Institute for Optoelectronics and Microsystems (ISOM) and ETSII, Universidad Politécnica de Madrid (UPM), José Gutiérrez Abascal 2, E-28006 Madrid, Spain.
Polymer Physics, Swiss Federal Institute of Technology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8049 Zurich, Switzerland.
Int J Mol Sci. 2009 Nov 23;10(11):5054-5089. doi: 10.3390/ijms10115054.
We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature.
我们回顾了一种层次建模方案的方法、算法实现和性能特征，用于在不同分子描述水平上生成、平衡和拓扑分析聚合物系统：从原子级聚乙烯样品到具有相同尺寸的相切硬球的自由连接链的随机堆积。我们的分析重点关注迄今讨论较少的实现蒙特卡罗（MC）程序的算法细节，用于系统生成和平衡，以及后处理步骤，在该步骤中，我们以原始路径的形式确定模拟系统的基础拓扑结构。为了证明我们的论点，我们研究了分子长度和堆积密度（体积分数）如何影响围绕链连接改变移动构建的 MC 方案的性能。同时，我们量化了有限系统大小、多分散性以及纠缠数（和相关的缠结分子量）的定义对原始路径网络结果的影响。沿着这些思路，我们批准了以前在文献中提出的主要概念。
