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Title: | A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser | Authors: | Yoon, C.H Yurkov, M.V Schneidmiller, E.A Samoylova, L Buzmakov, A Jurek, Z Ziaja, B Santra, R Loh, N.D Tschentscher, T Mancuso, A.P |
Keywords: | nitrogenase reductase oxidoreductase chemistry computer simulation devices electron laser photon procedures protein conformation theoretical model three dimensional imaging X ray crystallography X ray diffraction Computer Simulation Crystallography, X-Ray Electrons Imaging, Three-Dimensional Lasers Models, Theoretical Oxidoreductases Photons Protein Conformation X-Ray Diffraction |
Issue Date: | 2016 | Citation: | Yoon, C.H, Yurkov, M.V, Schneidmiller, E.A, Samoylova, L, Buzmakov, A, Jurek, Z, Ziaja, B, Santra, R, Loh, N.D, Tschentscher, T, Mancuso, A.P (2016). A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. Scientific Reports 6 : 24791. ScholarBank@NUS Repository. https://doi.org/10.1038/srep24791 | Rights: | Attribution 4.0 International | 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. © 2016, Nature Publishing Group. All rights reserved. | Source Title: | Scientific Reports | URI: | https://scholarbank.nus.edu.sg/handle/10635/178915 | ISSN: | 20452322 | DOI: | 10.1038/srep24791 | Rights: | Attribution 4.0 International |
Appears in Collections: | Elements Staff Publications |
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