The Experts below are selected from a list of 25422 Experts worldwide ranked by ideXlab platform
Zuoguang Ye - One of the best experts on this subject based on the ideXlab platform.
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origin of Diffuse Scattering in relaxor ferroelectrics
Physical Review B, 2010Co-Authors: Panchapakesan Ganesh, Eric Cockayne, Muhtar Ahart, R E Cohen, Benjamin P Burton, Russell J Hemley, Wenge Yang, Zuoguang YeAbstract:High-pressure and variable temperature single-crystal synchrotron x-ray measurements combined with first principles based molecular-dynamics simulations were used to study Diffuse Scattering in the relaxor ferroelectric system ${\text{PbSc}}_{1/2}{\text{Nb}}_{1/2}{\text{O}}_{3}$. Constant temperature experiments show a pressure-induced transition to the relaxor phase, in which butterfly- and rod-shaped Diffuse Scattering occurs around the {h00} and {hh0} Bragg spots. Simulations qualitatively reproduce the observed Diffuse Scattering features as well as their pressure-temperature behavior and show that they arise from polarization correlations between chemically ordered regions, which in previous simulations were shown to behave as polar nanoregions. Simulations also exhibit radial Diffuse Scattering [elongated toward and away from $\mathbf{Q}=(000)$] that persists even in the paraelectric phase; consistent with previous neutron experiments on ${\text{PbMg}}_{1/3}{\text{Nb}}_{2/3}{\text{O}}_{3}$.
J S Fraser - One of the best experts on this subject based on the ideXlab platform.
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predicting x ray Diffuse Scattering from translation libration screw structural ensembles
Acta Crystallographica Section D-biological Crystallography, 2015Co-Authors: Andrew H Van Benschoten, Pavel V Afonine, Thomas C Terwilliger, Michael E Wall, Colin J Jackson, Nicholas K Sauter, Paul D Adams, Alexandre Urzhumtsev, J S FraserAbstract:Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray Scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure Diffuse Scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.Diffuse, addresses this need by employing Guinier's equation to calculate Diffuse Scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.Diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of Diffuse Scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar Diffuse Scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray Diffuse Scattering could extend macromolecular structural refinement, validation and analysis.
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predicting x ray Diffuse Scattering from translation libration screw structural ensembles
bioRxiv, 2015Co-Authors: Andrew H Van Benschoten, Pavel V Afonine, Thomas C Terwilliger, Michael E Wall, Colin J Jackson, Nicholas K Sauter, Paul D Adams, Alexandre Urzhumtsev, J S FraserAbstract:Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. While Bragg diffraction describes the average positional distribution of crystalline atoms, many different models can fit this distribution equally well. Diffuse X-ray Scattering can reduce this degeneracy by directly reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure Diffuse Scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.Diffuse, addresses this need by employing Guinier’s equation to calculate Diffuse Scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.Diffuse is applied to Translation-Libration-Screw (TLS) refinement, which models rigid body displacement for segments of the macromolecule. To enable calculation of Diffuse Scattering from TLS refined structures, phenix.tls_models builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS group partitioning and different motional correlations between groups yield markedly dissimilar Diffuse Scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how X-ray Diffuse Scattering can extend macromolecular structural refinement, validation, and analysis.
Thomas Welberry - One of the best experts on this subject based on the ideXlab platform.
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Simulation of Diffuse Scattering in DL-norleucine.
Acta Crystallographica Section B Structural Science Crystal Engineering and Materials, 2019Co-Authors: Thomas Welberry, Carl Henrik GörbitzAbstract:The diffraction patterns of dl-norleucine (SR-2-aminohexanoic acid, dl-Nle) crystals may show obvious Diffuse Scattering, usually described as `streaking', between the Bragg peaks. This phenomenon is obviously related to the non-ideal behaviour of the crystal. The normal interpretation is disorder in the stacking of weakly interacting 2D layers, known also for a number of other racemates of amino acids with linear hydrophobic side chains, as well as 1:1 complexes between different l- and d-enantiomers (quasi-racemates). Presented here is the first attempt to extract the information hidden in the Diffuse Scattering for this group of compounds by applying Monte Carlo simulations to the site distributions of two polymorphs in a block of 48 × 48 × 48 unit cells (four sites in each unit cell, 442 368 in total). The results demonstrate that it is indeed possible to model the Diffuse Scattering and relate it to processes expected to take place during phase transitions, characterized by slipping of molecular bilayers (or parts of them) relative to their neighbours. The understanding of the (intermediate) mixed phases in terms of domain size and defect density is consequently brought to a new level.
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A neutron Diffuse Scattering study of PbZrO3 and Zr-rich PbZr1-xTixO3
Journal of Applied Crystallography, 2015Co-Authors: Nan Zhang, Thomas Welberry, Marek Pasciak, A. M. Glazer, Jirka Hlinka, Matthias J. Gutmann, Hazel A. Sparkes, Andrzej Majchrowski, Krystian Roleder, Yujuan XieAbstract:A combined neutron Diffuse Scattering study and model analysis of the antiferroelectric crystal PbZrO3 is described. Following on from earlier X-ray Diffuse Scattering studies, supporting evidence for disordering of oxygen octahedral tilts and Pb displacements is shown in the high-temperature cubic phase. Excess Diffuse Scattering intensity is found at the M and R points in the Brillouin zone. A shell-model molecular dynamics simulation closely reproduces the neutron Diffuse Scattering pattern. Both in-phase and antiphase tilts are found in the structural model, with in-phase tilts predominating. The transition between disordered and ordered structure is discussed and compared with that seen in Zr-rich PbZr1−xTixO3.
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One hundred years of Diffuse Scattering
Crystallography Reviews, 2015Co-Authors: Thomas Welberry, Thomas WeberAbstract:Over the 100 years since the discovery of the diffraction of X-rays by crystals, structure determination based on the analysis of Bragg peaks has grown into a very precise, widely applicable, and definitive tool. This conventional crystallography is based on the assumption that a crystal consists of a three-dimensional array of identical units. Real materials, however, only approximate this ideal and their diffraction patterns contain, in addition to sharp Bragg peaks, a weak continuous background known as Diffuse Scattering. Diffuse Scattering occurs when there are departures of any kind from the ideal lattice. The properties of many important materials are dependent not simply on the average crystal structure yielded by the Bragg analysis but are often crucially dependent on the departures from ideality (disorder) that can only be revealed by analysis of the Diffuse Scattering. Diffuse Scattering has been known and studied since the very earliest days of crystallography but because of the generally very...
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Diffuse Scattering resulting from macromolecular frustration
Acta Crystallographica Section B Structural Science, 2011Co-Authors: Thomas Welberry, Aidan Heerdegen, David C. Goldstone, Ian A. TaylorAbstract:Distinctive Diffuse Scattering in the form of Diffuse rings around Bragg positions has been observed in the diffraction patterns of a crystal of the N-terminal fragment of the Gag protein from Feline Foamy Virus. It is shown that these are caused by geometric frustration as molecules try to pack on the triangular b–c mesh of the space group P6122. In order to explain the strong Diffuse Scattering it is necessary for the crystal to contain occupational disorder such that each unit cell contains one or other of two different molecular arrangements, A and B. The frustration arises because the nearest-neighbour packing prefers neighbouring cells to be AB or BA, which cannot be achieved on all three sides of a triangle simultaneously. To explain the observation that reciprocal sections hk5n, where n = integer, contain only Bragg peaks it is necessary that A and B are identical molecular arrangements differing only by a translation of 0.2c. The implications of the disorder for solving the structure of the protein by conventional techniques as well as the possibility of using the Diffuse Scattering for this purpose are discussed.
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Diffuse Scattering from organic crystals
Molecular Crystals and Liquid Crystals, 2005Co-Authors: Thomas WelberryAbstract:ABSTRACT The measurement of Diffuse Scattering data over large volumes of reciprocal space is now relatively routine and this opens up the possibility of analysing the local atomic and molecular structure of crystals in a level of detail not possible via conventional crystallography. We describe the development of a general method by which such Diffuse Scattering data can be analysed. This involves Monte Carlo simulation of a model crystal from which diffraction patterns may be calculated and compared to the observed data. The method is illustrated using two contrasting organic molecular crystal examples. For benzil, C14H10O2, the Diffuse Scattering is purely thermal in origin while ClMe (p–methyl–N-(p-chlorobenzylidene) aniline, C14H12ClN) is very disordered with each molecular site being occupied by the molecule in one of four different basic orientations and considerable local relaxation of these basic positions and orientations is present.
Panchapakesan Ganesh - One of the best experts on this subject based on the ideXlab platform.
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origin of Diffuse Scattering in relaxor ferroelectrics
Physical Review B, 2010Co-Authors: Panchapakesan Ganesh, Eric Cockayne, Muhtar Ahart, R E Cohen, Benjamin P Burton, Russell J Hemley, Wenge Yang, Zuoguang YeAbstract:High-pressure and variable temperature single-crystal synchrotron x-ray measurements combined with first principles based molecular-dynamics simulations were used to study Diffuse Scattering in the relaxor ferroelectric system ${\text{PbSc}}_{1/2}{\text{Nb}}_{1/2}{\text{O}}_{3}$. Constant temperature experiments show a pressure-induced transition to the relaxor phase, in which butterfly- and rod-shaped Diffuse Scattering occurs around the {h00} and {hh0} Bragg spots. Simulations qualitatively reproduce the observed Diffuse Scattering features as well as their pressure-temperature behavior and show that they arise from polarization correlations between chemically ordered regions, which in previous simulations were shown to behave as polar nanoregions. Simulations also exhibit radial Diffuse Scattering [elongated toward and away from $\mathbf{Q}=(000)$] that persists even in the paraelectric phase; consistent with previous neutron experiments on ${\text{PbMg}}_{1/3}{\text{Nb}}_{2/3}{\text{O}}_{3}$.
Andrew H Van Benschoten - One of the best experts on this subject based on the ideXlab platform.
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predicting x ray Diffuse Scattering from translation libration screw structural ensembles
Acta Crystallographica Section D-biological Crystallography, 2015Co-Authors: Andrew H Van Benschoten, Pavel V Afonine, Thomas C Terwilliger, Michael E Wall, Colin J Jackson, Nicholas K Sauter, Paul D Adams, Alexandre Urzhumtsev, J S FraserAbstract:Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray Scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure Diffuse Scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.Diffuse, addresses this need by employing Guinier's equation to calculate Diffuse Scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.Diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of Diffuse Scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar Diffuse Scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray Diffuse Scattering could extend macromolecular structural refinement, validation and analysis.
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predicting x ray Diffuse Scattering from translation libration screw structural ensembles
bioRxiv, 2015Co-Authors: Andrew H Van Benschoten, Pavel V Afonine, Thomas C Terwilliger, Michael E Wall, Colin J Jackson, Nicholas K Sauter, Paul D Adams, Alexandre Urzhumtsev, J S FraserAbstract:Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. While Bragg diffraction describes the average positional distribution of crystalline atoms, many different models can fit this distribution equally well. Diffuse X-ray Scattering can reduce this degeneracy by directly reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure Diffuse Scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.Diffuse, addresses this need by employing Guinier’s equation to calculate Diffuse Scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.Diffuse is applied to Translation-Libration-Screw (TLS) refinement, which models rigid body displacement for segments of the macromolecule. To enable calculation of Diffuse Scattering from TLS refined structures, phenix.tls_models builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS group partitioning and different motional correlations between groups yield markedly dissimilar Diffuse Scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how X-ray Diffuse Scattering can extend macromolecular structural refinement, validation, and analysis.