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  • X-ray lasersXFELsbiologystructuredynamics  (2)
  • quasicrystalssuperspace crystallographystructure analysisphasonsX-ray diffuse scattering  (2)
  • Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy  (1)
  • International Union of Crystallography (IUCr)  (5)
  • American Institute of Physics
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  • International Union of Crystallography (IUCr)  (5)
  • American Institute of Physics
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  • 1
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2016-06-28
    Keywords: quasicrystalssuperspace crystallographystructure analysisphasonsX-ray diffuse scattering
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2016-06-15
    Description: The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.
    Keywords: quasicrystalssuperspace crystallographystructure analysisphasonsX-ray diffuse scattering
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
    Publication Date: 2018-11-09
    Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
    Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 4
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-07-01
    Keywords: X-ray lasersXFELsbiologystructuredynamics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 5
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-05-11
    Description: The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump–probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallography to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
    Keywords: X-ray lasersXFELsbiologystructuredynamics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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