Discrete hydrodynamics: Determination of equations of motion by simulation

A detailed procedure is described for computing discrete equations of motion for a fluid, to implement a new method which turns out to be substantially more efficient than previous methods for calculating transport coefficients. This paper describes the calculations of discrete averages from molecular dynamics data and the numerical extraction of the equation-of-motion coefficients in a way which makes maximum use of the geometric symmetry of the problem. Extrapolation to the infinite-system limit and eventual computation of transport coefficients by renormalization are discussed. The method described in detail here is briefly sketched and applied numerically to computing the viscosity of the soft-sphere liquid in a subsequent paper.     

基于基液连续假设的大体系Cu-H2O纳米流体输运特性的模拟研究

分子动力学模拟是研究纳米流体的输运特性的重要手段, 但计算量庞大. 为研究能体现流动传热过程的大体系纳米流体的输运特性, 本文对基液采用连续介质假设, 将基液的势能拟合在纳米团簇的势能中, 大幅度减小了计算量, 使得大体系输运特性的模拟成为可能, 且模拟结果与多组实验结果吻合较好. 采用此方法模拟研究了速度梯度剪切对Cu-H₂O纳米流体颗粒聚集过程和聚集特性的影响, 进而对Cu-H₂O纳米流体在流动传热过程中的热导率和黏度进行了模拟计算, 定量揭示了宏观流动传热过程中不同的速度梯度、速度、平均温度和温度梯度对于Cu-H₂O纳米流体热导率和黏度的影响.     

Characterization of adsorption mode of new B2 bradykinin receptor antagonists onto colloidal Ag substrate

In this paper, the surface‐enhanced Raman scattering (SERS) spectra of the potent B₂ bradykinin receptor antagonists, [D‐Arg⁰,Hyp³,Thi^5,8,L‐Pip⁷]BK, Aaa[D‐Arg⁰,Hyp³,Thi^5,8,L‐Pip⁷]BK, [D‐Arg⁰,Hyp³,Thi⁵,D‐Phe⁷,L‐Pip⁸]BK, and Aaa[D‐Arg⁰,Hyp³,Thi⁵,D‐Phe⁷,L‐Pip⁸]BK, were measured when immobilized onto a colloidal assembly of apparently randomly adhering Ag spheres with diameters of approximately 20 – 25 nm. The observed SERS bands corresponding to different vibrational modes of the molecule, attached to or near Ag, and the variations in these bands resulting from competitive interactions of the functional groups of the peptides with the SERS‐active Ag surfaces were analyzed in this study. Briefly, it was shown that Pip, in generally in vertical orientation, and Thi, in the edge‐on position, relative to the colloidal Ag surface interacted with this surface through their lone electron pairs on the nitrogen and sulfur atoms, respectively. The imide bond of the X‐Pro peptide linkage and the guanidine group of Arg were involved in the adsorption process. In addition, it was demonstrated that the specific differences in the amino acid sequences slightly influenced the mode of adsorption. For example, Aaa in Aaa[D‐Arg⁰,Hyp³,Thi^5,8,L‐Pip⁷]BK and Aaa[D‐Arg⁰,Hyp³,Thi⁵,D‐Phe⁷,L‐Pip⁸]BK and D‐Phe (vertical with respect to the colloidal Ag surface) in [D‐Arg⁰,Hyp³,Thi⁵,D‐Phe⁷,L‐Pip⁸]BK, and Aaa[D‐Arg⁰,Hyp³,Thi⁵,D‐Phe⁷,L‐Pip⁸]BK assisted in the adsorption of these peptides onto the colloidal Ag particles. To discuss these spectral alterations due to the different surface adsorption mechanisms of these peptides, the spectral changes were analyzed according to the adsorption process and Fourier‐transform‐Raman spectra. Copyright © 2013 John Wiley & Sons, Ltd.     

旋转光滑圆环约束质点问题研究

应用非线性动力学的原理和方法,从理论上分析了不动点的类型,并通过数值计算作出质点的相轨迹,从而更加直观地得出了多种初始条件下质点的运动情况.     

Simulation of plasma doping process by using the localized molecular dynamics method

Plasma doping is the candidate for semiconductor doping. Accurate simulation of the doping technology is needed for the advanced integrated circuit manufacturing. In this paper, the plasma doping process simulation is performed by using the localized molecular dynamics method. Models that involve the statistics of the implanted compositions, angles and energies are developed. The effect of the model on simulation results is studied. The simulation results about the doping concentration profile are supported by experimental data.     

微液滴动力学特性的耗散粒子动力学模拟

对传统的耗散粒子动力学方法进行了改进.改进的耗散粒子动力学方法采用了包含远程吸引力和近距排斥力的保守力势函数,从而使得用耗散粒子动力学方法模拟多相流动成为可能.应用改进的耗散粒子动力学方法,对微尺度下液滴的形成及液滴在微重力下的大幅度振荡变形进行了数值模拟.计算结果表明,改进的耗散粒子动力学(DPD)方法能够有效地描述微尺度下液滴的动力学特性,对研究复杂流体多相流动有着重要的意义. 关键词： 多相流 微液滴 耗散粒子动力学(DPD)方法 保守力势函数     

基于原子运动模型的类金刚石薄膜生长机理研究

利用分子动力学模拟方法，从原子尺度上研究了类金刚石(DLC)薄膜生长过程. 按照运动特点把入射原子在表面的行为分为表面冷冻、迁移、注入和反弹等四种，并由此提出原子运动模型. 入射原子的表面行为对DLC薄膜的微观结构以及生长方式有重要影响. 其中原子水平迁移是薄膜热弛豫的主要途径，入射原子的注入和迁移行为相互竞争，决定了薄膜生长的模式和最终结构. 利用统计分析手段给出了入射能量对原子表面行为进而对薄膜结构的影响，加深了对DLC薄膜生长机理的认识.     

分子动力学模拟BCC铁中级联碰撞产生的缺陷结构及其演变(英文)

用分子动力学模拟BCC铁中级联碰撞原子的演变过程.结果显示,级联碰撞的原子不仅可以临时地产生自间隙原子、空位、以及<100>,<110>和<111>哑铃型缺陷,也可以产生<110>和<111>,以及<110>和<110>哑铃型缺陷的复合缺陷.模拟显示在模拟的能量范围内,如果初级碰撞原子的能量越大,该原子引起的级联碰撞覆盖区域会越大.发现具有几千电子伏特初级碰撞能量的原子引起的级联碰撞覆盖区域大约为11~15个晶格常数大小.同时还发现在级联碰撞的初始阶段(0.0~0.75 ps)不仅会有自间隙原子与空位的生成,同时也会有少量的自间隙原子与空位缺陷复合而消失.     

Stochastic motion of a charged particle in a magnetic field: I Classical treatment

We study the dissipative, classical dynamics of a charged particle in the presence of a magnetic field. Two stochastic models are employed, and a comparative analysis is made, one based on diffusion processes and the other on jump processes. In the literature on collision-broadening of spectral lines, these processes go under the epithet of weak-collision model and Boltzmann-Lorentz model, respectively. We apply our model calculation to investigate the effect of magnetic field on the collision-broadened spectral lines, when the emitter carries an electrical charge. The spectral lines show narrowing as the magnetic field is increased, the narrowing being sharper in the Boltzmann-Lorentz model than in the weak collision model.     

Molecular dynamics simulations of hydrogen adsorption/desorption by palladium decorated single-walled carbon nanotube bundle

Utilising molecular dynamics simulations, the hydrogen molecules adsorption isotherms of the (8,?0) palladium decorated single-walled carbon nanotube (SWNT) were obtained. The hydrogen adsorption was studied on the external, interstial and internal surfaces of the SWNT bundle at several temperatures ranging from 77 to 400?K. The results were compared with the bare single-walled carbon nanotube bundle under the same conditions. The decorated carbon nanotube bundle hydrogen adsorption was significantly higher than that of the bare one. The hydrogen desorption and readsorption were studied using temperature as the readsorption/desorption variable. The rate constants were calculated for the hydrogen desorption at different temperatures. The calculated decorated SWNT bundle hydrogen desorption activation energy was higher than that for the bare SWNT bundle. The calculated activation energies for the hydrogen desorption in both nanotube bundles specified the temperature dependency of hydrogen desorption.     

液气共存的耗散粒子动力学模拟

传统的耗散粒子动力学方法(DPD)由于采用了纯排斥的守恒力相互作用,从而不能适应液气共存或者带有自由面流体的模拟.这里研究了DPD方法中新近提出的一种短程排斥、长程吸引相互作用,探索了这种改进势能对于DPD方法模拟液气共存的能力.模拟了这种新势能所形成的液气过渡界面,计算了过渡界面区的应力分布,发现应力分布与多体DPD方法所得结果一致.进一步对表面张力进行了研究,验证了这种势能所形成的界面满足Laplace定律,而通过理论公式与Laplace定律分别所得到的表面张力也彼此相符。     

能量粒子轰击金刚石的计算机模拟

利用Tersoff势和分子动力学方法研究了初始动能为500 eV的硼粒子注入金刚石的微观行为.结果表明：硼注入后产生温度为5000 K的热峰，其寿命为0.18 ps；同时产生半径为0.45 nm局部非晶化区域，三重配位原子数占该区域原子数的7%.薄膜表层原子向内弛豫，近表层原子向外弛豫，表面层与近表层原子的间距减少了15%，表面层表现为压应力.硼原子以B<110>分裂间隙的形式存在于金刚石结构中. 关键词： 分子动力学模拟 金刚石 硼 注入     

用分子模拟方法研究羟基乙叉二膦酸(HEDP)在方解石表面的吸附行为

建立了基于分子力学计算方法的分子模拟手段,用于研究羟基乙叉二膦酸(HEDP)在方解石{104}表面的吸附特性.分子模拟三维吸附图像显示,HEDP中的膦酸基团中的氧原子具有强烈的负电性,能与晶体表面的阳离子产生强烈的静电吸引作用,形成“立体匹配”吸附结构.计算结果显示,HEDP在方解石面上、台阶和扭折点位置的平均吸附能依次约为-5.2eV,-7.0eV和-23.5eV,表明HEDP强烈地吸附到扭折点位置上,从而影响和抑制台阶的生长. 关键词： 分子模拟 方解石 阻垢剂 表面吸附     

棱形石墨烯纳米孔道内离子传输性能的分子动力学模拟

纳米通道的尺寸、结构和表面化学对其内部溶液的分布结构和输运性质有着重大影响.本文研究了一种全新的菱形石墨烯纳米通道.这种理想的通道与最近被广泛研究的金属有机框架材料(MOF)的内部结构类似,有着与传统的碳纳米管截然不同的内部结构.本文使用分子动力学模拟的方法研究在不同尺寸的菱形石墨烯纳米通道内的KCl溶液的性质,并将其与同尺寸的单壁碳纳米管进行了比较.研究结果表明在小孔道内(<20?)其内部的溶液结构呈现若干个密度极高的聚集区域,即出现了结晶化的趋势．这一研究结果,将为MOF的结构设计提供思路,从而有望实现类似于生物离子通道的高选择性和高传输能力.     

Mo高压熔化的分子动力学模拟

 采用第一原理方法计算了钼在零温下的结构,表明钼在500 GPa以下一直保持bcc结构（常温）,与实验一致。在零压附近计算了E-V关系,利用Murnaghan物态方程拟合得到了零压体积及其模量,与实验结果符合得很好。采用第一原理分子动力学模拟了钼的高压熔化性质。采用NVT系综计算了128个原子的系统,初始构形为bcc结构,体积分别为0.015 48、0.012 19、0.010 98、0.009 84、0.009 10 nm³/atom,计算了几个温度点,拟合得到了熔化曲线,熔化温度明显高于金刚石压砧（DAC）实验结果;将初始构形改变为fcc结构,模拟其熔化特性,得到的熔化温度明显下降,与激光加载DAC实验结果一致,认为可能的原因是钼熔化后形成的液体结构类似于fcc结构,而不是常态时的bcc结构。     

Application of shell model in molecular dynamics simulation to MgO

The P－V－T equation of state of MgO has been simulated under high pressure and elevated temperature using the molecular dynamics (MD) method with the breathing shell model (BSM). It is found that the MD simulation with BSM is very successful in reproducing accurately the measured molar volumes of MgO over a wide range of temperature and pressure. In addition, the MD simulation reproduces accurately the measured volume compression data of MgO up to 100GPa at 300K. It is demonstrated that the MD simulated P－V－T equation of state of MgO could be applied as a useful internal pressure calibration standard at elevated temperatures and high pressures.     

Comparison of adsorption mechanism on colloidal silver surface of alafosfalin and its analogs

This study reports the Raman (FT‐RS) and absorption infrared (FT‐IR) spectra, based on calculated wavenumbers and normal modes of vibrations, of the following compounds: L ‐Ala‐L ‐NH‐CH(Me)‐PO₃H₂ (alafosfalin, A1), L ‐Ala‐D ‐NH‐CH(Me)‐PO₃H₂ (A2), L ‐Ala‐L ‐NH‐CH(Et)‐PO₃H₂ (A3), D ,L ‐Ala‐D,L ‐NH‐CH(Et)‐PO₃H₂ (A4), L ‐Ala‐D ‐NH‐CH(iPr)‐PO₃H₂ (A5), L ‐Ala‐D,L ‐NH‐CH(iPr)‐PO₃H₂ (A6), L ‐Ala‐D,L ‐NH‐CH(tBu)‐PO₃H₂ (A7), L ‐Ala‐D,L ‐NH‐CH(iBu)‐PO₃H₂ (A8), L ‐Ala‐D,L ‐NH‐CH(cBu)‐PO₃H₂ (A9), L ‐Ala‐D,L ‐NH‐CH(nPA)‐PO₃H₂ (A10), β‐Ala‐D ‐NH‐CH(Me)‐PO₃H₂ (A11), and D,L ‐Ala‐NH‐C(Me,Me)‐PO₃H₂ (A12). The equilibrium geometries and vibrational wavenumbers are calculated using density functional theory (DFT) at the B3LYP; 6–31 + + G** level of theory using Gaussian'03, GaussSum 0.8, and GAR2PED software. We briefly compare and analyze the experimental and calculated vibrational wavenumbers in the range of 3600–400 cm⁻¹. In addition, Raman wavenumbers are compared to those from surface‐enhanced Raman scattering (SERS) for the phosphonodipeptides of alanine (Ala) adsorbed on a colloidal silver surface. The geometry of these molecules etched on the silver surface is deduce from the observed changes in both the intensity and breadth of Raman bands in the spectra of the bound vs free species. For example, A7, A8, A1, A3, and A4 appear to adsorb onto the colloidal silver particles mainly through the phosphonate terminus, and for A3 and A4, through the  C‐NH₂ and  CONH fragments. The most dominant SERS bands of A5, A6, A9, A10, and A11 are due to the amide bond vibrations, as well as to the vibrations of the  C‐NH₂ group (A9 and A10) and the C C group (A6 and A11). The differences recorded for the A5, A6, A9, A10, and A11 and those of A2 and A12 are due to interactions between the amine and methyl groups with the silver surface, and they reflect vibrational characteristic of these groups. Copyright © 2008 John Wiley & Sons, Ltd.     

Simulation and experiment of the cooling effect of trapped ion by pulsed laser

We investigate the process of pulsed laser cooling using a self-constructed molecular dynamics simulation(MDSimulation) program. We simulate the Doppler cooling process and pulsed laser Doppler cooling process of a single ~(40)Ca~+ ion, and the comparison with the experimental results shows that this self-constructed MD-Simulation program works well in the weak laser intensity situation. Furthermore, we analyze the pulsed laser Doppler cooling process of a single ~(27)Al~+ ion. This program can be used to analyze the molecular dynamic process of various situations of Doppler cooling in an ion trap, which could give predictions and experimental guidance.     

超高压水的分子动力学模拟

 采用平衡分子动力学（EMD）方法,模拟研究了温度范围为243~348 K、压强范围为0.1~400 MPa条件下水的热力学性质、结构和动力学性质,模拟结果与实验值吻合较好。模拟结果表明,随着压强的增大,水分子间的氢键作用增强,扩散系数减小;随着温度的升高,水分子间的氢键作用减弱,有序程度下降,扩散系数增大。但在过冷水中,扩散系数随压强的增大有增加的趋势。