Journal Article

PUBDB-2016-01805

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

Yoon, C. H. (Corresponding author)CFEL*DESY* ; Yurkov, M.DESY* ; Schneidmiller, E. A.DESY* ; Samoylova, L.>Extern*XFEL.EU* ; Buzmakov, A.>Extern*XFEL.EU* ; Jurek, Z.CFEL*DESY* ; Ziaja, B.CFEL*DESY* ; Santra, R.CFEL*DESY* ; Loh, N. D. ; Tschentscher, T.>Extern*XFEL.EU* ; Mancuso, A. P. (Corresponding author)>Extern*XFEL.EU*

2016
Nature Publishing Group London

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Please use a persistent id in citations: doi:10.1038/srep24791  doi:10.3204/PUBDB-2016-01805

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.

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Contributing Institute(s):

1. CFEL-Coherent X-Ray Imaging (FS-CFEL-1)
2. CFEL-Theory (FS-CFEL-3)
3. European XFEL (Eur.XFEL)

Research Program(s):

1. 6211 - Extreme States of Matter: From Cold Ions to Hot Plasmas (POF3-621) (POF3-621)
2. 6G13 - XFEL (POF3-622) (POF3-622)
3. BIOSTRUCT-X - Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities (283570) (283570)
4. CUI - Hamburger Zentrum für ultraschnelle Beobachtung (194651731) (194651731)

Experiment(s):

1. SPB: Single Particles, clusters & Biomolecules (SASE1)

Appears in the scientific report 2016

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Database coverage:
; ; ; ; BIOSIS Previews ; IF >= 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection ; Zoological Record

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