Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on 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 imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation.

Center for Free Electron Laser Science CFEL Deutsches Elektronen Synchrotron DESY Notkestr 85 22607 Hamburg Germany

Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia

Department of Physics Universität Hamburg Notkestr 9 11 22607 Hamburg Germany

Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK

European XFEL Holzkoppel 4 22869 Schenefeld Germany

Institute of Nuclear Physics Polish Academy of Sciences Radzikowskiego 152 31 342 Krakow Poland

Institute of Physics Czech Academy of Sciences Na Slovance 2 182 21 Prague 8 Czech Republic

The Hamburg Centre for Ultrafast Imaging Luruper Chaussee 149 22761 Hamburg Germany

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Bogan MJ, et al. Single particle X-ray diffractive imaging. Nano Lett. 2008;8:310–316. doi: 10.1021/nl072728k. PubMed DOI

Seibert MM, et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature. 2011;470:78–81. doi: 10.1038/nature09748. PubMed DOI PMC

Sobolev E, et al. Megahertz single-particle imaging at the European XFEL. Commun. Phys. 2020 doi: 10.1038/s42005-020-0362-y. DOI

Bielecki J, Maia FRNC, Mancuso AP. Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources. Struct. Dynam. 2020;7:040901. doi: 10.1063/4.0000024. PubMed DOI PMC

Cheng Y. Single-particle cryo-em-how did it get here and where will it go. Science. 2018;361:876–880. doi: 10.1126/science.aat4346. PubMed DOI PMC

Nogales E. The development of cryo-em into a mainstream structural biology technique. Nat. Methods. 2016;13:24–27. doi: 10.1038/nmeth.3694. PubMed DOI PMC

Sun Z, Fan J, Li H, Jiang H. Current status of single particle imaging with x-ray lasers. Appl. Sci. 2018 doi: 10.3390/app8010132. DOI

Barty A, et al. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat. Photonics. 2012;6:35–40. doi: 10.1038/nphoton.2011.297. PubMed DOI PMC

Xu R, et al. Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses. Nat. Commun. 2014;5:4061. doi: 10.1038/ncomms5061. PubMed DOI

Mancuso AP, et al. The single particles, clusters and biomolecules and serial femtosecond crystallography instrument of the European XFEL: Initial installation. J. Synchrotron Radiat. 2019;26:660–676. doi: 10.1107/S1600577519003308. PubMed DOI PMC

Nass K, et al. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat. Commun. 2020;11:1814. doi: 10.1038/s41467-020-15610-4. PubMed DOI PMC

Chapman HN, et al. Femtosecond x-ray protein nanocrystallography. Nature. 2011;470:73–77. doi: 10.1038/nature09750. PubMed DOI PMC

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. 2015;2:256–269. doi: 10.3390/photonics2010256. DOI

Yoon CH, et al. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray free-electron laser. Sci. Rep. 2016 doi: 10.1038/srep24791. PubMed DOI PMC

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. 2017;4:560–568. doi: 10.1107/S2052252517009496. PubMed DOI PMC

Fortmann-Grote, C. & E, J. C. Simex. howpublishedhttps://github.com/PaNOSC-ViNYL/SimEx (2020).

Juncheng E, et al. Simex-lite: Easy access to start-to-end simulation for experiments at advanced light sources. Proc. SPIE. 2023 doi: 10.1117/12.2677299. DOI

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. 2021;11:17976. doi: 10.1038/s41598-021-97142-5. PubMed DOI PMC

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. 2023;13:16359. doi: 10.1038/s41598-023-43298-1. PubMed DOI PMC

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. 2009;102:205002. doi: 10.1103/PhysRevLett.102.205002. PubMed DOI

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. 2016;49:1048–1056. doi: 10.1107/S1600576716006014. DOI

Murphy BF, et al. Femtosecond X-ray-induced explosion of C 60 at extreme intensity. Nat. Commun. 2014;5:4281. doi: 10.1038/ncomms5281. PubMed DOI

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. 2022;27:4206. doi: 10.3390/molecules27134206. PubMed DOI PMC

Zhang W, Dunkle JA, Cate JHD. Structures of the ribosome in intermediate states of ratcheting. Science. 2009;325:1014–1017. doi: 10.1126/science.1175275. PubMed DOI PMC

Gibbon, P. PEPC: Pretty Efficient Parallel Coulomb-solver. Technical Report, FORSCHUNGSZENTRUM JÜLICH GmbH Zentralinstitut für Angewandte MathematikFZJ-ZAM-IB-2003-05 (2003).

Inoue I, et al. Femtosecond reduction of atomic scattering factors triggered by intense x-ray pulse. Phys. Rev. Lett. 2023;131:163201. doi: 10.1103/PhysRevLett.131.163201. PubMed DOI

Abdullah MM, 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. 2018;5:699–705. doi: 10.1107/S2052252518011442. PubMed DOI PMC