High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging

Single-particle coherent X-ray diffraction imaging using an X-ray free-electron laser has the potential to reveal the three-dimensional structure of a biological supra-molecule at sub-nanometer resolution. In order to realise this method, it is necessary to analyze as many as 1 × 10(6) noisy X-ray d...

Ausführliche Beschreibung

Bibliographische Detailangaben
Veröffentlicht in:Journal of synchrotron radiation. - 1994. - 20(2013), Pt 6 vom: 07. Nov., Seite 899-904
1. Verfasser: Tokuhisa, Atsushi (VerfasserIn)
Weitere Verfasser: Arai, Junya, Joti, Yasumasa, Ohno, Yoshiyuki, Kameyama, Toyohisa, Yamamoto, Keiji, Hatanaka, Masayuki, Gerofi, Balazs, Shimada, Akio, Kurokawa, Motoyoshi, Shoji, Fumiyoshi, Okada, Kensuke, Sugimoto, Takashi, Yamaga, Mitsuhiro, Tanaka, Ryotaro, Yokokawa, Mitsuo, Hori, Atsushi, Ishikawa, Yutaka, Hatsui, Takaki, Go, Nobuhiro
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2013
Zugriff auf das übergeordnete Werk:Journal of synchrotron radiation
Schlagworte:Journal Article K computer X-ray free-electron laser big-data analysis classification of diffraction patterns single-particle coherent diffraction imaging
LEADER 01000naa a22002652 4500
001 NLM231658346
003 DE-627
005 20231224091243.0
007 cr uuu---uuuuu
008 231224s2013 xx |||||o 00| ||eng c
024 7 |a 10.1107/S0909049513022152  |2 doi 
028 5 2 |a pubmed24n0772.xml 
035 |a (DE-627)NLM231658346 
035 |a (NLM)24121336 
040 |a DE-627  |b ger  |c DE-627  |e rakwb 
041 |a eng 
100 1 |a Tokuhisa, Atsushi  |e verfasserin  |4 aut 
245 1 0 |a High-speed classification of coherent X-ray diffraction patterns on the K computer for high-resolution single biomolecule imaging 
264 1 |c 2013 
336 |a Text  |b txt  |2 rdacontent 
337 |a ƒaComputermedien  |b c  |2 rdamedia 
338 |a ƒa Online-Ressource  |b cr  |2 rdacarrier 
500 |a Date Completed 22.05.2014 
500 |a Date Revised 21.10.2021 
500 |a published: Print-Electronic 
500 |a Citation Status MEDLINE 
520 |a Single-particle coherent X-ray diffraction imaging using an X-ray free-electron laser has the potential to reveal the three-dimensional structure of a biological supra-molecule at sub-nanometer resolution. In order to realise this method, it is necessary to analyze as many as 1 × 10(6) noisy X-ray diffraction patterns, each for an unknown random target orientation. To cope with the severe quantum noise, patterns need to be classified according to their similarities and average similar patterns to improve the signal-to-noise ratio. A high-speed scalable scheme has been developed to carry out classification on the K computer, a 10PFLOPS supercomputer at RIKEN Advanced Institute for Computational Science. It is designed to work on the real-time basis with the experimental diffraction pattern collection at the X-ray free-electron laser facility SACLA so that the result of classification can be feedback for optimizing experimental parameters during the experiment. The present status of our effort developing the system and also a result of application to a set of simulated diffraction patterns is reported. About 1 × 10(6) diffraction patterns were successfully classificatied by running 255 separate 1 h jobs in 385-node mode 
650 4 |a Journal Article 
650 4 |a K computer 
650 4 |a X-ray free-electron laser 
650 4 |a big-data analysis 
650 4 |a classification of diffraction patterns 
650 4 |a single-particle coherent diffraction imaging 
700 1 |a Arai, Junya  |e verfasserin  |4 aut 
700 1 |a Joti, Yasumasa  |e verfasserin  |4 aut 
700 1 |a Ohno, Yoshiyuki  |e verfasserin  |4 aut 
700 1 |a Kameyama, Toyohisa  |e verfasserin  |4 aut 
700 1 |a Yamamoto, Keiji  |e verfasserin  |4 aut 
700 1 |a Hatanaka, Masayuki  |e verfasserin  |4 aut 
700 1 |a Gerofi, Balazs  |e verfasserin  |4 aut 
700 1 |a Shimada, Akio  |e verfasserin  |4 aut 
700 1 |a Kurokawa, Motoyoshi  |e verfasserin  |4 aut 
700 1 |a Shoji, Fumiyoshi  |e verfasserin  |4 aut 
700 1 |a Okada, Kensuke  |e verfasserin  |4 aut 
700 1 |a Sugimoto, Takashi  |e verfasserin  |4 aut 
700 1 |a Yamaga, Mitsuhiro  |e verfasserin  |4 aut 
700 1 |a Tanaka, Ryotaro  |e verfasserin  |4 aut 
700 1 |a Yokokawa, Mitsuo  |e verfasserin  |4 aut 
700 1 |a Hori, Atsushi  |e verfasserin  |4 aut 
700 1 |a Ishikawa, Yutaka  |e verfasserin  |4 aut 
700 1 |a Hatsui, Takaki  |e verfasserin  |4 aut 
700 1 |a Go, Nobuhiro  |e verfasserin  |4 aut 
773 0 8 |i Enthalten in  |t Journal of synchrotron radiation  |d 1994  |g 20(2013), Pt 6 vom: 07. Nov., Seite 899-904  |w (DE-627)NLM09824129X  |x 1600-5775  |7 nnns 
773 1 8 |g volume:20  |g year:2013  |g number:Pt 6  |g day:07  |g month:11  |g pages:899-904 
856 4 0 |u http://dx.doi.org/10.1107/S0909049513022152  |3 Volltext 
912 |a GBV_USEFLAG_A 
912 |a SYSFLAG_A 
912 |a GBV_NLM 
912 |a GBV_ILN_40 
912 |a GBV_ILN_350 
912 |a GBV_ILN_2005 
951 |a AR 
952 |d 20  |j 2013  |e Pt 6  |b 07  |c 11  |h 899-904