A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser Academic Article uri icon


  • 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. 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.


  • Yoon, Chun Hong
  • Yurkov, Mikhail V
  • Schneidmiller, Evgeny A
  • Samoylova, Liubov
  • Buzmakov, Alexey
  • Jurek, Zoltan
  • Ziaja, Beata
  • Santra, Robin
  • Loh, N Duane
  • Tschentscher, Thomas
  • Mancuso, Adrian

publication date

  • 2016