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.     

超越技术 深入学科——对分子模拟技术融入化学教学的思考

分子模拟技术有助于学生形成心像、微观思维能力和表征转换能力。分析了影响化学教师使用分子模拟技术的2项因素,对如何消解国外分子模拟技术在国内化学教育领域科技扩散过程中出现的障碍、分子模拟技术如何更好地融入化学教学等问题提出建议。     

气体分子在纳米孔道材料中扩散传输的分子动力学研究进展

随着计算机科学技术的迅猛发展以及分子动力学(Molecular Dynamics,MD)模拟技术的不断完善,MD模拟已成为微观尺度上研究流体动态性质的有力工具,越来越多地应用到气体分子扩散传输的研究中.本文综述了近年来气体分子在纳米孔道材料中扩散传输的MD研究进展,包括单组分或多组分气体在人工纳米管、多孔膜材料、金属有机骨架多孔材料以及生物蛋白通道等的扩散传输,报道了温度、压强、气体组分以及纳米孔道材料结构等因素对扩散传输过程的影响.     

铵根离子在水溶液中的跳跃转动机理

铵根离子的动力学行为与生命体内的生物和化学过程密切相关.依据流体力学理论,由于铵根离子与水分子之间存在多个强氢键,其转动应较慢,但实验结果并非如此,其转动的微观机理尚不清晰.本文分子动力学模拟研究表明,水溶液中铵根离子主要以快速、大角度的跳跃方式进行转动,像水分子一样遵从扩展分子跳跃转动模型.通过微观转动模式的分解和两种转动弛豫时间的比较发现,相对其氢键骨架的扩散转动,跳跃转动对其转动速率贡献更大,并随浓度增大不断强化.与水分子氢键交换方式相比,铵根离子更倾向于在非氢键相连的水分子间发生交换.     

从分子水平研究电子传递

有机分子中电子传递受到诸多因素的影响, 纳米电极、界面、环境和分子本身都是必须要系统考察的因素. 本文从理论模拟和实验研究两个方面总结了在分子尺度上电子传递研究的最新进展. 着重讨论了分子动力学方法模拟纳米电极的制备, 量子化学方法研究电场作用下的分子构象及分子电导, 另外还讨论了扫描隧道显微术和电化学方法研究单分子结的电子传递. 分子电子传递的研究不仅涉及微观的实验测量, 从宏观的实验结果通过合理的分析推导, 也可以得到微观的信息.     

水和醇类分子及其混合物在纳米孔道材料中的传输扩散

随着计算机科学技术的飞速发展,理论计算特别是分子动力学模拟技术在研究受限流体的性质时发挥着独特的作用.本文综述了近年来水和醇类分子及其混合物在纳米孔道材料中传输扩散的研究进展,包括单组分水、甲醇和乙醇等在多种纳米孔道材料中的传输扩散,以及甲醇/水和乙醇/水等混合物在碳纳米管和沸石膜中的吸附和分离,讨论了体系温度、分子浓度以及纳米孔道材料结构等因素对水和醇类分子传输扩散过程的影响.     

锂铅合金中氚扩散行为的理论研究

锂铅合金是非常有前途的聚变堆、聚变-裂变混合堆包层产氚材料,研究氚在其中的扩散行为是很有意义的工作.从氢在金属中扩散的宏观规律出发,依据平板模型初步建立了氚-锂铅体系的扩散模型,利用相关文献数据,探讨了不同研究方式、氚浓度、温度对扩散行为的影响,分析了这种扩散的微观机制.计算结果表明:造成研究结论之间巨大差异的原因在于锂铅表面物理和化学状态的不同考虑;在一定温度范围内,氚浓度的升高引起扩散系数的下降,温度的升高引起扩散系数的增加.     

Ni(115)台阶面对氢表面微观动力学行为的影响

用５参数Ｍｏｒｓｅ势模拟氢－镍表面体系相互作用势，考察了氢原子在Ｎｉ（１１５）台面上吸附扩散行为。同时构造了氢分子与Ｎｉ（１００）和Ｎｉ（１１５）台阶面 相互作用推广的ＬＥＰＳ势面面，考察了氢分子解离化学吸附的微观动力学性质。     

基于分离粒子随机扩散理论的色谱模拟

为了对扩散分子的轨迹实施动态追踪与模拟, 深入理解分子扩散对色谱动力学的影响, 本文利用微尺度受限空间随机行走的模拟方法对色谱填充柱中的分子扩散过程进行了模拟. 重点考察了固定相的填充率、固定相的形状和柱长对色谱动力学行为的影响. 模拟结果表明短柱和大填充率具有较高的柱效; 在相同的密堆排列下, 固定相形状对分子扩散过程影响微弱; 待分离粒子的运动表现出微尺度空间限域的扩散特征, 但粒子的流动行为会随外部压力的增大而增加. 本论文提出的模拟方法对于发展高效能色谱, 开发新型分离技术等具有参考意义.     

分子在纯硅β分子筛内扩散的随机行走模型

建立了一个β分子筛上分子扩散的模型. 该模型中, 分子在β分子筛中运动是在不同吸附点位上作无规行走. β孔道的拓扑结构和在两种孔道吸附位上不同的跃迁几率导致分子沿两个主轴方向扩散, 扩散系数存在一个关联关系; 分子动力学对不同温度下苯分子在β分子筛上扩散模拟证实了这一关联关系. 氩原子在不同作用半径下的动力学模拟表明, 分子作用半径大小是满足随机行走假设的重要条件, 即该模型要求扩散分子作用半径足够大, 与分子筛孔径相近.     

Diffusion of spherical particles in microcavities

The diffusive motion of a colloidal particle trapped inside a small cavity filled with fluid is reduced by hydrodynamic interactions with the confining walls. In this work, we study these wall effects on a spherical particle entrapped in a closed cylinder. We calculate the diffusion coefficient along the radial, azimuthal, and axial direction for different particle positions. At all locations the diffusion is smaller than in a bulk fluid and it becomes anisotropic near the container's walls. We present a simple model which reasonably well describes the simulation results for the given dimensions of the cylinder, which are taken from the recent experimental work.     

Prediction of Brownian particle deposition in porous media using the constricted tube model

The deposition of colloidal particles onto the collector surfaces of porous media is investigated using the Brownian dynamics simulation method. The pore structure in a filter bed was characterized by the constricted tube model. The effects of various shapes of the total interaction energy curves of DLVO theory and the effects of different particle diameters on the collection efficiencies of particles are examined. The simulation results show that the particle collection efficiency is strongly dependent on the geometry of the tube and on the shape of the total interaction energy curve. In a comparison with the available experimental measurements of the filter coefficient, it is found that the present model can give a smaller discrepancy than that of the convective diffusion model in the unfavorable deposition region.     

Single particle tracking of complex diffusion in membranes: simulation and detection of barrier, raft, and interaction phenomena

Single particle tracking is being used increasingly to follow the motion of membrane-associated receptors and lipids. Anomalous and complex diffusive behaviors are generally found in cell membranes. We developed computational algorithms to simulate particle trajectories and to detect complex diffusive behaviors in two dimensions, including confined and convective diffusion, intramembrane barrier and raft phenomena, and interparticle interactions. Little useful information regarding barrier, raft, and interaction effects were provided by standard computational procedures for identification of anomalous diffusion, including analysis of mean squared displacement, distributions of diffusion rates and range, and time evolution of particle position. New algorithms were developed and optimized to detect complex diffusive behaviors from simulated single particle trajectories. A barrier detection algorithm was developed on the basis of spatial averaging of particle positions in trajectories. A raft detection algorithm utilized spatially resolved diffusion coefficients and particle density functions. An interaction algorithm utilized interparticle distance distributions. The algorithms developed here are applicable to identify biologically important diffusive phenomena in cell membranes.     

Theoretical simulation of chromatographic separation based on random diffusion in the restricted space

The diffusion behavior of particles in the chromatography is a fundamental issue of chromatographic dynamics. The understanding of the diffusion behaviors is particularly critical to optimize the operation conditions, improve the chromatographic performance and design a new separation device. Many of the present simulations focus on chromatographic thermodynamics, and very few aim at the overall diffusion and separation process. In order to dynamically trace the trajectory of the diffusing particles and to perform simulations of the whole chromatographic process, we have developed a model based on the framework of random walk in the restricted space and performed the simulation of a single particle diffusion in the gas chromatography. The simulation parameters were determined by comparing with the experimental data. The elution profiles of n-alkanes under different flow rates were accurately simulated with the method. The results show that the relative difference between the measures and the simulations are less than 2% and 10% for the retention time and the peak width, respectively. The simulation method shows great significance for the optimization of separation conditions and the development of novel technologies of chromatographic separation.     

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.     

基于随机扩散理论的气相色谱分离模拟

色谱分离过程中的粒子扩散问题是色谱动力学研究的基础,深入理解粒子的扩散行为对优化分离操作条件、提升色谱性能和开发新型色谱柱尤为关键.现有的模拟方法多集中于局部过程的热力学研究,而整体的扩散分离过程报道并不多见.为此,该文基于微尺度受限空间内随机扩散的方法,通过动态追踪粒子的运动轨迹,实现粒子在气相色谱开管柱内的扩散全过...     

核磁共振中多量子相干扩散行为的理论表述和计算机模拟

Self-diffusion is one of the most fundamental motions of particles in liquid. Nuclear magnetic resonance （NMR）provides a convenient and noninvasive means for accurately measuring the self-diffusion coefficient of molecules in solution. The theoretical expressions of apparent diffusion rates of MQCs are given and computer simulation based on the method to measure the self-diffusion coefficient by NMR was discussed and the random walk model of particles is used to simulate the apparent diffusion behaviors of intra-molecular and inter-molecular multiple-quantum coherences（MQCs）. The results of computer simulation agree well with theoretical predictions.     

EMULSION POLYMERIZATION IN A SEED-FED CONTINUOUS STIRRED-TANK REACTOR

A numerical method has been developed to predict the particle size distribution (PSD) of the product latex from a steady-state polydisperse-seeded continuous reactor. Simulations have been carried out for the emulsion polymerization of vinyl chloride based on the experimental conditions reported by Berens(l). The simulation results can be reasonably well fitted to the PSD data published by Berens. The radical desorption constant, k_d, for Berens’ vinyl chloride emulsion polymerization can be estimated by fitting the simulated PSD to experimental measurements. The simulation work presented in this article demonstrates that the combination of mathematical modeling and PSD measurements can be a useful tool in studying radical transport rates and aqueous phase termination phenomena. The simulation results also indicate that the continuum diffusion theory for free radical absorption by the particles leads to a better PSD fit than a model based on equal diffusion rates per unit area.     

Short-cut method for the correction of light attenuation influences in the experimental data obtained from confocal laser scanning microscopy

Based on Lambert-Beer law and the light attenuation model, a new method will be introduced in this work in order to eliminate the disturbances caused by signal attenuation in the experimental data measured by confocal laser scanning microscopy (CLSM). This new method considers the attenuation effects which depend on concentration of fluorophore-labelled protein as well as attenuation effects which are independent from protein concentration. Furthermore, no solvent additive is required in order to match the refraction index of solvent to bead material. The determination of correction factors is, thus, easily done using the currently investigated chromatographic phase system, so that the validity of the correction factors in the current system can be guaranteed. The introduced correction method has been applied for the investigation of intraparticle protein distribution inside an HIC (hydrophobic interaction chromatography) particle.