Computational methods for the structural alignment of molecules

In drug design, often enough, no structural information on a particular receptor protein is available. However, frequently a considerable number of different ligands is known together with their measured binding affinities towards a receptor under consideration. In such a situation, a set of plausible relative superpositions of different ligands, hopefully approximating their putative binding geometry, is usually the method of choice for preparing data for the subsequent application of 3D methods that analyze the similarity or diversity of the ligands. Examples are 3D-QSAR studies, pharmacophore elucidation, and receptor modeling. An aggravating fact is that ligands are usually quite flexible and a rigorous analysis has to incorporate molecular flexibility. We review the past six years of scientific publishing on molecular superposition. Our focus lies on automatic procedures to be performed on arbitrary molecular structures. Methodical aspects are our main concern here. Accordingly, plain application studies with few methodical elements are omitted in this presentation. While this review cannot mention every contribution to this actively developing field, we intend to provide pointers to the recent literature providing important contributions to computational methods for the structural alignment of molecules. Finally we provide a perspective on how superposition methods can effectively be used for the purpose of virtual database screening. In our opinion it is the ultimate goal to detect analogues in structure databases of nontrivial size in order to narrow down the search space for subsequent experiments.     

Evidence of red cell alignment in the magnetic field of an NMR spectrometer based on the diffusion tensor of water

The alignment of human erythrocytes in aqueous suspensions in the magnetic field B(0) (called the z-direction) of an NMR spectrometer was shown by calculating the diffusion tensor for water in the sample. The diffusion was measured using a pulsed-field-gradient spin-echo NMR method. The extent of diffusion anisotropy for water was exemplified by the values of the apparent diffusion coefficients with erythrocytes of normal shape and volume: for a typical experiment the values for the x-, y-, and z-directions were (6.88 +/- 0.17) x 10(-10), (7.07 +/- 0.17) x 10(-10), and (10.20 +/- 0.17) x 10(-10) m(2) s(-1), respectively. Cells in hypo- and hyperosmotic media were also studied and they too showed the anisotropy of the apparent diffusion coefficients but the extents were different. A new method of data analysis was developed using the Standard Add-On Packages in a Mathematica program. The experimental findings support evidence of erythrocyte alignment that was previously obtained with a high-field-gradient q-space method.     

大型Schmidt望远镜光学系统调整方法

安装于紫金山天文台盱眙观测站用以观测近地天体的大型Schmidt望远镜,采用了平场Schmidt光学系统,改正镜通光口径为1m,球面反射镜口径为1.2m,焦距为1.8m,接收器用了4K×4K的高灵敏度CCD。本文叙述了该仪器光轴调整的方法及调整后观测获得的初步结果。叙述了望远镜光轴校正方法、校正结果、CCD靶面的调整及望远镜极轴高度、方位的调整及相应的照片。经实际观测的结果是:露光1s可拍到18等星;露光4s可拍到19.3等星;露光20s可拍摄到21.2等星。     

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用火花预电离辅助介质阻挡放电装置在大气压空气中实现了均匀的类辉光放电。通过用光谱模拟法和波尔兹曼图解法对N 2 第一负带系B2Σ→X 2Σ(0,0)带发射谱线的分析,对放电过程中N 2 的转动温度进行了诊断。研究了不同频率和放电模式下转动温度的变化规律,对由两种方法计算所得的温度进行了对比。实验结果表明,转动温度会随着外加频率的增加而缓慢的增加;当放电从类辉光模式变到丝状放电模式时,转动温度会有70K左右的升高。     

Development of rotational CARS for combustion diagnostics using a polarization approach

Rotational Coherent anti-Stokes Raman spectroscopy (CARS) has the last decades been developed into a useful tool for thermometry and concentration measurements in combustion. In this paper, we present a novel polarization approach of the technique, which will enhance its potential and widen the range of conditions at which it can be utilized. The theory of the polarization approach is described in detail. It is shown that by specific arrangement of the polarizations of the laser beams, total suppression of the non-resonant background signal can be obtained, and thus by probing only the resonant CARS signal the diagnostic utility of the technique increases. The main benefit of the approach is in situations where the non-resonant background signal is relatively high in comparison with the resonant signal. The high potential of polarization rotational CARS for thermometry is demonstrated in some illustrative examples, for example, nitrogen thermometry on the fuel side of diffusion flames, and carbon monoxide thermometry in the product gas of ethylene/oxygen/argon-flames.     

The millimeter wave rotational spectrum of pyruvic acid

The rotational spectrum of pyruvic acid has been investigated for the first time in the millimeter-wave region, at 160-314 GHz, and also in supersonic expansion, at 10-17.4 GHz. The analysis of the broadband spectra recorded in this work was carried out with the newly developed AABS software package for Assignment and Analysis of Broadband Spectra, and precise spectroscopic constants are reported for the ground state, the first excited state of the low-frequency skeletal torsional mode ν₂₄, and the first excited state of the methyl torsional mode ν₂₃. Limited results have also been obtained for several higher excited states. The dataset for the ground state currently exceeds 1500 lines and for both the A and E internal rotor sublevels spans the complete range of values of K_a at the mid values of J for the measured transitions. The results were analysed with three freely available computer programs employing different strategies for dealing with internal rotation and a comparative discussion of their merits is made.     

Microwave spectroscopy of furfural in vibrationally excited states

The results of microwave spectrum investigation of the excited vibrational states of furfural in the frequency range between 49 and 149 GHz are reported. In total 15 excited vibrational states (9 for trans-furfural and 6 for cis-furfural) were assigned and analyzed. Six of the 15 investigated states were assigned for the first time. Accurate values of rigid rotor and quartic centrifugal distortion constants of asymmetric top Hamiltonian have been determined for 13 excited states. Also for some states several sextic and octic level constants were needed in order to fit the data within experimental accuracy. The v_t = 3 and v_s = 1, v_a = 1 states of trans-furfural were found to be strongly perturbed and only rotational transitions with low K_a values can be reliably identified in this study.     

Synthesis and nonlinear optical properties of novel Y‐type polyester containing tricyanovinylthiazolylazoresorcinoxy group with enhanced thermal stability of dipole alignment

Novel Y‐type polyester 4 containing 5‐methyl‐4‐{5‐(1,2,2‐tricyanovinyl)‐2‐thiazolylazo}resorcinoxy groups as nonlinear optical (NLO) chromophores, which are parts of the polymer backbone, was prepared, and its NLO properties were investigated. Polyester 4 is soluble in common organic solvents such as N,N‐dimethylformamide and dimethylsulfoxide. Polymer 4 shows a thermal stability up to 250 °C from thermogravimetric analysis with glass‐transition temperature obtained from differential scanning calorimetry of approximately 94 °C. The second harmonic generation (SHG) coefficient (d₃₃) of poled polymer film at 1560‐nm fundamental wavelength is 8.12 × 10^?9 esu. The dipole alignment exhibits a thermal stability even at 6 °C higher than glass‐transition temperature (T_g), and no significant SHG decay is observed below 100 °C due to the partial main‐chain character of polymer structure, which is acceptable for NLO device applications. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Modular Breath Analyzer (MBA): Introduction of a Breath Analyzer Platform Based on an Innovative and Unique,Modular eNose Concept for Breath Diagnostics and Utilization of Calibration Transfer Methods in Breath Analysis Studies

Exhaled breath analysis for early disease detection may provide a convenient method for painless and non-invasive diagnosis. In this work, a novel, compact and easy-to-use breath analyzer platform with a modular sensing chamber and direct breath sampling unit is presented. The developed analyzer system comprises a compact, low volume, temperature-controlled sensing chamber in three modules that can host any type of resistive gas sensor arrays. Furthermore, in this study three modular breath analyzers are explicitly tested for reproducibility in a real-life breath analysis experiment with several calibration transfer (CT) techniques using transfer samples from the experiment. The experiment consists of classifying breath samples from 15 subjects before and after eating a specific meal using three instruments. We investigate the possibility to transfer calibration models across instruments using transfer samples from the experiment under study, since representative samples of human breath at some conditions are difficult to simulate in a laboratory. For example, exhaled breath from subjects suffering from a disease for which the biomarkers are mostly unknown. Results show that many transfer samples of all the classes under study (in our case meal/no meal) are needed, although some CT methods present reasonably good results with only one class.     

Rotational invariance in the three-dimensional lattice Boltzmann method is dependent on the choice of lattice

The lattice Boltzmann method has recently gained popularity as a tool for simulating complex fluid flows. It uses discrete sets of velocity vectors, or lattices, to create a reduced model of the molecular dynamics of a continuum fluid. While several lattices are believed to behave isotropically, there are reports of qualitatively incorrect results. However, thus far, the reason as to why a lack of isotropy occurs is not known. Based on the hypothesis that lower order lattices may not display rotational invariance, this study tests the isotropy of the D3Q15, D3Q19 and D3Q27 lattices by performing simulations at intermediate Reynolds numbers (50–500) and low Knudsen number (<0.0005) in an axisymmetrical geometry with a nozzle leading to a throat followed by a sudden expansion. The symmetry properties of the results were examined. It was found that at Re ? 250 the D3Q15 and D3Q19 lattices produced different results depending on the plane of the lattice with which the flow was aligned. Lattice planes with fewer than six velocity vectors consistently produced results which were qualitatively different from the planes with six or more velocity vectors. These errors were not observed at Re = 50 or when a D3Q27 lattice was used. They appeared to be independent of grid density, collision operator and Ma. This suggests that the lattices which contain these planes are not fully isotropic and therefore do not properly replicate the behavior of a real fluid in this particular situation, notably downstream from the expansion. Predictions made using these models in more complex geometries may therefore be affected by the orientation of the lattice. When using LBM in CFD simulation (including validation) this study highlights the need for caution to ensure that the solution obtained is independent of the lattice orientation throughout the domain.