000606808 001__ 606808
000606808 005__ 20251017180823.0
000606808 0247_ $$2doi$$a10.1038/s41598-024-61314-w
000606808 0247_ $$2datacite_doi$$a10.3204/PUBDB-2024-01638
000606808 0247_ $$2altmetric$$aaltmetric:163438723
000606808 0247_ $$2pmid$$apmid:38720133
000606808 0247_ $$2WOS$$aWOS:001216325300001
000606808 0247_ $$2openalex$$aopenalex:W4396775398
000606808 037__ $$aPUBDB-2024-01638
000606808 041__ $$aEnglish
000606808 082__ $$a600
000606808 1001_ $$0P:(DE-H253)PIP1092209$$aStransky, Michal$$b0$$eCorresponding author
000606808 245__ $$aComputational study of diffraction image formation from XFEL irradiated single ribosome molecule
000606808 260__ $$a[London]$$bMacmillan Publishers Limited, part of Springer Nature$$c2024
000606808 3367_ $$2DRIVER$$aarticle
000606808 3367_ $$2DataCite$$aOutput Types/Journal article
000606808 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1724405762_903794
000606808 3367_ $$2BibTeX$$aARTICLE
000606808 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000606808 3367_ $$00$$2EndNote$$aJournal Article
000606808 520__ $$aSingle particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-rayFree-Electron Lasers. Such a capability would create great opportunity within the biological sciences, as high-resolutionstructural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we reporton a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule,containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX,available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imagingstudies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be usedfor simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for theseexperiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, makingthe best use of the resource-intensive XFEL operation.
000606808 536__ $$0G:(DE-HGF)POF4-631$$a631 - Matter – Dynamics, Mechanisms and Control (POF4-631)$$cPOF4-631$$fPOF IV$$x0
000606808 542__ $$2Crossref$$i2024-05-09$$uhttps://creativecommons.org/licenses/by/4.0
000606808 542__ $$2Crossref$$i2024-05-09$$uhttps://creativecommons.org/licenses/by/4.0
000606808 693__ $$0EXP:(DE-H253)XFEL-SPB-20150101$$1EXP:(DE-H253)XFEL-20150101$$5EXP:(DE-H253)XFEL-SPB-20150101$$6EXP:(DE-H253)XFEL-SASE1-20150101$$aXFEL$$eSPB: Single Particles, clusters & Biomolecules$$fSASE1$$x0
000606808 7001_ $$0P:(DE-H253)PIP1084165$$aE, Juncheng$$b1
000606808 7001_ $$0P:(DE-H253)PIP1013492$$aJurek, Zoltan$$b2
000606808 7001_ $$0P:(DE-H253)PIP1012203$$aSantra, Robin$$b3
000606808 7001_ $$0P:(DE-H253)PIP1016993$$aBean, Richard$$b4
000606808 7001_ $$0P:(DE-H253)PIP1003464$$aZiaja, Beata$$b5
000606808 7001_ $$0P:(DE-H253)PIP1006340$$aMancuso, Adrian$$b6$$eCorresponding author
000606808 77318 $$2Crossref$$3journal-article$$a10.1038/s41598-024-61314-w$$bSpringer Science and Business Media LLC$$d2024-05-09$$n1$$p10617$$tScientific Reports$$v14$$x2045-2322$$y2024
000606808 773__ $$0PERI:(DE-600)2615211-3$$a10.1038/s41598-024-61314-w$$n1$$p10617$$tScientific reports$$v14$$x2045-2322$$y2024
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/HTML-Approval_of_scientific_publication.html
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/PDF-Approval_of_scientific_publication.pdf
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/Supplementary%20Material.pdf$$yRestricted
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/Supplementary%20Material.pdf?subformat=pdfa$$xpdfa$$yRestricted
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/manuscript.pdf$$yOpenAccess$$zStatID:(DE-HGF)0510
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/s41598-024-61314-w.pdf$$yRestricted$$zStatID:(DE-HGF)0599
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/manuscript.pdf?subformat=pdfa$$xpdfa$$yOpenAccess$$zStatID:(DE-HGF)0510
000606808 8564_ $$uhttps://bib-pubdb1.desy.de/record/606808/files/s41598-024-61314-w.pdf?subformat=pdfa$$xpdfa$$yRestricted$$zStatID:(DE-HGF)0599
000606808 8767_ $$8SN-2024-00558-b$$92024-08-20$$d2024-08-23$$eAPC$$jDEAL$$lSpringerNature$$v17.12$$zXFEL, corresponding author erscheint mit XFEL Affiliation, Einzelnachweis Rechnung SN-2024-00558-b
000606808 8767_ $$8SN-2025-01342-e$$92025-09-25$$d2024-08-23$$ePayment fee$$jDEAL$$lSpringerNature$$v0.35$$zMPDL Gebühr
000606808 8767_ $$8SN-2024-00558-b$$92024-08-20$$d2024-08-23$$eAPC$$jStorniert$$lSpringerNature$$zDFG OAPK (Projekt)
000606808 8767_ $$8SN-2024-00558-b$$92024-08-20$$d2024-08-23$$eAPC$$jZahlung erfolgt$$lSpringerNature$$zDFG OAPK (Projekt)
000606808 8767_ $$8SN-2024-01904-b$$92024$$d2025-07-15$$ePayment fee$$jStorniert$$lSpringerNature$$v-10.81$$zKorrketur MwSt -> 7%
000606808 909CO $$ooai:bib-pubdb1.desy.de:606808$$pdnbdelivery$$popenCost$$pVDB$$pdriver$$pOpenAPC$$popen_access$$popenaire
000606808 9101_ $$0I:(DE-588b)2008985-5$$6P:(DE-H253)PIP1092209$$aDeutsches Elektronen-Synchrotron$$b0$$kDESY
000606808 9101_ $$0I:(DE-H253)_CFEL-20120731$$6P:(DE-H253)PIP1092209$$aCentre for Free-Electron Laser Science$$b0$$kCFEL
000606808 9101_ $$0I:(DE-HGF)0$$6P:(DE-H253)PIP1092209$$aExternal Institute$$b0$$kExtern
000606808 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1092209$$aEuropean XFEL$$b0$$kXFEL.EU
000606808 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1084165$$aEuropean XFEL$$b1$$kXFEL.EU
000606808 9101_ $$0I:(DE-588b)2008985-5$$6P:(DE-H253)PIP1013492$$aDeutsches Elektronen-Synchrotron$$b2$$kDESY
000606808 9101_ $$0I:(DE-H253)_CFEL-20120731$$6P:(DE-H253)PIP1013492$$aCentre for Free-Electron Laser Science$$b2$$kCFEL
000606808 9101_ $$0I:(DE-588b)2008985-5$$6P:(DE-H253)PIP1012203$$aDeutsches Elektronen-Synchrotron$$b3$$kDESY
000606808 9101_ $$0I:(DE-H253)_CFEL-20120731$$6P:(DE-H253)PIP1012203$$aCentre for Free-Electron Laser Science$$b3$$kCFEL
000606808 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1012203$$aEuropean XFEL$$b3$$kXFEL.EU
000606808 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1016993$$aEuropean XFEL$$b4$$kXFEL.EU
000606808 9101_ $$0I:(DE-588b)2008985-5$$6P:(DE-H253)PIP1003464$$aDeutsches Elektronen-Synchrotron$$b5$$kDESY
000606808 9101_ $$0I:(DE-H253)_CFEL-20120731$$6P:(DE-H253)PIP1003464$$aCentre for Free-Electron Laser Science$$b5$$kCFEL
000606808 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1003464$$aEuropean XFEL$$b5$$kXFEL.EU
000606808 9101_ $$0I:(DE-HGF)0$$6P:(DE-H253)PIP1006340$$aExternal Institute$$b6$$kExtern
000606808 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1006340$$aEuropean XFEL$$b6$$kXFEL.EU
000606808 9131_ $$0G:(DE-HGF)POF4-631$$1G:(DE-HGF)POF4-630$$2G:(DE-HGF)POF4-600$$3G:(DE-HGF)POF4$$4G:(DE-HGF)POF$$aDE-HGF$$bForschungsbereich Materie$$lVon Materie zu Materialien und Leben$$vMatter – Dynamics, Mechanisms and Control$$x0
000606808 9141_ $$y2024
000606808 915__ $$0LIC:(DE-HGF)CCBY4$$2HGFVOC$$aCreative Commons Attribution CC BY 4.0
000606808 915__ $$0StatID:(DE-HGF)0160$$2StatID$$aDBCoverage$$bEssential Science Indicators$$d2023-08-24
000606808 915__ $$0StatID:(DE-HGF)1190$$2StatID$$aDBCoverage$$bBiological Abstracts$$d2023-08-24
000606808 915__ $$0StatID:(DE-HGF)0113$$2StatID$$aWoS$$bScience Citation Index Expanded$$d2023-08-24
000606808 915__ $$0StatID:(DE-HGF)0700$$2StatID$$aFees$$d2023-08-24
000606808 915__ $$0StatID:(DE-HGF)0510$$2StatID$$aOpenAccess
000606808 915__ $$0StatID:(DE-HGF)0561$$2StatID$$aArticle Processing Charges$$d2023-08-24
000606808 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR$$bSCI REP-UK : 2022$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)0501$$2StatID$$aDBCoverage$$bDOAJ Seal$$d2024-07-29T15:28:26Z
000606808 915__ $$0StatID:(DE-HGF)0500$$2StatID$$aDBCoverage$$bDOAJ$$d2024-07-29T15:28:26Z
000606808 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bDOAJ : Anonymous peer review$$d2024-07-29T15:28:26Z
000606808 915__ $$0StatID:(DE-HGF)0600$$2StatID$$aDBCoverage$$bEbsco Academic Search$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bASC$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bClarivate Analytics Master Journal List$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)1040$$2StatID$$aDBCoverage$$bZoological Record$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)1150$$2StatID$$aDBCoverage$$bCurrent Contents - Physical, Chemical and Earth Sciences$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)1050$$2StatID$$aDBCoverage$$bBIOSIS Previews$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection$$d2024-12-18
000606808 915__ $$0StatID:(DE-HGF)9900$$2StatID$$aIF < 5$$d2024-12-18
000606808 915pc $$0PC:(DE-HGF)0000$$2APC$$aAPC keys set
000606808 915pc $$0PC:(DE-HGF)0001$$2APC$$aLocal Funding
000606808 915pc $$0PC:(DE-HGF)0002$$2APC$$aDFG OA Publikationskosten
000606808 915pc $$0PC:(DE-HGF)0178$$2APC$$aDEAL: Springer Nature 01.01.2024
000606808 915pc $$0PC:(DE-HGF)0003$$2APC$$aDOAJ Journal
000606808 9201_ $$0I:(DE-H253)FS-CFEL-XM-20210408$$kFS-CFEL-XM$$lGruppe CFEL-XM$$x0
000606808 9201_ $$0I:(DE-H253)FS-CFEL-3-20120731$$kFS-CFEL-3$$lCFEL-Theory$$x1
000606808 9201_ $$0I:(DE-H253)XFEL_E1_SPB_SFX-20210408$$kXFEL_E1_SPB/SFX$$lSPB/SFX$$x2
000606808 9801_ $$aFullTexts
000606808 980__ $$ajournal
000606808 980__ $$aVDB
000606808 980__ $$aI:(DE-H253)FS-CFEL-XM-20210408
000606808 980__ $$aI:(DE-H253)FS-CFEL-3-20120731
000606808 980__ $$aI:(DE-H253)XFEL_E1_SPB_SFX-20210408
000606808 980__ $$aUNRESTRICTED
000606808 980__ $$aAPC
000606808 999C5 $$1MJ Bogan$$2Crossref$$9-- missing cx lookup --$$a10.1021/nl072728k$$p310 -$$tNano Lett.$$uBogan, M. J. et al. Single particle X-ray diffractive imaging. Nano Lett. 8, 310–316. https://doi.org/10.1021/nl072728k (2008).$$v8$$y2008
000606808 999C5 $$1MM Seibert$$2Crossref$$9-- missing cx lookup --$$a10.1038/nature09748$$p78 -$$tNature$$uSeibert, M. M. et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470, 78–81. https://doi.org/10.1038/nature09748 (2011).$$v470$$y2011
000606808 999C5 $$1E Sobolev$$2Crossref$$9-- missing cx lookup --$$a10.1038/s42005-020-0362-y$$tCommun. Phys.$$uSobolev, E. et al. Megahertz single-particle imaging at the European XFEL. Commun. Phys.https://doi.org/10.1038/s42005-020-0362-y (2020).$$y2020
000606808 999C5 $$1J Bielecki$$2Crossref$$9-- missing cx lookup --$$a10.1063/4.0000024$$tStruct. Dynam.$$uBielecki, 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).$$v7$$y2020
000606808 999C5 $$1Y Cheng$$2Crossref$$9-- missing cx lookup --$$a10.1126/science.aat4346$$p876 -$$tScience$$uCheng, Y. Single-particle cryo-em-how did it get here and where will it go. Science 361, 876–880. https://doi.org/10.1126/science.aat4346 (2018).$$v361$$y2018
000606808 999C5 $$1E Nogales$$2Crossref$$9-- missing cx lookup --$$a10.1038/nmeth.3694$$p24 -$$tNat. Methods$$uNogales, 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).$$v13$$y2016
000606808 999C5 $$1Z Sun$$2Crossref$$9-- missing cx lookup --$$a10.3390/app8010132$$tAppl. Sci.$$uSun, 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).$$y2018
000606808 999C5 $$1A Barty$$2Crossref$$9-- missing cx lookup --$$a10.1038/nphoton.2011.297$$p35 -$$tNat. Photonics$$uBarty, 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).$$v6$$y2012
000606808 999C5 $$1R Xu$$2Crossref$$9-- missing cx lookup --$$a10.1038/ncomms5061$$p4061 -$$tNat. Commun.$$uXu, R. et al. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nat. Commun. 5, 4061. https://doi.org/10.1038/ncomms5061 (2014).$$v5$$y2014
000606808 999C5 $$1AP Mancuso$$2Crossref$$9-- missing cx lookup --$$a10.1107/S1600577519003308$$p660 -$$tJ. Synchrotron Radiat.$$uMancuso, 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).$$v26$$y2019
000606808 999C5 $$1K Nass$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41467-020-15610-4$$p1814 -$$tNat. Commun.$$uNass, K. et al. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat. Commun. 11, 1814. https://doi.org/10.1038/s41467-020-15610-4 (2020).$$v11$$y2020
000606808 999C5 $$1HN Chapman$$2Crossref$$9-- missing cx lookup --$$a10.1038/nature09750$$p73 -$$tNature$$uChapman, H. N. et al. Femtosecond x-ray protein nanocrystallography. Nature 470, 73–77. https://doi.org/10.1038/nature09750 (2011).$$v470$$y2011
000606808 999C5 $$1B Ziaja$$2Crossref$$9-- missing cx lookup --$$a10.3390/photonics2010256$$p256 -$$tPhotonics$$uZiaja, B. et al. Towards realistic simulations of macromolecules irradiated under the conditions of coherent diffraction imaging with an x-ray free-electron laser. Photonics 2, 256–269. https://doi.org/10.3390/photonics2010256 (2015).$$v2$$y2015
000606808 999C5 $$1CH Yoon$$2Crossref$$9-- missing cx lookup --$$a10.1038/srep24791$$tSci. Rep.$$uYoon, C. H. et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray free-electron laser. Sci. Rep.https://doi.org/10.1038/srep24791 (2016).$$y2016
000606808 999C5 $$1C Fortmann-Grote$$2Crossref$$9-- missing cx lookup --$$a10.1107/S2052252517009496$$p560 -$$tIUCrJ$$uFortmann-Grote, C. et al. Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray free-electron laser. IUCrJ 4, 560–568. https://doi.org/10.1107/S2052252517009496 (2017).$$v4$$y2017
000606808 999C5 $$2Crossref$$uFortmann-Grote, C. & E, J. C. Simex. howpublishedhttps://github.com/PaNOSC-ViNYL/SimEx (2020).
000606808 999C5 $$1E Juncheng$$2Crossref$$9-- missing cx lookup --$$a10.1117/12.2677299$$tProc. SPIE$$uJuncheng, E. et al. Simex-lite: Easy access to start-to-end simulation for experiments at advanced light sources. Proc. SPIEhttps://doi.org/10.1117/12.2677299 (2023).$$y2023
000606808 999C5 $$1E Juncheng$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41598-021-97142-5$$p17976 -$$tSci. Rep.$$uJuncheng, E. et al. Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray free-electron laser. Sci. Rep. 11, 17976. https://doi.org/10.1038/s41598-021-97142-5 (2021).$$v11$$y2021
000606808 999C5 $$1E Juncheng$$2Crossref$$9-- missing cx lookup --$$a10.1038/s41598-023-43298-1$$p16359 -$$tSci. Rep.$$uJuncheng, 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).$$v13$$y2023
000606808 999C5 $$1B Ziaja$$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevLett.102.205002$$tPhys. Rev. Lett.$$uZiaja, 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).$$v102$$y2009
000606808 999C5 $$1Z Jurek$$2Crossref$$9-- missing cx lookup --$$a10.1107/S1600576716006014$$p1048 -$$tJ. Appl. Crystallogr.$$uJurek, Z., Son, S.-K., Ziaja, B. & Santra, R. XMDYN and XATOM: Versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter. J. Appl. Crystallogr. 49, 1048–1056 (2016).$$v49$$y2016
000606808 999C5 $$1BF Murphy$$2Crossref$$9-- missing cx lookup --$$a10.1038/ncomms5281$$p4281 -$$tNat. Commun.$$uMurphy, 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).$$v5$$y2014
000606808 999C5 $$1M Stransky$$2Crossref$$9-- missing cx lookup --$$a10.3390/molecules27134206$$p4206 -$$tMolecules$$uStransky, M., Jurek, Z., Santra, R., Mancuso, A. & Ziaja, B. Tree-code based improvement of computational performance of the X-ray-matter-interaction simulation tool XMDYN. Molecules 27, 4206. https://doi.org/10.3390/molecules27134206 (2022).$$v27$$y2022
000606808 999C5 $$1W Zhang$$2Crossref$$9-- missing cx lookup --$$a10.1126/science.1175275$$p1014 -$$tScience$$uZhang, 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).$$v325$$y2009
000606808 999C5 $$2Crossref$$uGibbon, P. PEPC: Pretty Efficient Parallel Coulomb-solver. Technical Report, FORSCHUNGSZENTRUM JÜLICH GmbH Zentralinstitut für Angewandte Mathematik FZJ-ZAM-IB-2003-05 (2003).
000606808 999C5 $$1I Inoue$$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevLett.131.163201$$tPhys. Rev. Lett.$$uInoue, I. et al. Femtosecond reduction of atomic scattering factors triggered by intense x-ray pulse. Phys. Rev. Lett. 131, 163201 (2023).$$v131$$y2023
000606808 999C5 $$1MM Abdullah$$2Crossref$$9-- missing cx lookup --$$a10.1107/S2052252518011442$$p699 -$$tIUCrJ$$uAbdullah, M. M., Son, S.-K., Jurek, Z. & Santra, R. Towards the theoretical limitations of X-ray nanocrystallography at high intensity: the validity of the effective-form-factor description. IUCrJ 5, 699–705. https://doi.org/10.1107/S2052252518011442 (2018).$$v5$$y2018