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Physicochemical property based computational scheme for classifying DNA sequence elements of Saccharomyces cerevisiae

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computational BIOLOGY AND CHEMISTRY 2019年 79卷 193-201页

作者： Jaiswal, Atul Kumar Krishnamachari, Annangarachari JNU Sch Computat & Integrat Sci New Delhi 110067 India

GenerationE of huge "omics" data necessitates the development and application of computational methods to annotate the data in terms of biological features. In the context of DNA sequence, it is important to unravel the hidden physicochemical signatures. For this purpose, we have considered various sequence elements such as promoter, ACS, LTRs, telomere, and retrotransposon of the model organism Saccharomyces cerevisiae. Contributions due to di-nucleotides play a major role in studying the DNA conformation profile. The physicochemical parameters used are hydrogen bonding energy, stacking energy and solvation energy per base pair. Our computational study shows that all sequence elements in this study have distinctive physicochemical signatures and the same can be exploited for prediction experiments. The order that we see in a DNA sequence is dictated by biological regions and hence, there exists role of dependency in the sequence makeup, keeping this in mind we are proposing two computational schemes (a) using a windowing block size procedure and (b) using di-nucleotide transitions. We obtained better discriminating profile when we analyzed the sequence data in windowing manner. In the second novel approach, we introduced the di-nucleotide transition probability matrix (DTPM) to study the hidden layer of information embedded in the sequences. DTPM has been used as weights for scanning and predictions. This proposed computational scheme incorporates the memory property which is more realistic to study the physicochemical properties embedded in DNA sequences. Our analysis shows that the DTPM scheme performs better than the existing method in this applied region. Characterization of these elements will be a key to genome editing applications and advanced machine learning approaches may also require such distinctive profiles as useful input features.

关键词： DNA sequence elements Physicochemical properties DTPM computational scheme Machine learning

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A Modified computational scheme for the Stochastic Perturbation Finite Element Method

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LATIN AMERICAN JOURNAL OF SOLIDS AND STRUCTURES 2015年第13期12卷 2480-2505页

作者： Wu, Feng Gao, Qiang Xu, Xiao-Ming Zhong, Wan-Xie Dalian Univ Technol State Key Lab Struct Anal Ind Equipment Dept Engn Mech Fac Vehicle Engn & Mech Dalian 116023 Peoples R China

A modified computational scheme of the stochastic perturbation finite element method (SPFEM) is developed for structures with low-level uncertainties. The proposed scheme can provide second-order estimates of the mean and variance without differentiating the system matrices with respect to the random variables. When the proposed scheme is used, it involves finite analyses of deterministic systems. In the case of one random variable with a symmetric probability density function, the proposed computational scheme can even provide a result with fifth-order accuracy. Compared with the traditional computational scheme of SPFEM, the proposed scheme is more convenient for numerical implementation. Four numerical examples demonstrate that the proposed scheme can be used in linear or nonlinear structures with correlated or uncorrelated random variables.

关键词： Stochastic finite element method Uncertain structures Perturbation computational scheme

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Two Different computational schemes for Solving Chemical Dissolution-Front Instability Problems in Fluid-Saturated Porous Media

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TRANSPORT IN POROUS MEDIA 2022年第2期145卷 323-346页

作者： Zhao, Chongbin Hobbs, B. E. Ord, A. Cent South Univ Computat Geosci Res Ctr Changsha 410083 Peoples R China Cent South Univ Key Lab Metallogen Predict Nonferrous Met & Geol Minist Educ Changsha 410083 Peoples R China Univ Western Australia Sch Earth & Environm Crawley WA 6009 Australia

This paper deals with how to solve chemical dissolution-front instability problems, which are nonlinearly coupled by subsurface pore-fluid flow, reactive mass transport and porosity evolution processes in fluid-saturated porous media, through using two different computational schemes. In the first computational scheme, porosity, pressure of the pore-fluid and concentration of the solute are used as fundamental unknown variables to describe a chemical dissolution system, so that it can be named as the PPC scheme. In the second computational scheme, porosity, velocity of the pore-fluid and concentration of the solute are used as fundamental unknown variables to describe a chemical dissolution system, so that it can be named as the PVC scheme. Since the finite element equations of a chemical dissolution-front instability problem on the basis of using the PPC scheme is available, the main focus of this study is on deriving the finite element equations of a chemical dissolution-front instability problem on the basis of using the PVC scheme. In particular, analytical solutions for the property matrices of a four-node rectangular element have been derived and used in both the PVC scheme and the PPC scheme. Through comparing the computational simulation results obtained from using both the PPC scheme and the PVC scheme, it has demonstrated that: (1) if the chemical dissolution system is in a stable state, then the PPC scheme is superior to the PVC scheme because the PPC scheme uses less computational efforts than the PVC scheme;(2) if the chemical dissolution system is in an unstable state, then the PVC scheme is superior to the PPC scheme because the PVC scheme yields more accurate computational simulation results than the PPC scheme.

关键词： Chemical dissolution Mass transport computational scheme Solution accuracy Front instability Porous media

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Mathematical analysis and pattern formation in diffusive predator-prey system

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JOURNAL OF APPLIED MATHEMATICS AND COMPUTING 2025年第3期71卷 3037-3058页

作者： Ahmed, Nauman Yasin, Muhammad Waqas Akgul, Ali Baleanu, Dumitru Tintareanu-Mircea, Ovidiu Univ Lahore Dept Math & Stat Lahore Pakistan Lebanese Amer Univ Dept Comp Sci & Math Beirut Lebanon Univ Narowal Dept Math Narowal Pakistan SIMATS Saveetha Sch Engn Dept Elect & Commun Engn Chennai Tamilnadu India Siirt Univ Art & Sci Fac Dept Math TR-56100 Siirt Turkiye Biruni Univ Dept Comp Engn TR-34010 Istanbul Turkiye Near East Univ Math Res Ctr Dept Math Near East BlvdMersin 10 TR-99138 Nicosia Turkiye Inst Space Sci Subsidiary INFLPR Magurele Romania

Prey-predator interactions are modeled using various dynamical systems and these interactions are affected by several factors. The predation rate of prey, reproduction rate, and prey use various strategies to avoid predation, the movement of the prey and predator species, food, and secured shelter can lead to the emergence of various types of patterns. These patterns in the prey-predator dynamics explain the complicated ecosystem. A reaction-diffusion prey-predator model with harvesting in predator is numerically investigated. A conditionally positivity preserving scheme is used. The von Neumann technique is used for the stability analysis. The Taylor series is used for the consistency analysis and discrete approximation is consistent with the underlying model. Pattern formation is observed for the governing model. The spot, stripe, and spot-stripes patterns are successfully gained that describe the complicated dynamics of the prey-predator dynamics. 3D and 2D simulations are drawn for the underlying model. The underlying model has two equilibria, both are successfully gained. All the theoretical results are verified through the simulations.

关键词： Predator-prey model Pattern formation computational scheme Analysis Discussion

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computational analysis of radiation effects in Williamson fluid flow through a porous medium under an inclined magnetic field

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JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2025年第2期18卷

作者： Kerdid, Nabil Arif, Muhammad Shoaib Nawaz, Yasir Abodayeh, Kamaleldin Imam Mohammad Ibn Saud Islamic Univ IMSIU Coll Sci Dept Math & Stat POB 90950 Riyadh 11623 Saudi Arabia Prince Sultan Univ Coll Humanities & Sci Dept Math & Sci Riyadh 11586 Saudi Arabia Air Univ Dept Math PAF Complex E9 Islamabad 44000 Pakistan

Various technical and commercial processes, including polymer extrusion, biomedical transport, and improved oil recovery, depend on the simulation of non-Newtonian fluid behaviour. Of the non-Newtonian models, the Williamson fluid best reflects shear-thinning properties;nonetheless, its non-linear governing equations provide major difficulties for conventional numerical methods. This work tackles these issues by suggesting a unique twostage explicit computational method to solve the time-dependent flow of Williamson fluid through a DarcyForchheimer porous media under the effect of thermal radiation and an angled magnetic field. The approach uses a compact finite difference method for space (sixth-order accuracy) and a modified exponential integrator for time discretization (second-order accuracy). Including internal heat generation and chemical reaction, the model is nondimensionalized and solved under unsteady boundary conditions. The suggested approach shows better accuracy and lower numerical error when compared to the classical second-order Runge-Kutta scheme. Key results show that although larger reaction rates result in lower concentration, more velocity is produced by raising the Darcy number and lowering the magnetic field intensity. Apart from presenting a quick numerical framework, the paper offers physical insights on regulating transport phenomena in complicated porous and electromagnetic settings, suggesting uses in thermal management, fluid processing, and MHD systems.

关键词： computational scheme Stability Convergence Radiation effects Williamson fluid Darcy Forchheimer flow

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Investigation of spectral properties of ¹¹Be in breakup reactions

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CHINESE PHYSICS C 2025年第5期49卷 054111-054111页

作者： Valiolda, D. S. Janseitov, D. M. Melezhik, V. S. Al Farabi Kazakh Natl Univ Alma Ata 050074 Kazakhstan Inst Nucl Phys Alma Ata 050032 Kazakhstan Joint Inst Nucl Res Bogoliubov Lab Theoret Phys Dubna 141980 Russia Dubna State Univ Dubna 141980 Russia

We investigate the breakup of the halo nucleus on a light target (Be-11) within the quantum-quasiclassical approach in a wide range of beam energy (5-67 MeV/nucleon), including bound states and low-lying resonances in different partial and spin states of Be-11. The obtained results are in good agreement with existing experimental data at 67 MeV/nucleon. Furthermore, we demonstrate that the developed computational scheme can be used for investigating nuclei spectral properties in low-energy breakup experiments on different targets.

关键词： halo nucleus breakup cross section low-lying resonances computational scheme

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Spatio-temporal patterns and Turing-Hopf bifurcation in a spatially extended prey-predator model with ratio-dependent interactions

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MODELING EARTH SYSTEMS AND ENVIRONMENT 2025年第3期11卷 1-20页

作者： Yasin, Muhammad Waqas Ahmed, Nauman Akgul, Ali Baber, Muhammad Zafarullah Baleanu, Dumitru Tintareanu-Mircea, Ovidiu Univ Narowal Dept Math Narowal Pakistan Univ Lahore Dept Math & Stat Lahore Pakistan SIMATS Saveetha Sch Engn Dept Elect & Commun Engn Chennai Tamilnadu India Siirt Univ Art & Sci Fac Dept Math TR-56100 Siirt Turkiye Biruni Univ Dept Comp Engn TR-34010 Topkapi Istanbul Turkiye Near East Univ Math Res Ctr Dept Math Near East BlvdMersin 10 TR-99138 Nicosia Turkiye Univ Lahore Dept Math & Stat Sargodha Campus Sargodha Pakistan Lebanese Amer Univ Dept Comp Sci & Math Beirut Lebanon Inst Space Sci Subsidiary INFLPR Magurele Romania

In this manuscript, we investigate the (2+1)-dimensional ratio-dependent prey-predator system. Prey-predator dynamics are a vital component of the eco-system. It provides the basic food for the living organisms. So, we considered the extended prey-predator model. The underlying model has 2 equilibrium points and stability analysis is carried out about the coexistence equilibrium. The condition for the Hopf bifurcation and Turing instabilities are derived. These conditions help to analyze the formation of patterns in the prey-predator system. The dispersion relation shows the changing behavior of Hopf bifurcation and Turing instability from stable to unstable. The bifurcation and Turing instability simulation divide the parametric space into 4 Regions. In Region I, the solution is stable, in Region II there is purely Turing instability, in Region III, there is only Hopf instability and in Region IV there is Hopf as well as Turing instability. Different types of Turing patterns are produced to capture rate parameters. The numerical solution of the model is obtained by positivity preserving finite difference scheme. The applied scheme is von Neumann stable, and consistent with the model. The bounded behavior of a given scheme is established. Mainly, we are focused on the graphical simulations for pattern formation and steady-state analysis. The 3D and 2D visualization for the Turing pattern and numerical solution are drawn for the various parameter values. The numerical simulations endorsed the analytical results.

关键词： Population dynamics Turning patterns computational scheme Analysis of scheme Results

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computational aspects of nonlinear and multiscale analyses by the multipoint meshless FDM

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JOURNAL OF computational SCIENCE 2023年 70卷

作者： Jaworska, Irena Cracow Univ Technol Chair Computat Engn Krakow Poland

The paper focuses on the recently developed higher order extension of the MFDM - the multipoint meshless finite difference method and introduces the computational schemes and algorithms of the method application to the boundary value problems, especially to the nonlinear and multiscale analyses. There are two basic versions of the multipoint approach that allow accurate and effective solving of engineering problems. The main advantage of the multipoint general version is its generality - the basic relations of derivatives from the unknown function depend on the domain discretization only and are independent of the type of problem being solved. This feature allows to divide the multipoint computational strategy into two stages and is advantageous from the calculation efficiency point of view. The multipoint method algorithms, applied to such engineering problems as two-scale analysis of heterogeneous materials and nonlinear analysis, are developed and briefly presented. This manuscript is an extension of the paper Multipoint Meshless FD schemes Applied to Nonlinear and Multiscale Analysis by I. Jaworska (2022) published in Lecture Notes in Computer Science [1]. In this extended version computational aspects of the algorithms are deepened, the subsections explaining specific features of the multipoint meshless approach application to the numerical homogenization and nonlinear analysis are included, and finally, the advantages and disadvantages of the method are discussed. The paper is illustrated with several examples (completed in the extended version) of the multipoint numerical analysis.

关键词： Multipoint Meshless FDM computational scheme Homogenization Nonlinear analysis Elastic-plastic problem

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Efficient numerical analysis of finite FSS with multilayered media by MLACA

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IET MICROWAVES ANTENNAS & PROPAGATION 2019年第11期13卷 1804-1810页

作者： Hu, Yunqin Su, Ting Wan, Ting Nanjing Univ Posts & Telecommun Dept Commun Engn 66 Xinmofan Rd Nanjing Jiangsu Peoples R China Army Engn Univ PLA Nanjing Jiangsu Peoples R China

In this study, an efficient numerical technique for transmission characteristic analysis of finite planar frequency selective surface (FSS) with multilayered media is presented by using the multilevel adaptive cross approximation (MLACA). The computational scheme is based on the mixed-potential electric field integral equation (MPIE) with multilayered media Green's functions (MLGFs). The three-level modified discrete complex images method (DCIM) is presented for the spatial-domain MLGFs without any quasi-static and surface-wave extraction. For electrically large-size FSS structures, the MLACA method is then employed to alleviate the high computational complexity and memory requirement of method of moments. Numerical results are presented to demonstrate the accuracy and efficiency of the proposed method.

关键词： electric field integral equations frequency selective surfaces approximation theory method of moments numerical analysis Green's function methods finite FSS transmission characteristic analysis finite planar frequency selective surface multilevel adaptive cross approximation computational scheme mixed-potential electric field integral equation three-level modified discrete complex images method surface-wave extraction MLACA method high computational complexity numerical analysis numerical technique FSS structures spatial-domain MLGF multilayered media Green functions

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Parameter identification of fractional order system using enhanced response sensitivity approach

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COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION 2019年第Feb.期67卷 492-505页

作者： Liu, G. Wang, L. Luo, W. L. Liu, J. K. Lu, Z. R. Sun Yat Sen Univ Sch Aeronaut & Astronaut Dept Appl Mech & Engn 135 Xingang Rd Guangzhou 510275 Guangdong Peoples R China Guangzhou Univ Sch Civil Engn 230 Wai Huan West Rd Guangzhou 510006 Guangdong Peoples R China

This paper presents an investigation on parameters identification of fractional order system based on the enhanced response sensitivity approach. Compared with the integer order differential operator, fractional order operator can describe the characteristics of some phenomena more accurately such as hereditary and memory properties. In order to achieve the solution of the fractional order system, a new computational scheme is presented in this paper based on Adams-type scheme and the Newmark -beta method. Such an identification problem is classed as an inverse problem and can be modeled as an nonlinear optimization problem. In this paper, the enhanced response sensitivity approach is derived and used to identify the parameters of the fractional order system. To this end, the time domain response of the fractional order system is obtained by the proposed computational scheme, then the response sensitivity with respect to the parameter is achieved as well. Numerical examples illustrated the computing and identification procedure and shown the accuracy and the convergence of identification scheme. (C) 2018 Elsevier B.V. All rights reserved.

关键词： Fractional order system computational scheme Parameter identification Enhanced response sensitivity approach

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