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100 1 _ |a Stransky, Michal
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245 _ _ |a Computational study of diffraction image formation from XFEL irradiated single ribosome molecule
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520 _ _ |a Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-rayFree-Electron Lasers. Such a capability would create great opportunity within the biological sciences, as high-resolutionstructural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we reporton a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule,containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX,available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imagingstudies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be usedfor simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for theseexperiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, makingthe best use of the resource-intensive XFEL operation.
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999 C 5 |a 10.1021/nl072728k
|9 -- missing cx lookup --
|1 MJ Bogan
|p 310 -
|2 Crossref
|u Bogan, M. J. et al. Single particle X-ray diffractive imaging. Nano Lett. 8, 310–316. https://doi.org/10.1021/nl072728k (2008).
|t Nano Lett.
|v 8
|y 2008
999 C 5 |a 10.1038/nature09748
|9 -- missing cx lookup --
|1 MM Seibert
|p 78 -
|2 Crossref
|u Seibert, M. M. et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470, 78–81. https://doi.org/10.1038/nature09748 (2011).
|t Nature
|v 470
|y 2011
999 C 5 |a 10.1038/s42005-020-0362-y
|1 E Sobolev
|9 -- missing cx lookup --
|2 Crossref
|u Sobolev, E. et al. Megahertz single-particle imaging at the European XFEL. Commun. Phys.https://doi.org/10.1038/s42005-020-0362-y (2020).
|t Commun. Phys.
|y 2020
999 C 5 |a 10.1063/4.0000024
|1 J Bielecki
|9 -- missing cx lookup --
|2 Crossref
|u Bielecki, J., Maia, F. R. N. C. & Mancuso, A. P. Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources. Struct. Dynam. 7, 040901. https://doi.org/10.1063/4.0000024 (2020).
|t Struct. Dynam.
|v 7
|y 2020
999 C 5 |a 10.1126/science.aat4346
|9 -- missing cx lookup --
|1 Y Cheng
|p 876 -
|2 Crossref
|u Cheng, Y. Single-particle cryo-em-how did it get here and where will it go. Science 361, 876–880. https://doi.org/10.1126/science.aat4346 (2018).
|t Science
|v 361
|y 2018
999 C 5 |a 10.1038/nmeth.3694
|9 -- missing cx lookup --
|1 E Nogales
|p 24 -
|2 Crossref
|u Nogales, E. The development of cryo-em into a mainstream structural biology technique. Nat. Methods 13, 24–27. https://doi.org/10.1038/nmeth.3694 (2016).
|t Nat. Methods
|v 13
|y 2016
999 C 5 |a 10.3390/app8010132
|1 Z Sun
|9 -- missing cx lookup --
|2 Crossref
|u Sun, Z., Fan, J., Li, H. & Jiang, H. Current status of single particle imaging with x-ray lasers. Appl. Sci.https://doi.org/10.3390/app8010132 (2018).
|t Appl. Sci.
|y 2018
999 C 5 |a 10.1038/nphoton.2011.297
|9 -- missing cx lookup --
|1 A Barty
|p 35 -
|2 Crossref
|u Barty, A. et al. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat. Photonics 6, 35–40. https://doi.org/10.1038/nphoton.2011.297 (2012).
|t Nat. Photonics
|v 6
|y 2012
999 C 5 |a 10.1038/ncomms5061
|9 -- missing cx lookup --
|1 R Xu
|p 4061 -
|2 Crossref
|u Xu, R. et al. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nat. Commun. 5, 4061. https://doi.org/10.1038/ncomms5061 (2014).
|t Nat. Commun.
|v 5
|y 2014
999 C 5 |a 10.1107/S1600577519003308
|9 -- missing cx lookup --
|1 AP Mancuso
|p 660 -
|2 Crossref
|u Mancuso, A. P. et al. The single particles, clusters and biomolecules and serial femtosecond crystallography instrument of the European XFEL: Initial installation. J. Synchrotron Radiat. 26, 660–676. https://doi.org/10.1107/S1600577519003308 (2019).
|t J. Synchrotron Radiat.
|v 26
|y 2019
999 C 5 |a 10.1038/s41467-020-15610-4
|9 -- missing cx lookup --
|1 K Nass
|p 1814 -
|2 Crossref
|u Nass, K. et al. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat. Commun. 11, 1814. https://doi.org/10.1038/s41467-020-15610-4 (2020).
|t Nat. Commun.
|v 11
|y 2020
999 C 5 |a 10.1038/nature09750
|9 -- missing cx lookup --
|1 HN Chapman
|p 73 -
|2 Crossref
|u Chapman, H. N. et al. Femtosecond x-ray protein nanocrystallography. Nature 470, 73–77. https://doi.org/10.1038/nature09750 (2011).
|t Nature
|v 470
|y 2011
999 C 5 |a 10.3390/photonics2010256
|9 -- missing cx lookup --
|1 B Ziaja
|p 256 -
|2 Crossref
|u Ziaja, B. et al. Towards realistic simulations of macromolecules irradiated under the conditions of coherent diffraction imaging with an x-ray free-electron laser. Photonics 2, 256–269. https://doi.org/10.3390/photonics2010256 (2015).
|t Photonics
|v 2
|y 2015
999 C 5 |a 10.1038/srep24791
|1 CH Yoon
|9 -- missing cx lookup --
|2 Crossref
|u Yoon, C. H. et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray free-electron laser. Sci. Rep.https://doi.org/10.1038/srep24791 (2016).
|t Sci. Rep.
|y 2016
999 C 5 |a 10.1107/S2052252517009496
|9 -- missing cx lookup --
|1 C Fortmann-Grote
|p 560 -
|2 Crossref
|u Fortmann-Grote, C. et al. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray free-electron laser. IUCrJ 4, 560–568. https://doi.org/10.1107/S2052252517009496 (2017).
|t IUCrJ
|v 4
|y 2017
999 C 5 |2 Crossref
|u Fortmann-Grote, C. & E, J. C. Simex. howpublishedhttps://github.com/PaNOSC-ViNYL/SimEx (2020).
999 C 5 |a 10.1117/12.2677299
|1 E Juncheng
|9 -- missing cx lookup --
|2 Crossref
|u Juncheng, E. et al. Simex-lite: Easy access to start-to-end simulation for experiments at advanced light sources. Proc. SPIEhttps://doi.org/10.1117/12.2677299 (2023).
|t Proc. SPIE
|y 2023
999 C 5 |a 10.1038/s41598-021-97142-5
|9 -- missing cx lookup --
|1 E Juncheng
|p 17976 -
|2 Crossref
|u Juncheng, E. et al. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray free-electron laser. Sci. Rep. 11, 17976. https://doi.org/10.1038/s41598-021-97142-5 (2021).
|t Sci. Rep.
|v 11
|y 2021
999 C 5 |a 10.1038/s41598-023-43298-1
|9 -- missing cx lookup --
|1 E Juncheng
|p 16359 -
|2 Crossref
|u Juncheng, E. et al. Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser. Sci. Rep. 13, 16359. https://doi.org/10.1038/s41598-023-43298-1 (2023).
|t Sci. Rep.
|v 13
|y 2023
999 C 5 |a 10.1103/PhysRevLett.102.205002
|1 B Ziaja
|9 -- missing cx lookup --
|2 Crossref
|u Ziaja, B., Wabnitz, H., Wang, F. & Weckert, E. Energetics, ionization, and expansion dynamics of atomic clusters irradiated with short intense vacuum-ultraviolet pulses. Phys. Rev. Lett. 102, 205002 (2009).
|t Phys. Rev. Lett.
|v 102
|y 2009
999 C 5 |a 10.1107/S1600576716006014
|9 -- missing cx lookup --
|1 Z Jurek
|p 1048 -
|2 Crossref
|u Jurek, Z., Son, S.-K., Ziaja, B. & Santra, R. XMDYN and XATOM: Versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter. J. Appl. Crystallogr. 49, 1048–1056 (2016).
|t J. Appl. Crystallogr.
|v 49
|y 2016
999 C 5 |a 10.1038/ncomms5281
|9 -- missing cx lookup --
|1 BF Murphy
|p 4281 -
|2 Crossref
|u Murphy, B. F. et al. Femtosecond X-ray-induced explosion of C 60 at extreme intensity. Nat. Commun. 5, 4281. https://doi.org/10.1038/ncomms5281 (2014).
|t Nat. Commun.
|v 5
|y 2014
999 C 5 |a 10.3390/molecules27134206
|9 -- missing cx lookup --
|1 M Stransky
|p 4206 -
|2 Crossref
|u Stransky, M., Jurek, Z., Santra, R., Mancuso, A. & Ziaja, B. Tree-code based improvement of computational performance of the X-ray-matter-interaction simulation tool XMDYN. Molecules 27, 4206. https://doi.org/10.3390/molecules27134206 (2022).
|t Molecules
|v 27
|y 2022
999 C 5 |a 10.1126/science.1175275
|9 -- missing cx lookup --
|1 W Zhang
|p 1014 -
|2 Crossref
|u Zhang, W., Dunkle, J. A. & Cate, J. H. D. Structures of the ribosome in intermediate states of ratcheting. Science 325, 1014–1017. https://doi.org/10.1126/science.1175275 (2009).
|t Science
|v 325
|y 2009
999 C 5 |2 Crossref
|u Gibbon, P. PEPC: Pretty Efficient Parallel Coulomb-solver. Technical Report, FORSCHUNGSZENTRUM JÜLICH GmbH Zentralinstitut für Angewandte Mathematik FZJ-ZAM-IB-2003-05 (2003).
999 C 5 |a 10.1103/PhysRevLett.131.163201
|1 I Inoue
|9 -- missing cx lookup --
|2 Crossref
|u Inoue, I. et al. Femtosecond reduction of atomic scattering factors triggered by intense x-ray pulse. Phys. Rev. Lett. 131, 163201 (2023).
|t Phys. Rev. Lett.
|v 131
|y 2023
999 C 5 |a 10.1107/S2052252518011442
|9 -- missing cx lookup --
|1 MM Abdullah
|p 699 -
|2 Crossref
|u Abdullah, M. M., Son, S.-K., Jurek, Z. & Santra, R. Towards the theoretical limitations of X-ray nanocrystallography at high intensity: the validity of the effective-form-factor description. IUCrJ 5, 699–705. https://doi.org/10.1107/S2052252518011442 (2018).
|t IUCrJ
|v 5
|y 2018


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