Diffractive Imaging of Crystalline Materials at XFELs and Synchrotrons

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: 28 June 2024 | Viewed by 2522

Special Issue Editors


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Guest Editor
Center for Free-Electron Laser Science DESY, Hamburg, Germany
Interests: XFEL; serial femtosecond crystallography (SFX); coherent diffractive imaging; X-ray holography and diffraction microscopy

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Guest Editor
School of Science, RMIT University, Melbourne VIC 3000, Australia
Interests: XFEL; coherent diffractive imaging; data processing; serial crystallography; fluctuation X-ray scattering

Special Issue Information

Dear Colleagues,

Crystals, one of the most common forms of matter, are extremely fascinating and have been the focus of studies for centuries even before the birth of crystallography. Since the first X-ray diffraction experiments and the subsequent molecular structure determination from crystals in the early twentieth century, X-ray science and technologies have advanced dramatically over the past hundred years. The scientific community has witnessed and benefitted from the birth of large-scale brighter x-ray facilities like synchrotrons and more recently, the x-ray free-electron lasers (XFELs) in the last two decades. Meanwhile, along with crystallography, ultrafast diffractive imaging has emerged as a powerful technique providing unprecedented insights into the structure and dynamics of matter. With the rapid advancements in the design and capabilities of synchrotrons and XFELs, and with the advancements in the field of diffractive imaging, there is a significant interest among the community in condensing the recent knowledge on diffractive imaging of the structure and dynamics of crystalline materials at synchrotrons and XFELs. To realize this, we invite you—the scientific community, friends and colleagues, to contribute to this Special Issue focusing on “Diffractive Imaging of Crystalline Materials at XFELs and Synchrotrons”.

The scope of this Special Issue spans several aspects of coherent diffractive imaging (CDI) of crystals with a focus on nanoscale crystalline materials. The topics covered are serial/single-crystal diffractive imaging of macromolecular/inorganic materials (e.g.: serial macromolecular crystallography, fiber-diffraction, grain-mapping in case of inorganic nanocrystals), instrumentation and sample delivery for diffractive imaging, Bragg-CDI, ptychography, holography, x-ray microscopy, projection imaging, fluctuation imaging, and ultrafast pump-probe diffractive imaging of nanocrystals, data processing for high repetition rate XFELs including the development of software and algorithms including machine learning methods. Your contribution could either be a review article condensing the recent signs of progress in these areas or a perspective focusing on future developments of a specific technique or a class of crystalline materials or even a facility/instrument, or it could be a rapid communication/full-article with original theoretical or experimental research results!

Note: As this Special Issue focuses exclusively on crystalline materials and within the scope of the journal, articles on diffractive imaging of non-crystalline materials are not covered; however, the potential of extension of crystallographic methods to imaging non-crystalline materials can be discussed briefly in your submissions.

The submission deadline is July 31, 2023. Please get in touch with us, should you have any questions on this Special Issue!

Looking forward to receiving your contributions!

Dr. Chufeng Li
Dr. Andrew V. Martin
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • diffractive imaging
  • macromolecular, organic, and inorganic crystals
  • quasicrystals
  • liquid crystals
  • fiber diffraction
  • serial crystallography
  • data processing in diffractive imaging
  • holography of crystalline materials
  • sample delivery for diffractive imaging
  • free electron laser, X-ray diffraction, ultra-fast X-ray diffraction, serial femto-second crystallography, coherent diffractive imaging, X-ray diffraction microscopy, 3-dimensional X-ray diffraction (3DXRD)
  • grain orientation mapping, diffraction contrast tomography(DCT
  • X-ray topography
  • Bragg coherent diffractive imaging (BCDI)
  • Bragg ptychography
  • high volume and throughput data analysis
  • machine learning
  • multigrain crystallography
  • diffraction data analysis

Published Papers (2 papers)

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Research

15 pages, 2426 KiB  
Article
EXtra-Xwiz: A Tool to Streamline Serial Femtosecond Crystallography Workflows at European XFEL
by Oleksii Turkot, Fabio Dall’Antonia, Richard J. Bean, Juncheng E, Hans Fangohr, Danilo E. Ferreira de Lima, Sravya Kantamneni, Henry J. Kirkwood, Faisal H. M. Koua, Adrian P. Mancuso, Diogo V. M. Melo, Adam Round, Michael Schuh, Egor Sobolev, Raphaël de Wijn, James J. Wrigley and Luca Gelisio
Crystals 2023, 13(11), 1533; https://doi.org/10.3390/cryst13111533 - 24 Oct 2023
Cited by 2 | Viewed by 1073
Abstract
X-ray free electron lasers deliver photon pulses that are bright enough to observe diffraction from extremely small crystals at a time scale that outruns their destruction. As crystals are continuously replaced, this technique is termed serial femtosecond crystallography (SFX). Due to its high [...] Read more.
X-ray free electron lasers deliver photon pulses that are bright enough to observe diffraction from extremely small crystals at a time scale that outruns their destruction. As crystals are continuously replaced, this technique is termed serial femtosecond crystallography (SFX). Due to its high pulse repetition rate, the European XFEL enables the collection of rich and extensive data sets, which are suited to study various scientific problems, including ultra-fast processes. The enormous data rate, data complexity, and the nature of the pixelized multimodular area detectors at the European XFEL pose severe challenges to users. To streamline the analysis of the SFX data, we developed the semiautomated pipeline EXtra-Xwiz around the established CrystFEL program suite, thereby processing diffraction patterns on detector frames into structure factors. Here we present EXtra-Xwiz, and we introduce its architecture and use by means of a tutorial. Future plans for its development and expansion are also discussed. Full article
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12 pages, 2903 KiB  
Article
An Optimized Approach for Serial Crystallography Using Chips
by Marina Galchenkova, Aida Rahmani Mashhour, Patrick Y. A. Reinke, Sebastian Günther, Jan Meyer, Henry N. Chapman and Oleksandr M. Yefanov
Crystals 2023, 13(8), 1225; https://doi.org/10.3390/cryst13081225 - 9 Aug 2023
Viewed by 1063
Abstract
Serial crystallography is a rapidly developing method for the determination of the structure of biomolecules at room temperature at near-atomic resolution from an ensemble of small crystals. Numerous advances in detectors, data analysis pipelines, sample delivery methods, and crystallization protocols expand the scope [...] Read more.
Serial crystallography is a rapidly developing method for the determination of the structure of biomolecules at room temperature at near-atomic resolution from an ensemble of small crystals. Numerous advances in detectors, data analysis pipelines, sample delivery methods, and crystallization protocols expand the scope of structural biology to understand the fundamental processes that take place in living cells. Many experimental strategies for serial crystallography are in use, depending on the type and sizes of the crystals or other needs of the experiment. Such strategies should ideally minimize the wastage of samples or beamtime without compromising experimental goals. This paper proposes a way to optimize beamtime utilization in serial crystallography experiments that use fixed-target sample delivery methods, such as chips. The strategy involves two key steps. Firstly, a fast raster scan of the chip is performed to determine the positions of the crystals based on their diffraction. Subsequently, a rotational series is collected at each identified crystal position, covering a narrow range of chip orientations. This approach enables the exclusion of empty positions during data acquisition, resulting in significant savings in beam time utilization and a reduced volume of measured data. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Fiber Diffraction at XFELs and Synchrotrons
Authors: Paul Lourdu Xavier
Affiliation: 1.Center for Free-Electron Laser Science DESY, Hamburg, Germany 2.Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany

Title: Diffractive Imaging of Inorganic Nanocrystals at XFELs and Synchrotrons
Authors: Paul Lourdu Xavier; Chufeng Li
Affiliation: 1.Center for Free-Electron Laser Science DESY, Hamburg, Germany 2.Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany

Title: EXtra-Xwiz: a tool to streamline serial femtosecond crystallography workflows at European XFEL
Authors: Oleksii Turkot; Fabio Dall’Antonia; Richard J. Bean; Juncheng E; Hans Fangohr; Danilo E. Ferreira de Lima; Sravya Kantamneni; Henry Kirkwood; Faisal H. M. Koua; Adrian P. Mancuso[*]; Diogo Melo; Adam Round; Egor Sobolev; Raphael de Wijn; James J. Wrigley; Luca Gelisio
Affiliation: [all] European XFEL GmbH, Holzkoppel 4, 22069 Schenefeld, Germany. [*] La Trobe Institute for Molecular Science, Melbourne, VIC 3086, Australia.
Abstract: X-ray free electron lasers deliver photon pulses which are bright enough to observe diffraction from extremely small crystals, at a time scale outrunning their destruction. As crystals are continuously replaced, this technique is termed serial femtosecond crystallography (SFX). Due to its high pulse repetition rate, the European XFEL enables the collection of rich and extensive data sets, suited to study various scientific problems including ultrafast processes. The enormous data rate, data complexity, and the nature of the pixelized multi-modular area detectors at European XFEL pose severe challenges to users. To streamline the analysis of SFX data, we developed the semi-automated pipeline EXtra-Xwiz around the established CrystFEL program suite, processing diffraction patterns on detector frames into structure factors.

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