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  1. Article ; Online: Fourth-generation light sources.

    Chapman, Henry N

    IUCrJ

    2023  Volume 10, Issue Pt 3, Page(s) 246–247

    Abstract: New fourth-generation synchrotron radiation facilities bring large gains in X-ray source brightness, but also challenges in making full use of their potentials. Some of these challenges have been faced at X-ray free-electron laser facilities. ...

    Abstract New fourth-generation synchrotron radiation facilities bring large gains in X-ray source brightness, but also challenges in making full use of their potentials. Some of these challenges have been faced at X-ray free-electron laser facilities.
    Language English
    Publishing date 2023-05-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525 ; 2052-2525
    ISSN (online) 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252523003585
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  2. Article ; Online: DriftRec: Adapting Diffusion Models to Blind JPEG Restoration.

    Welker, Simon / Chapman, Henry N / Gerkmann, Timo

    IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

    2024  Volume 33, Page(s) 2795–2807

    Abstract: In this work, we utilize the high-fidelity generation abilities of diffusion models to solve blind JPEG restoration at high compression levels. We propose an elegant modification of the forward stochastic differential equation of diffusion models to ... ...

    Abstract In this work, we utilize the high-fidelity generation abilities of diffusion models to solve blind JPEG restoration at high compression levels. We propose an elegant modification of the forward stochastic differential equation of diffusion models to adapt them to this restoration task and name our method DriftRec. Comparing DriftRec against an L
    Language English
    Publishing date 2024-04-11
    Publishing country United States
    Document type Journal Article
    ISSN 1941-0042
    ISSN (online) 1941-0042
    DOI 10.1109/TIP.2024.3383776
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  3. Article ; Online: X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.

    Chapman, Henry N

    Annual review of biochemistry

    2019  Volume 88, Page(s) 35–58

    Abstract: X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources ... ...

    Abstract X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
    MeSH term(s) Crystallization/instrumentation ; Crystallization/methods ; Crystallography, X-Ray/history ; Crystallography, X-Ray/instrumentation ; Crystallography, X-Ray/methods ; Electrons ; History, 20th Century ; History, 21st Century ; Lasers/history ; Macromolecular Substances/ultrastructure ; Photons ; Synchrotrons/instrumentation ; Virion/ultrastructure ; X-Ray Diffraction/history ; X-Ray Diffraction/instrumentation ; X-Ray Diffraction/methods ; X-Rays
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2019-01-02
    Publishing country United States
    Document type Historical Article ; Journal Article ; Review
    ZDB-ID 207924-0
    ISSN 1545-4509 ; 0066-4154
    ISSN (online) 1545-4509
    ISSN 0066-4154
    DOI 10.1146/annurev-biochem-013118-110744
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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.209: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Ab initio spatial phase retrieval via intensity triple correlations.

    Peard, Nolan / Ayyer, Kartik / Chapman, Henry N

    Optics express

    2023  Volume 31, Issue 15, Page(s) 25082–25092

    Abstract: Second-order intensity correlations from incoherent emitters can reveal the Fourier transform modulus of their spatial distribution, but retrieving the phase to enable completely general Fourier inversion to real space remains challenging. Phase ... ...

    Abstract Second-order intensity correlations from incoherent emitters can reveal the Fourier transform modulus of their spatial distribution, but retrieving the phase to enable completely general Fourier inversion to real space remains challenging. Phase retrieval via the third-order intensity correlations has relied on special emitter configurations which simplified an unaddressed sign problem in the computation. Without a complete treatment of this sign problem, the general case of retrieving the Fourier phase from a truly arbitrary configuration of emitters is not possible. In this paper, a general method for ab initio phase retrieval via the intensity triple correlations is described. Simulations demonstrate accurate phase retrieval for clusters of incoherent emitters which could be applied to imaging stars or fluorescent atoms and molecules. With this work, it is now finally tractable to perform Fourier inversion directly and reconstruct images of arbitrary arrays of independent emitters via far-field intensity correlations alone.
    Language English
    Publishing date 2023-07-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1491859-6
    ISSN 1094-4087 ; 1094-4087
    ISSN (online) 1094-4087
    ISSN 1094-4087
    DOI 10.1364/OE.495920
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  5. Article ; Online: Crystal diffraction prediction and partiality estimation using Gaussian basis functions.

    Brehm, Wolfgang / White, Thomas / Chapman, Henry N

    Acta crystallographica. Section A, Foundations and advances

    2023  Volume 79, Issue Pt 2, Page(s) 145–162

    Abstract: The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction ... ...

    Abstract The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
    Language English
    Publishing date 2023-02-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2020844-3
    ISSN 2053-2733 ; 1600-5724 ; 0108-7673
    ISSN (online) 2053-2733 ; 1600-5724
    ISSN 0108-7673
    DOI 10.1107/S2053273323000682
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  6. Article ; Online: A detector for the sources.

    Chapman, Henry N

    Nature methods

    2018  Volume 15, Issue 10, Page(s) 774–775

    MeSH term(s) Crystallography ; Data Collection
    Language English
    Publishing date 2018-10-01
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-018-0150-8
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6022: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  7. Article ; Online: Structure Determination Using X-Ray Free-Electron Laser Pulses.

    Chapman, Henry N

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1607, Page(s) 295–324

    Abstract: The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to ...

    Abstract The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to macromolecular crystals by several orders of magnitude higher than usually tolerable in conventional measurements, allowing crystal size to be decreased dramatically in diffraction measurements and without the need to cool the sample. Such pulses lead to the eventual vaporization of the sample, which has required a measurement approach, called serial crystallography, of consolidating snapshot diffraction patterns of many individual crystals. This in turn has further separated the connection between dose and obtainable diffraction information, with the only requirement from a single pattern being that to give enough information to place it, in three-dimensional reciprocal space, in relation to other patterns. Millions of extremely weak patterns can be collected and combined in this way, requiring methods to rapidly replenish the sample into the beam while generating the lowest possible background . The method is suited to time-resolved measurements over timescales below 1 ps to several seconds, and opens new opportunities for phasing. Some straightforward considerations of achievable signal levels are discussed and compared with a wide variety of recent experiments carried out at XFEL, synchrotron, and even laboratory sources, to discuss the capabilities of these new approaches and give some perspectives on their further development.
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7000-1_12
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  8. Article ; Online: Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates.

    Stagno, Jason R / Knoska, Juraj / Chapman, Henry N / Wang, Yun-Xing

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2568, Page(s) 243–249

    Abstract: Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers ( ... ...

    Abstract Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers (XFEL), a new frontier has emerged in time-resolved crystallography whereby crystals can be mixed with ligand and then probed with X-rays (mix-and-inject) in real time and at room temperature. This chapter outlines the basic setup and procedures for mix-and-inject experiments for recording time-resolved crystallographic data of riboswitch RNA reaction states using serial femtosecond crystallography (SFX) and an XFEL.
    MeSH term(s) Crystallography/methods ; Crystallography, X-Ray ; Lasers ; Ligands ; RNA ; Riboswitch
    Chemical Substances Ligands ; Riboswitch ; RNA (63231-63-0)
    Language English
    Publishing date 2022-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2687-0_16
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  9. Article ; Online: Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions.

    Cardoch, Sebastian / Trost, Fabian / Scott, Howard A / Chapman, Henry N / Caleman, Carl / Timneanu, Nicusor

    Physical review. E

    2023  Volume 107, Issue 1-2, Page(s) 15205

    Abstract: Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the ... ...

    Abstract Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted x-ray laser pulses, but a detailed account of changes in opacity and emergence of resonances is still missing. In this computational work, we employ nonlocal thermodynamic equilibrium plasma simulations to study the interaction of femtosecond x rays and copper. Following the onset of frustrated absorption, we find that a K-M resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter x-ray pulses. Intense femtosecond x rays are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.
    Language English
    Publishing date 2023-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.107.015205
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  10. Article: Disruptive photon technologies for chemical dynamics.

    Chapman, Henry N

    Faraday discussions

    2014  Volume 171, Page(s) 525–543

    Abstract: A perspective of new and emerging technologies for chemical dynamics is given, with an emphasis on the use of X-ray sources that generate sub-picosecond pulses. The two classes of experimental techniques used for time-resolved measurements of chemical ... ...

    Abstract A perspective of new and emerging technologies for chemical dynamics is given, with an emphasis on the use of X-ray sources that generate sub-picosecond pulses. The two classes of experimental techniques used for time-resolved measurements of chemical processes and their effects are spectroscopy and imaging, where the latter includes microscopy, diffractive imaging, and crystallography. X-Ray free-electron lasers have brought new impetus to the field, allowing not only temporal and spatial resolution at atomic time and length scales, but also bringing a new way to overcome limitations due to perturbation of the sample by the X-ray probe by out-running radiation damage. Associated instrumentation and methods are being developed to take advantage of the new opportunities of these sources. Once these methods of observational science have been mastered it should be possible to use the new tools to directly control those chemical processes.
    Language English
    Publishing date 2014
    Publishing country England
    Document type Journal Article
    ISSN 1359-6640
    ISSN 1359-6640
    DOI 10.1039/c4fd00156g
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