Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

轮式仿人机器人的ZMP建模及动态稳定判据

介绍了ZMP的概念,比较常见的几种ZMP建模方法,提出将高效牛顿-欧拉算法(RENA)与ZMP的概念相结合的迭代ZMP建模方法,并利用该方法完成轮式仿人机器人的ZMP建模.通过模型分析,得出该轮式仿人机器人的ZMP简化计算公式.最后得出此类轮式仿人机器人的稳定性判据及稳定度的定义.

制造企业系统的一个集成化参考模型

指出当前用面向对象建模方法对制造企业进行建模活动中存在的问题 ,提出一种新的面向对象建模方法 ,该方法基本能克服现存问题 ,并用该方法为制造企业系统建立了一个参考模型。该模型覆盖了在工厂管理中的经营操作与制订决策的过程

基于广义正交多项式迭积微分算子的地震波场数值模拟研究

Seismic Numerical Modeling is one of bases of the Exploratory Seismology and Academic Seismology, also is a research field in great demand. Essence of seismic numerical modeling is to assume that structure and parameters of the underground media model are known, simulate the wave-field and calculate the numerical seismic record that should be observed. Seismic numerical modeling is not only a means to know the seismic wave-field in complex inhomogeneous media, but also a test to the application effect by all kinds of methods. There are many seismic numerical modeling methods, each method has its own merits and drawbacks. During the forward modeling, the computation precision and the efficiency are two pivotal questions to evaluate the validity and superiority of the method. The target of my dissertation is to find a new method to possibly improve the computation precision and efficiency, and apply the new forward method to modeling the wave-field in the complex inhomogeneous media. Convolutional Forsyte polynomial differentiator (CFPD) approach developed in this dissertation is robust and efficient, it shares some of the advantages of the high precision of generalized orthogonal polynomial and the high speed of the short operator finite-difference. By adjusting the operator length and optimizing the operator coefficient, the method can involve whole and local information of the wave-field. One of main tasks of the dissertation is to develop a creative, generalized and high precision method. The author introduce convolutional Forsyte polynomial differentiator to calculate the spatial derivative of seismic wave equation, and apply the time staggered grid finite-difference which can better meet the high precision of the convolutional differentiator to substitute the conventional finite-difference to calculate the time derivative of seismic wave equation, then creating a new forward method to modeling the wave-field in complex inhomogeneous media. Comparing with Fourier pseudo-spectral method, Chebyshev pseudo-spectral method, staggered- grid finite difference method and finite element method, convolutional Forsyte polynomial differentiator (CFPD) method has many advantages: 1. Comparing with Fourier pseudo-spectral method. Fourier pseudo-spectral method (FPS) is a local operator, its results have Gibbs effects when the media parameters change, then arose great errors. Therefore, Fourier pseudo-spectral method can not deal with special complex and random heterogeneous media. But convolutional Forsyte polynomial differentiator method can cover global and local information. So for complex inhomogeneous media, CFPD is more efficient. 2. Comparing with staggered-grid high-order finite-difference method, CFPD takes less dots than FD at single wave length, and the number does not increase with the widening of the studying area. 3. Comparing with Chebyshev pseudo-spectral method (CPS). The calculation region of Chebyshev pseudo-spectral method is fixed in , under the condition of unchangeable precision, the augmentation of calculation is unacceptable. Thus Chebyshev pseudo-spectral method is inapplicable to large area. CFPD method is more applicable to large area. 4. Comparing with finite element method (FE), CFPD can use lager grids. The other task of this dissertation is to study 2.5 dimension (2.5D) seismic wave-field. The author reviews the development and present situation of 2.5D problem, expatiates the essentiality of studying the 2.5D problem, apply CFPD method to simulate the seismic wave-field in 2.5D inhomogeneous media. The results indicate that 2.5D numerical modeling is efficient to simulate one of the sections of 3D media, 2.5D calculation is much less time-consuming than 3D calculation, and the wave dispersion of 2.5D modeling is obviously less than that of 3D modeling. Question on applying time staggered-grid convolutional differentiator based on CFPD to modeling 2.5D complex inhomogeneous media was not studied by any geophysicists before, it is a fire-new creation absolutely. The theory and practices prove that the new method can efficiently model the seismic wave-field in complex media. Proposing and developing this new method can provide more choices to study the seismic wave-field modeling, seismic wave migration, seismic inversion, and seismic wave imaging.

工程地质三维可视化技术及其工程应用研究

Study of 3D visualization technology of engineering geology and its application to engineering is a cross subject which includes geosciences, computer, software and information technology. Being an important part of the secondary theme of National Basic Research Program of China (973 Program) whose name is Study of Multi-Scale Structure and Occurrence Environment of Complicated Geological Engineering Mass(No.2002CB412701), the dissertation involves the studies of key problems of 3D geological modeling, integrated applications of multi-format geological data, effective modeling methods of complex approximately layered geological mass as well as applications of 3D virtual reality information management technology.The main research findings are listed below:Integrated application method of multi-format geological data is proposed,which has solved the integrated application of drill holes, engineering geology plandrawings, sectional drawings and cutting drawings as well as exploratory trenchsketch. Its application can provide as more as possible fundamental data for 3Dgeological modeling.A 3D surface construction method combined Laplace interpolation points withoriginal points is proposed, so the deformation of 3D model and the crossing error ofupper and lower surface of model resulted from lack of data when constructing alaminated stratum can be eliminated.3D modeling method of approximately layered geological mass is proposed,which has solved the problems of general modeling method based on the sections or points and faces when constructing terrain and concordant strata.The 3D geological model of VII dam site of Xiangjiaba hydropower stationhas been constructed. The applications of 3D geological model to the auto-plotting ofsectional drawing and the converting of numerical analysis model are also discussed.3D virtual reality information integrated platform is developed, whose mostimportant character is that it is a software platform having the functions of 3D virtualreality flying and multi-format data management simultaneously. Therefore, theplatform can load different 3D model so as to satisfy the different engineeringdemands.The relics of Aigong Cave of Longyou Stone Caves are recovered. Thereinforcement plans of 1# and 2# cave in phoenix hill also be expressed. The intuitiveexpression provided decision makers and designers a very good environment.The basic framework and specific functions of 3D geological informationsystem are proposed.The main research findings in the dissertation have been successfully applied to some important engineering such as Xiangjiaba hydropower station, a military airport and Longyou Stone Caves etc.

社会形势预警的几种建模方法比较

Based on social survey data conducted by local research group in some counties executed in the nearly past five years in China, the author proposed and solved two kernel problems in the field of social situation forecasting: i) How can the attitudes’ data on individual level be integrated with social situation data on macrolevel; ii) How can the powers of forecasting models’ constructed by different statistic methods be compared? Five integrative statistics were applied to the research: 1) algorithm average (MEAN); 2) standard deviation (SD); 3) coefficient variability (CV); 4) mixed secondary moment (M2); 5) Tendency (TD). To solve the former problem, the five statistics were taken to synthesize the individual and mocrolevel data of social situations on the levels of counties’ regions, and form novel integrative datasets, from the basis of which, the latter problem was accomplished by the author: modeling methods such as Multiple Regression Analysis (MRA), Discriminant Analysis (DA) and Support Vector Machine (SVM) were used to construct several forecasting models. Meanwhile, on the dimensions of stepwise vs. enter, short-term vs. long-term forecasting and different integrative (statistic) models, meta-analysis and power analysis were taken to compare the predicting power of each model within and among modeling methods. Finally, it can be concluded from the research of the dissertation: 1) Exactly significant difference exists among different integrative (statistic) models, in which, tendency (TD) integrative models have the highest power, but coefficient variability (CV) ones have the lowest; 2) There is no significant difference of the power between stepwise and enter models as well as short-term and long-term forecasting models; 3) There is significant difference among models constructed by different methods, of which, support vector machine (SVM) has the highest statistic power. This research founded basis in all facets for exploring the optimal forecasting models of social situation’s more deeply, further more, it is the first time methods of meta-analysis and power analysis were immersed into the assessments of such forecasting models.

Modeling, numerical methods, and simulation for particle-fluid two-phase flow problems

In this paper, we study the issues of modeling, numerical methods, and simulation with comparison to experimental data for the particle-fluid two-phase flow problem involving a solid-liquid mixed medium. The physical situation being considered is a pulsed liquid fluidized bed. The mathematical model is based on the assumption of one-dimensional flows, incompressible in both particle and fluid phases, equal particle diameters, and the wall friction force on both phases being ignored. The model consists of a set of coupled differential equations describing the conservation of mass and momentum in both phases with coupling and interaction between the two phases. We demonstrate conditions under which the system is either mathematically well posed or ill posed. We consider the general model with additional physical viscosities and/or additional virtual mass forces, both of which stabilize the system. Two numerical methods, one of them is first-order accurate and the other fifth-order accurate, are used to solve the models. A change of variable technique effectively handles the changing domain and boundary conditions. The numerical methods are demonstrated to be stable and convergent through careful numerical experiments. Simulation results for realistic pulsed liquid fluidized bed are provided and compared with experimental data. (C) 2004 Elsevier Ltd. All rights reserved.

Effect of Rock Mass Structure and Block Size on the Slope Stability-Physical Modeling and Discrete Element Simulation

This paper studies the stability of jointed rock slopes by using our improved three-dimensional discrete element methods (DEM) and physical modeling. Results show that the DEM can simulate all failure modes of rock slopes with different joint configurations. The stress in each rock block is not homogeneous and blocks rotate in failure development. Failure modes depend on the configuration of joints. Toppling failure is observed for the slope with straight joints and sliding failure is observed for the slope with staged joints. The DEM results are also compared with those of limit equilibrium method (LEM). Without considering the joints in rock masses, the LEM predicts much higher factor of safety than physical modeling and DEM. The failure mode and factor of safety predicted by the DEM are in good agreement with laboratory tests for any jointed rock slope.

Progress In Modeling Of Fluid Flows In Crystal Growth Processes

Modeling of fluid flows in crystal growth processes has become an important research area in theoretical and applied mechanics. Most crystal growth processes involve fluid flows, such as flows in the melt, solution or vapor. Theoretical modeling has played an important role in developing technologies used for growing semiconductor crystals for high performance electronic and optoelectronic devices. The application of devices requires large diameter crystals with a high degree of crystallographic perfection, low defect density and uniform dopant distribution. In this article, the flow models developed in modeling of the crystal growth processes such as Czochralski, ammonothermal and physical vapor transport methods are reviewed. In the Czochralski growth modeling, the flow models for thermocapillary flow, turbulent flow and MHD flow have been developed. In the ammonothermal growth modeling, the buoyancy and porous media flow models have been developed based on a single-domain and continuum approach for the composite fluid-porous layer systems. In the physical vapor transport growth modeling, the Stefan flow model has been proposed based on the flow-kinetics theory for the vapor growth. In addition, perspectives for future studies on crystal growth modeling are proposed. (c) 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

Molecular modeling on human CCR5 receptors and complex with CD4 antigens and HIV-1 envelope glycoprotein gp120

AIM: To investigate the interaction between human CCR5 receptors (CCR5) and HIV-1 envelope glycoprotein gp120 (HIV-1 gp120) and HIV-1 receptor CD4 antigens (CD4). METHODS: The structurally con served regions (SCR) of human CCR5 was built by the SYBYL/Biopolymer module using the corresponding transmembrane (TM) domain of bacteriorhodopsin (bR) as the template. The coordinates for amino-ter minal residue sequence, and carboxyl-terminal residue sequence, extracellular and cytoplasmic loops were generated using LOOP SEARCH algorithm. Subsequently the structural model was merged into the complex with HIV-1 gp120 and CD4. RESULTS: Human CCR5 interacted with both an HIV-1 gp120 and CD4. The N-terminal residues (especially Met1 and Gln4) of human CCR5, contacted with CD4 residues, mainly 7Nith one span (56 - 59) of CD4 in electrostatic interaction and hydrogen-bonds. The binding sites of human CCR5 were buried in a hydrophobic center surrounded by a highly basic periphery. On the other hand, direct interatomic contacts were made between ? CCR5 residues and 6 gp120 amino-acid residues, which included van der Waals contacts, hydrophobic interaction, and hydrogen bonds. CONCLUSION: The interaction model should be helpful for rational design of novel anti-HIV drugs.

Modeling of a coal-fired slagging combustor: Development of a slag submodel

In a slagging combustor or furnace, the high combustion temperature makes the molten slag layer cover the wall and capture the particles. If these particles contain combustible matter, they will continue to burn on the running slag. As a result, the total amount of ash deposition will be much greater than that in dry-wall combustors and the total heat flux through the deposition surface will change greatly. Considering the limitations of existing simulation methods for slagging combustion, this paper introduces a new wall burning model and slag flow model from the analysis; of particle deposition phenomena. Combined with a conventional combustion simulation program, the total computational frame is introduced. From comparisons of simulation results from several kinds of methods with experimental data, the conclusion is drawn that the conventional simulation methods are not very suitable for slagging combustion and the wall burning mechanism should be considered more thoroughly.

A finite-element algorithm for modeling variably saturated flows

A general numerical algorithm in the context of finite element scheme is developed to solve Richards’ equation, in which a mass-conservative, modified head based scheme (MHB) is proposed to approximate the governing equation, and mass-lumping techniques are used to keep the numerical simulation stable. The MHB scheme is compared with the modified Picard iteration scheme (MPI) in a ponding infiltration example. Although the MHB scheme is a little inferior to the MPI scheme in respect of mass balance, it is superior in convergence character and simplicity. Fully implicit, explicit and geometric average conductivity methods are performed and compared, the first one is superior in simulation accuracy and can use large time-step size, but the others are superior in iteration efficiency. The algorithm works well over a wide variety of problems, such as infiltration fronts, steady-state and transient water tables, and transient seepage faces, as demonstrated by its performance against published experimental data. The algorithm is presented in sufficient detail to facilitate its implementation.