高分子粗粒化分子动力学模拟进展

模拟与理论、实验相互补充,彼此验证,使我们在原子和分子尺度上理解相关实验现象中的微观物理机制。结合高性能计算机和计算技术的发展,模拟已发展成为独特的高分子科学研究手段,在高分子材料优化设计和性能与结构问的性能关系研究中起重要作用。高分子具有不同层次的结构,材料的性质和功能不仅取决于化学结构和分子性质,而且很大程度上取决...     

Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function

The present work proposes a novel methodology for constructing coarse-grained(CG) models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as a functional of their equilibrium conformational probability densities, then is estimated from equilibrium averages of many independent physical quantities denoted as basis functions. An orthonormalization strategy is adopted to get the independent basis functions from sufficiently preselected interesting physical quantities of the system. Thus the current method is named as probability density matching coarse-graining(PMCG) scheme, which effectively takes into account the overall characteristics of the original systems to construct CG model, and it is a natural improvement of the usual CG scheme wherein some physical quantities are intuitively chosen without considering their correlations. We verify the general PMCG framework in constructing a one-site CG water model from TIP3 P model. Both structure of liquids and pressure of the TIP3 P water system are found to be well reproduced at the same time in the constructed CG model.     

基于复杂度分析logistic映射和Lorenz模型的研究

采用三次粗粒化方法得到了logistic映射和Lorenz模型的符号序列，运用动态非线性时间序 列分析方法——Lemper-Ziv复杂度，分别对两组符号序列进行了对比分析.对于logistic映 射，其复杂度反映了时间序列的演化；Lorenz模型三个分量的复杂度序列都具有混沌性质， 即由许多振幅非常接近而长度完全不同的循环所组成，反映了Lorenz模型内在的准周期特性 .进一步研究发现，当取不同的窗口长度时，复杂度序列的特征基本相同，并且复杂度反映 了时间序列的时空特性.因此，可以借助复杂度的计算来反演观测资料的动力学结构. 关键词： 三次粗粒化 Lemper-Ziv复杂度 logistic映射 Lorenz模型     

Towards the Evaluation of the Relevant Degrees of Freedom in Nonlinear Partial Differential Equations

We investigate an operator renormalization group method to extract and describe the relevant degrees of freedom in the evolution of partial differential equations. The proposed renormalization group approach is formulated as an analytical method providing the fundamental concepts of a numerical algorithm applicable to various dynamical systems. We examine dynamical scaling characteristics in the short-time and the long-time evolution regime providing only a reduced number of degrees of freedom to the evolution process.     

On the connection between Zwanzig's classical projection operator formalism and coarse-graining

It is pointed out that the following two procedures are identical: (i) applying Zwanzig's projection operator to the distribution function; (ii) coarsegraining the distribution function with cells which are defined by means of the macroscopic variables and their inaccuracies, and going to the limit of vanishing inaccuracies.     

Probabilistic approach to homoclinic chaos

Three-dimensional systems possessing a homoclinic orbit associated to a saddle focus with eigenvalues ±i, – and giving rise to homoclinic chaos when the Shil'nikov condition < is satisfied are studied. The 2D Poincaré map and its 1D contractions capturing the essential features of the flow are given. At homoclinicity, these 1D maps are found to be piecewise linear. This property allows one to reduce the Frobenius—Perron equation to a master equation whose solution is analytically known. The probabilistic properties such as the time autocorrelation function of the state variablex are explicitly derived.     

Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

The development of ultracoarse-grained models for large biomolecules needs to derive the optimal number of coarse-grained (CG) sites to represent the targets. In this work, we propose to use the statistical internal cluster validation indexes to determine the optimal number of CG sites that are optimized based on the essential dynamics coarse-graining method. The calculated curves of Calinski-Harabasz and Silhouette Coefficient indexes exhibit the extrema corresponding to the similar CG numbers. The calculated ratios of the optimal CG numbers to the residue numbers of fine-grained models are in the range from 4 to 2. The comparison of the stability of index results indicates that Calinski-Harabasz index is the better choice to determine the optimal CG representation in coarse-graining. © 2019 Wiley Periodicals, Inc.     

基于条件熵长江三角洲温度的非线性动力学特征分析

通过粗粒化方法得到符号序列，如果两个符号序列的条件熵在相对位移为零时达到最小值，那么这两个时间序列可能属于同一个动力学系统.进一步可以判断两个时间序列之间的耦合强度并提取出两个动力学耦合信号之间的内在滞后关系.本文用条件熵算法分析了长江三角洲地区上海、南通、常州、南京和杭州的逐日气温资料，判断这些地区的温度是否属于同一个动力学系统以及它们之间的动力学耦合关系，并提取出它们之间的滞后信息. 关键词： 粗粒化 条件熵 动力学耦合 滞后时间