Structural basis for the mechanism of inhibition of uridine phosphorylase from <Emphasis Type="Italic">Salmonella typhimurium</Emphasis>

The three-dimensional structures of three complexes of Salmonella typhimurium uridine phosphorylase with the inhibitor 2,2′-anhydrouridine, the substrate PO₄, and with both the inhibitor 2,2′-anhydrouridine and the substrate PO₄ (a binary complex) were studied in detail by X-ray diffraction. The structures of the complexes were refined at 2.38, 1.5, and 1.75 Å resolution, respectively. Changes in the three-dimensional structure of the subunits in different crystal structures are considered depending on the presence or absence of the inhibitor molecule and (or) the phosphate ion in the active site of the enzyme. The presence of the phosphate ion in the phosphate-binding site was found to substantially change the orientations of the side chains of the amino-acid residues Arg30, Arg91, and Arg48 coordinated to this ion. A comparison showed that the highly flexible loop L9 is unstable. The atomic coordinates of the refined structures of the complexes and the corresponding structure factors were deposited in the Protein Data Bank (their PDB ID codes are 3DD0 and 3C74). The experimental data on the spatial reorganization of the active site caused by changes in its functional state from the unligated to the completely inhibited state suggest the structural basis for the mechanism of inhibition of Salmonella typhimurium uridine phosphorylase.     

Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from <Emphasis Type="Italic">Salmonella typhimurium</Emphasis> in the unligated state and in a complex with potassium ion

The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 Å resolution to R _work = 16.1% and R _free = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 Å, 1.042°, and 0.071°, respectively. The coordinate error estimated by the Luzzati plot is 0.166 Å. The coordinate error based on the maximum likelihood is 0.199 Å. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure of the homodimer St UPh in the complex with a K⁺ ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).     

Perspective fields of application of texture topography and further development of its apparatus

The applications of a new X-ray topography method designed for investigations of polycrystalline samples are closely related to reasons of different X-ray reflectivity from point to point in the surface of the specimen. The discussion of these relationships is followed by suggestions for an apparatus. The most simple one is based on the principle of the “camera obscura” locating the diaphragm of the camera at the place where a diffracted beam is focussed either according to the focussing principle of Guinier or according to Bragg-Brentano, respectively.     

Neutron scattering studies of the structure of a highly tetrahedral form of amorphous carbon

The structure of amorphous carbon prepared by plasma-arc deposition has been determined by neutron scattering and analysed to estimate the fraction of tetrahedrally and trigonally bonded carbon. The mean value of the nearest neighbour C-C distance is close to that of crystalline diamond and a fit to the data for the first interatomic distance gives about 86% tetrahedral bonding. This form of diamond-like carbon therefore appears to be the structural equivalent of a-Si and a-Ge. A somewhat different interpretation is obtained from an analysis of the measured first and second peak coordination numbers and an attempt is made to reconcile the two approaches.     

The influence of crystallization conditions on the onset of dendritic growth of calcium carbonate

Understanding the crystallization of calcium carbonate is relevant in numerous fields like biomineralization, geology and industrial applications where calcium carbonate forms. In order to enhance the knowledge about the formation of calcium carbonate with focus on the vaterite polymorph, in this work calcium carbonate has been crystallized in aqueous solutions at temperatures from 5 °C to 90 °C. Special attention has been directed to higher temperatures for which the effect of the initial supersaturation on the resulting crystal morphologies and the onset of dendritic growth have been studied. In analogy to snow crystal formation, it has been found that in a certain temperature range hexagonal plate‐like crystals form at low supersaturation whereas dendritic patterns start to appear at higher supersaturation. The symmetrical branches characteristic for dendritic growth get less pronounced as the temperature is decreased. The results reported here related to the interdependence between supersaturation, crystal morphology and growth mechanisms, can be used in future works to predict particle formation and to design crystal architectures. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Determination of light-scattering properties of glass surfaces

Glass surfaces were damaged in a defined manner by sandblasting with an adjustable sand blasting machine and subsequent etching with HF. Investigations with the scanning electron microscope (SEM) showed surface defects with an ellipsoidal shape. A quantitative evaluation of the exact profile of these defects was made using mathematical evaluation of stereographic pairs. A new method is described for characterizing surfaces with optical light scattering. In contrast to the usual method of a fixed specimen and a photocell moving on a circle around it, here the specimen revolves on an axis perpendicular to a laser beam and rotates on an axis parallel to it in order to average the scattering over a large area of the surface, thus preventing interferences of the coherent laser beam with surface defects. A theory is described which enables a numerical estimation of roughness parameters using a distribution function of angles of small mirrors to the average surface. In this special case the theory was extended for the special type of defects having an ellipsoidal shape. The results are discussed with respect to creation of surface defects by sandblasting, which are accompanied by subsurface cracks.     

Investigation of the effect of coefficient of thermal expansion on prediction of refractive index of thermally formed glass lenses using FEM simulation

During the cooling phase of thermal forming processes, the properties of glass undergo minor changes. These changes are a result of structural relaxation near the glass transition region. One such property, refractive index, is the most important material property that governs the optical performance of a glass lens. Therefore, it must be properly considered prior to manufacturing. A finite element model is established in this research to simulate structural relaxation behavior of glass during cooling. This is done in order to accurately predict the refractive index change which occurs during and after the forming process. This study shows that the success of the simulation model depends largely on the accuracy of material information available to the lens manufacturers. Specifically, the comparison between simulated and experimental data demonstrates that the published information for the generic coefficient of thermal expansion is inadequate for precisely predicting volume change. To resolve the issue, a reverse calculation method was presented. In addition, simulated finite element results showed that the value of the liquid coefficient of thermal expansion has a major effect on the simulated results, as compared to fraction parameter.     

Evidence of hopping of charge carriers in the clustered state of manganites

The electrical resistivity and magnetization measurements as a function of both temperature and magnetic field provide clear evidence for three temperature intervals in which the magnetic and transport properties are altered in the La_0.55Y_0.15Ca_0.3MnO₃ compound. The intermediated-T regime, called clustered state, involves the presence of both ferromagnetic and paramagnetic phases and is shown to be closely related to the colossal magnetoresistivity effect. An extra hopping conducting process is proposed to exist in this clustered state. We use both the Abeles’ model and microstructural parameters to estimate the hopping activation energy between ferromagnetic clusters. The size (density) temperature dependence and the shape of the ferromagnetic metallic clusters are revealed to play a major role in the clustered state of this manganite.     

Application of seeded batch crystallization methods for reduction of the scaling tendency of seawater – A study of growth kinetics of calcium carbonate in seawater

The objective of this study is to evaluate the applicability of a seeded batch crystallization method as a pre‐treatment stage to the reduction of the the scaling potential of seawater. The crystallization process of calcium carbonate in supersaturated seawater is studied experimentally in a seeded batch crystallizer. Results show that the initial pH value of seawater must be adjusted to be in the range of 8‐9. Calcite seeds will not have the potential to start the growth process in seawater at he the normal pH (7.36) compared to the above mentioned range. The growth kinetic parameters are determined from the measured desupersaturation curves. It is found that the growth process of calcite is controlled by surface integration step. The growth rate of calcite increases with increasing temperature and seeding ratio (up to 1 g/L), while it decreases with increasing the salinity of seawater. Crystals of calcite morphology are found to be growing faster than seeds of aragonite morphology. Stirrer speed has no distinct effect on the growth rate of calcite in seawater. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Numerical simulation of the LEC-growth of GaAs crystals with account of high-pressure gas convection

The influence of the inert gas pressure on the growth of 4 GaAs crystals by the liquid encapsulated Czochralski method (LEC) process is studied for a range of the Ar gas pressure up to 10 bar by using our finite-volume computer code STHAMAS. Up to the pressure of 0.6 bar we are considering laminar convection. For the pressure range from 5 to 10 bar we are using the buoyancy extended standard k-ε turbulence model with wall functions to simulate the gas flow. The numerical results show that the Argon gas pressure has a strong influence on the consumption of heater power in qualitative agreement with our experimental results. The convex curvature of the growth interface and the maximum thermal stress (von Mises criterion) are found to increase with increasing gas pressure both in the laminar and turbulent evaluations.     

A SAXS study of kinetics of aggregation of silica sols

SAXS in situ experiments on the evolution of TMOS solutions during hydrolysis and polycondensation lead to power laws with scaling exponents ≈ 2. It is suggested that this could be the result of the polydispersity of the samples and that only an apparent fractal dimension can be obtained in this way. Kinetic studies tend to indicate that agglomeration in the sol is the result of a diffusion-controlled process.     

Correlation of the basic parameters of unidirectional solidification of the Pb-Sn eutectic

General conditions of the unidirectional solidification are used to control the process of Pb-Sn eutectic solidification as well as to predict the desirable values of λ deciding about the physical properties of a final product.     

On the Theory of Reducing the Level of Statistical Noise and Filtering of 2D Images of Diffraction Tomography

Crystallography Reports - According to the diffraction tomography data, the efficiency of minimization algorithms used to reconstruct the displacement field of a defect in a crystal depends on the...     

稀释气体对CVD-SiC纤维性能的影响

在自行设计制造的直流电阻加热CVD装置上制备SiC纤维,研究了CH3SiHCl2-CH3SiCl3-H2-Ar体系中在W芯表面化学气相沉积SiC涂层工艺,考察了稀释气体Ar气含量对化学气相沉积SiC涂层的显微结构的影响。并对涂层表面形貌及成分进行了SEM,XRD分析。结果表明:Ar气不但起到了输送气体源,排出废气、增大流量、使反应室中前后端的反应气体比例尽量保持一致的作用,还一个重要原因是可以很好的平衡空间的温度差。当稀释气体的含量达到25%时,纤维的性能最好。     

Structure of the Nematic Phase of Pbaba

X-ray diffraction investigations of the nematic phase (191°C - 276°C) of p-n-propyloxybenzylidene-p-amino benzoic acid have shown that this phase is a skewed cybotactic nematic phase. The diffraction patterns, obtained with aligned samples, reveal an additional surprising structural feature, - the presence of one dimensional molecular correlation in a direction parallel to the nematic director. At 192°C, it is found that the molecular unit, thus correlated, is about 37 Å in length (dimer length) and the correlation range extends up to about seven such units. This l-d correlation persists up to the N-I transition.     

Effects of inertia of dislocations on the probability of unpinning by ultrasound

The paper is concerned with theoretical models of dislocation segments fixed at their ends to local obstacles of either the same or two different types. The dislocation inertial properties are shown to influence substantially the probability of unpinning from the local obstacles as the crystal is subjected to ultrasonic oscillations. The unpinning probability in the presence of oscillations can be much higher than that with a constant load of the same magnitude. In the case of two types of obstacles, the weaker can play a “provocative” role facilitating unpinning of dislocations from the stronger obstacles. The considered effects constitute admittedly one of microscopic mechanisms of the plasticizing and “softening” action of ultrasound.     

On the 70th anniversary of the Shubnikov Institute of Crystallography of the Russian Academy of Sciences

We are celebrating the 70th anniversary of the Shubnikov Institute of Crystallography. The institute has gone from being a small laboratory of piezoelectric crystals to a large internationally known scientific center. The 1990s was a decade of ruin, both literally and figuratively, for our institute; however, it is hard to believe that was the case when walking through the corridors of the institute today.     

Mesomorphism Dependence on the Position of Substitution of a Pair of Esters

A novel homologous series of ethylene derivatives of thermotropic liquid crystals has been synthesized. The methoxy to octyloxy derivatives are nematogenic, the decyloxy to tetradecyloxy derivatives are smectogenic, in addition to nematogenic, and the hexadecyloxy homologue is smectogenic only. All the members of the series are enantiotropically mesogenic. Thermotropic behavior was determined by an optical polarizing microscope equipped with a heating stage and Differential Scanning Calorimetry (DSC) study. Analytical and spectral data confirm the molecular structures of homologues (infrared, nuclear magnetic resonance, mass spectra, X-ray, and DSC data). Textures of the nematic phase are threaded or Schlieren and that of smectic phase are focal conic fan-shaped of smectic A or C. Transition curves of the phase diagram behave in a normal manner except one or two deviations from the normal trend. The mesophase range (Sm+N) varies from 3°C to 44°C. The average thermal stability for smectic is 93°C and that for nematic 117.4°C. The LC behavior of the novel series is compared with a structurally similar known series.     

Influence of low-temperature thermocycling on anisotropy of the structural state of commercial purity Beryllium

The influence of low-temperature cycling (300 ← 77 K) on the anisotropy of commerical purity beryllium structural state, obtained by uniaxial hot extrusion has been studied by means of X-ray method. In initial samples the anisotropy of structural state is shown by the preferential orientation of grains relative to extraction axis. Two types of experiments were carried out Two types of samples were investigated the samples cut out along and across the extrusion axis. It was shown that cycling in the samples oriented across the extrusion axis led to essential change in initial structural state due to intense twinning. Considerable changes in structures of the samples oriented along the extrusion axis were not observed. The effects are intensified by load application. Thermocycling leads to considerable decrease in grain size (form about 50 μm in initial state to about 30 μm after cycling) and decrease in structural state anisotropy. Nature of the phenomena found is discussed.     

Atomistic examinations of the solid-phase epitaxial growth of silicon

The low-temperature vapor deposition of silicon thin films and the ion implantation of silicon can result in the formation of amorphous silicon layers on a crystalline silicon substrate. These amorphous layers can be crystallized by a thermally activated solid-phase epitaxial (SPE) growth process. The transformations are rapid and initiate at the buried amorphous to crystalline interface within the film. The initial stages of the transformation are investigated here using a molecular dynamics simulation approach based upon a recently proposed bond order potential for silicon. The method is used first to predict an amorphous structure for a rapidly cooled silicon melt. The radial distribution function of this structure is shown to be similar to that observed experimentally. Molecular dynamics simulations of its subsequent crystallization indicate that the early stage, rate limiting mechanism appears to be removal of tetrahedrally coordinated interstitial defects in the nominally crystalline region just behind the advancing amorphous to crystalline transition front. The activation barriers for this interstitials migration within the bulk crystal lattice are calculated and are found to be comparable to the activation energy of the overall solid-phase epitaxial growth process simulated here.