Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model

We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo (kMC) simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion m, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed m, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size effects at the cost of reasonable computational time.     

非等活性加核自缩合乙烯基聚合体系回转半径的Monte Carlo模拟

利用Monte Carlo模拟方法研究了加核自缩合乙烯基聚合反应体系中超支化高分子的二次回转半径随双键转化率的变化情况. 在模拟中, 重点考察了两类活性基团的反应活性差异、 引发核的配比及基团数等因素对超支化高分子均方回转半径的影响. 结果表明, 上述因素对于超支化高分子的尺度有着显著影响, 从而可为调控体系中高分子的空间尺度提供有效途径.     

TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

A Theoretical study on the charge and discharge states of Na-ion battery cathode material,Na1+xFePO4F

Na₂FePO₄F is a promising cathode material for a Na-ion battery because of its high electronic capacity and good cycle performance. In this work, first principle calculations combined with cluster expansion and the Monte Carlo method have been applied to analyze the charge and discharge processes of Na₂FePO₄F by examining the voltage curve and the phase diagram. As a result of the density functional theory calculation and experimental verification with structural analysis, we found that the most stable structure of Na_1.5FePO₄F has the P2₁/b11 space group, which has not been reported to date. The estimated voltage curve has two clear plateaus caused by the two-phase structure composed of P2₁/b11 Na_1.5FePO₄F and Pbcn Na₂FePO₄F or Na₁FePO₄F and separated along the c-axis direction. The phase diagram shows the stability of the phase-separated structure. Considering that Na₂FePO₄F has diffusion paths in the a- and c-axis directions, Na₂FePO₄F has both innerphase and interphase diffusion paths. We suggest that the stable two-phase structure and the diffusion paths to both the innerphase and interphases are a key for the very clear plateau. We challenge to simulate a nonequilibrium state at high rate discharge with high temperature by introducing a coordinate-dependent chemical potential. The simulation shows agreement with the experimental discharge curve on the disappearance of the two plateaus. © 2018 Wiley Periodicals, Inc.     

Predicting Low-Pressure O2 Adsorption in Nanoporous Framework Materials for Sensing Applications

A set of 98 nanoporous framework material (NFM) structures was investigated by classical Grand canonical Monte Carlo simulations for low-pressure O₂ adsorption properties (Henry’s constant and isosteric heat of adsorption). The set of materials includes those that have shown high O₂ uptake experimentally as well as a subset of more than 2000 structures previously screened for noble-gas uptake. While use of the general force field UFF is fruitful for noble-gas adsorption studies, its use is shown to be limited for the case of O₂ adsorption—one distinct limitation is a lack of sufficient O₂–metal interactions to be able to describe O₂ interaction with open metal sites. Nonetheless, those structures without open metal sites that have very small pores (<2.5 Å) show increased O₂/N₂ selectivity. Additionally, O₂/N₂ mixture simulations show that in some cases, H₂O or N₂ can hinder O₂ uptake for NFMs with small pores due to competitive adsorption.     

参数法和非参数法估计组合样中被测组分含量的置信区间

本文以散装生铁块的随机样本分析结果为基础,应用Ｍｏｎｔｅ Ｃａｒｌｏ模拟法考察了组合样本中Ｓｉ、Ｍｎ,Ｃ,Ｓ,Ｐ含量（或份样平均值）的分布情况,研究了组分含量的置信区间,对参数法和非参数法的结果进行了比较。结果表明,对近似符合正态分布的原始总体或当组合样中的份样数目较多时,两种方法所估计的置信区间相近。但对偏离正态分布（或ｔ－分布）的总体且组合样中的份样数目较少时,非参数法较参数法的结果更符合实际     

端点附壁的高分子链形状的Monte Carlo模拟

分别基于简立方格点和四面体格点模型对一端吸附在无限大平面的高分子链（平面接枝高分子链）的形状进行了Ｍｏｎｔｅ Ｃａｒｌｏ模拟,结果表明,接枝高分子链的形状更偏离球形,〈Ｌ＾２１〉：〈Ｌ＾２２〉：〈Ｌ＾２３〉的极限值约为１：２．７５：１２．５,其中〈Ｌ＾２１〉,〈Ｌ＾２２〉和〈Ｌ＾２３〉分别为回转半径张量的本征值Ｌ＾２１,Ｌ＾２２和Ｌ＾２３（Ｌ＾２１〈Ｌ＾２２〈Ｌ＾２３）的统计平均;链长相同时,接枝     

A Theoretical Exploration of the Potential of ICAR ATRP for One‐ and Two‐Pot Synthesis of Well‐Defined Diblock Copolymers

Kinetic Monte Carlo simulations are performed to investigate the capability of ICAR ATRP for the synthesis of well‐defined poly(isobornyl acrylate‐b‐styrene) block(‐like) copolymers using one‐pot semi‐batch and two‐pot batch procedures. The block copolymer quality is quantified via a block deviation (〈BD〉) value. For 〈BD〉 values lower than 0.30, the quality is defined as good and for well‐chosen polymerization conditions the formation of homopolymer chains upon addition of the second monomer can be suppressed. A better block quality is obtained when isobornyl acrylate is polymerized first. For lower Cu levels a one‐pot semi‐batch procedure allows a much faster ATRP and better control over the polymer properties than a two‐pot batch procedure.