bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Expression of Photosynthesis and Nitrogen Fixation Genes in the Cyanobacterium Plectonema boryanum
Authors: Misra Hari S. , Tuli Rakesh
Published: July 2002

The filamentous non-heterocystous cyanobacterium Plectonema boryanum fixes dinitrogen at a high rate during microaerobic growth in continuous illumination by temporal separation of oxygen-evolving photosynthesis and oxygen-sensitive dinitrogen fixation. The onset of nitrogen fixation is preceded by a depression in photosynthesis that establishes a sufficiently low level of dissolved oxygen in the growth medium. A several-fold reduction in the level of transcripts coding for phycocyanin (cpcBA) and the chlorophyll abinding protein of photosystem II (psbC) andpsbA accompanied the depression in photosynthetic oxygen evolution. Unlike most of the other organisms examined to date, inP. boryanum, psbC and psbD do not appear to be co-transcribed. The psbC transcripts were down-regulated several fold, while the psbD transcript declined marginally during the nitrogen fixation phase. A decrease in dissolved oxygen and a dramatic increase in the level ofnifH transcripts and the enzyme activity of nitrogenase were characteristic of the nitrogen fixation phase. The level of transcript for glnA, which encodes glutamine synthetase, was not altered. Reciprocal regulation of gene expression was well orchestrated with the alternating cycles of photosynthesis and nitrogen fixation in P. boryanum.
Kinetics of Constant Gravitropic Stimulus Responses in Arabidopsis Roots Using a Feedback System,
Authors: Mullen Jack L. , Wolverton Chris , Ishikawa Hideo , Evans Michael L.
Published: July 2002

The study of gravitropism is hindered by the fact that as a root responds, the gravitational stimulus changes. Using a feedback system to connect a rotating stage platform to a video digitizer system, we were able to maintain a constant angle of gravistimulation to Arabidopsis roots for long time periods. The rate of curvature approximated the sine rule for angles of stimulation between 20° and 120°. For a given angle of stimulation, the rate of curvature also remained constant, with no observed diminishment of the response. Although previous reports of Arabidopsis root gravitropism suggest latent periods of approximately 30 min, using a smooth mechanical stage to reorient the root, we observed a mean time lag of approximately 10 min. This more rapid onset of curvature can, in part, be explained by reduced mechanical perturbation during the process of gravistimulation. This suggests that mechanical stimulation associated with rapid root re-orientation may confound investigations of early gravitropic events.
A Glucosinolate Mutant of Arabidopsis Is Thermosensitive and Defective in Cytosolic Hsp90 Expression after Heat Stress
Authors: Ludwig-Müller Jutta , Krishna Priti , Forreiter Christoph
Published: July 2002

The TU8 mutant of Arabidopsis previously described to be deficient in glucosinolate metabolism and pathogen-induced auxin accumulation was found to be remarkably less tolerant upon exposure to elevated temperatures than wild-type plants. Although moderately increased temperature only affected shoot growth, exposure to severe heat stress led to a dramatic decay of mutant plants. By contrast, wild-type seedlings showed little or no damage under the same conditions. Analysis of different heat stress proteins (Hsps) in TU8 seedlings revealed that only expression of cytoplasmic Hsp90 was affected in these plants. Although Hsp90 was present under control conditions, its level declined in mutant plants at elevated temperatures. Northern-blot analysis indicated that the decrease in Hsp90 protein was accompanied with a reduction of hsp90 transcript levels. Transient expression of Hsp90 in mutant protoplasts increased their survival rate at higher temperatures to near equivalent that of wild-type protoplasts. These data suggest that the reduced level of Hsp90 in TU8 mutants may be the primary cause for the observed reduction in thermostability.
Kinetics of Photoacclimation in Response to a Shift to High Light of the Red Alga Rhodella violacea Adapted to Low Irradiance
Authors: Ritz Mathilde , Thomas Jean-Claude , Spilar Agnès , Etienne Anne-Lise
Published: July 2002

The unicellular rhodophyte Rhodella violacea can adapt to a wide range of irradiances. To create a light stress, cells acclimated to low light were transferred to higher irradiance and the kinetics of various changes produced by the light shift were analyzed. The proton gradient generated by excess light led to a non-photochemical quenching of the chlorophyll fluorescence and some photoinhibition of photosystem II centers was also produced by the light stress. After the shift to higher irradiance, the mRNA levels of three chloroplast genes that encode phycoerythrin and phycocyanin apoproteins and heme oxygenase (the first enzyme specific to the bilin synthesis) were negatively regulated. A change in the amount of thylakoids and in the total pigment content of the cells occurred during light acclimation after a light stress. The change in the size of the phycobilisome was limited to dissapearance of the terminal phycoerythrin hexamers in some of the rods. The ability of R. violacea to photoacclimate depends both on large changes in thylakoid number and pigment content and on smaller changes in the antenna size of photosystem II.
Origin of the Cytoplasmic pH Changes during Anaerobic Stress in Higher Plant Cells. Carbon-13 and Phosphorous-31 Nuclear Magnetic Resonance Studies
Authors: Gout Elisabeth , Boisson Anne-Marie , Aubert Serge , Douce Roland , Bligny Richard
Published: July 2002

We tested the contribution of nucleoside triphosphate (NTP) hydrolysis, ethanol, and organic acid syntheses, and H+-pump ATPases activity in the acidosis of anoxic sycamore (Acer pseudoplatanus) plant cells. Culture cells were chosen to alter NTP pools and fermentation with specific nutrient media (phosphate [Pi]-deprived and adenine- or glycerol-supplied). In vivo 31P- and 13C-nuclear magnetic resonance (NMR) spectroscopy was utilized to noninvasively measure intracellular pHs, Pi, phosphomonoesters, nucleotides, lactate, and ethanol. Following the onset of anoxia, cytoplasmic (cyt) pH (7.5) decreased to 6.8 within 4 to 5 min, whereas vacuolar pH (5.7) and external pH (6.5) remained stable. The NTP pool simultaneously decreased from 210 to <20 nmol g−1 cell wet weight, whereas nuceloside diphosphate, nucleoside monophosphate, and cyt pH increased correspondingly. The initial cytoplasmic acidification was at a minimum in Pi-deprived cells containing little NTP, and at a maximum in adenine-incubated cells showing the highest NTP concentration. Our data show that the release of H+ ions accompanying the Pi-liberating hydrolysis of NTP was the principal cause of the initial cyt pH drop and that this cytoplasmic acidosis was not overcome by H+ extrusion. After 15 min of anoxia, a partial cyt-pH recovery observed in cells supplied with Glc, but not with glycerol, was attributed to the H+-consuming ATP synthesis accompanying ethanolic fermentation. Following re-oxygenation, the cyt pH recovered its initial value (7.5) within 2 to 3 min, whereas external pH decreased abruptly. We suggest that the H+-pumping ATPase located in the plasma membrane was blocked in anoxia and quickly reactivated after re-oxygenation.
Analysis of thermal-treatment-induced dislocation bundles in GaAs wafers by means of X-ray transmission topography and complementary methods
Authors: Möck P.
Published: July 2002

By means of a heat treatment that was part of a molecular beam epitaxy (MBE) growth procedure, dislocation bundles have been induced in two-inch-diameter undoped (001) GaAs substrates. On the basis of contrast variations in synchrotron-based single-crystal X-ray transmission topograms that were recorded under conditions of high anomalous transmission, these dislocation bundles have been classified into three different types. Dislocation bundles of the majority type start at the sample edges in regions around the four 〈100〉 peripheral areas, glide typically up to about 1.5 cm into the bulk of the wafer following perpendicular 〈110〉 line directions, and form a pseudo-symmetric fourfold set. There are dislocations with two different Burgers vectors in each majority-type dislocation bundle and the extended segments of all of these dislocations are of the 60° type. In order to explain complementary experimental results, it is suggested that dislocation pairs are formed in the majority-type dislocation bundles. Theoretical support for this hypothesis is derived from a model of plastic deformation of GaAs wafers during typical MBE growth. Dislocation bundles of two minority types, on the other hand, are not part of the fourfold set and originate in peripheral areas at and around 〈110〉.
Shape of precipitates in Ni-Al-Mo single crystals
Authors: Schneider J.-M. , Schönfeld B. , Demé B. , Kostorz G.
Published: July 2002

A method is presented to determine the shape of the average precipitate from anisotropic small-angle scattering patterns from single crystalline alloys during decomposition. The form factor squared of an average precipitate is described by an analytical expression with a single parameter, the morphology parameter α, to account for changes from spherical to cuboidal shape. The method is applied to microstructural states of Ni-12 at.% Al-2 at.% Mo and Ni10 at.% Al-5 at.% Mo after aging treatments of up to 10 h at 970 or 1070 K. The value of α increases with aging time and smaller Mo content, in good agreement with the average shape of precipitates obtained from transmission electron microscopy.
The determination of site occupancies using a new strategy in Rietveld refinements
Authors: Heuer M.
Published: July 2002

Using X-ray data, the determination of the cation distribution in crystals becomes problematic as a result of parameter correlations in the structure refinements. To circumvent the problem, a new refinement strategy (LOT analysis) was proposed by Krollet al.[Eur. J. Mineral.(1997), pp. 705–734] and successfully applied to X-ray single-crystal data. The purpose of the study reported here was to determine if the LOT method can also be used in Rietveld refinements. Model calculations in the form of refinements on calculated powder diffraction data were carried out to check the conditions required for a successful application of the LOT method. As a further test, the Fe2+, Mg2+distributions obtained from refinements on single-crystal and powder data of a natural olivine were compared. Model calculations and refinements show an improvement in the determination of the site occupancy factors when the LOT strategy is used. Their standard uncertainties are reduced from about σ(X) ≃ ±0.02 to σ(X) = ±0.004 for powder data.
Microstructural transformation of vanadium pentoxide powder obtained by high-energy vibrational ball-milling
Authors: Chatterjee Partha , Sen Gupta S. P. , Sen Suchitra
Published: July 2002

An X-ray powder profile analysis of vanadium pentoxide powder milled in a high-energy vibrational ball-mill is presented. The strain- and size-induced broadening of the Bragg reflection for two different crystallographic directions ([001] and [100]) were determined by Warren–Averbach (WA) analysis, using a pattern-decomposition method assuming a pseudo-Voigt function. The deformation process causes a decrease in the domain size, and a near isotropic saturation value of ∼10 nm is reached after severe milling. The initial stages of milling produce a propensity for size broadening, whereas, with increasing milling time, microstrain broadening is predominant. WA analysis indicated significant plastic strain along with spatial confinement of the internal strain fields, probably in the crystallite interfaces. Transmission electron microscopy revealed a drastic change in particle shape after 64 h of milling, indicating the existence of size anisotropy which, however, decreased with further increase of the milling time.
Background estimation using a robust Bayesian analysis
Authors: David W. I. F. , Sivia D. S.
Published: July 2002

A novel method for the estimation of the background in a powder diffraction pattern has been developed using a robust Bayesian analysis. In formulating a probabilistic approach to background fitting, the diffraction peaks are considered to be nuisance data that must be taken into account. The underlying probability theory is discussed in terms of going beyond the Gaussian approximation normally associated with counting statistics and least-squares analysis. Various examples are presented that illustrate the general applicability of this approach.
Interpretation of the optical rotatory dispersion in tellurium
Authors: Vyšín Ivo , Sváčková Kamila , Říha Jan
Published: July 2002

An interpretation of the most recent experimental data on the optical rotatory dispersion of tellurium is presented. The experimental data are approximated by theoretical equations which were derived using the model of three coupled oscillators. The applied mathematical method is based on the sum of least squares. The derived equations are also helpful when modelling the circular dichroism of tellurium and discussing the sense of the rotation of the linear polarized light with regard to the crystal structure.
TheComputational Crystallography Toolbox: crystallographic algorithms in a reusable software framework
Authors: Grosse-Kunstleve Ralf W. , Sauter Nicholas K. , Moriarty Nigel W. , Adams Paul D.
Published: July 2002

The advent of structural genomics initiatives has led to a pressing need for high-throughput macromolecular structure determination. To accomplish this, new methods and inevitably new software must be developed to accelerate the process of structure solution. To minimize duplication of effort and to generate maintainable code efficiently, a toolbox of basic crystallographic software components is required. The development of theComputational Crystallography Toolbox(cctbx) has been undertaken for this purpose. In this paper, the fundamental requirements for thecctbxare outlined and the decisions that have lead to its implementation are explained. Thecctbxcurrently contains algorithms for the handling of unit cells, space groups and atomic scatterers, and is released under an Open Source license to allow unrestricted use and continued development. It will be developed further to become a comprehensive library of crystallographic tools useful to the entire community of software developers.
Simultaneous determination of specimen temperature and specimen displacement in high-temperature X-ray diffractometry applying Bragg–Brentano geometry
Authors: Beck M. , Mittemeijer E. J.
Published: July 2002

Temperature uncertainty and unknown specimen displacement are the most severe errors in high-temperature X-ray diffractometry, in particular when using a strip heater mounted on a Bragg–Brentano goniometer. A method is presented that enables the simultaneous determination of the specimen displacement and the temperature of the sample. The method splits the determination of the aberrations into two steps: at room temperature and at elevated temperature. It is based on the use of a reference material as an internal standard. An experimental example applying the method to a specific material is given, and shows that the method provides correct data.
Thermal expansion and atomic displacement parameters of cubic KMgF3perovskite determined by high-resolution neutron powder diffraction
Authors: Wood I. G. , Knight K. S. , Price G. D. , Stuart J. A.
Published: July 2002

The structure of KMgF3has been determined by high-resolution neutron powder diffraction at 4.2 K, room temperature and at 10 K intervals from 373 K to 1223 K. The material remains cubic at all temperatures. The average volumetric coefficient of thermal expansion in the range 373–1223 K was found to be 7.11 (3) × 10−5 K−1. For temperatures between 4.2 and 1223 K, a second-order Grüneisen approximation to the zero-pressure equation of state, with the internal energy calculatedviaa Debye model, was found to fit well, with the following parameters: θD= 536 (9) K,Vo= 62.876 (6) Å3, K_{o}^{\,\prime} = 6.5 (1) and (VoKo/γ′) = 3.40 (2) × 10−18 J, where θDis the Debye temperature,Vois the volume atT= 0, K_{o}^{\,\prime} is the first derivative with respect to pressure of the incompressibility (Ko) and γ′ is a Grüneisen parameter. The atomic displacement parameters were found to increase smoothly withTand could be fitted using Debye models with θDin the range 305–581 K. At 1223 K, the displacement of the F ions was found to be much less anisotropic than that in NaMgF3at this temperature.
X-ray diffraction study of a one-dimensional GaAs–AlAs superlattice
Authors: Segmüller A. , Krishna P. , Esaki L.
Published: July 2002

Low- and high-angle X-ray diffraction patterns have been obtained from one-dimensional superlattice crystals prepared artificially by alternately depositing predetermined thicknesses of GaAs and AlAs, on the (001) face of a GaAs single-crystal by molecular-beam epitaxy. The positions and intensities of several superlattice reflections obtained along the 00l, 11l and 02l reciprocal lattice rows have been recorded. The structure of the superlattice can be approximated by a model which incorporates elastic strains in the unit cell due to the lattice mismatch between GaAs and AlAs. The number of Ga and Al layers in the superlattice unit cell can be accurately determined from the low-angle scattering data while the relative intensities of the high-angle superlattice reflections are a sensitive measure of the elastic strain present in the lattice. It is shown that the elastic strain agrees with the value computed theoretically on the assumption that the strain is not relieved by dislocations at the GaAs–AlAs interfaces.
Crystal data for β-Ga2Se3
Authors: Khan M. Y. , Ali S. Z.
Published: July 2002

The structure of the ordered form of the partially ordered cubic: α-Ga2Se3 is based on a tetragonal, body-centred cell, with space group I41/acd, a = 23.235 (5), c = 10.828 (2) Å, Z = 48, Dm
= 4.91 g cm−3 at 30°C. Diffractometer data up to θ ~ 80° from Cu Kα radiation are given for the β phase with nominal composition Ga2Se3.03.
X-ray topography of natural beryl using synchrotron and conventional sources
Authors: Herres N. , Lang A. R.
Published: July 2002

Continuous-spectrum synchrotron-radiation Laue transmission topographs of natural beryl have been compared with the corresponding projection topographs taken with conventional apparatus and Cu Kα
1 and Mo Kα
1 radiations in an analysis of configurations of grown-in lattice defects and of the diffraction contrast they produce. The natural defects studied included grown-in dislocations, impurity zoning and fault surfaces. A growth-sector map was constructed for the (0001) specimen slice examined. Differences of contrast among the various reflections appearing on the synchrotron-radiation topographs are discussed and it is demonstrated that the contrast characteristics of the synchrotron-radiation images which consist of a superimposition of 3{\bar 2\bar 1}1 and 6{\bar 4 \bar 2}2 reflections can be satisfactorily synthesized by a weighted superimposition of the 3{\bar 21}1 image recorded with Cu Kα
1 and the 6{\bar 4\bar 2}2 with Mo Kα
1. Synchrotron-radiation damage to the crystal manifested itself on the X-ray topographs both as area contrast and as contrast at the periphery of the irradiated area, yet no visual absorption or birefringence due to this damage was detected. Annealing at 770 K for 3 h completely removed the contrast due to radiation damage.
Twyman–Green interferometry for semi-quantitative analysis of homogeneity and nonlinearity of a mixing crystal
Authors: Schow F. L. , Riazi A. , Gandhi O. P. , Grow R. W.
Published: July 2002

Application of Twyman–Green interferometry is extended to achieve semi-quantitative assessment of optical qualities of a nonlinear crystal. Interferograms of a proustite crystal are analyzed and effects of crystal imperfections on the conversion efficiency of a parametric upconversion system are evaluated.
Routine recording of diffuse scattering from disordered molecular crystals
Authors: Welberry T. R.
Published: July 2002

We describe the use of conventional Weissenberg equipment to record in a routine manner the diffuse scattering from disordered molecular crystals. The diffuse image is digitized using an Optronics P1700 scanner and is corrected for background and other errors before subsequent rewriting as an undistorted reciprocal-lattice section in a form suitable for easy interpretation. The resolution of the method is discussed.
Reciprocal-lattice-compatible representation of linear position-sensitive detector output
Authors: McL Mathieson A.
Published: July 2002

For the X-ray case relating to a small crystal and not involving a monochromator, the (Δω, Δ2θ) intensity array for a Bragg reflection, derived from use of a linear position-sensitive detector and arranged as for an ω/θ scan, can be relatively simply scaled to correspond with the distribution around a reciprocal-lattice point in the plane of diffraction.
Enhancement of the `auto-indexing' method for cell determination in four-circle diffractometry
Authors: Clegg W.
Published: July 2002

Enhancements in the auto-indexing procedure for cell determination improve its power and reliability. A proper selection of three basis reflections for construction of an initial subcell is essential. A standard cell-reduction procedure applied to the subcell, and the calculation of appropriate limits for the direct-lattice-vector generation integers, make a comprehensive coverage of the direct space efficient and effective. Refinement of the generated lattice vectors against all the available reflection data makes assignment of the correct unit cell easier and more reliable. Generation of some additional long vectors is recommended in special cases.
Crystal data for 7HgI2Fe(C5H5)2
Authors: Votinský J. , Beneš L. , Klikorka J. , Kalousová J. , Horák J. , Lošťák P.
Published: July 2002

The new compound 7HgI2.Fe(C5H5)2 was prepared by the reaction of solid tetragonal mercuric iodide with ferrocene vapours at 423 K. The product is a dark green powder, stable in air, and decomposes at 463 K. The cubic unit-cell parameters (298 K) are: a = 20.12(2) Å, V = 8157.3 Å3, Z = 8, Mr
= 3366.8, Dx
= 5.49 Mg m−3; extinctions indicate a face-centered space group. X-ray (Cu Kα radiation) powder diffraction data (50 lines) are reported. The compound has interesting electrical properties. The JCPDS Diffraction File No. for 7HgI2.Fe(C5H5)2 is 35-2000.
Characterization of alumina powder using multiple small-angle neutron scattering. II. Experiment
Authors: Hardman-Rhyne K. A. , Berk N. F.
Published: July 2002

Small-angle neutron scattering techniques developed in the preceding paper [Berk & Hardman-Rhyne (1985). J. Appl. Cryst.
18, 467–472] are used to obtain microstructural parameters of high-purity alumina powder. The values of the particle size, volume fraction and surface area have been obtained and are compared to data from techniques such as laser light scattering, X-ray sedigraph and scanning electron microscopy. The particles exhibit a log–normal distribution and are spherical in shape with a mean particle size of 342 nm determined from SANS analyses of both beam broadening and Porod regions.
Coupled neutron – γ-ray diffraction: a method for accurate measurement of strains. Application to the study of the ferroelectric phase transition of KH2PO4
Authors: Bastie P. , Troussaut F. , Vallade M. , Zeyen C. M. E.
Published: July 2002

A method that employs simultaneous neutron and γ-ray diffraction techniques is proposed for accurate measurements of strains with or without an applied electric field (0–100 kV m−1). Instead of an absolute determination of the position of the neutron Bragg peak, a relative measurement of the neutron and γ peak positions is used and allows a determination of the lattice-parameter changes with an accuracy of within 2 × 10−6. This technique avoids systematic errors originating in sample rotations by taking advantage of a reference directly related to the crystal lattice. The method appears to be particularly important for crystals that exhibit structural phase transitions, as demonstrated by the measurement of the strain Uxx
in KH2PO4 crystals as a function of temperature and applied electric field. In this case the errors would amount to ±20%. The results demonstrate the need to re-examine the theory previously proposed by Uesu, Tanaka & Kobayashi [Ferroelectrics (1974), 7, 247–249] to interpret the electromechanical properties of KH2PO4.
The probabilistic determination of intensities of completely overlapping reflections in powder diffraction patterns
Authors: David W. I. F.
Published: July 2002

Two techniques are presented for the extraction of the individual intensities of completely overlapping reflections in a powder diffraction pattern. The first is analogous to Sayre's [Acta Cryst. (1952). 5, 60–65] squaring method while the second is based upon maximizing the entropy of the Patterson function subject to the constraints imposed by the observed intensities of single and overlapping groups of reflections. Although both methods are superior to a simple equipartition of intensities amongst overlapping reflections, the maximum-entropy (ME) technique is the more robust and scientifically justifiable. The ME Patterson map extracts the maximum amount of information from the available observed intensities and is thus optimal for Patterson-technique structure determination from powder diffraction patterns. The agreement between true |F|2 values of overlapping reflections and the values obtained by maximum entropy is, in most simulated cases, excellent.
The structure of Pt particles on γ-Al2O3 support
Authors: Pan M. , Cowley J. M. , Chan I. Y.
Published: July 2002

Samples of the catalyst Pt/γ-Al2O3 have been examined by high-resolution transmission electron microscopy (HRTEM), scanning transmission electron microscopy (STEM) and microdiffraction techniques. An epitaxic relationship of metallic Pt crystals on the γ-Al2O3 has been established. In both calcined and reduced samples, the crystalline oxide α-PtO2 was found along with metallic Pt. The oxide has a hexagonal lattice with unit-cell dimensions about 6% smaller than those previously reported. Microdiffraction from areas less than 20 Å in diameter, combined with HRTEM, STEM and secondary electron microscopy (SEM), has proved to be a very powerful technique for the study of the structures of particles less than 50 Å in size.
IMAGE, an interactive computer program for the visualization of molecular structures
Authors: Nayl C. , Lazzerini L. , Pierrot M.
Published: July 2002

An interactive program for creating and displaying molecular models on an inexpensive hardware system of medium performance is described. IMAGE is capable of (i) facilitating examination and interpretation of electron density maps and (ii) the depiction and manipulation of the covalent representation of molecules. IMAGE is written in Fortran 77 and is running on a PDP 11/44 under RSX 11 M version 4.1. The graphics screen is a DEC VT 125 and the plotter is a Tektronix 4662.
An automated full-symmetry Patterson search method
Authors: Rius J. , Miravitlles C.
Published: July 2002

A full-symmetry Patterson search method is presented that performs a molecular coarse rotation search in vector space and orientation refinement using the σ function. The oriented molecule is positioned using the fast translation function τ
0, which is based on the automated interpretation of τ projections using the sum function. This strategy reduces the number of Patterson-function values to be stored in the rotation search, and the use of the τ
0 function minimizes the required time for the development of all probable rotation search solutions. The application of this method to five representative test examples is shown.
Application of optimization to powder-pattern indexing
Authors: Paszkowicz W.
Published: July 2002

The optimization method of indexing powder diffraction patterns based on minimizing the suitable criterion function within a required range of unit-cell parameters is presented. The features of the method are discussed. A computer program is described which performs the optimization in two steps: systematic search and Powell method. The results are refined by the least-squares method. The actual version indexes patterns of orthorhombic or higher symmetry.
Incorporation of fast Fourier transforms to speed restrained least-squares refinement of protein structures
Authors: Finzel B. C.
Published: July 2002

Modifications to the restrained least-squares refinement program of Hendrickson & Konnert [Biomolecular Structure, Function, Conformation, and Evolution, edited by R. Srinivasan, pp. 43–57 (1980). Oxford: Pergamon Press] are described that result in dramatic acceleration of the refinement of protein structures. Proven fast-Fourier-transform-based algorithms for computing structure factors and least-squares matrix elements are incorporated that reduce up to a hundredfold the computation time required for a single cycle. The modified program is shown to give results comparable to refinement by conventional methods and has been successfully applied to the refinement of several protein crystal structures.
A small-angle X-ray camera using a two-dimensional multiwire proportional chamber
Authors: Furuno T. , Sasabe H. , Ikegami A.
Published: July 2002

The construction and performance of a small-angle X-ray camera equipped with a two-dimensional multiwire proportional chamber (two-dimensional MWPC) are described. The system has been used for studies of the structure of biological samples with a conventional rotating-anode X-ray source. The small-angle camera is of Franks type with two orthogonal platinum-coated bent optical flats placed in a helium-tight box. The specimen-to-detector distance is variable between 60 and 260 cm. The sensitive area of the two-dimensional MWPC is 256 × 256 mm with 256 × 256 resolution elements. The camera covers high angles up to about 5 Å, although diffraction line widths in this region are highly broadened owing to parallax. The electronic system comprises NIM modules, a hand-made module and a commercially available compact two-dimensional multichannel analyser (two-dimensional MCA). The two-dimensional MCA has a memory size of 256 × 256 channels (24 bits/channel). The estimated dead time of this system is approximately 5 μs, which permits a maximum count rate of 20 kHz at 10% loss. Diffraction patterns of a Langmuir–Blodgett film of arachidic acid and stacked purple membranes and a solution scattering of horse spleen apoferritin are demonstrated as examples.
Asymmetric X-ray line broadening of plastically deformed crystals. II. Evaluation procedure and application to [001]-Cu crystals
Authors: Ungár T. , Groma I. , Wilkens M.
Published: July 2002

In paper I [Groma, Ungár & Wilkens (1988). J. Appl. Cryst.
21, 47–53] a theory was developed to interpret the asymmetric X-ray line broadening of plastically deformed crystals. It was shown that the dislocation structure can be described by five distinct parameters, namely the dislocation density, the mean quadratic spatial fluctuation of the dislocation density, the effective outer cut-off radius, the dipole polarization and the spatial fluctuation of the dipole polarization of the dislocation structure. In this paper a procedure is developed to evaluate these parameters from the Fourier transform of the line profiles. The theory and this procedure are tested by applying it to the asymmetric line profiles of tensile-deformed Cu single crystals orientated for ideal multiple slip. The asymmetry of these profiles is assigned to the dipole polarization of the dislocation cell structure and is directly correlated to residual long-range internal stresses. It is shown that the data can be interpreted in terms of the quasi-composite model of the dislocation cell structure developed earlier for the same material.
Temperature dependence of spontaneous strain in ferroelastic thallous nitrate
Authors: Somayazulu M. S. , Wadhawan V. K.
Published: July 2002

TlNO3 is a ferroelastic crystal belonging to the orthorhombic Aizu species m3mFmmm(ss) at room temperature. Lattice-parameter measurements by X-ray powder diffraction at various temperatures are reported for this crystal. Spontaneous-strain components are calculated from the lattice parameters. The spontaneous strain has a large magnitude of 7.80 x 10−2 at room temperature. Its two components are found to be rather insensitive to change of temperature. This may be due in part to the improper nature of this ferroelastic. Anomalies indicating either new isomorphous phase transitions or crossover behaviour are observed at 309, 329 and 399 K. Between 352 and 416 K the crystal belongs to the rhombohedral Aizu species m3mF3. The critical exponent of the spontaneous strain for the rhombohedral phase is found to change from 0.72 (3) to 0.60 (5) at 399 K.
A high-pressure study of Ti3O5 by X-ray diffraction and synchrotron radiation. 1. Pressures up to 38.6 GPa
Authors: Åsbrink S. , Gerward L. , Olsen J. S.
Published: July 2002

High-pressure X-ray diffraction studies have been performed on powder samples of β-Ti3O5 (C2/m) for pressures up to 38.6 GPa using synchrotron radiation and a diamond-anvil cell. The compressibility is highly anisotropic. Thus, the compression Δl/l
0 for the maximum pressure investigated is 5.4, 0.8 and 6.7% for the unit-cell axis directions a, b and c, respectively. The anisotropy is reasonable, considering the crystal structure. The bulk modulus B
0, determined from the Murnaghan equation, is 173(10) GPa and B′0 is 7(1).
An X-ray monochromator system using successive reflection and its application to measurements of diffraction curves of annealed GaAs wafers
Authors: Fukumori T. , Futagami K.
Published: July 2002

To measure local lattice deformation on crystal surfaces, a monolithic monochromator system for Mo Kα
1 radiation was designed which uses successive 444 and 022 reflections from an Si crystal. The angular spread of the monochromated beam is 1.7′′ and the wavelength spread (Δλ/λ) is 1.9 × 10−5. The system has been applied to precise measurement of the Bragg-case diffraction curve from Ge and GaAs crystals with a triple-crystal arrangement. The percentage reflection and half-width of the diffraction curve at various points on semi-insulating GaAs wafers were measured before and after annealing at 1123 K, with the results that annealing processes are found to be very effective for improving the quality of the crystal.
Crystallization of low-molecular-weight organic compounds for X-ray crystallography
Authors: van der Sluis P. , Hezemans A. M. F. , Kroon J.
Published: July 2002

General strategies are described to obtain crystals of low-molecular-weight compounds suitable for X-ray structure determination. A survey is given of a variety of crystallization techniques together with their advantages and drawbacks, illustrated by experiences with notoriously crystallization-resisting compounds. The methods discussed range from preliminary investigations using evaporation, batch crystallization and liquid–liquid diffusion methods, via the most frequently used methods such as sitting-drop vapor-phase diffusion and change of temperature, to methods such as gel crystallization, sublimation and solidification. The most successful method appears to be the sitting-drop vapor-phase diffusion. Complete crystallization routes are described, taking into account the results of preliminary investigations. The hard-to-crystallize vecuronium bromide is presented as a case study.
Approximation of pole figures for the determination of crystal orientation in polymeric solids
Authors: Sajkiewicz P. , Wasiak A.
Published: July 2002

The approximation of experimentally measured angular intensity distributions of X-rays diffracted by oriented polycrystalline specimens is suggested as a method for the determination of orientation distribution characteristics for uniaxially oriented polymeric fibres. A non-linear optimization program based on a Hook–Jeeves algorithm is elaborated and incorporated into the method. As an example, the interpretation of the data from polyethylene specimens having various degrees of orientation is given. An important application of the method is the analysis of distributions (pole figures) using a superposition of two identical or similar functions with different parameters.
ABSCOR: a scaling and absorption correction program for the FAST area detector diffractometer
Authors: Messerschmidt A. , Schneider M. , Huber R.
Published: July 2002

A Fortran computer program is described which carries out scaling and absorption corrections and a post-correction of the non-uniformity of response of the detector for FAST area detector diffractometer data. The program runs under the VMS operating system.
Profile agreement indices in Rietveld and pattern-fitting analysis
Authors: Hill R. J. , Fischer R. X.
Published: July 2002

Two definitions of profile agreement indices are now in common use for estimating the degree of fit in Rietveld refinement and in structure-independent pattern-fitting methods of powder diffraction analysis. In the original program written by Rietveld, the background was subtracted and the `non-peak' regions of the pattern were removed from further consideration in a preliminary data-reduction stage prior to Structure refinement. However, the agreement indices used in many of the more recent programs retain the background counts in the observed step intensities and include all portions of the pattern in the sums. These latter definitions are strongly dependent on the signal-to-noise ratio and on the relative amount of `background-only' regions and do not, therefore, provide a sound basis for comparing the degree of fit of peak profile and crystal structure model refinements in the general case. The extent of this dependence is illustrated quantitatively using conventional and synchrotron X-ray and constant-wavelength and time-of-flight neutron data sets with different inherent background levels and peak densities. The unweighted background-corrected peak-only profile agreement index R′
p
= Σ
i
|Y

io
− Y
ic|/Σ
i
|Y

io
−Y

ib
| (and, to a lesser extent, its weighted equivalent) is recommended as the most appropriate criterion of fit for comparative work between diffraction patterns of all kinds.
Model-independent determination of the surface scattering-length-density profile from specular reflectivity data
Authors: Pedersen J. S.
Published: July 2002

An approach for analysing neutron and X-ray specular reflectivity data from stratified media having variation in the scattering-length density near the surface is described. The method has its origin in small-angle scattering and it is composed of two steps: (i) indirect Fourier transformation [Glatter (1977). J. Appl. Cryst.
10, 415–421] giving the profile correlation function p(z) of the derivative dρ/dz of the scattering-length density; (ii) square-root deconvolution [Glatter (1981). J. Appl. Cryst.
14, 101–108] giving dρ/dz and ρ, the scattering-length-density profile. The only requirement for applying the method is that the scattering-length density varies only in a limited range. In nearly all cases the approach does not require any knowledge of the chemical composition of the surface layer and consequently incorporates a certain degree of objectivity. The method gives the smoothest profile which agrees with the experimental reflectivity data. The method is tested on simulated reflectivity data for a series of different surface profiles and subsequently used for analysing experimental data on fluorocarbon amphiphiles in water and salt solutions. The tests on simulated data show that the indirect Fourier transformation gives correlation functions agreeing very well with the corresponding functions of the original profiles. It is further demonstrated that the square-root deconvolution gives reliable results for the scattering-length-density profiles.
A High-Resolution Multiple-Crystal Monochromator for X-ray Diffraction Studies
Authors: Giannini C. , Tapfer L.
Published: July 2002

This work proposes a new four-crystal monochromator particularly indicated for applications in the field of high-resolution X-ray diffraction. The monochromator is made of two monolithic crystal elements. The first one is a channel-cut crystal consisting of two symmetrically cut components set in a parallel nondispersive geometry. The second monolithic crystal is composed of two crystal components in a parallel nondispersive geometry but the crystal surfaces are miscut with respect to the diffraction planes. The diffraction geometry for both components of the second monochromator crystal element is the glancing-incidence condition. The peculiar properties of this monochromator are investigated theoretically. An appropriate rotation of the second component of the second monolithic block with respect to the first components corrects the beam deviation caused by the refraction effect. This monochromator system may allow one to obtain highly monochromated and collimated beams with high angular resolution (about 0.01 mrad) and wavelength dispersion of about 4 × 10−5. The intensity reduction of the proposed crystal arrangement in comparison with other monochromators is discussed, including wavelength spread and beam size increase.
Diffraction elastic constants of a cubic polycrystal
Authors: de Wit R.
Published: July 2002

New expressions for the diffraction elastic constants are presented for a cubic polycrystal that is statistically homogeneous, isotropic and disordered. The results are an extension of the theory of statistical continuum mechanics and differ from a previous derivation given by Bollenrath, Hauk, & Müller [Z Metallkde (1967), 58, 76–82].
Defect Structure of Ion-Irradiated Amorphous SiO2
Authors: Eyal Y. , Evron R. , Cohen Y.
Published: July 2002

Uniformly enhanced small-angle X-ray scattering intensities of amorphous SiO2, measured following irradiation with 320 keV H+ and He+ beams, are shown to be correlated, irrespective of the incident ion, with the O and Si cumulative displacement yields. Damage by both beams originated primarily from nuclear stopping but, under H+-ion irradiation, contributions from ionization processes were significant as well. At low beam fluences, the irradiated structure is compatible with the presence of stable radiation-induced interstitial-like O and Si atoms and complementary O and Si vacancy-like sites. There is no evidence for recovery near room temperature of the modified structure to the pre-irradiated state or for formation of colloidal-size scattering centers, such as gas bubbles or voids. Thus, ion-irradiation-induced changes in physical and chemical properties of silica seem to be due to the effect of the preserved primary atomic displacement damage.
Performance of a New Small-Angle Neutron Scattering Instrument at the Malaysian TRIGA Reactor
Authors: Sufi M. A. M. , Radiman S. , Wiedenmann A. , Mortensen K.
Published: July 2002

The set-up and alignment of a new small-angle neutron scattering (SANS) instrument, installed at the 1 MW light-water-moderated MINT TRIGA research reactor, are described. The wavelength distribution and the flux at the sample position have been determined. First neutron scattering measurements were made on two reference samples with strong scattering power; the results prove that the SANS signal is well reproduced on the instrument when samples of typical size are used, despite the high level of the background of fast and epithermal neutrons.
Carbamyl Phosphate Modifies the T Quaternary Structure of Aspartate Transcarbamylase, thereby Facilitating the Structural Transition Associated with Cooperativity
Authors: Fetler L. , Tauc P. , Vachette P.
Published: July 2002

The allosteric enzyme aspartate transcarbamylase from Escherichia coli (ATCase) displays regulatory properties that involve various conformational changes, including a large quaternary structure rearrangement. This entails a major change in its solution X-ray scattering curve upon binding substrate analogues, thereby providing a direct means to monitor the amount of different quaternary structures present in solution. Scattering curves in the presence of variable concentrations of several such substrate analogues were recorded using an area detector. Data were analyzed by singular-value decomposition without any prior assumption as to the number of quaternary structure states. They can all be accounted for with only two states. The structural transition appears to be concerted, a conclusion whose validity has been extended to higher resolution and to other combinations of ligands than previously studied using a linear detector. The titration curve with the bisubstrate analogue N-(phosphonacetyl)-l-aspartate (PALA) alone is identical to that previously obtained, while that in the additional presence of carbamyl phosphate (CP) shows a clear R shift. However, the scattering pattern of the ATCase–CP complex is shown to be different from the T pattern of the unligated enzyme, though not a linear combination of the Tand R patterns. Therefore, we conclude that CP acts by modifying the quaternary structure of the unligated enzyme to a T-like structure, a structure more easily converted to the R conformation by subsequent addition of PALA.
Speckle Structure in Small-Angle Coherent X-ray Scattering
Authors: Mainville J. , Bley F. , Livet F. , Geissler E. , Legrand J. F. , Abernathy D. , Grübel G. , Mochrie S. G. J. , Sutton M.
Published: July 2002

Small-angle coherent X-ray scattering measurements on a polymer gel and on a single crystal of Al–9at.% Li are reported. Speckle structures were recorded using a direct-illumination CCD camera. A speckle intensity fluctuation of ~20% was observed. Time and space statistics for the signal provided estimates of the coherence effects and the measurements demonstrate the wavevector dependence of the coherence effects. Preliminary intensity-fluctuation spectroscopy was performed for Al–Li.
The design and implementation ofSnBversion 2.0
Authors: Weeks Charles M. , Miller Russ
Published: July 2002

SnBis a direct-methods program based on theShake-and-Bakemethodology. It has been used to solve difficult or large structures that could not be solved by traditional reciprocal-space routines based on the tangent formula. Recently, it has also been used to determine the Se sites in large selenomethionyl-substituted proteins.SnBversion 1.5 has been available for several years and is being used regularly in many laboratories. In this paper, we introduceSnBversion 2.0, which incorporates a graphical user interface written in Java, a dynamic histogram display, and an interactive Java/VRML-based visualization facility. In addition, it provides the user with several utility routines and a variety of new algorithmic options.
Effect of pressure on phase transitions in K1−xNaxMnF3(x = 0.04)
Authors: Åsbrink S. , Waśkowska A. , Krane H. G. , Gerward L. , Olsen J. Staun
Published: July 2002

The pressure-induced phase transition sequence in the title compound, potassium sodium fluoromanganate, has been investigated by single-crystal X-ray diffraction using synchrotron radiation and a diamond anvil pressure cell. Na^+ ions at 4% of the K^+ sites shift the ferrodistortive phase transition to the lower pressure P_{c1} of 2.75 (5) GPa compared to 3.12 GPa in the parent compound KMnF3. The transition is illustrated by the critical behaviour of the unit-cell dimensions, the pressure-dependent evolution of the MnF_6 ^- octahedral rotation and related macroscopic spontaneous strain. As far as precision of the present experiment allows, the observations show that the 4% of Na^+ admixture at the K^+ sites does not substantially change the nature of the transition at P_{c1}. The main effect of pressure is to stabilize the tetragonal phase II. The expected further evolution of the MnF_6 ^- octahedral tiltings, leading to the orthorhombic and monoclinic phases, has not been observed up to 8.33 GPa.