KdV)方程[4,5,6],正弦

关键词： computational methods compound KdV equation(CKdV) stability analysis phase error.

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A cellular automata model for simulating grain structures with straight and hyperbolic interfaces

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International Journal of Minerals,Metallurgy and Materials 2012年第8期19卷 699-710页

作者： A.Ramírez-López M.Palomar-Pardavé D.Muñoz-Negrón C.Duran-Valencia S.López-Ramirez G.Soto-Cortés Materials and Energy Department Metropolitan Autonomous UniversityMexico Department of Industrial Engineering Technological Autonomous Institute of MexicoMexico Department of Molecular Engineering Mexican Institute of PetroleumMexico

A description of a mathematical algorithm for simulating grain structures with straight and hyperbolic interfaces is shown. The presence of straight and hyperbolic interfaces in many grain structures of metallic materials is due to different solidification conditions, in- eluding different solidification speeds, growth directions, and delaying on the nucleation times of each nucleated node. Grain growth is a complex problem to be simulated; therefore, computational methods based on the chaos theory have been developed for this purpose. Straight and hyperbolic interfaces are between columnar and equiaxed grain structures or in transition zones. The algorithm developed in this work involves random distributions of temperature to assign preferential probabilities to each node of the simulated sample for nucleation according to previously defined boundary conditions. Moreover, more than one single nucleation process can be established in order to gen- erate hyperbolic interfaces between the grains. The appearance of new nucleated nodes is declared in sequences with a particular number of nucleated nodes and a number of steps for execution. This input information influences directly on the final grain structure （grain size and dislribution）. Preferential growth directions are also established to obtain equiaxed and columnar grains. The simulation is done using rou- tines for nucleation and growth nested inside the main function. Here, random numbers are generated to place the coordinates of each new nucleated node at each nucleation sequence according to a solidification probability. Nucleation and growth routines are executed as a func- tion of nodal availability in order to know if a node will be part of a grain. Finally, this information is saved in a two-dimensional computa- tional array and displayed on the computer screen placing color pixels on the corresponding position forming an image as is done in cellular automaton.

关键词： grain growth interfaces grain size and shape computational methods algorithms cellular automata computer simulation

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Algorithm for Computation of Unstructured Real Stability Radius and Its Applications

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International Journal of Minerals,Metallurgy and Materials 1998年第4期12卷 245-250页

作者： Xiaodan Zhang Lequan Min(Applied Science School, University of Science and Technology Beijing, Beijing 100083, China) Applied Science School University of Science and Technology Beijing Beijing 100083 China

An algorithm for the computation of the unstructured real stability radius of high dimensional linearsystem is presented. Using the accurate formula of the real stability radius of 2-dimensional system linear systemchecks the algorithm. The result shows that the algorithm is reliable and efficient. As applications, the unstructuredreal stability radii of 2-dimensional Chua's circuit and 3-dimensional piecewise-linear system are calculated, thedynamical orbits of the corresponding perturbed systems are simulated.

关键词： lincar systems stability robustness parameter perturbation computational methods

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