Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data

Toshiyuki Nishiyama, Akinobu Niozu, Christoph Bostedt, Ken R. Ferguson, Yuhiro Sato, Christopher Hutchison, Kiyonobu Nagaya, Hironobu Fukuzawa, Koji Motomura, Shin Ichi Wada, Tsukasa Sakai, Kenji Matsunami, Kazuhiro Matsuda, Tetsuya Tachibana, Yuta Ito, Weiqing Xu, Subhendu Mondal, Takayuki Umemoto, Christophe Nicolas, Catalin MironTakashi Kameshima, Yasumasa Joti, Kensuke Tono, Takaki Hatsui, Makina Yabashi, Kiyoshi Ueda

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


With the emergence of X-ray free-electron lasers, it is possible to investigate the structure of nanoscale samples by employing coherent diffractive imaging in the X-ray spectral regime. In this work, we developed a refinement method for structure reconstruction applicable to low-quality coherent diffraction data. The method is based on the gradient search method and considers the missing region of a diffraction pattern and the small number of detected photons. We introduced an initial estimate of the structure in the method to improve the convergence. The present method is applied to an experimental diffraction pattern of an Xe cluster obtained in an X-ray scattering experiment at the SPring-8 Angstrom Compact free-electron LAser (SACLA) facility. It is found that the electron density is successfully reconstructed from the diffraction pattern with a large missing region, with a good initial estimate of the structure. The diffraction pattern calculated from the reconstructed electron density reproduced the observed diffraction pattern well, including the characteristic intensity modulation in each ring. Our refinement method enables structure reconstruction from diffraction patterns under difficulties such as missing areas and low diffraction intensity, and it is potentially applicable to the structure determination of samples that have low scattering power.

Original languageEnglish
Pages (from-to)10-17
Number of pages8
Publication statusPublished - 2020 Jan 1


  • XFELs
  • clusters
  • coherent diffractive imaging
  • computation
  • electron density
  • phase problem
  • single particles
  • structure reconstruction

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry
  • Materials Science(all)
  • Condensed Matter Physics


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