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Title: Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

Abstract

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. In conclusion, it is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [1];  [5];  [6];  [1];  [6];  [7];  [6];  [8];  [1]
  1. European XFEL GmbH, Schenefeld (Germany)
  2. Russian Academy of Sciences, Moscow (Russian Federation)
  3. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany)
  4. National Univ. of Singapore (Sinagpore)
  5. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  7. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  8. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Center for Ultrafast Imaging, Hamburg (Germany); Polish Academy of Sciences, Krakow (Poland)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1394070
Grant/Contract Number:  
AC02-76SF00515; 654220
Resource Type:
Accepted Manuscript
Journal Name:
IUCrJ
Additional Journal Information:
Journal Volume: 4; Journal Issue: 5; Journal ID: ISSN 2052-2525
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; single-particle imaging; X-ray free-electron lasers; simulations; diffraction; scattering

Citation Formats

Fortmann-Grote, Carsten, Buzmakov, Alexey, Jurek, Zoltan, Loh, Ne-Te Duane, Samoylova, Liubov, Santra, Robin, Schneidmiller, Evgeny A., Tschentscher, Thomas, Yakubov, Sergey, Yoon, Chun Hong, Yurkov, Michael V., Ziaja-Motyka, Beata, and Mancuso, Adrian P. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser. United States: N. p., 2017. Web. doi:10.1107/S2052252517009496.
Fortmann-Grote, Carsten, Buzmakov, Alexey, Jurek, Zoltan, Loh, Ne-Te Duane, Samoylova, Liubov, Santra, Robin, Schneidmiller, Evgeny A., Tschentscher, Thomas, Yakubov, Sergey, Yoon, Chun Hong, Yurkov, Michael V., Ziaja-Motyka, Beata, & Mancuso, Adrian P. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser. United States. doi:10.1107/S2052252517009496.
Fortmann-Grote, Carsten, Buzmakov, Alexey, Jurek, Zoltan, Loh, Ne-Te Duane, Samoylova, Liubov, Santra, Robin, Schneidmiller, Evgeny A., Tschentscher, Thomas, Yakubov, Sergey, Yoon, Chun Hong, Yurkov, Michael V., Ziaja-Motyka, Beata, and Mancuso, Adrian P. Fri . "Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser". United States. doi:10.1107/S2052252517009496. https://www.osti.gov/servlets/purl/1394070.
@article{osti_1394070,
title = {Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser},
author = {Fortmann-Grote, Carsten and Buzmakov, Alexey and Jurek, Zoltan and Loh, Ne-Te Duane and Samoylova, Liubov and Santra, Robin and Schneidmiller, Evgeny A. and Tschentscher, Thomas and Yakubov, Sergey and Yoon, Chun Hong and Yurkov, Michael V. and Ziaja-Motyka, Beata and Mancuso, Adrian P.},
abstractNote = {Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. In conclusion, it is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.},
doi = {10.1107/S2052252517009496},
journal = {IUCrJ},
number = 5,
volume = 4,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

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Cited by: 2 works
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Figures / Tables:

Figure 1 Figure 1: The temporal structure of the simulated X-ray pulse, the average number of bound electrons (Zbound, dashed curves) and the average atomic displacements (solid curves) in the 2nip sample as a function of time for pulse durations of (a) 3 fs, (b) 9 fs and (c) 30 fs.

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