Journal of Applied Crystallography最新文献_第2页

Application of signal separation to diffraction image compression and serial crystallography.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576724011038

Jérôme Kieffer, Julien Orlans, Nicolas Coquelle, Samuel Debionne, Shibom Basu, Alejandro Homs, Gianluca Santoni, Daniele De Sanctis

引用次数: 0

An extended thermal pressure equation of state for sodium fluoride.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576725000330

Lewis A Clough, Nicholas P Funnell, Christopher J Ridley, Dominik Daisenberger, Joseph A Hriljac, Matic Lozinšek, Ross J Angel, Simon Parsons

{"title":"An extended thermal pressure equation of state for sodium fluoride.","authors":"Lewis A Clough, Nicholas P Funnell, Christopher J Ridley, Dominik Daisenberger, Joseph A Hriljac, Matic Lozinšek, Ross J Angel, Simon Parsons","doi":"10.1107/S1600576725000330","DOIUrl":"10.1107/S1600576725000330","url":null,"abstract":"The effect of pressure and temperature on the unit-cell volume of NaF has been measured by X-ray powder diffraction at ambient pressure between 12 and 300 K and neutron powder diffraction up to 5 GPa between 140 and 350 K. These data have been combined with high-pressure volume data at 300 and 950 K to 25 GPa and adiabatic bulk modulus data to 650 K to define an equation of state for NaF relating molar volume to both temperature and pressure. The model combines a fourth-order Birch-Murnaghan equation of state at 295 K with a Mie-Grüneisen-Debye model for thermal pressure. The parameters of the model set at 295 K and ambient pressure are as follows: reference unit-cell volume V 0 = 14.9724 (5) cm3 mol-1, isothermal bulk modulus K 0T = 46.79 (14) GPa, first derivative of the bulk modulus K'0T = 5.72 (12), second derivative of the bulk modulus K''0T = -0.43 (4) GPa-1, Debye temperature T MGD = 459 (3) K, and Anderson Grüneisen parameters γ0 = 1.547 (11) and q = 0.94 (18).","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 1","pages":"227-232"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11798522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization and calibration of DECTRIS PILATUS3 X CdTe 2M high-Z hybrid pixel detector for high-precision powder diffraction measurements.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576724010033

Gavin B M Vaughan, Stefano Checchia, Marco Di Michiel

引用次数: 0

A new technical solution to the problem of increasing the resolution of X-ray diffraction methods.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576724011130

H R Drmeyan, S A Mkhitaryan, A H Mkrtchyan

{"title":"A new technical solution to the problem of increasing the resolution of X-ray diffraction methods.","authors":"H R Drmeyan, S A Mkhitaryan, A H Mkrtchyan","doi":"10.1107/S1600576724011130","DOIUrl":"https://doi.org/10.1107/S1600576724011130","url":null,"abstract":"A new technical solution to the problem of increasing the resolution of X-ray diffraction methods has been proposed and implemented, based on linearly enlarging the X-ray topographic patterns. For implementation of the suggested method, a novel device has been developed, created and tested that makes it possible to scan synchronously the slit for transmitting separate parts of the X-ray diffraction pattern and the X-ray film with a predetermined speed ratio. The possibility of significantly increasing the resolution of X-ray diffraction patterns with the suggested new scanning method has been experimentally proven. It was shown that if individual parts of the diffracted beam are passed successively through a narrow slit, which is synchronously scanned along with the X-ray detecting film, we obtain an enlargement in topographic patterns. A proposed scheme for enlarging the image in parts and a description and the operating principle of the scanning device are also presented. The relationship between the ratio of the speeds of the slit and the X-ray film movement and the parameters of the scanning device and the sample (slit width, total thickness of thin crystals, thickness of a thick crystal etc.) was revealed. The speeds of the reciprocating motion of the slit and the X-ray film were calculated. It has been experimentally proven that the scanning process does not introduce new information into the interference pattern but only enlarges it, since these patterns in sectional topograms differ only in size in the scattering plane.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 1","pages":"71-75"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11798520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microcalcifications in breast cancer tissue studied by X-ray absorption, emission, scattering and diffraction.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576724011750

Thomas Huthwelker, Camelia N Borca, Davide Altamura, Liberato De Caro, Renzo Vanna, Fabio Corsi, Carlo Morasso, Greta Banfi, Giovanni Arpa, Oliver Bunk, Cinzia Giannini

{"title":"Microcalcifications in breast cancer tissue studied by X-ray absorption, emission, scattering and diffraction.","authors":"Thomas Huthwelker, Camelia N Borca, Davide Altamura, Liberato De Caro, Renzo Vanna, Fabio Corsi, Carlo Morasso, Greta Banfi, Giovanni Arpa, Oliver Bunk, Cinzia Giannini","doi":"10.1107/S1600576724011750","DOIUrl":"10.1107/S1600576724011750","url":null,"abstract":"Microcalcifications (MC) are observed in various tissues and in relation to several diseases. For breast cancer, recent studies have reported differences in the nature of the MC and correlations to the degree of malignancy of the neoplasm. Here, investigations of benign, ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) breast MC using X-ray fluorescence, X-ray absorption spectroscopy and wide-angle X-ray scattering are reported. While Mg has been observed in all MC, only for the benign MC has a rim of crystalline whitlockite been identified as a minor crystalline phase in addition to the major hy-droxy-apatite (HAP) one. MC in DCIS and IDC tissue exhibit a higher abundance of a high-crystallinity HAP phase in comparison with the less well ordered MC in the benign tissue. Moreover, the distribution of other trace elements in the MC, such as Na, S, Cl, Sr and Y, is observed. For the quantitative analysis of the elemental maps, the experimentally determined sample thickness in each pixel has been incorporated as an additional parameter in the fitting process to account for sample roughness.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 1","pages":"233-250"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11798518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Top dusted adhesive tape sample preparation method for the X-ray diffraction analysis of small powder sample volumes with the Bragg-Brentano setup.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576724011920

Daniel Dickes, Uwe Glatzel

引用次数: 0

Hydro-static behaviour of highly inert Fomblin and Halocarbon fluids as pressure-transmitting media in high-pressure experiments.

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-02-01 DOI: 10.1107/S1600576725000342

Klemen Motaln, Erik Uran, Nico Giordano, Simon Parsons, Matic Lozinšek

{"title":"Hydro-static behaviour of highly inert Fomblin and Halocarbon fluids as pressure-transmitting media in high-pressure experiments.","authors":"Klemen Motaln, Erik Uran, Nico Giordano, Simon Parsons, Matic Lozinšek","doi":"10.1107/S1600576725000342","DOIUrl":"10.1107/S1600576725000342","url":null,"abstract":"A pressure-transmitting medium (PTM) plays an important role in diamond anvil cell (DAC) experiments as it ensures that the sample is exposed to hydro-static pressure. Although PTMs that are liquids under ambient conditions are the easiest to handle and load, the selection of chemically inert liquid media with established hydro-static properties is limited. To widen the choice of highly inert PTMs for high-pressure experiments, the hydro-static behaviours of Fomblin Z60, Fomblin Z25, Fomblin Y LVAC 06/6 and Halocarbon Oil 11-14 were investigated. The ruby fluorescence method was used to monitor the evolution of pressure gradients across the DAC sample chamber during compression and decompression. Fomblin Z60 and Fomblin Z25 perfluoro-polyethers, which are hydro-static to 1.7 and 1.5 GPa, respectively, exhibited the best hydro-static performance, followed by Halocarbon Oil 11-14 with a limit of 1.2 GPa, whereas the non-hydro-static behaviour of Fomblin Y LVAC 06/6 was observed above only 0.6 GPa.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 1","pages":"221-226"},"PeriodicalIF":6.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11798517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RAPID: an ImageJ macro for indexing electron diffraction zone axis spot patterns of cubic materials. 快速：一个用于标引立方材料的电子衍射区轴斑图案的ImageJ宏。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-11-26 eCollection Date: 2024-12-01 DOI: 10.1107/S1600576724010215

Thomas E Weirich

{"title":"RAPID: an ImageJ macro for indexing electron diffraction zone axis spot patterns of cubic materials.","authors":"Thomas E Weirich","doi":"10.1107/S1600576724010215","DOIUrl":"10.1107/S1600576724010215","url":null,"abstract":"As an extension to previous work, the ImageJ macro script RAPID (ratio-method pattern indexing) has been developed to allow instant indexing of calibrated and uncalibrated zone axis aligned electron diffraction patterns of cubic lattices using the Rn ratio principle. The program can be used to index zone axis aligned selected-area electron diffraction patterns, nanobeam electron diffraction patterns, transmission electron microscopy (TEM) Kikuchi patterns and even fast Fourier transforms of high-resolution (scanning) TEM images. The program allows the user to quickly assess whether the material under investigation belongs to the cubic crystal system, is pseudo-cubic or is not cubic at all by adjusting the boundary parameters and allowed errors for lattice indexing. The software also allows one to distinguish between the P, I and F Bravais lattices for certain zone axis directions. For calibrated diffraction patterns, the lattice parameters can be obtained, allowing verification of the material under investigation or phase identification in connection with a structural database. In addition, the program can be employed for determination or verification of the used instrument's camera constant when reference materials are used. Therefore, it is a convenient tool for on-site crystallographic analysis in TEM laboratories.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"2017-2029"},"PeriodicalIF":6.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GRASP Integrated 3D Plotter: GRIP. 集成3D绘图仪：抓地力。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-11-26 eCollection Date: 2024-12-01 DOI: 10.1107/S1600576724010379

Paul M Neves, Jonathan S White

{"title":"GRASP Integrated 3D Plotter: GRIP.","authors":"Paul M Neves, Jonathan S White","doi":"10.1107/S1600576724010379","DOIUrl":"10.1107/S1600576724010379","url":null,"abstract":"In research on mesoscale structure and correlations, small-angle neutron scattering (SANS) is increasingly being employed to map fully three-dimensional distributions of scattered intensity at low momentum transfer. While traditionally SANS experiments and data analysis methods are designed to prioritize the determination of salient information in only one or two dimensions, the trend towards volumetric intensity mapping experiments calls for new software tools to assist with analyzing the resulting datasets. In this paper, we describe the development of a new software module, the GRASP Integrated 3D Plotter (GRIP). GRIP adds numerous features to GRASP, a widely used SANS analysis program that was written in MATLAB and developed at the Institut Laue-Langevin, France. The GRIP module provides multiple methods of three-dimensional SANS data visualization and new abilities to perform 1D and 2D cuts in various momentum-space coordinate systems, including reciprocal lattice units relevant for single-crystal studies. GRIP also includes the ability to fit diffraction peaks to a fully three-dimensional ellipsoidal Gaussian function to extract peak parameters including peak intensity, location and width, as well as a built-in calculator for estimating the resolution-deconvolved 3D coherence lengths in a sample. GRIP thus represents a significant addition to GRASP which extends the utility and application of SANS. Valuable advantages are provided, in particular, for 'small-angle neutron diffraction' studies of mesoscale correlations in single crystals, such as those due to incommensurate magnetic spin textures like spirals and topological skyrmion lattices.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"2030-2042"},"PeriodicalIF":6.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures. 蛋白质-配体晶体结构中卤化抑制剂和配体的特异性辐射损伤。

IF 6.1 3区材料科学

Journal of Applied Crystallography Pub Date : 2024-11-26 eCollection Date: 2024-12-01 DOI: 10.1107/S1600576724010549

Matthew J Rodrigues, Marc Cabry, Gavin Collie, Michael Carter, Craig McAndrew, Robin L Owen, Benjamin R Bellenie, Yann-Vaï Le Bihan, Rob L M van Montfort

{"title":"Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures.","authors":"Matthew J Rodrigues, Marc Cabry, Gavin Collie, Michael Carter, Craig McAndrew, Robin L Owen, Benjamin R Bellenie, Yann-Vaï Le Bihan, Rob L M van Montfort","doi":"10.1107/S1600576724010549","DOIUrl":"10.1107/S1600576724010549","url":null,"abstract":"Protein-inhibitor crystal structures aid medicinal chemists in efficiently improving the potency and selectivity of small-molecule inhibitors. It is estimated that a quarter of lead molecules in drug discovery projects are halogenated. Protein-inhibitor crystal structures have shed light on the role of halogen atoms in ligand binding. They form halogen bonds with protein atoms and improve shape complementarity of inhibitors with protein binding sites. However, specific radiation damage (SRD) can cause cleavage of carbon-halogen (C-X) bonds during X-ray diffraction data collection. This study shows significant C-X bond cleavage in protein-ligand structures of the therapeutic cancer targets B-cell lymphoma 6 (BCL6) and heat shock protein 72 (HSP72) complexed with halogenated ligands, which is dependent on the type of halogen and chemical structure of the ligand. The study found that metrics used to evaluate the fit of the ligand to the electron density deteriorated with increasing X-ray dose, and that SRD eliminated the anomalous signal from brominated ligands. A point of diminishing returns is identified, where collecting highly redundant data reduces the anomalous signal that may be used to identify binding sites of low-affinity ligands or for experimental phasing. Straightforward steps are proposed to mitigate the effects of C-X bond cleavage on structures of proteins bound to halogenated ligands and to improve the success of anomalous scattering experiments.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 6","pages":"1951-1965"},"PeriodicalIF":6.1,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142769072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0