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. 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.
European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.|Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Chun Hong
CH
Yoon
DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Mikhail V
MV
Yurkov
DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Evgeny A
EA
Schneidmiller
European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.
Liubov
L
Samoylova
Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow 119333, Russia.
Alexey
A
Buzmakov
Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.|The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.
Zoltan
Z
Jurek
Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.|The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.|Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland.
Beata
B
Ziaja
Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.|The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.|Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany.
Robin
R
Santra
Centre for Bio-Imaging Sciences, National University of Singapore, Singapore.|Department of Biological Sciences, National University of Singapore, Singapore.|Department of Physics, National University of Singapore, Singapore.
N Duane
ND
Loh
European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.
Thomas
T
Tschentscher
European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.
Adrian P
AP
Mancuso
D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000295:instrumentation* / Q000379:methods; D004583:Electrons; D021621:Imaging, Three-Dimensional; D007834:Lasers; D008962:Models, Theoretical; D010088:Oxidoreductases / Q000737:chemistry*; D017785:Photons; D011487:Protein Conformation; D014961:X-Ray Diffraction
D010088:Oxidoreductases; C029130:nitrogenase reductase