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| Home > Publications database > A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser > print |
| 001 | 297261 | ||
| 005 | 20250730110122.0 | ||
| 024 | 7 | _ | |a 10.1038/srep24791 |2 doi |
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| 024 | 7 | _ | |a 10.3204/PUBDB-2016-01805 |2 datacite_doi |
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| 037 | _ | _ | |a PUBDB-2016-01805 |
| 041 | _ | _ | |a English |
| 082 | _ | _ | |a 000 |
| 100 | 1 | _ | |a Yoon, Chun Hong |0 P:(DE-H253)PIP1016300 |b 0 |e Corresponding author |u desy |
| 245 | _ | _ | |a A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser |
| 260 | _ | _ | |a London |c 2016 |b Nature Publishing Group |
| 336 | 7 | _ | |a article |2 DRIVER |
| 336 | 7 | _ | |a Output Types/Journal article |2 DataCite |
| 336 | 7 | _ | |a Journal Article |b journal |m journal |0 PUB:(DE-HGF)16 |s 1464096512_19290 |2 PUB:(DE-HGF) |
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| 336 | 7 | _ | |a Journal Article |0 0 |2 EndNote |
| 520 | _ | _ | |a The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design. |
| 536 | _ | _ | |a 6211 - Extreme States of Matter: From Cold Ions to Hot Plasmas (POF3-621) |0 G:(DE-HGF)POF3-6211 |c POF3-621 |f POF III |x 0 |
| 536 | _ | _ | |a 6G13 - XFEL (POF3-622) |0 G:(DE-HGF)POF3-6G13 |c POF3-622 |f POF III |x 1 |
| 536 | _ | _ | |a BIOSTRUCT-X - Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities (283570) |0 G:(EU-Grant)283570 |c 283570 |f FP7-INFRASTRUCTURES-2011-1 |x 2 |
| 536 | _ | _ | |a CUI - Hamburger Zentrum für ultraschnelle Beobachtung (194651731) |0 G:(GEPRIS)194651731 |c 194651731 |x 3 |
| 588 | _ | _ | |a Dataset connected to CrossRef |
| 693 | _ | _ | |a XFEL |e SPB: Single Particles, clusters & Biomolecules |f SASE1 |1 EXP:(DE-H253)XFEL-20150101 |0 EXP:(DE-H253)XFEL-SPB-20150101 |5 EXP:(DE-H253)XFEL-SPB-20150101 |6 EXP:(DE-H253)XFEL-SASE1-20150101 |x 0 |
| 700 | 1 | _ | |a Yurkov, Mikhail |0 P:(DE-H253)PIP1001234 |b 1 |u desy |
| 700 | 1 | _ | |a Schneidmiller, Evgeny Alexanrdovich |0 P:(DE-H253)PIP1001599 |b 2 |u desy |
| 700 | 1 | _ | |a Samoylova, Liubov |0 P:(DE-H253)PIP1006674 |b 3 |
| 700 | 1 | _ | |a Buzmakov, Alexey |0 P:(DE-H253)PIP1014327 |b 4 |
| 700 | 1 | _ | |a Jurek, Zoltan |0 P:(DE-H253)PIP1013492 |b 5 |u desy |
| 700 | 1 | _ | |a Ziaja, Beata |0 P:(DE-H253)PIP1003464 |b 6 |u desy |
| 700 | 1 | _ | |a Santra, Robin |0 P:(DE-H253)PIP1012203 |b 7 |u desy |
| 700 | 1 | _ | |a Loh, N. Duane |0 P:(DE-HGF)0 |b 8 |
| 700 | 1 | _ | |a Tschentscher, Thomas |0 P:(DE-H253)PIP1001329 |b 9 |
| 700 | 1 | _ | |a Mancuso, Adrian Paul |0 P:(DE-H253)PIP1006340 |b 10 |e Corresponding author |
| 773 | _ | _ | |a 10.1038/srep24791 |g Vol. 6, p. 24791 - |0 PERI:(DE-600)2615211-3 |p 24791 |t Scientific reports |v 6 |y 2016 |x 2045-2322 |
| 856 | 4 | _ | |u http://www.nature.com/articles/srep24791 |
| 856 | 4 | _ | |u https://bib-pubdb1.desy.de/record/297261/files/Sci.Rep.2016Yoon.pdf |y OpenAccess |
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