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Recent Progress in numerical methods for the Poisson-Boltzmann Equation in Biophysical Applications

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Communications in Computational Physics 2008年第5期3卷 973-1009页

作者： B.Z.Lu Y.C.Zhou M.J.Holst J.A.McCammon Howard Hughes Medical Institute University of CaliforniaSan Diego 9500 Gilman DriveDept.0112La JollaCA 92093-0112USA. Department of Mathematics University of CaliforniaSan Diego 9500 Gilman DriveDept.0112La JollaCA 92093-0112USA. Center for Theoretical Biological Physics University of CaliforniaSan Diego 9500 Gilman DriveDept.0112La JollaCA 92093-0112USA. Department of Chemistry and Biochemistry University of CaliforniaSan Diego 9500 Gilman DriveDept.0112La JollaCA 92093-0112USA. Department of Pharmacology University of CaliforniaSan Diego 9500 Gilman DriveDept.0112La JollaCA 92093-0112USA.

Efficiency and accuracy are two major concerns in numerical solutions of the Poisson-Boltzmann equation for applications in chemistry and *** developments in boundary element methods,interface methods,adaptive methods,finite element methods,and other approaches for the Poisson-Boltzmann equation as well as related mesh generation techniques are *** also discussed the challenging problems and possible future work,in particular,for the aim of biophysical applications.

关键词： Biomolecular electrostatics Poisson-Boltzmann equation numerical methods finite difference methods finite element methods boundary element methods adaptive methods hybrid methods mesh generation electrostatic forces

Analysis of Bone Remodeling Under Piezoelectricity Effects Using Boundary Elements

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Journal of Bionic Engineering 2017年第4期14卷 659-671页

作者： Miguel Cerrolaza Vannessa Duarte Diego Garzon-Alvarado National Institute of Bioengineering Central University of Venezuela Caracas Venezuela International Center for numerical methods in Engineering ( CIMNE) Polytechnic University of Catalonia Barcelona Spain Virtual Rooms Program ( CIMNE) Polytechnic University of Catalonia Barcelona Spain Laboratory of Biomimetics Group of Mechanobiology of Organs and Tissues Biotechnology Institute Department of Mechanical Engineering and Mechatronics National University of Colombia Bogota Colombia

Piezoelectric materials exhibit a response to mechanical-electrical coupling, which represents an important contribution to the electrical-mechanical interaction in bone remodeling process. Therefore, the study of the piezoelectric effect on bone re- modeling has high interest in applied biomechanics. The effects of mechano-regulation and electrical stimulation on bone healing are explained. The Boundary Element Method （BEM） is used to simulate piezoelectric effects on bones when shearing forces are applied to collagen fibers to make them slip past each other. The piezoelectric fundamental solutions are obtained by using the Radon transform. The Dual Reciprocity Method （DRM） is used to simulate the particular solutions in time-dependent problems. BEM analysis showed the strong influence of electrical stimulation on bone remodeling. The examples discussed in this work showed that, as expected, the electrically loaded bone surfaces improved the bone deposition. BEM results confirmed previous findings obtained by using the Finite Element Method （FEM）. This work opens very promising doors in biomechanics research, showing that mechanical loads can be replaced, in part, by electrical charges that stimulate strengthening bone density. The obtained results herein are in good agreement with those found in literature from experimental testing and/or other simu- lation approaches.

关键词： bone remodeling numerical methods piezoelectricity boundary element anisotropy

An element decomposition method with variance strain stabilization

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Science China(Physics,Mechanics & Astronomy) 2015年第7期58卷 57-66页

作者： CUI XiangYang LIU PengWei LI GuangYao State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body Hunan University

An element decomposition method with variance strain stabilization(EDM-VSS) is proposed. In the present EDM-VSS, the quadrilateral element is first divided into four sub-triangular cells, and the local strains in sub-triangular cells are obtained using linear interpolation function. For each quadrilateral element, the strain of the whole quadrilateral is the weighted average value of the local strains, which means only one integration point is adopted to construct the stiffness matrix. The stabilization item of the stiffness matrix is constructed by variance of the local strains, which can eliminate the instability of the one-point integration formulation and largely increase the accuracy of the element. Compared with conventional full integration quadrilateral element, the EDM-VSS achieves more accurate results and expends much lower computational cost. More importantly, as no mapping or coordinate transformation is involved in the present EDM-VSS, the restriction on the conventional quadrilateral elements can be removed and problem domain can be discretized in more flexible ways. To verify the accuracy and stability of the present formulation, a number of numerical examples are studied to demonstrate the efficiency of the present EDM-VSS.

关键词： numerical methods element decomposition method variance strain stabilization one-point integration quadrilateralelement

Cross-spectral recognition method of bridge deck aerodynamic admittance function

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Earthquake Engineering and Engineering Vibration 2015年第4期14卷 595-609页

作者： Zhao Lin Ge Yaojun State Key Lab for Disaster Reduction in Civil Engineering Tongji University

This study proposes a new identification algorithm about the admittance function, which can estimate the full set of six aerodynamic admittance functions considering cross power spectral density functions about the forces and the turbulence components. The method was first numerically validated through Monte Carlo simulations, and then adopted to estimate the aerodynamic admittance of a streamlined bridge deck. The identification method was further validated through a comparison between the numerical calculation and wind tunnel tests on a moving bridge section. © 2015, Institute of Engineering Mechanics, China Earthquake Administration and Springer-Verlag Berlin Heidelberg.

关键词： Algorithms Bridge decks Intelligent systems Monte Carlo methods numerical methods Power spectral density Spectral density Wind stress Wind tunnels

MUSCL TYPE SCHEMES AND DISCRETE ENTROPY CONDITIONS

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Journal of Computational Mathematics 1997年第1期15卷 72-80页

作者： Zhao, N Wu, HM NANJING UNIV DEPT AERODYNAMNANJING 210008PEOPLES R CHINA CHINESE ACAD SCI STATE KEY LAB SCI & ENGN COMPICMSECBEIJINGPEOPLES R CHINA

In this paper, the semi-discrete entropy conditions with so called the proper discrete entropy flux of a class of high resolution MUSCL type schemes are discussed for genuinely nonlinear scalar conservation laws. It is shown that the high resolution schemes satisfying such;semi-discrete entropy conditions cannot preserve second order accuracy in the rarefaction region.

关键词： Computational fluid dynamics Convergence of numerical methods Nonlinear equations numerical methods

Novel polarimetric detector for target detection in heterogeneous clutter

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Journal of Systems Engineering and Electronics 2016年第6期27卷 1135-1141页

作者： Xu Cheng Longfei Shi Yuliang Chang Yongzhen Li Xuesong Wang State Key Laboratory of Complex Electromagnetic Environment Effects on Electronics and Information System College of Electronic Science and Engineering National University of Defense Technology

A detection of static or slowly moving targets in the inhomogeneous clutter of polarimetric radar is researched and a new detector without exploiting the training set is developed, which has a good performance against the inhomogeneous clutter. The decision rule ensures the constant false alarm rate (CFAR) with respect to the disturbance covariance matrix. numerical results show the robustness of the proposed method against the inhomogeneous clutter. © 2016 Beijing Institute of Aerospace Information.

关键词： Clutter (information theory) Covariance matrix numerical methods Polarimeters Radar Radar clutter Radar signal processing Signal processing

Structural transition dynamics of the formation of warm dense gold: From an atomic scale view

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Science China(Physics,Mechanics & Astronomy) 2020年第6期63卷 33-41页

作者： QiYu Zeng JiaYu Dai Department of Physics National University of Defense TechnologyChangsha 410073China

With the highly optimized embedded-atom-method(EAM)potential and electron-phonon coupling factor obtained from experimental data,the dynamics of the formation of warm dense gold and the nuclear response of gold foils upon intense laser excitation were investigated using two-temperature molecular dynamics *** laser energy densities ranging from 0.18 to 1.17 MJ/kg,we provide a microscopic picture of the formation of warm dense gold.A threshold(0.19 MJ/kg)for the laser energy density was determined,identifying two different melting *** an energy density below 0.19 MJ/kg,the melting of the foil is controlled by the propagation of melt fronts from external surfaces,which results in heterogeneous melting on the time scale of hundreds of *** an energy density above 0.19 MJ/kg,homogeneous nucleation and growth of liquid regions inside the foil play the leading role,and homogeneous melting occurs with several *** with previous simulations and experimental measurements,the evaluated different threshold value indicates that the improvement in the electron heat capacity for the two-temperature model by including the kinetic information of electrons may predict better laser-matter interactions under such extreme non-equilibrium conditions.

关键词： molecular dynamics numerical methods solid-liquid transitions laser ablation of solids

Simulation of heat transfer in steel billets during continuous casting

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International Journal of Minerals,Metallurgy and Materials 2010年第4期17卷 403-416页

作者： A.Ramirez-López R.Aguilar-López M.Palomar-Pardavé M.A.Romero-Romo D.Muoz-Negrón Department of Materials Metropolitan Autonomous University Mexico City C.P.02200Mexico Institute Polytechnic National Mexico City C.P.07300Mexico Institute Technologic Autonomous of Mexico Mexico City C.P.01080Mexico Institute Polytechnic National Mexico City C.P.07300 Mexico

This work is focused on the development of computational algorithms to create a simulator for solving the heat transfer during the continuous casting process of steel. The temperatures and the solid shell thickness profiles were calculated and displayed on the screen for a billet through a defined continuous casting plant （CCP）. The algorithms developed to calculate billet temperatures, involve the solutions of the corresponding equations for the heat removal conditions such as radiation, forced convection, and conduction according to the billet posi- tion through the CCP. This is done by a simultaneous comparison with the kinematics model previously developed. A finite difference method known as Cmnk-Nicholson is applied to solve the two-dimensional computational array （2D model）. Enthalpy （HIJ） and temperature （TIL） in every node are updated at each step time. The routines to display the results have been developed using a graphical user interface （GUI） in the programming language C＋＋. Finally, the results obtained are compared with those of industrial trials for the surface temperature of three steel casters with different plant configurations in different casting conditions.

关键词： continuous casting heat transfer heat removal simulation numerical methods

LOCAL ARTIFICIAL BOUNDARY CONDITIONS FOR THEINCOMPRESSIBLE VISCOUS FLOW IN A SLIP CHANNEL

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Journal of Computational Mathematics 1997年第4期15卷 335-344页

作者： Wei-zhu Bao Hou-de Han (Department of Applied Mathematics, Tsinghua University, Beijing, China) 清华大学应用数学系北京

In this paper we consider numerical simulation of incompressible viscous flow in a infinite slip channel. Local artificial boundary conditions at an artificial boundary are derived by the continuity of velocity and normal stress at the segment artificial boundary. The the original problem is reduced to a boundary value problem on a bounded computational domain. numerical example shows that our artificial boundary conditions are very effective.

关键词： Boundary value problems Computational methods Computer simulation Navier Stokes equations numerical methods Viscous flow