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000297261 1001_ $$0P:(DE-H253)PIP1016300$$aYoon, Chun Hong$$b0$$eCorresponding author$$udesy
000297261 245__ $$aA comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser
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000297261 520__ $$aThe advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.
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000297261 7001_ $$0P:(DE-H253)PIP1001234$$aYurkov, Mikhail$$b1$$udesy
000297261 7001_ $$0P:(DE-H253)PIP1001599$$aSchneidmiller, Evgeny Alexanrdovich$$b2$$udesy
000297261 7001_ $$0P:(DE-H253)PIP1006674$$aSamoylova, Liubov$$b3
000297261 7001_ $$0P:(DE-H253)PIP1014327$$aBuzmakov, Alexey$$b4
000297261 7001_ $$0P:(DE-H253)PIP1013492$$aJurek, Zoltan$$b5$$udesy
000297261 7001_ $$0P:(DE-H253)PIP1003464$$aZiaja, Beata$$b6$$udesy
000297261 7001_ $$0P:(DE-H253)PIP1012203$$aSantra, Robin$$b7$$udesy
000297261 7001_ $$0P:(DE-HGF)0$$aLoh, N. Duane$$b8
000297261 7001_ $$0P:(DE-H253)PIP1001329$$aTschentscher, Thomas$$b9
000297261 7001_ $$0P:(DE-H253)PIP1006340$$aMancuso, Adrian Paul$$b10$$eCorresponding author
000297261 773__ $$0PERI:(DE-600)2615211-3$$a10.1038/srep24791$$gVol. 6, p. 24791 -$$p24791$$tScientific reports$$v6$$x2045-2322$$y2016
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