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Bloß D, Trinter F, Unger I, Zindel C, Honisch C, Viehmann J, Kiefer N, Marder L, Küstner-Wetekam C, Heikura E, Cederbaum LS, Björneholm O, Hergenhahn U, Ehresmann A, Hans A. X-ray radiation damage cycle of solvated inorganic ions. Nat Commun 2024; 15:4594. [PMID: 38816362 PMCID: PMC11139941 DOI: 10.1038/s41467-024-48687-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024] Open
Abstract
X-ray-induced damage is one of the key topics in radiation chemistry. Substantial damage is attributed to low-energy electrons and radicals emerging from direct inner-shell photoionization or produced by subsequent processes. We apply multi-electron coincidence spectroscopy to X-ray-irradiated aqueous solutions of inorganic ions to investigate the production of low-energy electrons (LEEs) in a predicted cascade of intermolecular charge- and energy-transfer processes, namely electron-transfer-mediated decay (ETMD) and interatomic/intermolecular Coulombic decay (ICD). An advanced coincidence technique allows us to identify several LEE-producing steps during the decay of 1s vacancies in solvated Mg2+ ions, which escaped observation in previous non-coincident experiments. We provide strong evidence for the predicted recovering of the ion's initial state. In natural environments the recovering of the ion's initial state is expected to cause inorganic ions to be radiation-damage hot spots, repeatedly producing destructive particles under continuous irradiation.
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Affiliation(s)
- Dana Bloß
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany.
| | - Florian Trinter
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
- Institut für Kernphysik, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Isaak Unger
- Chemical and Biomolecular Physics, Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Christina Zindel
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Carolin Honisch
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Johannes Viehmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Nils Kiefer
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Lutz Marder
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Catmarna Küstner-Wetekam
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Emilia Heikura
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Lorenz S Cederbaum
- Theoretical Chemistry, Institute of Physical Chemistry, University of Heidelberg, Heidelberg, Germany
| | - Olle Björneholm
- Chemical and Biomolecular Physics, Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Uwe Hergenhahn
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
| | - Arno Ehresmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Andreas Hans
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany.
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2
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Stransky M, E J, Jurek Z, Santra R, Bean R, Ziaja B, Mancuso AP. Computational study of diffraction image formation from XFEL irradiated single ribosome molecule. Sci Rep 2024; 14:10617. [PMID: 38720133 PMCID: PMC11078940 DOI: 10.1038/s41598-024-61314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
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.
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Affiliation(s)
- Michal Stransky
- 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.
| | - Juncheng E
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Krakow, Poland
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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3
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Wollter A, De Santis E, Ekeberg T, Marklund EG, Caleman C. Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging. J Chem Phys 2024; 160:114108. [PMID: 38506290 DOI: 10.1063/5.0188772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins' orientation as each protein is randomly oriented when exposed to x-rays. Algorithms such as the expand, maximize, and compress (EMC) exist that can solve the orientation problem and reconstruct the three-dimensional diffraction intensity space, given sufficient measurements. If information about orientation were known, for example, by using an electric field to orient the particles, the reconstruction would benefit and potentially reach better results. We used simulated diffraction experiments to test how the reconstructions from EMC improve with particles' orientation to a preferred axis. Our reconstructions converged to correct maps of the three-dimensional diffraction space with fewer measurements if biased orientation information was considered. Even for a moderate bias, there was still significant improvement. Biased orientations also substantially improved the results in the case of missing central information, in particular in the case of small datasets. The effects were even more significant when adding a background with 50% the strength of the averaged diffraction signal photons to the diffraction patterns, sometimes reducing the data requirement for convergence by a factor of 10. This demonstrates the usefulness of having biased orientation information in single particle imaging experiments, even for a weaker bias than what was previously known. This could be a key component in overcoming the problems with background noise that currently plague these experiments.
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Affiliation(s)
- August Wollter
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Husargatan 3, 75124 Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Husargatan 3, 75124 Uppsala, Sweden
| | - Erik G Marklund
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, DE-22607 Hamburg, Germany
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4
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Round A, Jungcheng E, Fortmann-Grote C, Giewekemeyer K, Graceffa R, Kim C, Kirkwood H, Mills G, Round E, Sato T, Pascarelli S, Mancuso A. Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:141-162. [PMID: 38507205 DOI: 10.1007/978-3-031-52193-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.
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Affiliation(s)
| | | | | | | | | | - Chan Kim
- European XFEL, Schenefeld, Germany
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5
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Guest TW, Bean R, Kammering R, van Riessen G, Mancuso AP, Abbey B. A phenomenological model of the X-ray pulse statistics of a high-repetition-rate X-ray free-electron laser. IUCRJ 2023; 10:708-719. [PMID: 37782462 PMCID: PMC10619450 DOI: 10.1107/s2052252523008242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Many coherent imaging applications that utilize ultrafast X-ray free-electron laser (XFEL) radiation pulses are highly sensitive to fluctuations in the shot-to-shot statistical properties of the source. Understanding and modelling these fluctuations are key to successful experiment planning and necessary to maximize the potential of XFEL facilities. Current models of XFEL radiation and their shot-to-shot statistics are based on theoretical descriptions of the source and are limited in their ability to capture the shot-to-shot intensity fluctuations observed experimentally. The lack of accurate temporal statistics in simulations that utilize these models is a significant barrier to optimizing and interpreting data from XFEL coherent diffraction experiments. Presented here is a phenomenological model of XFEL radiation that is capable of capturing the shot-to-shot statistics observed experimentally using a simple time-dependent approximation of the pulse wavefront. The model is applied to reproduce non-stationary shot-to-shot intensity fluctuations observed at the European XFEL, whilst accurately representing the single-shot properties predicted by FEL theory. Compared with previous models, this approach provides a simple, robust and computationally inexpensive method of generating statistical representations of XFEL radiation.
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Affiliation(s)
- Trey W. Guest
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Raimund Kammering
- Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Grant van Riessen
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Adrian P. Mancuso
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Brian Abbey
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
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6
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E J, Stransky M, Shen Z, Jurek Z, Fortmann-Grote C, Bean R, Santra R, Ziaja B, Mancuso AP. 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. [PMID: 37773512 PMCID: PMC10541445 DOI: 10.1038/s41598-023-43298-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023] Open
Abstract
The noise caused by sample heterogeneity (including sample solvent) has been identified as one of the determinant factors for a successful X-ray single-particle imaging experiment. It influences both the radiation damage process that occurs during illumination as well as the scattering patterns captured by the detector. Here, we investigate the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. Orientation recovery is a critical step for single-particle imaging. It enables to sort a set of diffraction patterns scattered by identical particles placed at unknown orientations and assemble them into a 3D reciprocal space volume. The recovery quality is characterized by a "disconcurrence" metric. Our results show that while a water layer mitigates protein damage, the noise generated by the scattering from it can introduce challenges for orientation recovery and is anticipated to cause problems in the phase retrieval process to extract the desired protein structure. Compared to these disadvantageous effects due to the thick water layer, the effects of radiation damage on the orientation recovery are relatively small. Therefore, minimizing the amount of residual sample solvent should be considered a crucial step in improving the fidelity and resolution of X-ray single-particle imaging experiments.
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Affiliation(s)
- Juncheng E
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Michal Stransky
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland
| | - Zhou Shen
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607, Hamburg, Germany
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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E J, Kim Y, Bielecki J, Sikorski M, de Wijn R, Fortmann-Grote C, Sztuk-Dambietz J, Koliyadu JCP, Letrun R, Kirkwood HJ, Sato T, Bean R, Mancuso AP, Kim C. Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:064101. [PMID: 36411869 PMCID: PMC9675053 DOI: 10.1063/4.0000169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 05/15/2023]
Abstract
The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.
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Affiliation(s)
- Juncheng E
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Bielecki
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Sikorski
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R. de Wijn
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - R. Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - T. Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - R. Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - C. Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Author to whom correspondence should be addressed:
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8
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Stransky M, Jurek Z, Santra R, Mancuso AP, Ziaja B. Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN. Molecules 2022; 27:molecules27134206. [PMID: 35807452 PMCID: PMC9267930 DOI: 10.3390/molecules27134206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 12/04/2022] Open
Abstract
In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL.
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Affiliation(s)
- Michal Stransky
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany;
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland;
- Correspondence: (M.S.); (Z.J.)
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany;
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence: (M.S.); (Z.J.)
| | - Robin Santra
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany;
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607 Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany;
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland;
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany;
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