Guillaume Evrard  Fabien Mareuil  Francois Bontems  Christina Sizun  Javier Perez 《Journal of Applied Crystallography》2011,44(6):1264-1271

DADIMODO is a program for refining atomic models of multidomain proteins or complexes against small‐angle X‐ray scattering data. Interdomain distance and orientational restraints, such as those derived from NMR measurements, can be included in the optimization process. While domain structures are mainly kept rigid, flexible regions can be user defined. Stepwise generic conformational changes, specified by the user, are applied cyclically in a stochastic optimization algorithm that performs a search in the protein conformation space. The convergence for this genetic algorithm is driven by an adaptable selection pressure. The algorithmic structure guarantees that a physically acceptable full atomic model of the structure is present at all stages of the optimization. A graphical user interface ensures user‐friendly handling.  相似文献   

    

Dazhi Liu  Kunlun Hong  Carrie Y. Gao  Yuri Melnichenko  Ken Littrell  Greg Smith  Jinkui Zhao 《Journal of Applied Crystallography》2011,44(5):1120-1122

Initial experimental results are reported from the extended Q‐range small‐angle neutron scattering (EQ‐SANS) diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory (ORNL). A generation‐8 polyamidoamine dendrimer was measured and the conformation parameters (radius of gyration, thickness of the soft shell etc.) extracted by model fitting to the scattering data. The results are compared with data collected at the general‐purpose small‐angle neutron scattering (GP‐SANS) beamline at the High‐Flux Isotopic Reactor at ORNL and show that EQ‐SANS is ready for scientific studies for the small‐angle neutron scattering community.  相似文献   

    

Martin Rosenthal  Denis V. Anokhin  Matthieu Defaux  Giuseppe Portale  Dimitri A. Ivanov 《Journal of Applied Crystallography》2011,44(4):805-811

Small‐angle X‐ray scattering interface distribution function (IDF) analysis is successfully applied to evaluate the two‐ and three‐phase inter‐platelet gallery structure in synthetic montmorillonite (MMT) modified with a mixture of chemically grafted and physically adsorbed chains of a typical organic modifier, octadecyl trimethyl ammonium bromide. Two distinctly different states of adsorbed chains in the inter‐platelet galleries are identified. The first one corresponds to a fully cation‐exchanged structure with an inter‐platelet distance of about 21 Å. In this case the organic modifier is in a liquid‐like state, and the system does not exhibit any structural or thermal transitions between ambient temperature and 433 K. When the number of adsorbed chains exceeds the cation‐exchange capacity of the MMT platelets the inter‐platelet spacing is increased to 43 Å. In this case, the variable‐temperature IDFs reveal partially crystalline order in the inter‐platelet galleries, which vanishes at the melting point of the alkyl tails confined in the galleries.  相似文献   

    

Brian R. Pauw  Martin E. Vigild  Kell Mortensen  Jens W. Andreasen  Enno A. Klop 《Journal of Applied Crystallography》2011,44(6):1297-1299

Determining the effects of stress on the internal structure of high‐performance fibres may provide insight into their structure–property relationships. The deformation of voids inside a poly(p‐phenylene terephthalamide) (PPTA) fibre upon application of stress is one such effect which may be observed using in situ small‐angle X‐ray scattering. For this purpose, a compact in‐vacuum stretching device is described here, capable of applying a force of up to 500 N using specially designed fibre clamps. Furthermore, a small radiative heater is placed around the fibre at the measurement position, so that the effects of the application of heat during tensile load can also be determined. Initial results show a slight but significant effect of stress and heating on the internal void structure of PPTA fibres. The effects on the void structure of heating and stress appear to be markedly different.  相似文献   

    

Shuji Akiyama  Takaaki Hikima 《Journal of Applied Crystallography》2011,44(6):1294-1296

A new octuple cuvette has been developed to reduce the experimental time in small‐angle X‐ray scattering (SAXS). Since each chamber has uniform dimensions, identical scattering curves for bovine serum albumin are obtained within an average deviation of 1%. The cuvette can be used to record SAXS curves for seven sample concentrations quasi‐simultaneously by interchamber subtraction, i.e. calculating the difference in scattering intensity between the sample in any of the first seven chambers and a matching buffer in the eighth chamber. This enables fast acquisition of a data set and its extrapolation to infinite dilution, and increases the throughput of SAXS experiments.  相似文献   

    

Steen Hansen 《Journal of Applied Crystallography》2011,44(2):265-271

The effect of deviation from spherical symmetry is studied for the structure factor. This is done by combining the analytical expression for the excluded volume of an ellipsoid of revolution with the expression for the excluded volume correlation function for a sphere. This approach makes it possible to estimate the effect of small deviations from spherical symmetry as a function of axial ratio and volume fraction for relatively low volume fractions. The calculations are relevant for the case of short‐range potentials where the Percus–Yevick formula is frequently applied, and indicate that even minor deviations from spherical symmetry may lead to significant effects on the structure factor at low scattering angles.  相似文献   

    

Christian M. Schlepütz  Simon O. Mariager  Stephan A. Pauli  Robert Feidenhans'l  Philip R. Willmott 《Journal of Applied Crystallography》2011,44(1):73-83

Angle calculations for a (2+3)‐type diffractometer are presented with comprehensive derivations for both cases of either a vertical or horizontal sample configuration. This work focuses on some particular aspects of using area detectors in surface X‐ray diffraction, namely the role of the detector rotation and the direct conversion of the angle‐resolved diffraction signal recorded by the detector into a two‐dimensional slice through reciprocal space.  相似文献   

    

Hiroki Iwase  Hitoshi Endo  Masaki Katagiri  Mitsuhiro Shibayama 《Journal of Applied Crystallography》2011,44(3):558-568

The small‐angle neutron scattering spectrometer SANS‐U at the research reactor (JRR‐3) of the Japan Atomic Energy Agency, Tokai, Japan, has been successfully upgraded. This major upgrade was undertaken in order to install a high‐resolution position‐sensitive detector consisting of a cross‐wired position‐sensitive photomultiplier tube combined with a ZnS/⁶LiF scintillator on the SANS‐U spectrometer. Without changing the total length of the spectrometer, the aim was to extend the accessible low‐Q limit (Q is the magnitude of the scattering vector) and to shorten the measurement time by employing focusing small‐angle neutron scattering (FSANS). By using both spherical MgF₂ biconcave lenses and the new high‐resolution position‐sensitive detector, the accessible low‐Q limit was extended from 2.5 × 10⁻³ to 3.8 × 10⁻⁴ Å⁻¹. As a result, SANS‐U can continuously cover a wide Q range from 3.8 × 10⁻⁴ to 0.35 Å⁻¹ with a wavelength of 7 Å. FSANS can be utilized not only to improve the accessible low‐Q limit but also to increase the intensity of incident neutrons passing through the sample in the conventional Q range from 2.5 × 10⁻³ to 0.35 Å⁻¹. The use of `high‐intensity' FSANS also allowed a reduction of the measuring time by approximately 1/3.16 by increasing the incident neutron intensity.  相似文献   

    

Xi Wang  Helen A. Hanson  Xinsheng Sean Ling  Charles F. Majkrzak  Brian B. Maranville 《Journal of Applied Crystallography》2011,44(2):414-417

The vortex matter in bulk type II superconductors serves as a prototype system for studying the random pinning problem in condensed matter physics. Since the vortex lattice is embedded in an atomic lattice, small‐angle neutron scattering (SANS) is the only technique that allows for direct structural studies. In traditional SANS methods, the scattering intensity is a measure of the structure factor averaged over the entire sample. Recent studies in vortex physics have shown that it is highly desirable to develop a SANS technique that is capable of resolving the spatial inhomogeneities in the bulk vortex state. This article reports a novel slicing neutron diffraction technique using atypical collimation and an areal detector, which allows for observing the three‐dimensional disorder of the vortex matter inside an as‐grown Nb single crystal.  相似文献   

    

F. Zhang  A. J. Allen  L. E. Levine  J. Ilavsky  G. G. Long  A. R. Sandy 《Journal of Applied Crystallography》2011,44(1):200-212

This paper describes the development of ultra‐small‐angle X‐ray scattering–X‐ray photon correlation spectroscopy (USAXS–XPCS). This technique takes advantage of Bonse–Hart crystal optics and is capable of probing the long‐time‐scale equilibrium and non‐equilibrium dynamics of optically opaque materials with prominent features in a scattering vector range between those of dynamic light scattering and conventional XPCS. Instrumental parameters for optimal coherent‐scattering operation are described. Two examples are offered to illustrate the applicability and capability of USAXS–XPCS. The first example concerns the equilibrium dynamics of colloidal dispersions of polystyrene microspheres in glycerol at 10, 15 and 20% volume concentrations. The temporal intensity autocorrelation analysis shows that the relaxation time of the microspheres decays monotonically as the scattering vector increases. The second example concerns the non‐equilibrium dynamics of a polymer nanocomposite, for which it is demonstrated that USAXS–XPCS can reveal incipient dynamical changes not observable by other techniques.  相似文献