Journal of Applied Crystallography最新文献_第4页

On the use of beam precession for serial electron crystallography. 束流进动在连续电子晶体学中的应用。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-25 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725005606

Sergi Plana-Ruiz, Penghan Lu, Govind Ummethala, Rafal E Dunin-Borkowski

{"title":"On the use of beam precession for serial electron crystallography.","authors":"Sergi Plana-Ruiz, Penghan Lu, Govind Ummethala, Rafal E Dunin-Borkowski","doi":"10.1107/S1600576725005606","DOIUrl":"10.1107/S1600576725005606","url":null,"abstract":"During the past few years, serial electron crystallography (serial electron diffraction) has been gaining attention for the structure determination of crystalline compounds that are sensitive to irradiation by an electron beam. By recording a single electron diffraction pattern per crystal, indexing thousands to tens of thousands of such patterns and merging the reflection intensities of the successfully indexed patterns, one can retrieve crystal structure models with strongly mitigated beam damage contributions. However, one of the technique's bottlenecks is the need to obtain so many well indexed diffraction patterns, which leads to the collection of raw diffraction data in an automated way that usually yields low indexing rates. This work demonstrates how to overcome this limitation by performing the serial crystallography experiment following a semi-automated routine with a precessed electron beam (serial precession electron diffraction). The precession movement increases the number of reflections present in the diffraction patterns, and dynamical effects related to specific orientations of the crystals with respect to the electron beam are greatly minimized. This leads to more uniform reflection intensities across the serial data set, and a smaller number of patterns are required to merge the reflection intensities for good statistics. Furthermore, structure refinements based on the dynamical diffraction theory become possible due to the diffraction volume integration of beam precession, providing a novel approach for more accurate structure models. In this context, the use of beam precession is presented as an advantageous tool for serial electron crystallography, as it enables reliable crystal structure analysis with a lower amount of diffraction data.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1249-1260"},"PeriodicalIF":2.8,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789139","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

Inversion of the X-ray restrained wavefunction equations: a first step towards the development of exchange-correlation functionals based on X-ray data. x射线约束波函数方程的反演：基于x射线数据的交换相关函数发展的第一步。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-25 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725004765

Alessandro Genoni, Maurizio Sironi

{"title":"Inversion of the X-ray restrained wavefunction equations: a first step towards the development of exchange-correlation functionals based on X-ray data.","authors":"Alessandro Genoni, Maurizio Sironi","doi":"10.1107/S1600576725004765","DOIUrl":"10.1107/S1600576725004765","url":null,"abstract":"The X-ray restrained wavefunction (XRW) method is a quantum crystallographic technique that enables the determination of wavefunctions compatible with experimental X-ray diffraction data. Extensive research has demonstrated that this strategy inherently captures electron correlation and polarization effects on the electron density, while also providing consistent electron distributions. These findings suggest that the approach could be valuable in the development of new exchange-correlation (xc) functionals for density functional theory (DFT) calculations. This is particularly relevant in light of recent observations and recommendations by Medvedev et al. [Science (2017), 355, 49-52], who stressed the importance that xc functionals give both accurate energy values and exact electron densities, in line with the original spirit of DFT. Motivated by this perspective, this paper presents a preliminary investigation that aims at extracting and visualizing for the first time the perturbation potentials arising from the use of X-ray diffraction data as restraints in XRW calculations. In the present work, these potentials are simply obtained as orbital-averaged potentials through straightforward inversions of the XRW equations, where theoretical or high-quality experimental X-ray structure factors are employed in XRW computations at the restricted Hartree-Fock level for atoms (neon, argon and krypton) and simple molecules (dilithium and urea). Features and limitations of the resulting preliminary potentials are illustrated, while future perspectives on the use of the XRW method for the development of xc functionals are also discussed.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1106-1121"},"PeriodicalIF":2.8,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789234","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

Opportunities for near-surface small-angle neutron scattering to probe magnetic nanostructures within thin-film volumes. 近表面小角中子散射探测薄膜内磁性纳米结构的机会。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-22 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725005503

Grace L Causer

{"title":"Opportunities for near-surface small-angle neutron scattering to probe magnetic nanostructures within thin-film volumes.","authors":"Grace L Causer","doi":"10.1107/S1600576725005503","DOIUrl":"10.1107/S1600576725005503","url":null,"abstract":"Near-surface small-angle neutron scattering (NS-SANS) is a highly versatile, yet under-utilized, technique in condensed matter research. It addresses the shortcomings of transmission SANS to enable the characterization of nano-structures within extremely small sample volumes in the thin-film limit. NS-SANS stands out in its capacity to resolve 1D, 2D or 3D structural, chemical and magnetic correlations beneath the surfaces of thin films with nanometre resolution. By varying the incident angle above the critical angle of reflection, NS-SANS delivers tuneable depth sensitivity across nano-confined volumes, effectively minimizing noise contributions from substrates while surpassing the surface-sensitive capabilities of grazing-incidence SANS. This perspective highlights the future potential of NS-SANS to study condensed matter thin films and heterostructures, with a special focus on nanoscale magnetic phenomena, such as topological skyrmion lattices, superconducting vortex lattices and chiral domain walls, which are of timely interest to the magnetism and quantum materials communities.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1455-1461"},"PeriodicalIF":2.8,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789140","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

Optimization of magnetic reference layer for neutron reflectometry. 中子反射计磁参比层的优化。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-22 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725004674

Anton Zubayer, Fredrik Eriksson, Naureen Ghafoor, Jochen Stahn, Jens Birch, Artur Glavic

{"title":"Optimization of magnetic reference layer for neutron reflectometry.","authors":"Anton Zubayer, Fredrik Eriksson, Naureen Ghafoor, Jochen Stahn, Jens Birch, Artur Glavic","doi":"10.1107/S1600576725004674","DOIUrl":"10.1107/S1600576725004674","url":null,"abstract":"Neutron reflectivity is a powerful technique for probing density profiles in films, with applications across physics, chemistry and biology. However, challenges arise when dealing with samples characterized by high roughness, unknown scattering length density (SLD) with low contrast, very thin layers or complex multi-layered structures that cannot be uniquely resolved due to the phase problem. Incorporating a magnetic reference layer (MRL) and using polarized neutron reflectivity improves the sensitivity and modelling accuracy by providing complementary information. In this study, we introduce a quantitative means of comparing MRL systems in a model-free way. We apply this approach to demonstrate that CoTi alloys offer a superior solution as MRLs compared with the commonly used Fe or Ni MRLs. The low nuclear and magnetic scattering length densities of CoTi significantly enhance sensitivity, making it particularly advantageous for soft-matter research. Furthermore, the tunable Co versus Ti ratio allows for optimization of the SLD to achieve maximum sensitivity, establishing CoTi as a highly effective choice for MRL applications. The applied simulation framework for optimizing MRL sensitivity to a specific materials system and research question is a generic approach that can be used prior to growing the MRL for a given experiment.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1299-1310"},"PeriodicalIF":2.8,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789141","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

Powder diffraction data beyond the pattern: a practical review. 粉末衍射数据超越模式：实用回顾。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-22 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725004728

Nicola Casati, Elena Boldyreva

引用次数: 0

A systematic approach for quantitative orientation and phase fraction analysis of thin films through grazing-incidence X-ray diffraction. 用掠入射x射线衍射分析薄膜定量取向和相分数的系统方法。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-22 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725004935

Fabian Gasser, Sanjay John, Jorid Smets, Josef Simbrunner, Mario Fratschko, Víctor Rubio-Giménez, Rob Ameloot, Hans-Georg Steinrück, Roland Resel

{"title":"A systematic approach for quantitative orientation and phase fraction analysis of thin films through grazing-incidence X-ray diffraction.","authors":"Fabian Gasser, Sanjay John, Jorid Smets, Josef Simbrunner, Mario Fratschko, Víctor Rubio-Giménez, Rob Ameloot, Hans-Georg Steinrück, Roland Resel","doi":"10.1107/S1600576725004935","DOIUrl":"10.1107/S1600576725004935","url":null,"abstract":"Grazing-incidence X-ray diffraction (GIXD) is widely used for the structural characterization of thin films, particularly for analyzing phase composition and the orientation distribution of crystallites. While various tools exist for qualitative evaluation, a widely applicable systematic procedure to obtain quantitative information has not yet been developed. This work presents a first step in that direction, allowing accurate quantitative information to be obtained through the evaluation of radial line profiles from GIXD data. An algorithm is introduced for computing radial line profiles based on the crystal structure of known compounds. By fitting experimental data with calculated line profiles, accurate quantitative information about orientation distribution and phase composition is obtained, along with additional parameters such as mosaicity and total crystal volume. The approach is demonstrated using three distinct thin film systems, highlighting the broad applicability of the algorithm. This method provides a systematic and general approach to obtaining quantitative information from GIXD data.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1288-1298"},"PeriodicalIF":2.8,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789224","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

Accounting for instrument resolution in the pair distribution functions obtained from total scattering data using Hermite functions. 利用埃尔米特函数计算从总散射数据得到的对分布函数中的仪器分辨率。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-22 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725004340

Shaojie Wang, Min Gao, Yinze Qin, Sijie Zhang, Lei Tan, Martin T Dove

{"title":"Accounting for instrument resolution in the pair distribution functions obtained from total scattering data using Hermite functions.","authors":"Shaojie Wang, Min Gao, Yinze Qin, Sijie Zhang, Lei Tan, Martin T Dove","doi":"10.1107/S1600576725004340","DOIUrl":"10.1107/S1600576725004340","url":null,"abstract":"The use of Hermite functions to describe pair distribution functions (PDFs) from total scattering data was previously proposed by Krylov & Vvedenskii [J. Non-Cryst. Solids (1995), 192-193, 683-687]. Hermite functions have a suitable form for describing both the total scattering data and the PDF, and have the useful feature that they are eigenfunctions of the Fourier transform operation. We demonstrate that, by fitting Hermite functions to total scattering data, it is possible to take into account the effects of experimental resolution when deriving the PDF from the scattering data. This is particularly advantageous for neutron time-of-flight data, where different banks of detectors have different resolution functions and the resolution widths vary with the size of the scattering vector. A number of technical points are discussed and illustrated using examples of synthetic data, including both amorphous and crystalline materials. These include a solution to the problem of handling the sharp Bragg peaks, and how to scale the scattering function and PDF to match the scale of the Hermite functions. A number of examples using real scattering data, both synchrotron X-ray and spallation neutron data, are also shown. To account for uncertainties in the levels of the scattering functions, we have modified a method of Billinge & Farrow [J. Phys. Condens. Matter (2013), 25, 454202] to remove backgrounds by fitting with low-order orthogonal (Chebyshev) functions.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1269-1287"},"PeriodicalIF":2.8,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789225","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

Small-angle X-ray scattering profile calculation for high-resolution models of biomacromolecules. 高分辨率生物大分子模型的小角度x射线散射剖面计算。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-16 eCollection Date: 2025-08-01 DOI: 10.1107/S160057672500562X

Kristian Lytje, Jan Skov Pedersen

{"title":"Small-angle X-ray scattering profile calculation for high-resolution models of biomacromolecules.","authors":"Kristian Lytje, Jan Skov Pedersen","doi":"10.1107/S160057672500562X","DOIUrl":"10.1107/S160057672500562X","url":null,"abstract":"We introduce a new approach to calculating small-angle X-ray scattering (SAXS) profiles from high-resolution atomic structures, which is realized in the open-source software AUSAXS. We employ an efficient implementation of the Debye equation, incorporating both accurate excluded volume models and a novel hydration shell model based on explicit dummy atoms. Two new excluded volume models are presented: (i) a simple, heterogeneous equivalent atom model, and (ii) a grid-based model. The two approaches reduce the risk of overfitting by either eliminating fitting parameters or introducing a safer volume scaling method. These models are compared with the traditional Gaussian sphere method, which is widely used in existing software. The comparisons reveal significant shortcomings in previously accepted methods, suggesting they may be more prone to overfitting than previously thought. This underscores the importance of a well tested and openly accessible baseline implementation like AUSAXS. AUSAXS is freely available at https://github.com/AUSAXS/AUSAXS.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1332-1346"},"PeriodicalIF":2.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789145","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

Superstability of micrometre jets surrounded by a polymeric shell. 被聚合外壳包围的微米射流的超稳定性。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-16 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725004790

A Rubio, J M Montanero, M Vakili, F H M Koua, S Bajt, H N Chapman, A M Gañán-Calvo

引用次数: 0

The {010} form of polar brushite (CaHPO₄·2H₂O) deposits as an epi-growing crystal on a non-polar {010} substrate of gypsum (CaSO₄·2H₂O). 极性电刷石（CaHPO4·2H2O）的{010}形式在非极性的{010}石膏（CaSO4·2H2O）基体上呈外延生长晶体沉积。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2025-07-16 eCollection Date: 2025-08-01 DOI: 10.1107/S1600576725005060

Dino Aquilano, Stefano Ghignone, Marco Bruno

{"title":"The {010} form of polar brushite (CaHPO4·2H2O) deposits as an epi-growing crystal on a non-polar {010} substrate of gypsum (CaSO4·2H2O).","authors":"Dino Aquilano, Stefano Ghignone, Marco Bruno","doi":"10.1107/S1600576725005060","DOIUrl":"10.1107/S1600576725005060","url":null,"abstract":"The mechanisms of crystal growth from solution are more complicated than those from vapor or melt growth. These mechanisms are important in bio-mineralization (bones, teeth, shells) and in the characterization of optically non-linear crystals, perfectly crystallized proteins, nucleic acids and complex viruses. This motivated studies on new basic phenomena, including the crystal interfaces of biological macromolecules and those of low-solubility inorganic salts. Generalization of the Gibbs-Thomson effect has been questioned when describing isotropic (circular) or anisotropic (polygonized) spiral steps spreading onto a crystal face. This work focuses on the brushite crystal (CaHPO4·2H2O) since it can grow freely or as a deposit on a gypsum (CaSO4·2H2O) substrate. Brushite looks like a 2D crystal built by a flat {010} form limited by {h0l} polar and thin faces running as straight steps. Moreover, it is worth investigating the {010} gypsum to {010} brushite transformation since mineralogy and geochemistry play an important role in the crystal growth. Here, we study the freely growing brushite and, subsequently, its {010} form arising from gypsum. The epitaxy {010} gypsum/{010} brushite is also examined because brushite twins are involved. A new way of thinking about the epi-relations is proposed, along with more rigorous constraints; this new approach emphasizes the physical importance of the adhesion energy connected to every epitaxy.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1220-1226"},"PeriodicalIF":2.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789148","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