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


ABSTRACT: 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.

SUBMITTER: Yoon CH 

PROVIDER: S-EPMC4842992 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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

Yoon Chun Hong CH   Yurkov Mikhail V MV   Schneidmiller Evgeny A EA   Samoylova Liubov L   Buzmakov Alexey A   Jurek Zoltan Z   Ziaja Beata B   Santra Robin R   Loh N Duane ND   Tschentscher Thomas T   Mancuso Adrian P AP  

Scientific reports 20160425


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) simu  ...[more]

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