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  1. Article: X-ray lasers for structure and dynamics in biology.

    Spence, John C H

    IUCrJ

    2018  Volume 5, Issue Pt 3, Page(s) 236–237

    Abstract: Recent advances in the application of X-ray lasers to structural biology are providing time-resolved high-resolution imaging of many processes, from enzyme kinetics to the riboswitch in action, drug action, and light-sensitive proteins. ...

    Abstract Recent advances in the application of X-ray lasers to structural biology are providing time-resolved high-resolution imaging of many processes, from enzyme kinetics to the riboswitch in action, drug action, and light-sensitive proteins.
    Language English
    Publishing date 2018-04-12
    Publishing country England
    Document type Editorial
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252518005365
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Outrunning damage: Electrons vs X-rays-timescales and mechanisms.

    Spence, John C H

    Structural dynamics (Melville, N.Y.)

    2017  Volume 4, Issue 4, Page(s) 44027

    Abstract: Toward the end of his career, Zewail developed strong interest in fast electron spectroscopy and imaging, a field to which he made important contributions toward his aim of making molecular movies free of radiation damage. We therefore compare here the ... ...

    Abstract Toward the end of his career, Zewail developed strong interest in fast electron spectroscopy and imaging, a field to which he made important contributions toward his aim of making molecular movies free of radiation damage. We therefore compare here the atomistic mechanisms leading to destruction of protein samples in diffract-and-destroy experiments for the cases of high-energy electron beam irradiation and X-ray laser pulses. The damage processes and their time-scales are compared and relevant elastic, inelastic, and photoelectron cross sections are given. Inelastic mean-free paths for ejected electrons at very low energies in insulators are compared with the bioparticle size. The dose rate and structural damage rate for electrons are found to be much lower, allowing longer pulses, reduced beam current, and Coulomb interactions for the formation of smaller probes. High-angle electron scattering from the nucleus, which has no parallel in the X-ray case, tracks the slowly moving nuclei during the explosion, just as the gain of the XFEL (X-ray free-electron laser) has no parallel in the electron case. Despite reduced damage and much larger elastic scattering cross sections in the electron case, leading to not dissimilar elastic scattering rates (when account is taken of the greatly increased incident XFEL fluence), progress for single-particle electron diffraction is seen to depend on the effort to reduce emittance growth due to Coulomb interactions, and so allow formation of intense sub-micron beams no larger than a virus.
    Language English
    Publishing date 2017-06-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2758684-4
    ISSN 2329-7778
    ISSN 2329-7778
    DOI 10.1063/1.4984606
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  3. Article ; Online: Reprint of: Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021).

    Spence, John C H / Donatelli, Jeffrey J

    Ultramicroscopy

    2021  Volume 231, Page(s) 113409

    Abstract: A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. ... ...

    Abstract A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unit ary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
    Language English
    Publishing date 2021-10-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1479043-9
    ISSN 1879-2723 ; 0304-3991
    ISSN (online) 1879-2723
    ISSN 0304-3991
    DOI 10.1016/j.ultramic.2021.113409
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Ondrej Krivanek's early scientific research.

    Spence, John C H

    Ultramicroscopy

    2017  Volume 180, Page(s) 8–13

    Abstract: In 1806, Humphrey Davey said that "nothing promotes the advancement of science so much as a new instrument". This paper reviews some of the lesser-known achievements of Ondrej's early career, and reminds us of the level of performance of instruments in ... ...

    Abstract In 1806, Humphrey Davey said that "nothing promotes the advancement of science so much as a new instrument". This paper reviews some of the lesser-known achievements of Ondrej's early career, and reminds us of the level of performance of instruments in those days, in order to appreciate how great has been the progress in instrumentation, much of it due to Ondrej and his leadership, since then. Some new results in the field of EELS are described, including extraction of the time-dependence of the dielectric response (with better time resolution than an X-ray free electron laser (XFEL)) from Nion EELS data. An approximation for atomic-resolution imaging which includes multiple scattering effects is given for biological samples, for use with aberration-corrected instruments when these become needed at the higher beam energies required to preserve the projection approximation, on which the 3D merging of single-particle cryo-EM images is based. We also discuss the requirements for out-running radiation damage using pulsed electron beams, a worthy final challenge for OLK.
    Language English
    Publishing date 2017
    Publishing country Netherlands
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1479043-9
    ISSN 1879-2723 ; 0304-3991
    ISSN (online) 1879-2723
    ISSN 0304-3991
    DOI 10.1016/j.ultramic.2016.12.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021).

    Spence, John C H / Donatelli, Jeffrey J

    Ultramicroscopy

    2021  Volume 222, Page(s) 113214

    Abstract: A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. ... ...

    Abstract A method for recovering complex structure factors from many simultaneously excited Bragg beam in- tensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unit ary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
    Language English
    Publishing date 2021-01-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1479043-9
    ISSN 1879-2723 ; 0304-3991
    ISSN (online) 1879-2723
    ISSN 0304-3991
    DOI 10.1016/j.ultramic.2021.113214
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data.

    Donatelli, Jeffrey J / Spence, John C H

    Physical review letters

    2020  Volume 125, Issue 6, Page(s) 65502

    Abstract: An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate multiple scattering artifacts from electron diffraction data, solving ... ...

    Abstract An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate multiple scattering artifacts from electron diffraction data, solving the phase problem and increasing the thicknesses of samples used in materials science, solid-state chemistry, and small molecule crystallography. For high-energy transmission electron diffraction, we show that the algorithm recovers accurate complex structure factors from a wide range of thicknesses, orientations, and relativistic beam energies, and does not require known thickness or atomic-resolution data if sufficient multiple scattering occurs. Extensions to Cryo-electron microscopy and Micro-electron diffraction are suggested.
    Language English
    Publishing date 2020-08-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.125.065502
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    In stock of ZB MED Bonn / Germany

    Z 4' 58/153: Show issues

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  7. Article: X-ray lasers and serial crystallography.

    Spence, John C H

    IUCrJ

    2015  Volume 2, Issue Pt 3, Page(s) 305–306

    Abstract: A summary is given of the achievements and opportunities which resulted from the first use of an X-ray laser for serial crystallography and related methods in 2009. ...

    Abstract A summary is given of the achievements and opportunities which resulted from the first use of an X-ray laser for serial crystallography and related methods in 2009.
    Language English
    Publishing date 2015-04-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252515008027
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  8. Article: Split-Second Reactions.

    Fromme, Petra / Spence, John C H

    Scientific American

    2017  Volume 316, Issue 5, Page(s) 62–67

    MeSH term(s) Crystallization ; Crystallography, X-Ray/methods ; Eye ; Humans ; Lasers ; Ocular Physiological Phenomena ; Photosynthesis ; Plant Leaves/metabolism ; Plant Leaves/radiation effects ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Plant Proteins/ultrastructure ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/ultrastructure ; Sunlight ; Vision, Ocular ; X-Rays
    Chemical Substances Plant Proteins ; Receptors, G-Protein-Coupled
    Language English
    Publishing date 2017-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 246-x
    ISSN 1946-7087 ; 0036-8733
    ISSN (online) 1946-7087
    ISSN 0036-8733
    DOI 10.1038/scientificamerican0517-62
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1209: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article: X-ray lasers and crystallography.

    Spence, John C H

    IUCrJ

    2014  Volume 1, Issue Pt 3, Page(s) 151–152

    Abstract: The development of X-ray lasers and their applications in crystallography is described. In the birth of this new field, IUCrJ is ideally positioned to present this research to both specialists in crystallography, and to the wider audience in structural ... ...

    Abstract The development of X-ray lasers and their applications in crystallography is described. In the birth of this new field, IUCrJ is ideally positioned to present this research to both specialists in crystallography, and to the wider audience in structural biology.
    Language English
    Publishing date 2014-04-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252514009567
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  10. Article: Approaches to time-resolved diffraction using an XFEL.

    Spence, John C H

    Faraday discussions

    2014  Volume 171, Page(s) 429–438

    Abstract: We describe several schemes for time-resolved imaging of molecular motion using a free-electron laser (XFEL), in response to the many challenges and opportunities which XFEL radiation has created for accurate time-resolved measurement of structure. For ... ...

    Abstract We describe several schemes for time-resolved imaging of molecular motion using a free-electron laser (XFEL), in response to the many challenges and opportunities which XFEL radiation has created for accurate time-resolved measurement of structure. For pump-probe experiments using crystals, the problem of recording full Bragg reflections (not partials) in each shot arises. Two solutions, the use of the large bandwith which necesarily results from using attosecond pulses, and the use the coherent convergent beam mode are suggested. We also show that with attosecond recording times shorter than the temporal coherence time, Bragg reflections excited by different wavelengths from different reflections can interfere, providing structure factor phase information. For slower processes, a mixing jet sample-delivery device is described to allow snapshot solution scattering during molecular reactions on the microsecond scale. For optically excited membrane proteins, we suggest the use of the lipid cubic phase sample delivery device operating at atmospheric pressure. The use of two-color and split-and-delay schemes is suggested for improved accuracy in the Monte-Carlo method of serial femtosecond crystallography (SFX).
    MeSH term(s) Crystallography, X-Ray/methods ; Lasers ; Monte Carlo Method ; X-Ray Diffraction
    Language English
    Publishing date 2014
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1359-6640
    ISSN 1359-6640
    DOI 10.1039/c4fd00025k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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