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Title: 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. Furthermore, 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.

Authors:
 [1];  [2];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [3];  [3]
  1. European XFEL GmbH, Hamburg (Germany); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  2. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  3. European XFEL GmbH, Hamburg (Germany)
  4. Russian Academy of Sciences, Moscow (Russia)
  5. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany)
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); he Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Polish Academy of Sciences, Krakow (Poland)
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
  8. National Univ. of Singapore (Singapore)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1253731
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
42 ENGINEERING; atomic and molecular interactions with photons; single-molecule biophysics; X-rays

Citation Formats

Yoon, Chun Hong, Yurkov, Mikhail V., Schneidmiller, Evgeny A., Samoylova, Liubov, Buzmakov, Alexey, Jurek, Zoltan, Ziaja, Beata, Santra, Robin, Loh, N. Duane, Tschentscher, Thomas, and Mancuso, Adrian P. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. United States: N. p., 2016. Web. doi:10.1038/srep24791.
Yoon, Chun Hong, Yurkov, Mikhail V., Schneidmiller, Evgeny A., Samoylova, Liubov, Buzmakov, Alexey, Jurek, Zoltan, Ziaja, Beata, Santra, Robin, Loh, N. Duane, Tschentscher, Thomas, & Mancuso, Adrian P. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. United States. doi:10.1038/srep24791.
Yoon, Chun Hong, Yurkov, Mikhail V., Schneidmiller, Evgeny A., Samoylova, Liubov, Buzmakov, Alexey, Jurek, Zoltan, Ziaja, Beata, Santra, Robin, Loh, N. Duane, Tschentscher, Thomas, and Mancuso, Adrian P. Mon . "A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser". United States. doi:10.1038/srep24791. https://www.osti.gov/servlets/purl/1253731.
@article{osti_1253731,
title = {A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser},
author = {Yoon, Chun Hong and Yurkov, Mikhail V. and Schneidmiller, Evgeny A. and Samoylova, Liubov and Buzmakov, Alexey and Jurek, Zoltan and Ziaja, Beata and Santra, Robin and Loh, N. Duane and Tschentscher, Thomas and Mancuso, Adrian P.},
abstractNote = {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. Furthermore, 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.},
doi = {10.1038/srep24791},
journal = {Scientific Reports},
number = ,
volume = 6,
place = {United States},
year = {Mon Apr 25 00:00:00 EDT 2016},
month = {Mon Apr 25 00:00:00 EDT 2016}
}

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Works referenced in this record:

RELION: Implementation of a Bayesian approach to cryo-EM structure determination
journal, December 2012