Megavariate Analysis of Environmental QSAR Data. Part II – Investigating Very Complex Problem Formulations Using Hierarchical, Non-Linear and Batch-Wise Extensions of PCA and PLS

Summary Three extensions of the basic PCA and PLS methodologies are described. These extensions are hierarchical, non-linear and batch-based in nature. The objectives of these methods are to assist in problem understanding and problem solving in very complex (QSAR) problem formulations. The method extensions are illustrated using two example QSAR data sets containing many X- and Y-variables.     

Effects of pressure on structural,electronic, and mechanical properties of α,β,and γ uranium

The first-principles methods have been employed to calculate the structural, electronic, and mechanical properties of the α, β, and γ phases of uranium under pressure up to 100 GPa. The electronic structure has been viewed in forms of density of states and band structure. The mechanical stability of metal U in the α, β, and γ phases have been examined.The independent elastic constants, polycrystalline elastic moduli, as well as Poisson's ratio have been obtained. Upon compression, the elastic constants, elastic moduli, elastic wave velocities, and Debye temperature of α phase are enhanced pronouncedly. The value of B/G illustrates that α and γ phases are brittle in ground state.     

Toward the computer-aided discovery of FabH inhibitors. Do predictive QSAR models ensure high quality virtual screening performance?

Antibiotic resistance has increased over the past two decades. New approaches for the discovery of novel antibacterials are required and innovative strategies will be necessary to identify novel and effective candidates. Related to this problem, the exploration of bacterial targets that remain unexploited by the current antibiotics in clinical use is required. One of such targets is the \(\beta \) -ketoacyl-acyl carrier protein synthase III (FabH). Here, we report a ligand-based modeling methodology for the virtual-screening of large collections of chemical compounds in the search of potential FabH inhibitors. QSAR models are developed for a diverse dataset of 296 FabH inhibitors using an in-house modeling framework. All models showed high fitting, robustness, and generalization capabilities. We further investigated the performance of the developed models in a virtual screening scenario. To carry out this investigation, we implemented a desirability-based algorithm for decoys selection that was shown effective in the selection of high quality decoys sets. Once the QSAR models were validated in the context of a virtual screening experiment their limitations arise. For this reason, we explored the potential of ensemble modeling to overcome the limitations associated to the use of single classifiers. Through a detailed evaluation of the virtual screening performance of ensemble models it was evidenced, for the first time to our knowledge, the benefits of this approach in a virtual screening scenario. From all the obtained results, we could arrive to a significant main conclusion: at least for FabH inhibitors, virtual screening performance is not guaranteed by predictive QSAR models.     

Features of Calculation of the Equation of State,Composition, and Conductivity for a Plasma of Dense,Supercritical Metal Vapors—a Plasma Fluid

Journal of Experimental and Theoretical Physics - The caloric and thermal equations of state, composition, and conductivity have been calculated for a supercritical aluminum plasma fluid. A...     

Nanoscale PhysiCs ＆ Devlces Laboratory , nstitute of Physics, Chinese Academy of Sciences

概况 中国科学院物理研究所纳米物理与器件实验室的前身是中国科学院北京真空物理开放实验室,成立于1985年。二十多年来,实验室在科研工作中取得了一系列具有国际先进水平和国际领先水平的成果。目前实验室有四个研究组构成,实验室的运作特色是加强各研究组之间的交叉合作,发挥集体智慧,     

Nanoscale Physics ＆ Devices Laboratory,Institute of Physics,Chinese Academy of Sciences

Brief History Formerly known as Beijing Vacuum Physics Laboratory of Chinese Academy of Sciences since 1985, Nanoscale Physics ＆ Devices Laboratory （NPDL） was established in 2001. The mission of NPDL is to construct and study nanomaterials that address the challenges presented bythe national research strategy. For more than 20 years, NPDL has been dedicated to the study of fundamental physics related to nanomaterials and their applications in information and energy devices.     

Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong

在近代量子力学的图像中，环绕着原子与分子的电子云具有各种不同的形态结构，一般在某一测定时间内，其形状为球状或哑铃状．这类形状通常称为电子轨道，它们可在飞秒量级的时间内明显地观测到．这些电子轨道也可在简并态(具有相同能量的量子态)间相互跃迁；如在相同轴上由垂直哑铃转变为水平哑铃等．     

First-principles calculation of the structural,electronic, elastic,and optical properties of sulfur-doping ε-GaSe crystal

The structural,electronic,mechanical properties,and frequency-dependent refractive indexes of GaSe_(1-x)S_x(x=0,0.25,and 1) are studied by using the first-principles pseudopotential method within density functional theory.The calculated results demonstrate the relationships between intralayer structure and elastic modulus in GaSe_(1-x)S_x(x=0,0.25,and 1).Doping of ε-GaSe with S strengthens the Ga-X bonds and increases its elastic moduli of C_(11) and C_(66).Born effective charge analysis provides an explanation for the modification of cleavage properties about the doping of e-GaSe with S.The calculated results of band gaps suggest that the distance between intralayer atom and substitution of S_(Se),rather than interlayer force,is a key factor influencing the electronic exciton energy of the layer semiconductor.The calculated refractive indexes indicate that the doping of ε-GaSe with S reduces its refractive index and increases its birefringence.     

三维全息原子场作用矢量用于苦味二肽QSAR研究

本文利用三维全息原子场作用矢量(3D-Ho VAIF)对苦味二肽分子结构进行表征,并利用逐步回归结合多元线性回归建立苦味二肽定量构效关系模型,同时采用内外部双重验证的方法检验模型的稳定性.所建模型相关统计参量如下:复相关系数(R_(cum)~2)、留一法(LOO)交互验证相关系数(R_(cv)~2)、外部样本验证相关系数(Q_(ext)~2)和均方根误差(RMSE)分别为0.983、0.934、0.876和0.145.结果表明,3D-VAIF能较好地表征苦味二肽结构,优于传统的氨基酸描述子.为强活性肽类药物分子设计和改造提供指导.     

Assignment of Photoelectron Spectra of MC2 （M= V, Cr, Fe, and Co）

Hybrid density functional theory （DFT） calculations are performed to study MC2 （M= V, Cr, Fe and Co） clusters in the neutral and anionic charge states. We find that the equilibrium geometries of MC2 and their anions are all cyclic structures with C2v symmetry, which agrees well with the previous theoretical studies. The Mulliken charge and spin populations of MC2 clusters and their anions are also calculated, and it is found that the electron charge transformations from anions to neutral molecules mainly take place on the M atoms. Time-dependent DFT is used to calculate the excited states, and a theoretical assignment for the features in the experimental photoelectron spectrum is given, which are in good agreement with the available experimental data.     

Synthesis,Characterization of 9, 9＇-Bianthracene and Fabrication of 9, 9＇-Bianthracene Field-Effect Transistors

We synthesize and purify 9, 9＇-bianthracene with the purity up to 96.4%. The electronic and crystallographic structures of 9, 9＇-bianthracene are studied. The results of a joint experimental investigation based on a combination of x-ray diffraction （XRD） spectra, hydrogen nuclear magnetic （HNMR） spectra, infrared absorption （FT-IR） spectra, and mass spectra （MS） of 9, 9＇-bianthracene are obtained. The uniform compact film is observed by an atomic-force microscope （AFM）. Organic field effect transistors （OFETs） with an active layer based on the synthesized 9, 9＇-bianthracene are fabricated for the first time. Its field-effect mobility is as large as 0.067 cm^2 /（V·s） and the on/off ratio is above 5 ×10^4. The result demonstrates that the oligomerization of a small semiconductor molecule is an effective method to develop high-mobility organic semiconductors.     

Study of Hard-sealed,Tunable,Photoelastic Birefringent Dual-frequency Lasers

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Reconstruction of all-electron orbitals from one-electron pseudowave functions and calculations of the intensities of Si X-ray emission spectra of Si, β-SiC,stishovite, and β-cristobalite crystals

The intensities of Si X-ray emission spectra of Si, β-SiC, stishovite, and β-cristobalite crystals are calculated. The wave functions of the initial and final states are obtained in the framework of the density-functional theory with the use of the norm-conserving and ultrasoft pseudopotentials. The all-electron crystal orbitals are reconstructed from the one-electron pseudowave functions. The probabilities of X-ray emission transitions are calculated by reconstructing the all-electron orbitals in two different gauges, namely, the length and velocity gauges. The calculated intensities are compared with the experimental spectra and the partial densities of states.     

Application of the multireference equation of motion coupled cluster method,including spin–orbit coupling,to the atomic spectra of Cr,Mn, Fe and Co

The recently introduced multireference equation of motion (MR-EOM) approach is combined with a simple treatment of spin–orbit coupling, as implemented in the ORCA program. The resulting multireference equation of motion spin–orbit coupling (MR-EOM-SOC) approach is applied to the first-row transition metal atoms Cr, Mn, Fe and Co, for which experimental data are readily available. Using the MR-EOM-SOC approach, the splittings in each L-S multiplet can be accurately assessed (root mean square (RMS) errors of about 70 cm^?1). The RMS errors for J-specific excitation energies range from 414 to 783 cm^?1 and are comparable to previously reported J-averaged MR-EOM results using the ACESII program. The MR-EOM approach is highly efficient. A typical MR-EOM calculation of a full spin–orbit spectrum takes about 2 CPU hours on a single processor of a 12-core node, consisting of Intel XEON 2.93 GHz CPUs with 12.3 MB of shared cache memory.     

Analysis of the common characteristics of the Hartmann,Ronchi, and Shack–Hartmann tests

An overview of the settings of the planes for the filters and observed patterns in the Hartmann and Ronchi tests is presented. Also a new set of filters for both test were developed. In a similar way, it is easy to extend this analysis to the Shack–Hartmann test, and to propose a new Null Shack–Hartmann filter.     

Quantitative estimates of the content of the metastable Si-XII,Si-III,and α-Si phases of silicon in the areas of indenter impressions

A quantitative estimate is presented of the specific and total volumes of the metastable Si-XII, Si-III, and α-Si phases of silicon in a locally strained (Berkovich pyramid) area. Calculations are performed using experimental data obtained via Raman spectroscopy and in situ registration of the Si-I → Si-II phase transitions of silicon under the indenter.