On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

磁场下有原子自旋轨道耦合的各向异性量子点的精确解析传播子

量子力学中很少有系统能够精确地计算传播子, 特别是在考虑了自旋轨道耦合效应的情况下. 利用相空间的群论方法, 首先导出了有原子自旋轨道耦合的各向异性量子点传播子的精确解析表达式. 随后利用传播子来计算自旋高斯波包的演化与相应的概率密度, 并研究了原子自旋轨道耦合效应和磁场强度对距离期望值的影响.     

6英寸低位错锗单晶生长热场设计

锗片作为衬底材料已在空间太阳电池领域得到广泛的应用,新型锗基空间太阳能电池对锗片的需求由4英寸(1英寸=2.54 cm)提高到6英寸后,低位错锗单晶的生长难度增大。本文设计开发了一种适用于直拉法生长大尺寸、低位错锗单晶的双加热器热场系统,模拟研究了不同形状主加热器的热场分布,从而得到最优的热场环境。研究发现:渐变长度为L/h=1/2、渐变率α为65°的渐变型主加热器热场结构能够获得最佳的热场分布,有利于低位错单晶的生长。经验证,生长的锗单晶热应力较低,位错密度在310～450 cm^-2范围内。     

Synthesis of conjugated polymers possessing diketopyrrolopyrrole units bearing phenyl,pyridyl, and thiazolyl groups by direct arylation polycondensation: Effects of aromatic groups in DPP on physical properties

Conjugated polymers containing phenyl‐, pyridyl‐, and thiazolyl‐flanked diketopyrrolopyrrole (DPP) were synthesized by direct arylation polycondensation of 3,4‐ethylenedioxythiophene derivatives and dibrominated DPP‐based monomers, in order to probe the effects of the aromatic groups in the DPP units on the absorption property, energy level, and crystallinity. A polymer possessing thiazolyl‐flanked DPP units was found to display long‐wavelength absorption properties and higher crystallinity than the polymers bearing phenyl‐ and pyridyl‐flanked DPP units. These features of the thiazolyl‐based polymer were afforded by its coplanar structure of the main chain. The synthesized polymers showed semiconducting properties in organic field effect transistors and organic photovoltaics. Direct arylation polycondensation is an efficient synthetic method that affords a series of DPP‐based polymers in a simple fashion and, thus, helping in a comprehensive understanding on the relationship between the aromatic groups in DPP units and their physical properties. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2337–2345     

Nonrigid image registration using similarity measure based on spatially weighted global probability distribution function

In nonrigid image registration, similarity measures including spatial information have been shown to perform better than those measures without spatial information. In this work, we provide new insight to the relationships among regional mutual information, regional probability distribution functions (PDFs) and global PDFs, and propose a novel nonrigid registration scheme with spatially weighted global probability distribution function (SWGPDF). Similarity measures based on SWGPDF (SWGPDFSM) are constructed. Three different spatial sub-region division methods are compared: the equally spaced sub-region (ESSR), the local binary pattern sub-region (LBPSR) and the gradient sub-region (GSR). The registration scheme applies B-spline based free form deformations (FFDs) as the transformation model. A Parzen window and linear interpolation are used to construct histograms. The SWGPDFSM registration scheme with ESSR space division is compared with the traditional global mutual information (gMI), the traditional global normalized mutual information (gNMI), regional mutual information and the SWGPDFSM with LBPSR or GSR space division. The test results show that SWGPDFSM scheme with ESSR space division outperforms the other schemes for elastically aligning images in the presence of big geometrical transformations, bias fields and illumination changes.     

Constructing permutation polynomials from piecewise permutations

We present a construction of permutation polynomials over finite fields by using some piecewise permutations. Based on a matrix approach and an interpolation approach, several classes of piecewise permutation polynomials are obtained.