基于密度泛函理论研究二元排斥Yukawa流体的表面结构性质

基于自由能密度泛函理论(DFT)考察了二元排斥Yukawa (HCRY)流体在不同外场下的密度分布. 基于微扰理论, 体系的Helmholtz自由能泛函采用硬球排斥部分和长程色散部分贡献之和, 其中Kierlik和Rosinberg的加权密度近似(WDA)被用来计算硬球排斥部分, 而色散部分采用平均场理论(MFT)进行描述. 为了验证DFT计算结果的合理性, 研究中采用巨正则Monte Carlo(GCMC)模拟计算了在不同主体相密度、硬核直径和位能参数比的条件下二元HCRY混合流体的密度分布. 结果表明, 该DFT计算结果与GCMC模拟值吻合良好.     

对含重元素体系的接合二分量-标量相对论密度泛函计算方法

在相对论密度泛函ZORA方法的基础上,提出一种用于含重元素体系的接合二分量-标量相对论密度泛函计算方法.对于只含少数几个重元素的较大体系,仅对其中旋轨耦合作用强的重元素作二分量相对论计算,而对体系的其余部分则作标量相对论计算,通过对动能矩阵元的近似处理实现两种计算的接合.对一系列含6p区重元素分子进行计算的结果表明,当非重元素是第三周期以前的元素时,此方法与二分量ZO-RA方法的计算结果吻合得很好.当非重元素为第四周期元素时,计算结果有一定偏差,表明在后一种情况下旋轨耦合作用已比较显著,但误差仍在目前近似密度泛函计算的精度范围内.此方法可以有效地节省计算量,而且避免了Dyall方法的缺点.     

缓蚀剂膜抑制腐蚀介质扩散行为的分子动力学模拟

采用分子动力学模拟方法研究了4种腐蚀介质粒子(H₂O, H₃O⁺, HS^-和Cl^-)在6种不同烷基链长的1-(2-羟乙基)-2-烷基-咪唑啉缓蚀剂膜中的扩散行为. 计算了腐蚀介质粒子在不同缓蚀剂膜中的扩散系数、膜的自由体积分数、粒子与膜的相互作用能等, 并对缓蚀剂膜抑制腐蚀介质粒子扩散行为的微观机理进行了分析. 计算结果表明, 6种缓蚀剂膜均可有效阻碍腐蚀介质粒子向金属表面的扩散, 从而达到抑制或延缓腐蚀的目的; 随烷基链长的增加, 缓蚀剂膜对腐蚀介质粒子扩散行为的抑制能力逐渐增强; 同种缓蚀剂膜对正负离子H₃O⁺, HS^-和Cl^-比对中性的H₂O分子具有更强的扩散抑制能力.     

氯化钠水溶液的monte Carlo分子模拟研究

采用MonteCarlo计算机分子模拟方法,研究了氯化钠水溶液在常温和高温情况下粒子的径向分布函数和粒子间各种作用位能的热力学性质。模拟过程采用了NTV正则系综,粒子间的作用能包括离子库仑静电作用,偶极子作用以及色散作用,这些作用构成了电解质溶液的基本框架,模拟结果与微扰理论和平均球近似积分方程理论的预测值进行了比较。     

基于布朗棘轮的单通道分离体系的模拟研究

分子在微尺度受限空间内的扩散行为是微观化学的重要研究领域. 本文利用布朗棘轮效应构建了一种微型单通道分离器件模型, 并基于随机行走理论对其中分子的扩散分离运动进行了模拟研究, 阐明了该体系的分离机理并考察了不同条件对分子扩散分离运动的影响. 模拟结果表明, 通过调节驱动力对各组分粒子的作用周期, 可以控制粒子与分离通道两端势垒发生不同程度的相互作用, 从而在单分离通道内实现粒子向不同方向的有效分离. 同时, 也给出了利用该分离体系进行分离的组分粒子本身的扩散运动与受外力驱动运动的相对大小需满足的条件. 通过调整分离器件的结构参数, 可在实现最佳分离效果的同时节约时间成本. 本文提出的模拟方法对开发微型分离器件及优化操作参数等具有参考意义.     

密度泛函与分子模拟计算介孔孔径分布比较

用巨正则系综Monte Carlo模拟(GCMC)方法和密度泛函理论（ DFT）结合统计积分方程（SIE）计算了介孔材料的孔径分布.为比较这两种方法,以77 K氮气在介孔活性碳微球中的吸附数据为依据,求出其孔径分布.在GCMC模拟和DFT计算中,流体分子模型化为单点的Lerrnard-Jones球;流体分子与吸附剂材料之间的作用采用平均场理论中的10-4-3模型.在DFT方法中,自由能采用Tarazona 提出的加权近似密度泛函方法(weighted density approximation,WDA)求解.结果表明,对于孔径大于1.125 nm的介孔材料,GCMC和DFT两种方法都可以用来研究介孔材料的孔径分布;对于小于1.125 nm的介孔材料,不能用DFT方法计算孔径分布（DFT方法本身的近似产生了误差）,只能用分子模拟方法.     

温度对半胱氨酸缓蚀性能影响的实验评价与机理研究

通过实验对不同温度条件下半胱氨酸抑制盐酸对碳钢腐蚀的性能进行评价, 并采用分子动力学模拟(Molecular Dynamics Simulation, 简称MD)方法, 从缓蚀剂膜抑制腐蚀粒子扩散的角度对其缓蚀机理进行深入研究. 静态失重实验显示: 随温度的升高(25～65 ℃), 半胱氨酸缓蚀剂的缓蚀效率呈逐渐下降趋势, 其数值从88.36%降至61.64%. MD模拟发现: 随温度升高, 半胱氨酸缓蚀剂膜的自由体积逐渐增大, 且腐蚀粒子与缓蚀剂膜的相互作用也逐渐减弱, 更有利于腐蚀粒子在膜中的主动扩散; 同时膜内半胱氨酸分子的自扩散能力也随温度升高而增强, 腐蚀粒子在缓蚀剂膜携带下被动迁移的过程也随之加剧. 主动扩散和被动迁移两方面的变化表明, 腐蚀粒子在缓蚀剂膜中扩散能力随温度升高而增大; 也就是说, 随温度升高, 半胱氨酸缓蚀剂膜对腐蚀粒子的扩散抑制能力逐渐降低, 腐蚀粒子更易扩散运移至金属表面, 导致半胱氨酸缓蚀剂缓蚀效率的降低.     

端羟基聚丁二烯/增塑剂共混物相容性的分子动力学模拟和介观模拟

应用分子动力学(MD)和介观动力学(MesoDyn)模拟方法对固体推进剂中端羟基聚丁二烯(HTPB)与增塑剂癸二酸二辛酯(DOS)、硝化甘油(NG)的相容性进行了研究. 采用MD模拟方法在COMPASS力场下, 对纯物质、HTPB/增塑剂共混物的密度、内聚能密度、溶度参数和共混物分子间的Flory-Huggins作用参数及结合能等进行了模拟计算, 通过比较溶度参数差值(Δδ)的大小、模拟前后体系密度变化情况均可以预测HTPB与增塑剂的相容性, 结合能的分析揭示了HTPB/增塑剂共混物组分间的相互作用及本质. 将Flory-Huggins作用参数转化为MesoDyn模拟的输入参数, 采用MesoDyn模拟方法对HTPB/增塑剂共混体系的介观形貌与动力学演变过程进行了研究, 通过模拟得到的等密度图、自由能密度和有序度参数等可以判断共混体系的相容性. MD和MesoDyn模拟结果均表明: HTPB/DOS属于相容体系, 而HTPB/NG属于不相容体系, 其结论与实验结果一致.     

腐蚀介质在缓蚀剂膜中扩散行为的分子动力学模拟

采用分子动力学模拟方法,从缓蚀剂膜阻碍腐蚀介质粒子(H2O、H3O+和HCO3-)向金属表面扩散的角度,研究了4种1-R1-2-十一烷基-咪唑啉缓蚀剂(R1:羧甲基(A),羟乙基(B),氨乙基(C),氢(D))抑制碳钢CO2腐蚀的缓蚀机理,并对其缓蚀性能进行了理论评价.腐蚀介质粒子在不同缓蚀剂膜中的扩散系数、粒子与膜的相互作用能以及膜的自扩散性能的计算结果表明:4种缓蚀剂均可形成稳定的缓蚀剂膜,能有效阻碍腐蚀介质粒子向金属表面的扩散,达到抑制或延缓腐蚀的目的;随亲水支链(R1)极性的增加,缓蚀剂膜对腐蚀介质粒子扩散行为的抑制能力逐渐增强;同种缓蚀剂膜对正负离子H3O+和HCO3-比对中性的H2O分子具有更强的扩散抑制能力.综合计算及分析结果,4种缓蚀剂缓蚀性能的理论评价结果为ABCD,与文献实验结果吻合.     

MMP-2和Hydroxamate类抑制剂绝对自由能的计算

采用基于线性响应近似的自由能计算方法计算了一类hydroxamate抑制剂和MMP-2的绝对结合自由能。计算中,催化锌离子和MMP-2以及配体之间采用了非键模型。分子动力学模拟结果显示,采用非键模型时,催化Zn离子采用五配位的形式,但配位键的形式和初始结构比较有很大的差别。通过拟合,分别得到了单参数、双参数以及三参数的自由能预测模型,其中,含有常数校正项的三参数模型具有最佳的预测能力,预测自由能和实际自由能之间平均绝对误差仅为2.38kJ/mol。     

Theory of pressure-driven transport of neutral solutes and ions in porous ceramic nanofiltration membranes

Hindered transport theory and homogeneous electro-transport theory are used to calculate the limiting, high volume flux, rejection of, respectively, neutral solutes and binary electrolytes by granular porous nanofiltration membranes. For ceramic membranes prepared from metal oxides it is proposed that the membrane structural and charge parameters entering into the theory, namely the effective pore size and membrane charge density, can be estimated from independent measurements: the pore radius from the measured hydraulic radius using a model of sintered granular membranes and the effective membrane charge density from the hydraulic radius and the electrophoretic mobility measurements on the ceramic powder used to prepare the membrane. The electro-transport theory adopted here is valid when the membrane surface charge density is low enough and the pore radius is small enough for there to be strong electrical double layer overlap in the pores. Within this approximation the filtration streaming potential is also derived for binary electrolytes.     

Influence of diffusion on the kinetics of excited-state association--dissociation reactions: comparison of theory and simulation

Several recent theories of the kinetics of diffusion influenced excited-state association--dissociation reactions are tested against accurate Brownian dynamics simulation results for a wide range of parameters. The theories include the relaxation time approximation (RTA), multiparticle kernel decoupling approximations and the so-called kinetic theory. In the irreversible limit, none of these theories reduce to the Smoluchowski result. For the pseudo-first-order target problem, we show how the RTA can be modified so that the resulting formalism does reduce correctly in the irreversible limit. We call this the unified Smoluchowski approximation, because it unites modern theories of reversible reactions with Smoluchowski's theory of irreversible reactions.     

Thermodiffusion of charged colloids: single-particle diffusion

An expression for the single-particle thermal diffusion coefficient of a charged colloidal sphere is derived on the basis of force balance on the Brownian time scale in combination with thermodynamics. It is shown that the single-particle thermal diffusion coefficient is related to the temperature dependence of the reversible work necessary to build the colloidal particle, including the core, the solvation layer, and the electrical double layer. From this general expression, an explicit expression for the contribution of the electrical double layer to the single-particle thermal diffusion coefficient is derived in terms of the surface charge density of the colloidal sphere, the electrostatic screening length, and its core radius, to within the Debye-Hückel approximation. This result is shown to explain experimental data, for both thin and thick double layers. In addition, a comparison with other theories is made.     

Ensembles of microelectrodes: A digital- simulation

The rate of diffusion to ensembles of microelectrodes is calculated by digital simulation, based on the explicit finite-difference technique. Two limiting cases are shown in the current-time relationship at short times, when the diffusion layer is small in comparison to the radius of each microelectrode, the current behaves as in the case of semi-infinite planar diffusion to the active area on the surface. At long times, when the diffusion layers of adjacent electrodes overlap significantly, the current approaches the case of planar diffusion to the total area of the surface, including the non-active regions. The results are compared with previous calculations based on analytical solutions, which were derived on the basis of different approximations. Good agreement between reported experimental data and results based on simulation is observed.Edge effects arising as a result of contributions of radial components to the total diffusion rate are shown to be significant, even on relatively large electrodes. The errors which arise due to such effects are estimated as a function of the size of the electrode and the duration of measurement.     

Sensitive light-scattering detection–magnetophoretic acceleration mass analysis of single microparticles in an atmosphere

Optically detected magnetophoretic acceleration mass analysis of an individual micro-particle in an atmosphere has been remarkably improved in sensitivity by using a reflective microscope objective, by which forward scattered light from a particle could be effectively collected. From the light-scattering simulation, the detection limit for the radius of a micro-particle was estimated to be smaller than 0.4 μm, and about 60 times intensity enhancement was observed for a polystyrene particle with a radius of 2.8 μm. For both paramagnetic and diamagnetic micro-particles, the mass magnetic susceptibility and the relaxation time could be determined without knowing any parameters of the particles. From the relaxation time, the mass of a particle was obtained if the radius or the density of the particle was known. For a test sample silica particles were used to adsorb paramagnetic dysprosium(III), the surface concentration of dysprosium(III) on a single particle could be successfully determined by use of this method.     

Comparison of flux approximations in electrochemical digital simulation. Part 2: Complications due to homogeneous chemical reactions, charge estimation and application to the ultramicrodisk electrode

In numerical simulation of electrochemical systems the estimation of current flow or passed charge from simulated concentrations plays a crucial role and various approaches within the framework of finite differences are examined in this paper. Both on an exponentially expanding grid in X-space, and the corresponding equidistant grid in transformed Y-space, fluxes were expressed as either gradient approximations using a variable number of points, or as the spatial integral of rates of changes of the concentrations with time over the whole diffusion space, in the presence of homogeneous chemical reactions. Also, the passed charge was computed for these cases. The cases of chronoamperometric boundary conditions at a shrouded plane and an ultramicrodisk electrode (UMDE) were simulated. Results show that in all cases, fluxes computed on the basis of the spatial concentration gradient at the electrode are the most accurate provided that the Rudolph modification of the two-point flux in Y-space is used; it also works very well in the presence of homogeneous chemical reactions. The flux approximation on the basis of spatial integration of the time derivative of concentration comes a close second in Y-space in the case of one-dimensional simulations when K is not too large, and also works rather well in the case of the UMDE in transformed space. Charge computed as the time integral of flux can be quite accurate if two separate simulation runs are carried out, combining the results by extrapolation. Charge computed as the spatial integration of concentration loss in the diffusion space (not practical in the presence of a homogeneous chemical reaction) can also be quite accurate, both in the one- and two-dimensional case.     

Mobility matrix of a spherical particle translating and rotating in a viscous fluid confined in a spherical cell, and the rate of escape from the cell

The mobility matrix of a spherical particle moving in a spherical cavity, filled with a viscous incompressible fluid, and with no-slip boundary condition at the wall of the cavity, is evaluated from the Oseen tensor for the cavity by the method used by Lorentz for a particle near a planar wall. For the case that the particle is a rigid sphere with no-slip boundary condition the comparison with exact calculations shows that the approximation is quite accurate, provided the radius of the particle is small relative to that of the cavity, and provided the particle is not too close to the wall. The translational mobility is used to derive the diffusion tensor of a Brownian particle via an Einstein relation. The approximate result for the diffusion tensor is employed to estimate the rate of escape of a Brownian particle from a cavity with semipermeable wall.     

Numerical simulation of coupled‐stress case II diffusion in one dimension

This article is concerned with the robust and efficient numerical simulation of case II diffusion, which constitutes an important regime of solvent diffusion into glassy polymers. Even in the one‐dimensional case considered here, the numerical simulation of case II diffusion is made difficult by the extreme nonlinearities and coupling in the governing model equations due to a nonlinear flux law needed to produce sharp solvent fronts, a concentration‐dependent relaxation time of the polymer used to model the glass‐rubber transition, and coupling between the diffusion and deformation phenomena. Having an efficient and accurate solution to such equations is central to advancing a clear understanding of the meaning of such models. The difficulties due to coupling and nonlinearities are highlighted by the consideration of a specific, normalized, one‐dimensional case II diffusion model laid out in a general framework of balance laws. Issues such as the stiffness of the spatially discrete differential algebraic equations obtained from the finite element discretization of the governing equations and their bearing on the choice of time‐stepping schemes are discussed. The key requirements of numerical schemes, namely, robustness and efficiency, are addressed by the use of an implicit, adaptive, second‐order backward differentiation formula with error control for time discretization. Error control is used to maximize the step size to satisfy a target error and the radius of convergence requirements while nonlinear algebraic equations are solved at each time step. An example of an initial boundary value problem is solved numerically to show that the chosen model reproduces case II behavior and to validate that the stated objectives for the numerical simulation are met. Finally, the features and numerical implementation of this model are compared with those of a closely related case II diffusion model due to Wu and Peppas. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2091–2108, 2003     

Diffusion models of protein folding

In theory and in the analysis of experiments, protein folding is often described as diffusion along a single coordinate. We explore here the application of a one-dimensional diffusion model to interpret simulations of protein folding, where the parameters of a model that "best" describes the simulation trajectories are determined using a Bayesian analysis. We discuss the requirements for such a model to be a good approximation to the global dynamics, and several methods for testing its accuracy. For example, one test considers the effect of an added bias potential on the fitted free energies and diffusion coefficients. Such a bias may also be used to extend our approach to determining parameters for the model to systems that would not normally explore the full coordinate range on accessible time scales. Alternatively, the propagators predicted from the model at different "lag" times may be compared with observations from simulation. We then present some applications of the model to protein folding, including Kramers-like turnover in folding rates of coarse-grained models, the effect of non-native interactions on folding, and the effect of the chosen coordinate on the observed position-dependence of the diffusion coefficients. Lastly, we consider how our results are useful for the interpretation of experiments, and how this type of Bayesian analysis may eventually be applied directly to analyse experimental data.