采用加权直方图分析和蒙特卡洛重采样法对自由能级的校正研究（英文）

本文采用加权直方图分析方法和蒙特卡洛重采样方法进行自山基校正研究.生成的自由能表面几乎可以收敛到具有足够采样情况的精准表面,并且比常规的加权直方图分析校正方法能更稳定地处理采样不足的情况,为检测能级校正表面的不确定性提供指南,并且定义了明确的标准用以确定能改善其视觉效果的自山能表面平滑程度.本文通过水中的丙氨酸二肽和KillerRed蛋白质子转移的自山能图证明该方法的优势,说明蒙特卡洛重采样法可以作为在产生自由能表面实际的系统中的实用工具.     

窗口竞争性自适应重加权采样策略的近红外特征变量选择方法

通过消除光谱中的冗余信息变量,挑选出代表样品性质的特征变量代替全谱建立定量模型,可以提高近红外分析结果的准确性。基于进化论中适者生存原理的竞争性自适应重加权采样（CARS）算法因具有计算速度快、筛选得到的特征波长少等优点,在近红外特征变量筛选方面得到了广泛的应用。然而该方法在计算过程中容易出现校正集和验证集结果不一致情况。这是因为算法过于强调校正集交叉验证结果,且并未考虑相邻变量之间的协同作用。为了建立更加稳健的变量筛选方法,通过结合“窗口”以及CARS算法的优势,提出了一种基于窗口竞争性自适应重加权采样（WCARS）策略的近红外特征变量筛选方法,并将其应用于复杂植物样品近红外光谱与其化学成分含量之间的建模分析。采用WCARS方法可以实现准确定量分析,且通过与竞争性自适应重加权采样（CARS）方法结果相比较,WCARS方法得到的校正集和预测集结果一致,在一定程度上减少了过拟合问题的出现。该策略能有效增强特征变量选择的稳健性,提高了定量模型的可信度,具有一定的应用价值。     

基于Savitzky-Golay加权拟合的红外图像非均匀性条带校正方法

针对红外成像探测器单元响应不一致等因素导致的图像非均匀性条带问题, 提出了基于直方图加权和Savitzky-Golay拟合的非均匀性条带校正方法。首先, 计算每列的归一化直方图函数并将其作为权值对图像进行加权运算;然后, 利用Savitzky-Golay滤波器对加权后的图像列均值和列方差进行拟合, 并将结果带入校正公式, 通过可调参数的迭代完成校正。实验结果表明:该方法能有效地去除非均匀性条带, 保留图像的光谱辐射信息和纹理细节, 各项评价指标均提高10%。     

基于广义平面校正的图像对最小化畸变重投影

提出了一种基于广义平面校正的最小化畸变重投影方法,通过建立广义平面校正坐标系并对其虚拟规范化,在虚拟坐标系内考虑最小化畸变和最小化重采样效果,减少了因旋转造成的重采样畸变问题,校正后图像的可视性大大改善.     

基于自由变形技术的多投影颜色校正

为了解决多通道投影显示系统中各投影仪投影画面之间颜色不一致的问题,设计了一种基于自由变形技术的多投影颜色校正方法。首先,通过Bernstein基函数建立自由变形技术模型,建立各投影仪原始图像和摄像机拍摄图像之间的颜色转换关系;其次,采集原始图像集和摄像机拍摄的投影显示画面集,确定自由变形技术模型的参数;然后,通过Matlab分析验证投影图像各颜色通道之间是相互影响的;最后,对原始图像进行颜色扭曲,将本文颜色校正方法与传统方法进行直方图相似性评估对比。实验结果表明：对比广义颜色校正方法和基于B样条曲线的颜色校正方法,本文方法将投影画面的颜色强度平均差值在B通道减少了2.50,在G通道减少了2.34,在R通道减少了3.57,直方图的相关性提高了8.9%,巴氏距离降低了9.7%。基于自由变形技术的多投影颜色校正方法使投影画面衔接流畅,给用户带来更好的沉浸感受。     

蒙特卡洛方法计算材料表面激发参数

电子非弹性散射平均自由程（IMFP）是用表面电子能谱进行表面化学定量分析时极为重要的一个参数,它可以用测量的弹性峰电子能谱分析以及蒙特卡洛模拟来确定.为了更加精确地确定电子非弹性散射平均自由程,必须对弹性峰电子能谱中的表面激发效应进行修正,通常使用介电响应理论方法计算得到的表面激发参数.然而,通过理论计算得到的表面激发参数不能包含电子在材料内部输运过程中弹性散射的影响,进而影响所测的电子非弹性散射平均自由程的准确度.在这个工作中,我们采用蒙特卡洛方法来确定包含弹性散射效应时的表面激发参数.所得到的表面激发参数在不同能量、角度情况下,尤其是在弹性散射效应显著的60°以上的大角度入射、出射情况下,都与实验测量值符合得非常好.基于这些新确定的表面激发参数,可以在弹性峰电子能谱测量中获得更为准确的电子非弹性散射平均自由程数据.     

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

运用二维的键长涨落模型和蒙特卡洛方法研究高分子链从一个受限空间到自由空间穿孔过程中,链单体与纳米孔之间的相互作用.结果表明,在不同的链长和纳米孔交互作用下,高分子链成功穿越自由能能垒取决于链长和纳米孔长度,并且由于交互作用降低了自由能能垒,导致高分子链在纳米管的平均捕获时间缩短.     

自适应加权直方图均衡化的红外图像增强

鉴于现有的红外图像增强方法存在欠增强、过增强和放大噪声等缺陷,提出了自适应加权直方图均衡化的红外图像增强方法。该方法提出了直方图的自适应加权系数,其反比于每个灰度级对应直方图频次的平方根,适当地提升频次较小的直方图,而适当压制频次较大的直方图。用自适应加权系数对各个灰度级的直方图频次进行加权后,进行直方图均衡化处理,最后经灰度级映射得到增强图像。实验结果显示,相对于现有的方法,本方法的增强图像对比度更高,边缘细节信息更丰富,信息熵、平均梯度和标准差分别比现有方法高出0.23、2.2和3.7以上。因此,本文方法的红外图像增强效果优于最新提出的现有方法。     

随机反应扩散格气模型上钙动力学的粗粒化模拟

发展了一种基于随机格气模型的粗粒化方法,该方法能有效模拟内质网表面钙动力学信息. 首先将相邻的微观节点合并成粗粒化节点,再根据局域平均场近似推导出粗粒化反应速率,然后执行粗粒化动力学蒙特卡洛模拟. 发现粗粒化动力学蒙特卡洛模拟结果和微观模拟结果非常吻合. 有趣的是,存在一个最佳的粗粒化比m,使得粗粒化模拟与微观模拟的相变点偏差最小. 固定m,发现临界点随体系尺度增加而单调增加,而且相变点的偏差与体系尺度存在一个标度关系.此外,该粗粒化方法大大地加快了蒙特卡洛模拟速率,并且与微观模拟直接相关. 该方法可以广泛用来研究体系尺度效应,而节省大量计算时间.     

Mo纳米薄膜热力学性质的分子动力学模拟

采用改进嵌入原子法(MAEAM),通过经典的分子动力学(MD)模拟计算了高熔点过渡金属体心立方(bcc) Mo块体Gibbs自由能和表面能. 对于纳米薄膜的热力学数据,比如Gibbs自由能等,可以看成是薄膜内部原子和表面原子两部分数据之和,然后根据薄膜的体表原子之比就可以直接计算出总的自由能,并由此可以得到热力学性质与薄膜尺寸及温度的定量关系式. 分别计算了bcc Mo块体及其纳米尺寸薄膜的自由能和热容,结果表明,Mo纳米薄膜的热力学性质具有尺寸效应,并且在薄膜尺寸小于15—20nm时,这种效应变得非常明 关键词： 改进嵌入原子法 Mo纳米薄膜 表面自由能 热容     

Optimized convergence for multiple histogram analysis

We propose a new algorithm for solving the weighted histogram analysis method (WHAM) equations to estimate free energies out of a set of Monte Carlo (MC) or molecular dynamics (MD) simulations. The algorithm, based on free-energy differences, provides a more natural way of approaching the problem and improves convergence compared to the widely used direct iteration method. We also study how parameters (temperature, pressure, etc.) of the independent simulations should be chosen to optimize the accuracy of the set of free energies.     

微液滴在不同能量表面上润湿状态的分子动力学模拟

微小液滴在不同能量表面上的润湿状态对于准确预测非均相核化速率和揭示界面效应影响液滴增长微观机理具有重要意义. 通过分子动力学模拟, 研究了纳米级液滴在不同能量表面上的铺展过程和润湿形态. 结果表明, 固液界面自由能随固液作用强度增加而增加, 并呈现不同液滴铺展速率和润湿特性. 固液作用强度小于1.6的低能表面呈现疏水特征, 继续增强固液作用强度时表面变为亲水, 而固液作用强度大于3.5的高能表面上液体呈完全润湿特征. 受微尺度条件下非连续、非对称作用力影响, 微液滴气液界面存在明显波动, 呈现与宏观液滴不同的界面特征. 统计意义下, 微小液滴在不同能量表面上铺展后仍可以形成特定接触角, 该接触角随固液作用强度增加而线性减小, 模拟结果与经典润湿理论计算获得的结果呈现相似变化趋势. 模拟结果从分子尺度为核化理论中的毛细假设提供了理论支持, 揭示了液滴气液界面和接触角的波动现象, 为核化速率理论预测结果和实验测定结果之间的差异提供了定性解释.     

蒙特卡罗与离散纵标耦合方法在压水堆堆腔漏束计算中的应用

为克服蒙特卡罗(MC)方法计算时间长和离散纵标(SN)方法复杂几何描述不精确的困难,采用SN-MC耦合计算流程,研究了基于蒙特卡罗方法和离散纵标方法的耦合方法。耦合方法的主要思想是根据离散纵标程序提供的中子角通量,利用接口程序计算出面源的分布概率,然后由修改后的源抽样子程序生成包括上下圆面源和圆柱面源的组合源,提供给蒙特卡罗程序进行计算分析。初步计算结果表明,该耦合方法是正确的,可用于压水堆堆腔漏束的计算分析。     

Reconstructed (1 1 0) surfaces of FCC transition metals

The energies of the ideal, missing row (MR) and missing column (MC) (1 1 0) surfaces have been calculated by using modified embedded atom method (MEAM) for seven face centered cubic (FCC) transition metals Au, Pt, Ag, Pd, Rh, Cu and Ni. The results, that the MC reconstruction can not be formed for all metals, while the MR reconstruction can be formed naturally for Au and Pt, inductively for Ag, Pd, Rh and Cu and difficultly for Ni, are better than EAM calculated results in comparing with experimental results. In addition to the surface energy explanation, the results are also related to the surface topography and valence electron structure.     

Hydration Free Energies by Energetic Partitioning of the Potential Distribution Theorem

In the quasichemical theory of molecular solutions, the hydration free energy is spatially partitioned in a three-step thermodynamic process: cavity formation, solute insertion into the cavity, and relaxation of the cavity constraint. In the alternative local molecular field theory that focuses on the relationship of fluid structure and forces, the interaction energies are directly partitioned into local and far-field components; a restructured local potential incorporates information from the far-field interactions at the mean-field level. Here the quasichemical and local molecular field theories are related via energetic partitioning of the potential distribution theorem free energy. The resulting theory leads to a free energy division in which the local contribution requires direct evaluation, but the far-field component can be accurately estimated at the Gaussian level. A numerical approach for computing hydration free energies is developed that employs interaction energy distributions from several sampling states. Classical model problems of nonpolar, polar, and ionic hydration are presented to illustrate the theory. Extensions of the theory for estimating free energies at the quantum level are also discussed.     

Angle- and energy-dependent core-level photoelectron energy loss studies in Al and In

Electron energy loss structures of Al and In core-level photoemission spectra, in particular surface and bulk plasmon losses, have been investigated as functions of photon energy (i.e., photoelectron kinetic energy). These studies utilized synchrotron radiation to provide a variable photon source in the ultra-soft X-ray region, thus allowing these loss processes to be studied at photoelectron kinetic energies for which the mean free path of the electrons is minimal. The Al plasmon loss structure was also studied with soft X-ray radiation in an angle-resolved mode, allowing the variation of effective photoelectron sampling depth with different electron take-off (collection) angles. These results for the relative intensity of the bulk and surface plasmons as a function of electron kinetic energy and electron exit angle are in qualitative agreement with the predictions of ?unji? and ?ok?evi?. The core-level binding energies of surface atoms have also been studied with the result that no significant shift has been observed with respect to bulk-atom core levels.     

A reactive force-field (ReaxFF) Monte Carlo study of surface enrichment and step structure on yttria-stabilized zirconia

To investigate surface segregation in yttria-stabilized zirconia (YSZ), DFT energies describing surface energy as a function of yttrium lattice position were used to parameterize a reactive-force field (ReaxFF). We used ReaxFF to perform Monte Carlo (MC) simulated annealing to sample structural configurations of flat YSZ (111) and vicinal YSZ (111) stepped surfaces. We evaluated yttrium surface segregation, oxygen vacancy position, and surface step composition for flat and stepped YSZ surfaces. It is thermodynamically favorable for yttrium atoms to segregate to the surface of YSZ, and specifically to step edge sites. Surface saturation of yttrium occurs at approximately 40% (40:60 Y:Zr ratio) while yttrium concentration at the step edge does not approach a saturation value, suggesting that steps on the YSZ surface are mainly yttria-terminated. We found that it is thermodynamically favorable for oxygen vacancies to occupy positions in the subsurface layer of YSZ, and a higher fraction of vacancies occupy positions NN to Y than NN to Zr. Yttrium segregation to step edges on the YSZ surface does not lower the surface formation energy of the stepped surface below that of the flat (111) termination, suggesting that the stability of YSZ surface steps observed experimentally is due to kinetic barriers for surface re-ordering.     

Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.     

Wetting behaviour of plasma sprayed oxide coatings

Wetting behaviour of several plasma sprayed oxide surfaces were characterised using contact angle measurements. Since surfaces contained pores and cracks, the evaluation of wetting angles led only to rough estimation of surface free energies. In order to find out the effect of atmospheric contamination the wetting behaviour of plasma-etched surfaces was followed as a function of time.It was found out that the sample preparation method had great influence on the contact angle of plasma sprayed oxide surfaces. The contact angle of plasma-etched surfaces increased when the surfaces were exposed to air. The probable reason for that was adsorption of low surface free energy contaminants to the sample surfaces.     

Magnetic and binding properties of metal-divacancy complexes at MgO (0 0 1) surface: DFT calculations

We have analyzed the magnetic and binding properties of Ni, Cr, Mo, and Pt metals deposited on the defect free and defect containing surfaces of MgO by means of density functional theory calculations and embedded cluster model. Clusters of moderate sizes with no border anions, to avoid artificial polarization effects, were embedded in the simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. Spin quenching occurs for Cr and Mo complexes at the defect free (terrace) surface, and Cr, Mo, and Pt complexes at the defect containing “pit” divacancy surface. The binding energies of the metals are significantly enhanced on the cationic vacancy end of the divacancy. The adsorption energies of the low spin states of spin quenched complexes are always greater than those of the high spin states. The metal-support interactions stabilize the low spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. The encountered variations in magnetic properties of free metals and of metal complexes are correlated with the energy gaps of the frontier orbitals. Spin contamination affect the adsorbate-substrate distances, Mulliken charges, Mulliken spin densities, natural charge, natural orbital population, and provide rationalization for the reported magnetic and binding properties. The electrostatic potential energy curves provide clearer understanding of the nature of magnetic and binding interactions. The magnetic and binding properties of a single metal atom adsorbed on a particular surface result from a competition between Hund's rule for the adsorbed metal, and the formation of a chemical bond at the interface.