分子模拟在分子识别中的应用

随着计算机化学及量子化学理论的发展,其在化学、材料及生物医药等领域得到了广泛的应用。综述了分子模拟的方法:分子对接和分子动力学方法。着重介绍了分子动力学方法及其在分子识别领域的应用。分子对接方法是分子结构设计中的重要技术之一,可以预测生物分子复合物的结构和功能。分子动力学模拟可以使我们从原子尺度理解并预测物质的宏观性质,从而精确预测真实系统的物理性质。     

聚合物材料力学性能的计算机模拟

聚合物材料的宏观力学性能与其微观结构具有密切的关系,计算机模拟是研究这种结构与性能关系的重要手段之一,近年来国内外学者已经发展了多种模拟方法并从不同尺度来模拟聚合物材料的力学性能。本文综述了不同方法在聚合物材料力学性能模拟研究中的应用,重点介绍了Monte Carlo模拟、分子动力学模拟和基于弹簧格子模型的多尺度模拟这3种常见模拟方法的应用情况,如在分子动力学模拟中重点关注无定形聚合物玻璃态、结晶聚乙烯和部分非均质体系,而在多尺度模拟中则重点关注复杂的非均质聚合物体系,并讨论了各种方法的应用前景及亟待解决的问题。     

化学外加剂与水化硅酸钙相互作用的分子动力学研究进展EI北大核心CSCD

掺入化学外加剂是提升水泥基材料性能的有效方法。然而,各类化学外加剂在分子尺度上的作用机制仍需进一步明晰。水化硅酸钙(C–S–H)作为水泥水化的主要产物,控制着水泥基材料的各项宏观性能。分子动力学模拟可在分子/原子尺度上揭示化学外加剂分子与C–S–H的相互作用及其对C–S–H性能的影响。综述了近年来针对有机和无机化学外加剂与C–S–H在分子尺度上的相互作用及其对C–S–H性能影响机理的分子动力学研究进展,并展望了关于化学外加剂–(C–S–H)体系分子动力学模拟的后续研究方向。总结的化学外加剂包括有机小分子、树脂和纤维、水溶性聚合物等有机外加剂,以及(改性)石墨烯、硅烯、碳纳米管、各类纳米粒子等无机外加剂。分子动力学模拟研究重点关注各类外加剂与C–S–H界面的相互作用,这一作用的理解有助于揭示外加剂对C–S–H材料力学性能的提升机理。此外,针对有机小分子、水溶性聚合物及部分纳米粒子等外加剂,大量研究采用分子动力学方法,揭示此类外加剂对C–S–H层状结构的吸附、插层、聚集阻塞等微观作用,从而阐明这些外加剂对C–S–H力学性能、传输性能,乃至收缩行为的作用机理。这些认识,为有效提升水泥基材料性能、外加剂分子结构设计提供理论启发。     

蒙皂石层间结构与性质关系的分子模拟研究进展

综述了计算机模拟中的分子力学、Monte Carlo和分子动力学模拟方法及其在蒙皂石层间结构中的应用进展,涉及粘土-水-离子体系的位能函数、粘土的水化和层间结构、热力学性质、物理机械性质和柱撑蒙脱石等各个方面.指出分子模拟对蒙皂石层间分子行为的基础研究将发挥重要作用.     

分子模拟在化学工程中的应用

总结了不同尺度分子模拟技术在化工中的发展现状,利用量化计算的方法,可以研究纳微尺度表界面的活性及其对催化反应的影响。采用分子动力学模拟可很方便地研究受限条件下流体行为,采用粗粒化模拟技术可研究介观结构。最后介绍了反应力场模拟这种涵盖反应和传递的模拟新方法。随着模拟理论和并行技术的进步,分子模拟的定量化程度越来越高,必将与化工应用的实验结果越来越有可比性,从而在化工生产和实践中担当更重要的角色。     

分子模拟与化学工程

从分子水平来研究化工过程及产品的开发和设计是21世纪化学工程的一个重要方向.综述了计算机分子模拟中的MonteCarlo分子模拟和分子动力学模拟两种方法及其在化工中的应用,涉及分子模拟在建立状态方程和研究分子微观结构、相界面、扩散性质等方面的应用进展.指出分子模拟对化学工程的基础研究、工艺过程以及新产品开发将发挥巨大作用.     

复杂材料的微相分离和结构演变

共聚高分子和表面活性剂系统常常能够形成不同尺度的复杂结构,在材料和生物技术领域具有广泛的用途.这种结构及其形成过程与自然界中大量存在的斑图及其演化过程具有非常类似的机理,受到不同学科研究者的广泛关注.在高分子系统的分子热力学、微相分离及结构演变过程领域已经开展了大量的研究工作,已成为凝聚态物理、高分子物理、统计力学理论和计算机模拟的热点之一.在分子尺度上,基于格子和自由空间的分子热力学模型、计算机分子模拟方法可以用于描述高分子系统的相平衡和分子的聚集形态.在介观尺度上,时间相关的Ginzberg-Landau理论、元胞动力学方法等可以有效地研究微相分离结构的演变过程及其受外场的影响.而耗散粒子动力学模拟则可以将分子尺度和介观尺度的研究结合起来,是一种跨尺度的研究方法.多尺度研究方法的发展将成为今后研究的重点.本文总结了该领域的某些研究进展.     

分子筛数值模拟的研究进展

随着数值模拟方法的不断完善和发展,利用数值模拟计算分子筛各种物化性能逐渐成为研究的热点.数值模拟方法可从原子或分子尺度上揭示分子筛各种性质及其反应机理,为分子筛的应用提供理论数据.对分子筛数值模拟方法:密度泛函理论方法、分子动力学方法、蒙特卡洛法和组合方法进行了概括总结,对比了这几种方法优缺点,为各种方法的选择应用提供了参考.     

分子模拟技术在分子筛的吸附扩散研究中的应用

二分子模拟是近年发展起来的一门新兴计算化学技术.简要介绍了分子模拟技术的基本原理及其优点和缺点,重点阐述了分子模拟中的Monte Carlo分子模拟和分子动力学模拟两种方法及其在分子筛的吸附扩散研究中的应用.同时介绍了这两种组合方法的应用,最后展望了分子模拟技术的发展方向.     

静电作用力算法对分子动力学模拟结果的影响分析

蛋白质分子和界面之间的作用在药物输送以及生物分离等领域至关重要。利用分子动力学模拟考察蛋白质分子在界面附近的行为是最近10年研究的热点。在早期的工作中,Wang等发现同电荷离子交换介质可用于辅助蛋白质复性,但其机理不甚明确。在利用分子动力学模拟研究其分子机理时发现,不同静电作用力参数对模拟结果有直接的影响。因此,通过全原子分子动力学模拟考察不同静电参数条件对模拟结果的影响,展示此过程的构象和能量变化,分析了造成结果差异的原因。研究结果揭示了不同静电参数对模拟结果的影响,为进一步研究蛋白质在界面表面的行为奠定了一定的理论基础。     

Spatial simulations in systems biology: from molecules to cells

Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods.     

A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics

This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment.     

Multiscale modeling for polymer systems of industrial interest

Atomistic-based simulations such as molecular mechanics (MM), molecular dynamics (MD), and Monte Carlo-based methods (MC) have come into wide use for materials design. Using these atomistic simulation tools, one can analyze molecular structure on the scale of 0.1–10 nm. Although molecular structures can be studied easily and extensively by these atom-based simulations, it is less realistic to predict structures defined on the scale of 100–1000 nm with these methods. For the morphology on these scales, mesoscopic modeling techniques such as the dynamic mean field density functional theory (Mesodyn) and dissipative particle dynamics (DPD) are now available as effective simulation tools. Furthermore, it is possible to transfer the simulated mesoscopic structure to finite element modeling tools (FEM) for calculating macroscopic properties for a given system of interest. In this paper, we present a hierarchical procedure for bridging the gap between atomistic and macroscopic modeling passing through mesoscopic simulations. In particular, we will discuss the concept of multiscale modeling, and present examples of applications of multiscale procedures to polymer–organoclay nanocomposites. Examples of application of multiscale modeling to immiscible polymer blends and polymer–carbon nanotubes systems will also be presented.     

Multiscale modeling of ion transport in porous electrodes

Ion transport through nanoporous materials is of fundamental importance for the design and development of filtration membranes, electrocatalysts, and electrochemical devices. Recent experiments have shown that ion transport across porous materials is substantially different from that in individual pores. Here, we report a new theoretical framework for ion transport in porous materials by combining molecular dynamics (MD) simulations at nanopore levels with the effective medium approximation to include pore network properties. The ion transport is enhanced with the combination of strong confinement and dominating surface properties at the nanoscale. We find that the overlap of electric double layers and ion–water interaction have significant effects on the ionic distribution, flux, and conductance of electrolytes. We further evaluate the gap between individual nanopores and complex pore networks, focusing on pore size distribution and pore connectivity. This article highlights unique mechanisms of ion transport in porous materials important for practical applications.     

Multiscale molecular modeling in nanostructured material design and process system engineering

Atomistic-based simulations such as molecular mechanics, molecular dynamics, and Monte Carlo-based methods have come into wide use for material design. Using these atomistic simulation tools, we can analyze molecular structure on the scale of 0.1–10 nm. However, difficulty arises concerning limitations of the time and length scale involved in the simulation. Although a possible molecular structure can be simulated by the atom-based simulations, it is less realistic to predict the mesoscopic structure defined on the scale of 100–1000 nm, for example the morphology of polymer blends and composites, which often dominates actual material properties. For the morphology on these scales, mesoscopic simulations such as the dynamic mean field density functional theory and dissipative particle dynamics are available as alternatives to atomistic simulations. It is therefore inevitable to adopt a mesoscopic simulation technique and bridge the gap between atomistic and mesoscopic simulations for an effective material design. Furthermore, it is possible to transfer the simulated mesoscopic structure to finite elements modeling tools for calculating macroscopic properties for the systems of interest.In this contribution, a hierarchical procedure for bridging the gap between atomistic and macroscopic modeling passing through mesoscopic simulations will be presented and discussed. The concept of multiscale (or many scale) modeling will be outlined, and examples of applications of single scale and multiscale procedures for nanostructured systems of industrial interest will be presented. In particular the following industrial applications will be considered: (i) polymer-organoclay nanocomposites of a montmorillonite–polymer–surface modifier system; (ii) mesoscale simulation for diblock copolymers with dispersion of nanoparticels; (iii) polymer–carbon nanotubes system and (iv) applications of multiscale modeling for process systems engineering.     

Analytical multi-scale method for multi-phase complex systems in process engineering—Bridging reductionism and holism

Multi-scale spatio-temporal structures, the dominant feature for all complex systems, are identified and discussed as a common challenge and frontier in process engineering, as well as in science and technology of many different fields and disciplines. Emphasis is paid to the correlation between different scales, which is one of the focuses in complexity science. The energy minimization multi-scale (EMMS) model for particle-fluid flow is revisited as an implementation of the analytical multi-scale method to elucidate its principles, in which the correlation between scales is established by analyzing the compromise between dominant mechanisms. This strategy has been extended to six other systems, covering single-phase flow, gas-liquid flow, granular flow and emulsions. A general framework of the method and the common feature of the compromise processes are then presented together with an introduction to some practical applications of the analytical multi-scale method and its extensions. We conclude with prospects on the multi-scale method as a reasonable approach to complex systems that bridges reductionism and holism.     

Molecular dynamics simulations of thermal transport in porous nanotube network structures

Carbon nanotube based 3D nanostructures have shown a lot of promise towards designing next generation of multi-functional systems, such as nano-electronic devices. Motivated by their recent successful experimental synthesis as well as characterization, and realizing that thermal dissipation is an important concern in proposed devices because of ever-increasing power density, we have investigated the phononic thermal transport behavior in 3D porous nanotube network structures using reverse non-equilibrium molecular dynamics simulations. Based on our study, the length scale associated with the distance between nanotube junctions emerges as the most dominating parameter that governs phonon scattering (hence the characteristic mean free path) and the heat flow in these nanostructures at molecular length scales. However, because of their spatial inhomogeneity, we show that the aerial density of carbon nanotubes (normal to heat flow) is also of critical importance in determining their system-level thermal conductivity. Based on our findings, we postulate that both parameters should be considered while designing nano-devices where thermal management is relevant.     

A hybrid method of turbulent flow modelling in packings of complex geometry

In this work, experimental investigations and computational simulations were combined into a hybrid method of complex phenomena modelling. In particular, the thermo-anemometric technique and the multi-scale methodology of modelling were applied to investigate air turbulent flow within a rectangular container filled with spheres in cubic arrangement and different baffles alternatively inserted between the spheres. The model systems formed the complex geometric structures where three length scales were distinguished. Hence, the local fluctuations of air velocity were examined in the micro-scale determined by the size of the anemometric probe. The interstitial flow distributions, in turn, were investigated in the cell scale related to the sphere diameter. At last, the pressure drop changes caused by the superficial flow distributions were analysed in the apparatus scale. In each case, the particular experimental data were approximated by numerical modelling. However, when the information exchange between the complementary models was arranged, the significance of the flow mechanisms dominating in particular length scales could be confirmed in relation to all the experimental data determined in this work. In recapitulation, it was indicated how experimental and numerical investigations can be effectively combined in searching for a “profitable” anisotropy of the packing resistance to flow.