Multiscale modelling.
Multiscale modelling.
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DOI：
10.1039/c1cp90072b
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发表时间：
2011
期刊：
影响因子：
--
通讯作者：
L. Visscher;P. Bolhuis;F. Bickelhaupt
中科院分区：
文献类型：
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作者：
L. Visscher;P. Bolhuis;F. Bickelhaupt
多尺度建模可以定义为同时研究与复杂化学、物理或生物过程相关的不同时间和长度尺度。虽然这个概念已经应用于物理和材料科学的许多领域（如工程、流体和空气动力学），但它在物理化学和化学物理中的实现仍然相对较新。在这些学科中，多尺度方法连接了量子化学、经典分子动力学、计算材料科学和生物信息学等已建立的领域。这种整体观点对于光合作用、蛋白质折叠、DNA复制、催化等重要过程的重要性是显而易见的。随着上述领域理论模型的成熟，连接量子力学（QM）、分子力学（MM）、粗粒度（CG）和连续体描述的复杂仿真工作流程正在出现。因此，重点从改进工作流程的各个组成部分、在单一长度和/或时间尺度上的计算，转变为改进整个模型和在各级之间传递信息。用从头算参数从较低的长度尺度提供更大的长度尺度模拟需要在两个模型中的物理彻底匹配和整个工作流程的有效实现。由于多尺度模型的发展主要在母体领域的文献中讨论，不同领域之间的交叉受精仍然有限。这个主题的问题，收集跨物理化学和化学物理广泛领域的多尺度建模的想法，因此旨在加强跨学科的思想交流。这些贡献解决了在广泛的长度和时间尺度上的方法之间的耦合。对于最小的长度尺度，考虑量子力学对原子核运动的影响是有意义的，理想情况下，在一种自适应方案中，允许以动态方式在量子和经典力学描述之间切换（DOI: 10.1039/c0cp02865g）。更成熟的技术是将电子的显式量子力学（QM）描述连接到隐式分子力学（MM）模型（DOI: 10.1039/c0cp02957b）。虽然这两种模型都采用库仑算符来描述静电相互作用，但要准确处理量子力学系统中的离域电子密度与量子力学部分中的局域电荷之间的相互作用是一项挑战。因此，这些电荷的参数化和在MM描述中包含极化仍然是一个活跃的研究领域（DOI: 10.1039/c0cp02850a和DOI: 10.1039/c1cp20646j）。遗传算法可以改进力场参数化的优化（DOI: 10.1039/c0cp02889d）。QM/MM与本体溶剂边界势的结合提高了效率（DOI: 10.1039/c0cp02828b）。QM/MM分区的另一种选择是采用冻结密度分析器，从而包括非静电组件
Multiscale modelling can be defined as the concurrent study of the different time and length scales relevant for complex chemical, physical or biological processes. While this concept is already used in many areas of physics and material science (eg engineering, fluids, and aerodynamics), its realization in physical chemistry and chemical physics is still relatively new. Within these disciplines, a multiscale approach connects the established fields of quantum chemistry, classical molecular dynamics, computational materials science, and bioinformatics. The importance of such an integral view for important processes such as photosynthesis, protein folding, DNA replication, catalysis, etc. is evident. With the theoretical models in the above-mentioned fields reaching maturity, complex simulation workflows are emerging that link quantum mechanical (QM), molecular mechanics (MM), coarse-grained (CG), and continuum descriptions. The focus is thereby changed from the improvement of individual components of a workflow, calculations at a single length and/or time scale, to the improvement of the complete model and the transfer of information between the levels. Feeding the larger length scale simulations with ab initio parameters from lower length scales requires a thorough matching of the physics in the two models and efficient implementation of the entire workflow.As multiscale modelling developments are primarily discussed in the literature of the parent fields, cross-fertilization between the different fields is still limited. This themed issue, collecting ideas on multiscale modelling across the broad field of physical chemistry and chemical physics, therefore aims to enhance the interdisciplinary exchange of ideas. The contributions address coupling between methods at a wide range of length and time scales. For the smallest length scales it is of interest to consider quantum mechanical effects on the motion of nuclei, ideally in an adaptive scheme that allows for switching between quantum and classical mechanical descriptions in a dynamical fashion (DOI: 10.1039/c0cp02865g). More established are techniques that connect an explicit quantum mechanical (QM) description of the electrons to an implicit molecular mechanics (MM) model (DOI: 10.1039/c0cp02957b). Although both these models employ the Coulomb operator to describe electrostatic interactions, it is challenging to accurately handle the interaction between the delocalized electron density in the QM system and the localized charges in the MM part. Parameterization of such charges and inclusion of polarization in the MM description therefore remains an active field of research (DOI: 10.1039/c0cp02850a and DOI: 10.1039/c1cp20646j). Genetic algorithms can improve optimization of force field parameterization (DOI: 10.1039/c0cp02889d). The combination of QM/MM with a boundary potential for bulk solvent enhances efficiency (DOI: 10.1039/c0cp02828b). An alternative to the QM/MM partitioning is to employ a frozen density ansatz and thereby include non-electrostatic components