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Title: A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.
 [1] ;  [2] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [3] ;  [3]
  1. European XFEL GmbH, Hamburg (Germany); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  2. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  3. European XFEL GmbH, Hamburg (Germany)
  4. Russian Academy of Sciences, Moscow (Russia)
  5. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany)
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); he Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Polish Academy of Sciences, Krakow (Poland)
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
  8. National Univ. of Singapore (Singapore)
Publication Date:
Grant/Contract Number:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2045-2322
Nature Publishing Group
Research Org:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
42 ENGINEERING; atomic and molecular interactions with photons; single-molecule biophysics; X-rays
OSTI Identifier: