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Study for a similarity detection algorithm between very noisy diffraction patterns from XFEL

Research Project

Project/Area Number 26870852
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Quantum beam science
Biophysics
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Tokuhisa Atsushi  国立研究開発法人理化学研究所, 計算科学研究機構, 研究員 (60455300)

Research Collaborator GO Nobuhiro  京都大学, 名誉教授
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords類似性判定法 / X線回折像 / 生体高分子 / 実験条件 / X線自由電子レーザー / 単粒子構造解析 / XFEL / CDI / 性能評価 / ROC解析 / 分類器 / 到達分解能 / 計算コスト削減 / 類似性判定 / コヒーレントイメージング / 回折像
Outline of Final Research Achievements

In order to realize single particle diffraction imaging with high resolution, it is needed to extract useful signal from noisy diffraction pattern. In this research, we developed and improved an automatic algorithm to detect similarity between pairs of coherent diffraction patterns from an orientation-unknown single particle. We developed a Pre-Analysis step with optimized parameters to realize low computational cost by performing an efficiency evaluation based on ROC curves. We also aimed to construct multi steps similarity detection algorithm by combing with Pre-Analysis step and Main-Analysis step to realize similarity detection algorithm with the high-performance and low computational cost. We elucidated the switching wave-number between Pre-Analysis step and Main-Analysis step.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (10 results)

All 2016 2015 2014 Other

All Journal Article (1 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 1 results,  Acknowledgement Compliant: 1 results) Presentation (8 results) (of which Int'l Joint Research: 1 results) Remarks (1 results)

  • [Journal Article] Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns2016

    • Author(s)
      Atsushi Tokuhisa, Slavica Jonic, Florence Tama, Osamu Miyashita
    • Journal Title

      Journal of Structural Biology

      Volume: 194-3 Issue: 3 Pages: 325-336

    • DOI

      10.1016/j.jsb.2016.03.009

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Multistep similarity detection algorithm for single particle X-ray coherent diffraction imaging2016

    • Author(s)
      Tokuhisa, A., Miyashita, O., Tama, F.
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      筑波国際会議場(茨城県・つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] XFELによる単粒子構造解析へ向けて2016

    • Author(s)
      徳久淳師
    • Organizer
      第87回AICS caf
    • Place of Presentation
      計算科学研究機構(兵庫県・神戸市)
    • Year and Date
      2016-04-13
    • Related Report
      2015 Research-status Report
  • [Presentation] A hybrid approach to extract structural information from small number of 2D X-ray coherent diffraction patterns2016

    • Author(s)
      Tokuhisa, A., Jonic, S., Miyashita, O., Tama, F.
    • Organizer
      The 6th AICS International Symposium
    • Place of Presentation
      計算科学研究機構(兵庫県・神戸市)
    • Year and Date
      2016-02-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] A hybrid approach to extract structural information from a few coherent diffraction patterns obtained by XFEL2016

    • Author(s)
      徳久淳師
    • Organizer
      医薬基盤研究開発機構セミナー
    • Place of Presentation
      医薬基盤研究所(大阪府・茨木市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] Examination of a new approach for single particle CXDI by use of computational structural models and the pattern matching on coherent X-ray diffractions2015

    • Author(s)
      Tokuhisa, A.
    • Organizer
      The Second Project Report Meeting of the HPCI System Including K computer
    • Place of Presentation
      日本科学未来館(東京都・江藤区)
    • Year and Date
      2015-10-26
    • Related Report
      2015 Research-status Report
  • [Presentation] Computational algorithms to extract structural information from X-ray coherent diffractions2015

    • Author(s)
      Tokuhisa, A., Miyashita, O., Tama, F.
    • Organizer
      The 53rd Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      金沢大学【石川県・金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] X 線自由電子レーザーを用いたパターンマッチング法による第一原理構造モデリングの検討2014

    • Author(s)
      徳久淳師
    • Organizer
      日本生物物理学会
    • Place of Presentation
      札幌コンベンションセンター(北海道・札幌市)
    • Year and Date
      2014-09-27
    • Related Report
      2014 Research-status Report
  • [Presentation] 回折像類似性判定法による構造モデルの構築2014

    • Author(s)
      徳久淳師
    • Organizer
      日本放射光学会第6回若手研究会「コヒーレントX線が拓く構造可視化の新しい世界」
    • Place of Presentation
      理研播磨研究所(兵庫県・佐用郡)
    • Year and Date
      2014-08-22 – 2014-08-23
    • Related Report
      2014 Research-status Report
  • [Remarks] Google Scholar個人ページ (My Citations)

    • URL

      https://scholar.google.com/citations?view_op=list_works&hl=en&user=0gahzakAAAAJ&cstart=0&pagesize=20

    • Related Report
      2016 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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