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

Abstract

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.

Authors:
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Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1605029
Grant/Contract Number:  
[AC02-76SF00515; 11604003]
Resource Type:
Accepted Manuscript
Journal Name:
IUCrJ
Additional Journal Information:
[ Journal Volume: 7; Journal Issue: 1]; Journal ID: ISSN 2052-2525
Country of Publication:
United States
Language:
English

Citation Formats

Nishiyama, Toshiyuki, Niozu, Akinobu, Bostedt, Christoph, Ferguson, Ken R., Sato, Yuhiro, Hutchison, Christopher, Nagaya, Kiyonobu, Fukuzawa, Hironobu, Motomura, Koji, Wada, Shin-ichi, Sakai, Tsukasa, Matsunami, Kenji, Matsuda, Kazuhiro, Tachibana, Tetsuya, Ito, Yuta, Xu, Weiqing, Mondal, Subhendu, Umemoto, Takayuki, Nicolas, Christophe, Miron, Catalin, Kameshima, Takashi, Joti, Yasumasa, Tono, Kensuke, Hatsui, Takaki, Yabashi, Makina, and Ueda, Kiyoshi. Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data. United States: N. p., 2020. Web. doi:10.1107/s2052252519014222.
Nishiyama, Toshiyuki, Niozu, Akinobu, Bostedt, Christoph, Ferguson, Ken R., Sato, Yuhiro, Hutchison, Christopher, Nagaya, Kiyonobu, Fukuzawa, Hironobu, Motomura, Koji, Wada, Shin-ichi, Sakai, Tsukasa, Matsunami, Kenji, Matsuda, Kazuhiro, Tachibana, Tetsuya, Ito, Yuta, Xu, Weiqing, Mondal, Subhendu, Umemoto, Takayuki, Nicolas, Christophe, Miron, Catalin, Kameshima, Takashi, Joti, Yasumasa, Tono, Kensuke, Hatsui, Takaki, Yabashi, Makina, & Ueda, Kiyoshi. Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data. United States. doi:10.1107/s2052252519014222.
Nishiyama, Toshiyuki, Niozu, Akinobu, Bostedt, Christoph, Ferguson, Ken R., Sato, Yuhiro, Hutchison, Christopher, Nagaya, Kiyonobu, Fukuzawa, Hironobu, Motomura, Koji, Wada, Shin-ichi, Sakai, Tsukasa, Matsunami, Kenji, Matsuda, Kazuhiro, Tachibana, Tetsuya, Ito, Yuta, Xu, Weiqing, Mondal, Subhendu, Umemoto, Takayuki, Nicolas, Christophe, Miron, Catalin, Kameshima, Takashi, Joti, Yasumasa, Tono, Kensuke, Hatsui, Takaki, Yabashi, Makina, and Ueda, Kiyoshi. Wed . "Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data". United States. doi:10.1107/s2052252519014222.
@article{osti_1605029,
title = {Refinement for single-nanoparticle structure determination from low-quality single-shot coherent diffraction data},
author = {Nishiyama, Toshiyuki and Niozu, Akinobu and Bostedt, Christoph and Ferguson, Ken R. and Sato, Yuhiro and Hutchison, Christopher and Nagaya, Kiyonobu and Fukuzawa, Hironobu and Motomura, Koji and Wada, Shin-ichi and Sakai, Tsukasa and Matsunami, Kenji and Matsuda, Kazuhiro and Tachibana, Tetsuya and Ito, Yuta and Xu, Weiqing and Mondal, Subhendu and Umemoto, Takayuki and Nicolas, Christophe and Miron, Catalin and Kameshima, Takashi and Joti, Yasumasa and Tono, Kensuke and Hatsui, Takaki and Yabashi, Makina and Ueda, Kiyoshi},
abstractNote = {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.},
doi = {10.1107/s2052252519014222},
journal = {IUCrJ},
number = [1],
volume = [7],
place = {United States},
year = {2020},
month = {1}
}

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