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RMCProfile7: reverse Monte Carlo for multiphase systems. RMCProfile7:多相系统的反向蒙特卡罗。
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-31 eCollection Date: 2024-08-01 DOI: 10.1107/S1600576724004175
Wojciech A Sławiński, Christopher J Kerr, Yuanpeng Zhang, Helen Y Playford, Martin T Dove, Anthony E Phillips, Matthew G Tucker

This work introduces a completely rewritten version of the program RMCProfile (version 7), big-box, reverse Monte Carlo modelling software for analysis of total scattering data. The major new feature of RMCProfile7 is the ability to refine multiple phases simultaneously, which is relevant for many current research areas such as energy materials, catalysis and engineering. Other new features include improved support for molecular potentials and rigid-body refinements, as well as multiple different data sets. An empirical resolution correction and calculation of the pair distribution function as a back-Fourier transform are now also available. RMCProfile7 is freely available for download at https://rmcprofile.ornl.gov/.

这项工作介绍了一个完全重写版本的程序 RMCProfile(第 7 版),这是一个用于分析全散射数据的大型反向蒙特卡罗建模软件。RMCProfile7 的主要新功能是能够同时细化多个相,这与当前的许多研究领域(如能源材料、催化和工程)息息相关。其他新功能包括改进了对分子势和刚体细化以及多个不同数据集的支持。现在还提供了经验分辨率校正和计算对分布函数的反傅里叶变换。RMCProfile7 可在 https://rmcprofile.ornl.gov/ 免费下载。
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引用次数: 0
On the feasibility of time-resolved X-ray powder diffraction of macromolecules using laser-driven ultrafast X-ray sources. 利用激光驱动超快 X 射线源对大分子进行时间分辨 X 射线粉末衍射的可行性。
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-29 eCollection Date: 2024-08-01 DOI: 10.1107/S1600576724005028
Krishna Prasad Khakurel, Gabriel Žoldák, Borislav Angelov, Jakob Andreasson

With the emergence of ultrafast X-ray sources, interest in following fast processes in small molecules and macromolecules has increased. Most of the current research into ultrafast structural dynamics of macromolecules uses X-ray free-electron lasers. In parallel, small-scale laboratory-based laser-driven ultrafast X-ray sources are emerging. Continuous development of these sources is underway, and as a result many exciting applications are being reported. However, because of their low flux, such sources are not commonly used to study the structural dynamics of macromolecules. This article examines the feasibility of time-resolved powder diffraction of macromolecular microcrystals using a laboratory-scale laser-driven ultrafast X-ray source.

随着超快 X 射线源的出现,人们对跟踪小分子和大分子中快速过程的兴趣与日俱增。目前对大分子超快结构动力学的研究大多使用 X 射线自由电子激光器。与此同时,基于实验室的小型激光驱动超快 X 射线源也在不断涌现。这些光源正在不断开发中,因此许多令人兴奋的应用也被报道出来。然而,由于其通量较低,这类光源并不常用于研究大分子结构动力学。本文探讨了使用实验室规模的激光驱动超快 X 射线源对大分子微晶体进行时间分辨粉末衍射的可行性。
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引用次数: 0
Operando pair distribution function analysis of nanocrystalline functional materials: the case of TiO2-bronze nanocrystals in Li-ion battery electrodes. 纳米晶体功能材料的操作数对分布函数分析:锂离子电池电极中的 TiO2-青铜纳米晶体。
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-29 eCollection Date: 2024-08-01 DOI: 10.1107/S1600576724005624
Martin A Karlsen, Jonas Billet, Songsheng Tao, Isabel Van Driessche, Simon J L Billinge, Dorthe B Ravnsbæk

Structural modelling of operando pair distribution function (PDF) data of complex functional materials can be highly challenging. To aid the understanding of complex operando PDF data, this article demonstrates a toolbox for PDF analysis. The tools include denoising using principal component analysis together with the structureMining, similarityMapping and nmfMapping apps available through the online service 'PDF in the cloud' (PDFitc, https://pdfitc.org/). The toolbox is used for both ex situ and operando PDF data for 3 nm TiO2-bronze nanocrystals, which function as the active electrode material in a Li-ion battery. The tools enable structural modelling of the ex situ and operando PDF data, revealing two pristine TiO2 phases (bronze and anatase) and two lithiated Li x TiO2 phases (lithiated versions of bronze and anatase), and the phase evolution during galvanostatic cycling is characterized.

对复杂功能材料的操作数对分布函数(PDF)数据进行结构建模极具挑战性。为了帮助理解复杂的操作数对分布函数数据,本文展示了一个 PDF 分析工具箱。工具包括利用主成分分析法进行去噪,以及通过在线服务 "云中的 PDF"(PDFitc,https://pdfitc.org/)提供的 structureMining、similarityMapping 和 nmfMapping 应用程序。该工具箱适用于 3 nm TiO2-青铜纳米晶体的原位和操作 PDF 数据,该晶体是锂离子电池的活性电极材料。该工具可对原位和运行状态下的 PDF 数据进行结构建模,揭示出两种原始 TiO2 相(青铜相和锐钛矿相)和两种锂化 Li x TiO2 相(青铜相和锐钛矿相的锂化版本),并对电静力循环过程中的相演化进行表征。
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引用次数: 0
Rapid detection of rare events from in situX-ray diffraction data using machine learning. 利用机器学习从原位 X 射线衍射数据中快速检测罕见事件。
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-17 eCollection Date: 2024-08-01 DOI: 10.1107/S160057672400517X
Weijian Zheng, Jun-Sang Park, Peter Kenesei, Ahsan Ali, Zhengchun Liu, Ian Foster, Nicholas Schwarz, Rajkumar Kettimuthu, Antonino Miceli, Hemant Sharma

High-energy X-ray diffraction methods can non-destructively map the 3D microstructure and associated attributes of metallic polycrystalline engineering materials in their bulk form. These methods are often combined with external stimuli such as thermo-mechanical loading to take snapshots of the evolving microstructure and attributes over time. However, the extreme data volumes and the high costs of traditional data acquisition and reduction approaches pose a barrier to quickly extracting actionable insights and improving the temporal resolution of these snapshots. This article presents a fully automated technique capable of rapidly detecting the onset of plasticity in high-energy X-ray microscopy data. The technique is computationally faster by at least 50 times than the traditional approaches and works for data sets that are up to nine times sparser than a full data set. This new technique leverages self-supervised image representation learning and clustering to transform massive data sets into compact, semantic-rich representations of visually salient characteristics (e.g. peak shapes). These characteristics can rapidly indicate anomalous events, such as changes in diffraction peak shapes. It is anticipated that this technique will provide just-in-time actionable information to drive smarter experiments that effectively deploy multi-modal X-ray diffraction methods spanning many decades of length scales.

高能 X 射线衍射方法可以非破坏性地绘制金属多晶工程材料的三维微观结构和相关属性。这些方法通常与热机械加载等外部刺激相结合,以拍摄随时间演变的微观结构和属性的快照。然而,传统的数据采集和还原方法数据量巨大、成本高昂,阻碍了快速提取可行见解和提高这些快照的时间分辨率。本文介绍了一种能够在高能 X 射线显微镜数据中快速检测可塑性开始的全自动技术。该技术的计算速度比传统方法至少快 50 倍,而且适用于比完整数据集稀疏 9 倍的数据集。这项新技术利用自监督图像表征学习和聚类,将海量数据集转化为紧凑、语义丰富的视觉显著特征(如峰值形状)表征。这些特征可迅速显示异常事件,如衍射峰形状的变化。预计这项技术将提供及时可操作的信息,以推动更智能的实验,有效部署跨越数十年长度尺度的多模态 X 射线衍射方法。
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引用次数: 0
Demonstration of neutron time-of-flight diffraction with an event-mode imaging detector 利用事件模式成像探测器演示中子飞行时间衍射
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-11 DOI: 10.1107/s1600576724004448
Tim T. Jäger, A. Losko, A. Wolfertz, Søren Schmidt, Mads Bertelsen, A. Khaplanov, Sean R. Agnew, F. Funama, Manuel Morgano, M. Roth, J. R. Gochanour, A. M. Long, Luca Lutterotti, S. Vogel
Neutron diffraction beamlines have traditionally relied on deploying large detector arrays of 3He tubes or neutron-sensitive scintillators coupled with photomultipliers to efficiently probe crystallographic and microstructure information of a given material. Given the large upfront cost of custom-made data acquisition systems and the recent scarcity of 3He, new diffraction beamlines or upgrades to existing ones demand innovative approaches. This paper introduces a novel Timepix3-based event-mode imaging neutron diffraction detector system as well as first results of a silicon powder diffraction measurement made at the HIPPO neutron powder diffractometer at the Los Alamos Neutron Science Center. Notably, these initial measurements were conducted simultaneously with the 3He array on HIPPO, enabling direct comparison. Data reduction for this type of data was implemented in the MAUD code, enabling Rietveld analysis. Results from the Timepix3-based setup and HIPPO were benchmarked against McStas simulations, showing good agreement for peak resolution. With further development, systems such as the one presented here may substantially reduce the cost of detector systems for new neutron instrumentation as well as for upgrades of existing beamlines.
中子衍射光束线传统上依赖于部署大型 3He 管探测器阵列或中子敏感闪烁体,再加上光电倍增管来有效探测特定材料的晶体学和微观结构信息。鉴于定制数据采集系统的前期成本高昂以及近期 3He 的稀缺,新的衍射光束线或现有光束线的升级需要创新的方法。本文介绍了基于 Timepix3 的新型事件模式成像中子衍射探测器系统,以及在洛斯阿拉莫斯中子科学中心的 HIPPO 中子粉末衍射仪上进行的硅粉末衍射测量的初步结果。值得注意的是,这些初步测量是与 HIPPO 上的 3He 阵列同时进行的,因此可以进行直接比较。MAUD 代码对这类数据进行了还原,从而实现了里特维尔德分析。基于 Timepix3 的设置和 HIPPO 的结果与 McStas 模拟进行了比对,结果表明峰值分辨率具有良好的一致性。随着进一步的发展,像本文介绍的系统可能会大大降低新中子仪器和现有光束线升级探测器系统的成本。
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引用次数: 0
Evolution of elliptical SAXS patterns in aligned systems 排列系统中椭圆形 SAXS 图案的演变
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-11 DOI: 10.1107/s1600576724004503
N. S. Murthy, David T. Grubb
Small-angle X-ray and neutron scattering (SAXS and SANS) patterns from certain semicrystalline polymers and liquid crystals contain discrete reflections from ordered assemblies and central diffuse scattering (CDS) from uncorrelated structures. Systems with imperfectly ordered lamellar structures aligned by stretching or by a magnetic field produce four distinct SAXS patterns: two-point `banana', four-point pattern, four-point `eyebrow' and four-point `butterfly'. The peak intensities of the reflections lie not on a layer line, or the arc of a circle, but on an elliptical trajectory. Modeling shows that randomly placed lamellar stacks modified by chain slip and stack rotation or interlamellar shear can create these forms. On deformation, the isotropic CDS becomes an equatorial streak with an oval, diamond or two-bladed propeller shape, which can be analyzed by separation into isotropic and oriented components. The streak has elliptical intensity contours, a natural consequence of the imperfect alignment of the elongated scattering objects. Both equatorial streaks and two- and four-point reflections can be fitted in elliptical coordinates with relatively few parameters. Equatorial streaks can be analyzed to obtain the size and orientation of voids, fibrils or surfaces. Analyses of the lamellar reflection yield lamellar spacing, stack orientation (interlamellar shear) angle α and chain slip angle ϕ, as well as the size distribution of the lamellar stacks. Currently available computational tools allow these microstructural parameters to be rapidly refined.
某些半结晶聚合物和液晶的小角 X 射线和中子散射(SAXS 和 SANS)图样包含有序集合体的离散反射和非相关结构的中心漫散射(CDS)。通过拉伸或磁场对齐不完全有序层状结构的系统会产生四种不同的 SAXS 图案:两点 "香蕉"、四点图案、四点 "眉毛 "和四点 "蝴蝶"。反射的峰值强度不在层线或圆弧上,而是在椭圆轨迹上。建模结果表明,随机放置的薄片堆通过链滑移、堆旋转或薄片间剪切力的作用,可以形成这些形状。变形时,各向同性的 CDS 会变成赤道条纹,其形状为椭圆形、菱形或双叶螺旋桨形,可通过将其分离为各向同性和定向成分进行分析。条纹具有椭圆形的强度轮廓,这是拉长的散射物体不完全对齐的自然结果。赤道条纹以及两点和四点反射都可以用相对较少的参数在椭圆坐标中拟合。通过分析赤道条纹,可以获得空隙、纤维或表面的大小和方向。片层反射分析可得出片层间距、叠层取向(层间剪切)角 α 和链滑移角 ϕ,以及片层叠层的尺寸分布。目前可用的计算工具可以快速完善这些微观结构参数。
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引用次数: 0
Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III 自动流水线处理 PETRA III 极端条件光束线动态压缩实验的 X 射线衍射数据
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-04 DOI: 10.1107/s1600576724004114
Mikhail Karnevskiy, K. Glazyrin, Yuelong Yu, Anshuman Mondal, Carmen Sanchez-Valle, Hauke Marquardt, R. Husband, Earl O'Bannon, C. Prescher, Anton Barty, H. Liermann
Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.
本文介绍和讨论的软件解决方案可在动态金刚石砧室技术中进行的快速动态压缩实验期间提供及时的 X 射线衍射数据分析。它包括高效的数据收集、将数据和元数据流传输到高性能集群(HPC)、在集群上进行快速方位数据整合,以及使用 DIOPTAS 软件包控制数据处理步骤和可视化数据的工具。这一数据处理管道对大量研究都非常宝贵。以高压下的氨水混合物和多相矿物集合体的数据采集为例,说明了该管道的潜力。该管道的设计具有通用性,可随时调整,为许多其他 X 射线衍射技术提供快速反馈,例如大体积压制研究、原位应力/应变研究、相变研究、利用高分辨率衍射研究化学反应等。
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引用次数: 0
Subgradient-projection-based stable phase-retrieval algorithm for X-ray ptychography 基于子梯度投影的 X 射线断层扫描稳定相位检索算法
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-04 DOI: 10.1107/s1600576724004709
Natsuki Akaishi, Koki Yamada, Kohei Yatabe, Yuki Takayama
X-ray ptychography is a lensless imaging technique that visualizes the nanostructure of a thick specimen which cannot be observed with an electron microscope. It reconstructs a complex-valued refractive index of the specimen from observed diffraction patterns. This reconstruction problem is called phase retrieval (PR). For further improvement in the imaging capability, including expansion of the depth of field, various PR algorithms have been proposed. Since a high-quality PR method is built upon a base PR algorithm such as ePIE, developing a well performing base PR algorithm is important. This paper proposes an improved iterative algorithm named CRISP. It exploits subgradient projection which allows adaptive step size and can be expected to avoid yielding a poor image. The proposed algorithm was compared with ePIE, which is a simple and fast-convergence algorithm, and its modified algorithm, rPIE. The experiments confirmed that the proposed method improved the reconstruction performance for both simulation and real data.
X 射线层析成像技术是一种无透镜成像技术,可观察到电子显微镜无法观察到的厚试样的纳米结构。它根据观察到的衍射图样重建试样的复值折射率。这种重建问题被称为相位检索(PR)。为了进一步提高成像能力,包括扩大景深,人们提出了各种相位检索算法。由于高质量的相位检索方法建立在 ePIE 等基本相位检索算法的基础上,因此开发一种性能良好的基本相位检索算法非常重要。本文提出了一种名为 CRISP 的改进迭代算法。该算法利用子梯度投影,允许自适应步长,可望避免产生不良图像。本文将提出的算法与 ePIE(一种简单、收敛快的算法)及其改进算法 rPIE 进行了比较。实验证实,所提出的方法提高了模拟和真实数据的重建性能。
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引用次数: 0
On the analysis of two-time correlation functions: equilibrium versus non-equilibrium systems. 关于双时相关函数的分析:平衡与非平衡系统。
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-04 eCollection Date: 2024-08-01 DOI: 10.1107/S1600576724004618
Anastasia Ragulskaya, Vladimir Starostin, Fajun Zhang, Christian Gutt, Frank Schreiber

X-ray photon correlation spectroscopy (XPCS) is a powerful tool for the investigation of dynamics covering a broad range of timescales and length scales. The two-time correlation function (TTC) is commonly used to track non-equilibrium dynamical evolution in XPCS measurements, with subsequent extraction of one-time correlations. While the theoretical foundation for the quantitative analysis of TTCs is primarily established for equilibrium systems, where key parameters such as the diffusion coefficient remain constant, non-equilibrium systems pose a unique challenge. In such systems, different projections ('cuts') of the TTC may lead to divergent results if the underlying fundamental parameters themselves are subject to temporal variations. This article explores widely used approaches for TTC calculations and common methods for extracting relevant information from correlation functions, particularly in the light of comparing dynamics in equilibrium and non-equilibrium systems.

X 射线光子相关光谱(XPCS)是研究涵盖广泛时间尺度和长度尺度的动力学的强大工具。在 XPCS 测量中,双时相关函数(TTC)通常用于跟踪非平衡动力学演化,并随后提取单时相关性。虽然定量分析 TTC 的理论基础主要是针对平衡系统建立的,在平衡系统中,扩散系数等关键参数保持不变,但非平衡系统带来了独特的挑战。在这类系统中,如果基本参数本身会发生时间变化,那么对 TTC 的不同预测("切割")可能会导致不同的结果。本文探讨了广泛使用的 TTC 计算方法,以及从相关函数中提取相关信息的常用方法,特别是在比较平衡和非平衡系统的动力学时。
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引用次数: 0
Mix and measure II: joint high-energy laboratory powder diffraction and microtomography for cement hydration studies. 混合与测量 II:联合高能实验室粉末衍射和显微层析技术进行水泥水化研究。
IF 6.1 3区 材料科学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2024-07-04 eCollection Date: 2024-08-01 DOI: 10.1107/S1600576724004527
Jaime Fernandez-Sanchez, Ana Cuesta, Shiva Shirani, Cinthya Redondo-Soto, Angeles G De la Torre, Isabel Santacruz, Ines R Salcedo, Laura Leon-Reina, Miguel A G Aranda

Portland cements (PCs) and cement blends are multiphase materials of different fineness, and quantitatively analysing their hydration pathways is very challenging. The dissolution (hydration) of the initial crystalline and amorphous phases must be determined, as well as the formation of labile (such as ettringite), reactive (such as portlandite) and amorphous (such as calcium silicate hydrate gel) components. The microstructural changes with hydration time must also be mapped out. To address this robustly and accurately, an innovative approach is being developed based on in situ measurements of pastes without any sample conditioning. Data are sequentially acquired by Mo Kα1 laboratory X-ray powder diffraction (LXRPD) and microtomography (µCT), where the same volume is scanned with time to reduce variability. Wide capillaries (2 mm in diameter) are key to avoid artefacts, e.g. self-desiccation, and to have excellent particle averaging. This methodology is tested in three cement paste samples: (i) a commercial PC 52.5 R, (ii) a blend of 80 wt% of this PC and 20 wt% quartz, to simulate an addition of supplementary cementitious materials, and (iii) a blend of 80 wt% PC and 20 wt% limestone, to simulate a limestone Portland cement. LXRPD data are acquired at 3 h and 1, 3, 7 and 28 days, and µCT data are collected at 12 h and 1, 3, 7 and 28 days. Later age data can also be easily acquired. In this methodology, the amounts of the crystalline phases are directly obtained from Rietveld analysis and the amorphous phase contents are obtained from mass-balance calculations. From the µCT study, and within the attained spatial resolution, three components (porosity, hydrated products and unhydrated cement particles) are determined. The analyses quantitatively demonstrate the filler effect of quartz and limestone in the hydration of alite and the calcium aluminate phases. Further hydration details are discussed.

硅酸盐水泥(PCs)和水泥混合料是不同细度的多相材料,对其水化途径进行定量分析非常具有挑战性。必须确定初始结晶相和无定形相的溶解(水化)情况,以及易溶组分(如埃特林特)、活性组分(如波长石)和无定形组分(如硅酸钙水合物凝胶)的形成情况。还必须绘制出微观结构随水化时间的变化图。为了稳健而准确地解决这一问题,我们正在开发一种创新方法,该方法基于对浆料的原位测量,无需对样品进行任何调节。通过 Mo Kα1 实验室 X 射线粉末衍射 (LXRPD) 和显微层析 (µCT) 顺序获取数据,在扫描过程中对同一体积进行扫描,以减少变化。宽毛细管(直径 2 毫米)是避免伪影(如自干燥)和获得优异颗粒平均性的关键。该方法在三种水泥浆样品中进行了测试:(i) 商品 PC 52.5 R,(ii) 80 wt% PC 和 20 wt% 石英的混合料,用于模拟添加胶凝补充材料,以及 (iii) 80 wt% PC 和 20 wt% 石灰石的混合料,用于模拟石灰石波特兰水泥。在 3 小时和 1、3、7 和 28 天时采集 LXRPD 数据,在 12 小时和 1、3、7 和 28 天时采集 µCT 数据。后期龄期数据也可轻松获取。在这种方法中,结晶相的数量可直接通过里特维尔德分析法获得,而非晶相的含量则可通过质量平衡计算获得。通过 µCT 研究,在达到的空间分辨率范围内,可以确定三种成分(孔隙率、水化产物和未水化水泥颗粒)。分析从数量上证明了石英和石灰石在水合铝土矿和铝酸钙相中的填充作用。还讨论了进一步的水化细节。
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引用次数: 0
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Journal of Applied Crystallography
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