1
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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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2
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Inoue I, Yamada J, Kapcia KJ, Stransky M, Tkachenko V, Jurek Z, Inoue T, Osaka T, Inubushi Y, Ito A, Tanaka Y, Matsuyama S, Yamauchi K, Yabashi M, Ziaja B. Femtosecond Reduction of Atomic Scattering Factors Triggered by Intense X-Ray Pulse. PHYSICAL REVIEW LETTERS 2023; 131:163201. [PMID: 37925726 DOI: 10.1103/physrevlett.131.163201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 11/07/2023]
Abstract
X-ray diffraction of silicon irradiated with tightly focused femtosecond x-ray pulses (photon energy, 11.5 keV; pulse duration, 6 fs) was measured at various x-ray intensities up to 4.6×10^{19} W/cm^{2}. The measurement reveals that the diffraction intensity is highly suppressed when the x-ray intensity reaches of the order of 10^{19} W/cm^{2}. With a dedicated simulation, we confirm that the observed reduction of the diffraction intensity can be attributed to the femtosecond change in individual atomic scattering factors due to the ultrafast creation of highly ionized atoms through photoionization, Auger decay, and subsequent collisional ionization. We anticipate that this ultrafast reduction of atomic scattering factor will be a basis for new x-ray nonlinear techniques, such as pulse shortening and contrast variation x-ray scattering.
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Affiliation(s)
- Ichiro Inoue
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Jumpei Yamada
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Konrad J Kapcia
- Institute of Spintronics and Quantum Information, Faculty of Physics, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 2, PL-61614 Poznań, Poland
- Center of Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michal Stransky
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
| | - Victor Tkachenko
- Center of Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Zoltan Jurek
- Center of Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Takato Inoue
- Department of Materials Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603, Japan
| | - Taito Osaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yuichi Inubushi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Atsuki Ito
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yuto Tanaka
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Satoshi Matsuyama
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Department of Materials Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603, Japan
| | - Kazuto Yamauchi
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Center for Ultra-Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Beata Ziaja
- Center of Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
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3
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Mazza T, Baumann TM, Boll R, De Fanis A, Grychtol P, Ilchen M, Montaño J, Music V, Ovcharenko Y, Rennhack N, Rivas DE, Rörig A, Schmidt P, Usenko S, Ziołkowski P, La Civita D, Vannoni M, Sinn H, Keitel B, Plönjes E, Jastrow UF, Sorokin A, Tiedtke K, Mann K, Schäfer B, Breckwoldt N, Son SK, Meyer M. The beam transport system for the Small Quantum Systems instrument at the European XFEL: optical layout and first commissioning results. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:457-467. [PMID: 36891860 PMCID: PMC10000793 DOI: 10.1107/s1600577522012085] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
The Small Quantum Systems instrument is one of the six operating instruments of the European XFEL, dedicated to the atomic, molecular and cluster physics communities. The instrument started its user operation at the end of 2018 after a commissioning phase. The design and characterization of the beam transport system are described here. The X-ray optical components of the beamline are detailed, and the beamline performances, transmission and focusing capabilities are reported. It is shown that the X-ray beam can be effectively focused as predicted by ray-tracing simulations. The impact of non-ideal X-ray source conditions on the focusing performances is discussed.
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Affiliation(s)
- Tommaso Mazza
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Rebecca Boll
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Markus Ilchen
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Valerija Music
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Physics, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | | | - Nils Rennhack
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Sergey Usenko
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Harald Sinn
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Barbara Keitel
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Elke Plönjes
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ulf Fini Jastrow
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Andrey Sorokin
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Kai Tiedtke
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Klaus Mann
- IFNANO Institut für Nanophotonik Göttingen e.V., Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Bernd Schäfer
- IFNANO Institut für Nanophotonik Göttingen e.V., Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Niels Breckwoldt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9–11, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Meyer
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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4
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Banerjee S, Jurek Z, Abdullah MM, Santra R. Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054101. [PMID: 36329869 PMCID: PMC9625838 DOI: 10.1063/4.0000166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN toolkit to treat chemical bonds using the reactive force field. In order to study its impact, a highly intense x-ray pulse was made to interact with the simplest amino acid, glycine. Different model variants were used to highlight the consequences of charge rearrangement and chemical bonds on the time evolution. The charge-rearrangement-enhanced x-ray ionization of molecules effect is also discussed to address the capability of a classical MD based approach, i.e., XMDYN, to capture such a molecular phenomenon.
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Affiliation(s)
- Sourav Banerjee
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607 Hamburg, Germany
| | - Zoltan Jurek
- Authors to whom correspondence should be addressed: and
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5
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Probing C60 Fullerenes from within Using Free Electron Lasers. ATOMS 2022. [DOI: 10.3390/atoms10030075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Fullerenes, such as C60, are ideal systems to investigate energy redistribution following substantial excitation. Ultra-short and ultra-intense free electron lasers (FELs) have allowed molecular research in a new photon energy regime. FELs have allowed the study of the response of fullerenes to X-rays, which includes femtosecond multi-photon processes, as well as time-resolved ionization and fragmentation dynamics. This perspective: (1) provides a general introduction relevant to C60 research using photon sources, (2) reports on two specific X-ray FEL-based photoionization investigations of C60, at two different FEL fluences, one static and one time-resolved, and (3) offers a brief analysis and recommendations for future research.
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6
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Jin R, Jurek Z, Santra R, Son SK. Plasma environmental effects in the atomic structure for simulating x-ray free-electron-laser-heated solid-density matter. Phys Rev E 2022; 106:015206. [PMID: 35974549 DOI: 10.1103/physreve.106.015206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
High energy density (HED) matter exists extensively in the Universe, and it can be created with extreme conditions in laboratory facilities such as x-ray free-electron lasers (XFEL). In HED matter, the electronic structure of individual atomic ions is influenced by a dense plasma environment, and one of the most significant phenomena is the ionization potential depression (IPD). Incorporation of the IPD effects is of great importance in accurate modeling of dense plasmas. All theoretical treatments of IPD so far have been based on the assumption of local thermodynamic equilibrium, but its validity is questionable in ultrafast formation dynamics of dense plasmas, particularly when interacting with intense XFEL pulses. A treatment of transient IPD, based on an electronic-structure calculation of an atom in the presence of a plasma environment described by classical particles, has recently been proposed [Phys. Rev. E 103, 023203 (2021)2470-004510.1103/PhysRevE.103.023203], but its application to and impact on plasma dynamics simulations have not been investigated yet. In this work, we extend XMDYN, a hybrid quantum-classical approach combining Monte Carlo and molecular dynamics, by incorporating the proposed IPD treatment into plasma dynamics simulations. We demonstrate the importance of the IPD effects in theoretical modeling of aluminum dense plasmas by comparing two XMDYN simulations: one with electronic-structure calculations of isolated atoms (without IPD) and the other with those of atoms embedded in a plasma (with IPD). At equilibrium, the mean charge obtained in the plasma simulation with IPD is in good agreement with the full quantum-mechanical average-atom model. The present approach promises to be a reliable tool to simulate the creation and nonequilibrium evolution of dense plasmas induced by ultraintense and ultrashort XFEL pulses.
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Affiliation(s)
- Rui Jin
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 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, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestrasse 9-11, 22607 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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7
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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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8
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Gargiulo S, Madan I, Carbone F. Nuclear Excitation by Electron Capture in Excited Ions. PHYSICAL REVIEW LETTERS 2022; 128:212502. [PMID: 35687469 DOI: 10.1103/physrevlett.128.212502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/10/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
A nuclear excitation following the capture of an electron in an empty orbital has been recently observed for the first time. So far, the evaluation of the cross section of the process has been carried out widely using the assumption that the ion is in its electronic ground state prior to the capture. We show that by lifting this restriction new capture channels emerge resulting in a boost of more than three orders of magnitude to the electron capture resonance strength.
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Affiliation(s)
- Simone Gargiulo
- Institute of Physics (IPhys), Laboratory for Ultrafast Microscopy and Electron Scattering (LUMES), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015 CH, Switzerland
| | - Ivan Madan
- Institute of Physics (IPhys), Laboratory for Ultrafast Microscopy and Electron Scattering (LUMES), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015 CH, Switzerland
| | - Fabrizio Carbone
- Institute of Physics (IPhys), Laboratory for Ultrafast Microscopy and Electron Scattering (LUMES), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015 CH, Switzerland
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9
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Bouskila G, Landau A, Haritan I, Moiseyev N, Bhattacharya D. Complex energies and transition dipoles for shape-type resonances of uracil anion from stabilization curves via Padé. J Chem Phys 2022; 156:194101. [PMID: 35597649 DOI: 10.1063/5.0086887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absorption of slow moving electrons by neutral ground state nucleobases has been known to produce resonance metastable states. There are indications that such metastable states may play a key role in DNA/RNA damage. Therefore, herein, we present an ab initio non-Hermitian investigation of the resonance positions and decay rates for the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has already been successfully applied to many small molecular systems, and herein, we present the first application of RVP to a medium-sized system. The presented resonance energies are optimized with respect to the size of the basis set and compared with previous theoretical studies and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the optimal basis set. The ability to calculate ab initio energies and lifetimes of biologically relevant systems paves the way for studying reactions of such systems in which autoionization takes place, while the ability to also calculate their complex transition dipoles opens the door for studying photo-induced dynamics of such biological molecules.
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Affiliation(s)
- Gal Bouskila
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Arie Landau
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Idan Haritan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Debarati Bhattacharya
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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10
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Hui J, Yu J, Luo Y, Hu W, Liu Y, Hu Q, Wang K, Li T, Zhou X, Huang J, Zhang X, Ren Y, Wang H. Synchrotron X-ray-induced Synthesis of Copper Hydroxide Nitrate Nanoplates on Cu Thin Films in an Ambient Atmosphere. ACS APPLIED MATERIALS & INTERFACES 2022; 14:23342-23347. [PMID: 35549025 DOI: 10.1021/acsami.2c01329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synchrotron X-rays are widely used for material characterizations. However, they can also ionize atoms and molecules to damage and manipulate probed materials. We report here an X-ray-induced growth of copper hydroxide nitrate, Cu2(OH)3NO3, on copper thin films in the ambient atmosphere without solvents and thermal treatment. In situ synchrotron X-ray diffraction measurements showed that the time-dependent growth process of theCu2(OH)3NO3 is accompanied by the consumption of Cu metal and can be described by a sigmoidal model. The growth rate was reduced after the initial fast growth period. Scanning electron microscopy (SEM) images show that the isolated islands of Cu2(OH)3NO3 nanoplates formed in the beginning, which grew together with new nanoplates formed under continued X-ray irradiation. The result demonstrated that high-flux synchrotron X-rays may provide an unconventional approach to synthesizing and manipulating materials, which will inspire future investigation both experimentally and theoretically.
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Affiliation(s)
- Jian Hui
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Yu
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yuxi Luo
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenhui Hu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Qingyun Hu
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kailin Wang
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tianyi Li
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xinwei Zhou
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Jier Huang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Xiaoyi Zhang
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yang Ren
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong, China
- Centre for Neutron Scattering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Hong Wang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
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11
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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. [PMID: 34504156 PMCID: PMC8429720 DOI: 10.1038/s41598-021-97142-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/19/2021] [Indexed: 11/08/2022] Open
Abstract
We present a computational case study of X-ray single-particle imaging of hydrated proteins on an example of 2-Nitrogenase-Iron protein covered with water layers of various thickness, using a start-to-end simulation platform and experimental parameters of the SPB/SFX instrument at the European X-ray Free-Electron Laser facility. The simulations identify an optimal thickness of the water layer at which the effective resolution for imaging the hydrated sample becomes significantly higher than for the non-hydrated sample. This effect is lost when the water layer becomes too thick. Even though the detailed results presented pertain to the specific sample studied, the trends which we identify should also hold in a general case. We expect these findings will guide future single-particle imaging experiments using hydrated proteins.
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12
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Limitations of Structural Insight into Ultrafast Melting of Solid Materials with X-ray Diffraction Imaging. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11115157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this work, we analyze the application of X-ray diffraction imaging techniques to follow ultrafast structural transitions in solid materials using the example of an X-ray pump–X-ray probe experiment with a single-crystal silicon performed at a Linac Coherent Light Source. Due to the spatially non-uniform profile of the X-ray beam, the diffractive signal recorded in this experiment included contributions from crystal parts experiencing different fluences from the peak fluence down to zero. With our theoretical model, we could identify specific processes contributing to the silicon melting in those crystal regions, i.e., the non-thermal and thermal melting whose occurrences depended on the locally absorbed X-ray doses. We then constructed the total volume-integrated signal by summing up the coherent signal contributions (amplitudes) from the various crystal regions and found that this significantly differed from the signals obtained for a few selected uniform fluence values, including the peak fluence. This shows that the diffraction imaging signal obtained for a structurally damaged material after an impact of a non-uniform X-ray pump pulse cannot be always interpreted as the material’s response to a pulse of a specific (e.g., peak) fluence as it is sometimes believed. This observation has to be taken into account in planning and interpreting future experiments investigating structural changes in materials with X-ray diffraction imaging.
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13
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Medvedev N, Noei H, Toleikis S, Ziaja B. Response of free-standing graphene monolayer exposed to ultrashort intense XUV pulse from free-electron laser. J Chem Phys 2021; 154:204706. [PMID: 34241156 DOI: 10.1063/5.0041261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The response of a free-standing graphene monolayer exposed to a few tens of femtoseconds long extreme ultraviolet (XUV) pulse was studied theoretically in order to analyze and compare contributions of various mechanisms to the graphene damage, understood here as a global atomic disintegration. Our simulation results indicate that nonthermal disintegration of the atomic structure is the predominant damage mechanism for a free-standing graphene layer. Only at high absorbed doses, charge-induced disintegration of the graphene structure prevails. We also demonstrate that the progressing damage can be probed by femtosecond optical pulses in the soft UV regime (4 eV photon energy). The achieved quantitative understanding of the damage mechanisms may enable a better control of graphene-based devices when they are exposed to x-ray radiation, as well as an efficient processing of graphene layers with ultrashort intense XUV pulses.
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Affiliation(s)
- N Medvedev
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 8 18221, Czech Republic
| | - H Noei
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - S Toleikis
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - B Ziaja
- Center of Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
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14
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Ho PJ, Fouda AEA, Li K, Doumy G, Young L. Ultraintense, ultrashort pulse X-ray scattering in small molecules. Faraday Discuss 2021; 228:139-160. [PMID: 33576361 DOI: 10.1039/d0fd00106f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We examine X-ray scattering from an isolated organic molecule from the linear to nonlinear absorptive regime. In the nonlinear regime, we explore the importance of both the coherent and incoherent channels and observe the onset of nonlinear behavior as a function of pulse duration and energy. In the linear regime, we test the sensitivity of the scattering signal to molecular bonding and electronic correlation via calculations using the independent atom model (IAM), Hartree-Fock (HF) and density functional theory (DFT). Finally, we describe how coherent X-ray scattering can be used to directly visualize femtosecond charge transfer and dissociation within a single molecule undergoing X-ray multiphoton absorption.
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Affiliation(s)
- Phay J Ho
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.
| | - Adam E A Fouda
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.
| | - Kai Li
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA. and Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.
| | - Linda Young
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA. and Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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15
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Ben-Asher A, Landau A, Moiseyev N. Uniform vs Partial Scaling within Resonances via Padé Based on the Similarities to Other Non-Hermitian Methods: Illustration for the Beryllium 1 s22 p3 s State. J Chem Theory Comput 2021; 17:3435-3444. [PMID: 33945263 DOI: 10.1021/acs.jctc.1c00223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Resonance via Padé (RVP) is an efficient method for calculating autoionization resonance states. It is based on the stabilization technique in which the basis set is scaled. The scaling can be uniform (i.e., all basis functions are scaled) or partial. Herein, we compare the two RVP scaling schemes for calculating an autoionization eigenvalue; moreover, the effect of freezing the core electrons is intertwined within this comparison. In order to study the different behavior of the RVP schemes, we associate each RVP scaling scheme with a complex contour of integration. Similarities between RVP and other non-Hermitian methods emerge from the generated contours, which suggest that RVP introduces similar outgoing boundary conditions as the complex scaling (CS), complex basis function (CBF), and reflection-free complex absorbing potential (RF-CAP) methods. A uniform-RVP contour, unlike a partial one, immediately penetrates the complex plane and influences the interaction region. Hence, uniform scaling within RVP destroys the description of the core electrons, as well as the description of the reference state, and yields less reliable results than partial scaling. The 1s22p3s 1P autoionization state of Be, at the equation-of-motion coupled-cluster level, is used as our case study model.
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Affiliation(s)
- Anael Ben-Asher
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Landau
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry, Department of Physics and Russell-Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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16
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Inoue I, Deguchi Y, Ziaja B, Osaka T, Abdullah MM, Jurek Z, Medvedev N, Tkachenko V, Inubushi Y, Kasai H, Tamasaku K, Hara T, Nishibori E, Yabashi M. Atomic-Scale Visualization of Ultrafast Bond Breaking in X-Ray-Excited Diamond. PHYSICAL REVIEW LETTERS 2021; 126:117403. [PMID: 33798368 DOI: 10.1103/physrevlett.126.117403] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/09/2020] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Ultrafast changes of charge density distribution in diamond after irradiation with an intense x-ray pulse (photon energy, 7.8 keV; pulse duration, 6 fs; intensity, 3×10^{19} W/cm^{2}) have been visualized with the x-ray pump-x-ray probe technique. The measurement reveals that covalent bonds in diamond are broken and the electron distribution around each atom becomes almost isotropic within ∼5 fs after the intensity maximum of the x-ray pump pulse. The 15 fs time delay observed between the bond breaking and atomic disordering indicates nonisothermality of electron and lattice subsystems on this timescale. From these observations and simulation results, we interpret that the x-ray-induced change of the interatomic potential drives the ultrafast atomic disordering underway to the following nonthermal melting.
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Affiliation(s)
- Ichiro Inoue
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yuka Deguchi
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Beata Ziaja
- Center of Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
| | - Taito Osaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Malik M Abdullah
- Center of Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607, Germany
| | - Zoltan Jurek
- Center of Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607, Germany
| | - Nikita Medvedev
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 8, 18221, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 3, 182 00 Prague 8, Czech Republic
| | - Victor Tkachenko
- Center of Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yuichi Inubushi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Hidetaka Kasai
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Faculty of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Toru Hara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Eiji Nishibori
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Faculty of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
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17
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Jin R, Abdullah MM, Jurek Z, Santra R, Son SK. Transient ionization potential depression in nonthermal dense plasmas at high x-ray intensity. Phys Rev E 2021; 103:023203. [PMID: 33735970 DOI: 10.1103/physreve.103.023203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/22/2021] [Indexed: 11/07/2022]
Abstract
The advent of x-ray free-electron lasers (XFELs), which provide intense ultrashort x-ray pulses, has brought a new way of creating and analyzing hot and warm dense plasmas in the laboratory. Because of the ultrashort pulse duration, the XFEL-produced plasma will be out of equilibrium at the beginning, and even the electronic subsystem may not reach thermal equilibrium while interacting with a femtosecond timescale pulse. In the dense plasma, the ionization potential depression (IPD) induced by the plasma environment plays a crucial role for understanding and modeling microscopic dynamical processes. However, all theoretical approaches for IPD have been based on local thermal equilibrium (LTE), and it has been controversial to use LTE IPD models for the nonthermal situation. In this work, we propose a non-LTE (NLTE) approach to calculate the IPD effect by combining a quantum-mechanical electronic-structure calculation and a classical molecular dynamics simulation. This hybrid approach enables us to investigate the time evolution of ionization potentials and IPDs during and after the interaction with XFEL pulses, without the limitation of the LTE assumption. In our NLTE approach, the transient IPD values are presented as distributions evolving with time, which cannot be captured by conventional LTE-based models. The time-integrated ionization potential values are in good agreement with benchmark experimental data on solid-density aluminum plasma and other theoretical predictions based on LTE. The present work is promising to provide critical insights into nonequilibrium dynamics of dense plasma formation and thermalization induced by XFEL pulses.
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Affiliation(s)
- Rui Jin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240 Shanghai, China
| | | | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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18
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Nass K, Gorel A, Abdullah MM, V Martin A, Kloos M, Marinelli A, Aquila A, Barends TRM, Decker FJ, Bruce Doak R, Foucar L, Hartmann E, Hilpert M, Hunter MS, Jurek Z, Koglin JE, Kozlov A, Lutman AA, Kovacs GN, Roome CM, Shoeman RL, Santra R, Quiney HM, Ziaja B, Boutet S, Schlichting I. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat Commun 2020; 11:1814. [PMID: 32286284 PMCID: PMC7156470 DOI: 10.1038/s41467-020-15610-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics. The local X-ray-induced dynamics that occur in protein crystals during serial femtosecond crystallography (SFX) measurements at XFELs are not well understood. Here the authors performed a time-resolved X-ray pump X-ray probe SFX experiment, and they observe distinct structural changes in the disulfide bridges and peptide backbone of proteins; complementing theoretical approaches allow them to further characterize the details of the X-ray induced ionization and local structural dynamics.
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Affiliation(s)
- Karol Nass
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Alexander Gorel
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Malik M Abdullah
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew V Martin
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC, 3000, Australia
| | - Marco Kloos
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - Andrew Aquila
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Elisabeth Hartmann
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Mark S Hunter
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jason E Koglin
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Alexander Kozlov
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Alberto A Lutman
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355, Hamburg, Germany
| | - Harry M Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Beata Ziaja
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany. .,Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland.
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.
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19
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Ho PJ, Daurer BJ, Hantke MF, Bielecki J, Al Haddad A, Bucher M, Doumy G, Ferguson KR, Flückiger L, Gorkhover T, Iwan B, Knight C, Moeller S, Osipov T, Ray D, Southworth SH, Svenda M, Timneanu N, Ulmer A, Walter P, Hajdu J, Young L, Maia FRNC, Bostedt C. The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters. Nat Commun 2020; 11:167. [PMID: 31919346 PMCID: PMC6952381 DOI: 10.1038/s41467-019-13905-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/04/2019] [Indexed: 11/09/2022] Open
Abstract
Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The large-scale dynamic scattering calculations reveal that transient phenomena driven by non-linear x-ray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments. X-ray free electron lasers provide high photon flux to explore single particle diffraction imaging of biological samples. Here the authors present dynamic electronic structure calculations and benchmark them to single-particle XFEL diffraction data of sucrose clusters to predict optimal single-shot imaging conditions.
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Affiliation(s)
- Phay J Ho
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.,Chemistry Research Laboratory, Department of Chemistry, Oxford University, 12 Mansfield Rd, Oxford, OX1 3TA, UK
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.,European XFEL GmbH, Holzkoppel 4, D-22869, Schenefeld, Germany
| | - Andre Al Haddad
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Maximilian Bucher
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Gilles Doumy
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ken R Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Leonie Flückiger
- ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Tais Gorkhover
- Stanford Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Bianca Iwan
- Stanford Pulse Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher Knight
- Computational Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Stefan Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Timur Osipov
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Dipanwita Ray
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.,Department of Physics and Astronomy, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Anatoli Ulmer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623, Berlin, Germany
| | - Peter Walter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Linda Young
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Department of Physics and James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Christoph Bostedt
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA. .,Paul-Scherrer Institute, CH-5232, Villigen PSI, Switzerland. .,LUXS Laboratory for Ultrafast X-ray Sciences, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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20
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Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses. Nat Commun 2019; 10:4761. [PMID: 31628306 PMCID: PMC6802401 DOI: 10.1038/s41467-019-12717-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.
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21
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Yamazaki K, Niitsu N, Kanno M, Ueda K, Kono H. Capturing the photo-induced dynamics of nano-molecules by X-ray free electron laser induced Coulomb explosion. J Chem Phys 2019; 151:124305. [PMID: 31575189 DOI: 10.1063/1.5115072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We performed reaction dynamics simulations to demonstrate that the vibrational dynamics of C60 induced by infrared (IR) pulses can be traced by triggering Coulomb explosion with intense femtosecond X-ray free electron laser (XFEL) probe pulses. The time series of the angular anisotropy β(t) of fast C+ and C2+ fragments of C60 60+ produced by such an XFEL pulse reflects the instantaneous structure of C60 vibrationally excited by IR pulses. The phases and amplitudes of excited vibrational modes and the coupling between excited modes can be successfully extracted from the expansion of β(t) in terms of vibrational modes. This proof-of-principle simulation clearly demonstrates that various information of the structures and reaction dynamics of large clusters or biomolecules can be retrieved by decomposing the experimentally determined β(t) into vibrational modes.
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Affiliation(s)
- Kaoru Yamazaki
- Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan
| | - Naoyuki Niitsu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-9578, Japan
| | - Manabu Kanno
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-9578, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Hirohiko Kono
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-9578, Japan
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22
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Obaid R, Schnorr K, Wolf TJA, Takanashi T, Kling NG, Kooser K, Nagaya K, Wada SI, Fang L, Augustin S, You D, Campbell EEB, Fukuzawa H, Schulz CP, Ueda K, Lablanquie P, Pfeifer T, Kukk E, Berrah N. Photo-ionization and fragmentation of Sc 3N@C 80 following excitation above the Sc K-edge. J Chem Phys 2019; 151:104308. [PMID: 31521092 DOI: 10.1063/1.5110297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have investigated the ionization and fragmentation of a metallo-endohedral fullerene, Sc3N@C80, using ultrashort (10 fs) x-ray pulses. Following selective ionization of a Sc (1s) electron (hν = 4.55 keV), an Auger cascade leads predominantly to either a vibrationally cold multiply charged parent molecule or multifragmentation of the carbon cage following a phase transition. In contrast to previous studies, no intermediate regime of C2 evaporation from the carbon cage is observed. A time-delayed, hard x-ray pulse (hν = 5.0 keV) was used to attempt to probe the electron transfer dynamics between the encapsulated Sc species and the carbon cage. A small but significant change in the intensity of Sc-containing fragment ions and coincidence counts for a delay of 100 fs compared to 0 fs, as well as an increase in the yield of small carbon fragment ions, may be indicative of incomplete charge transfer from the carbon cage on the sub-100 fs time scale.
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Affiliation(s)
- Razib Obaid
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
| | | | - Thomas J A Wolf
- SLAC National Accelerator Laboratory, PULSE Institute, Menlo Park, California 94025, USA
| | - Tsukasa Takanashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Nora G Kling
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Kuno Kooser
- Deparment of Physics, University of Turku, Turku, Finland
| | - Kiyonobu Nagaya
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - Shin-Ichi Wada
- Department of Physical Science, Hiroshima University, Higashihiroshima 739-8526, Japan
| | - Li Fang
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Sven Augustin
- Max-Planck-Institut für Kernphysik, Heidelberg, Germany
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Eleanor E B Campbell
- EastCHEM and School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Hironobu Fukuzawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | | | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Pascal Lablanquie
- Laboratoire de Chimie Physique-Matière et Rayonnement, Sorbonne Université, CNRS, 4 place Jussieu, 75005 Paris, France
| | | | - Edwin Kukk
- Deparment of Physics, University of Turku, Turku, Finland
| | - Nora Berrah
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
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23
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Östlin C, Timneanu N, Caleman C, Martin AV. Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers? STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:044103. [PMID: 31463335 PMCID: PMC6701976 DOI: 10.1063/1.5098309] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/31/2019] [Indexed: 05/24/2023]
Abstract
The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors for achieving subnanometer X-ray imaging of single particles and that X-ray pulses need to be as short as possible. Based on the molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs, and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of high-resolution single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.
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Affiliation(s)
- C Östlin
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - N Timneanu
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - C Caleman
- Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - A V Martin
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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24
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Toyota K, Jurek Z, Son SK, Fukuzawa H, Ueda K, Berrah N, Rudek B, Rolles D, Rudenko A, Santra R. xcalib: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1017-1030. [PMID: 31274423 DOI: 10.1107/s1600577519003564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
The xcalib toolkit has been developed to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence-dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core-hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.
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Affiliation(s)
- Koudai Toyota
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Sang Kil Son
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
| | - Hironobu Fukuzawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Nora Berrah
- Physics Department, University of Connecticut, Storrs, CT, USA
| | - Benedikt Rudek
- Physikalisch-Technische Bundesanstalt, Braunschweig, Germany
| | - Daniel Rolles
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
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25
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Landau A, Haritan I. The Clusterization Technique: A Systematic Search for the Resonance Energies Obtained via Padé. J Phys Chem A 2019; 123:5091-5105. [DOI: 10.1021/acs.jpca.8b12573] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arie Landau
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Idan Haritan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
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26
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Abdullah MM, Jurek Z, Son SK, Santra R. Ultrafast x-ray-driven phenomena in nanocrystals: development and application of powerful simulation tools. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920505022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the radiation damage dynamics of nanocrystals at high x-ray intensity, by using time-resolved scattering patterns. We present dynamics simulations for biologically relevant molecules using XMDYN extended to nanocrystals and scattering simulation with XSINC.
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27
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Imaging electron-density fluctuations by multidimensional X-ray photon-coincidence diffraction. Proc Natl Acad Sci U S A 2018; 116:395-400. [PMID: 30584098 DOI: 10.1073/pnas.1816730116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ultrafast spontaneous electron-density fluctuation dynamics in molecules is studied theoretically by off-resonant multiple X-ray diffraction events. The time- and wavevector-resolved photon-coincidence signals give an image of electron-density fluctuations expressed through the four-point correlation function of the charge density in momentum space. A Fourier transform of the signal provides a real-space image of the multipoint charge-density correlation functions, which reveal snapshots of the evolving electron density in between the diffraction events. The proposed technique is illustrated by ab initio simulations of the momentum- and real-space inelastic scattering signals from a linear cyanotetracetylene molecule.
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28
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Abdullah MM, Son SK, 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. [PMID: 30443354 PMCID: PMC6211521 DOI: 10.1107/s2052252518011442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/10/2018] [Indexed: 06/09/2023]
Abstract
X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed. Additionally, the importance of temporal configurational fluctuations at high intensities, shaping these quantities besides the average electron loss, is shown. An analysis regarding the applicability of the approach to targets consisting of several atomic species is made, both theoretically and via realistic radiation-damage simulations. It is concluded that, up to intensities relevant for XFEL-based nanocrystallography, the effective-form-factor description is sufficiently accurate. This work justifies treating measured scattering patterns using conventional structure-reconstruction algorithms.
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Affiliation(s)
- Malik Muhammad Abdullah
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
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29
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Rudek B, Toyota K, Foucar L, Erk B, Boll R, Bomme C, Correa J, Carron S, Boutet S, Williams GJ, Ferguson KR, Alonso-Mori R, Koglin JE, Gorkhover T, Bucher M, Lehmann CS, Krässig B, Southworth SH, Young L, Bostedt C, Ueda K, Marchenko T, Simon M, Jurek Z, Santra R, Rudenko A, Son SK, Rolles D. Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays. Nat Commun 2018; 9:4200. [PMID: 30305630 PMCID: PMC6180123 DOI: 10.1038/s41467-018-06745-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022] Open
Abstract
An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report results on multiple ionization of xenon atoms by ultra-intense (about 1019 W/cm2) femtosecond X-ray pulses at photon energies from 5.5 to 8.3 keV and present a theoretical model capable of reproducing the experimental data in the entire energy range. Our analysis shows that the interplay of resonant and relativistic effects results in strongly structured charge state distributions, which reflect resonant positions of relativistically shifted electronic levels of highly charged ions created during the X-ray pulse. The theoretical approach described here provides a basis for accurate modeling of radiation damage in hard X-ray imaging experiments on targets with high-Z constituents.
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Affiliation(s)
- Benedikt Rudek
- Physikalisch-Technische Bundesanstalt, Braunschweig, Germany
| | - Koudai Toyota
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Erk
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Rebecca Boll
- Max Planck Institute for Nuclear Physics, Heidelberg, Germany
- European XFEL GmbH, Schenefeld, Germany
| | - Cédric Bomme
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jonathan Correa
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- California Lutheran University, Thousand Oaks, CA, USA
| | | | - Garth J Williams
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- NSLS-II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ken R Ferguson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Tais Gorkhover
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Stanford PULSE Institute, SLAC, Menlo Park, CA, USA
| | - Maximilian Bucher
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Argonne National Laboratory, Lemont, IL, USA
| | - Carl Stefan Lehmann
- Argonne National Laboratory, Lemont, IL, USA
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | | | - Linda Young
- Argonne National Laboratory, Lemont, IL, USA
- Department of Physics and The James Franck Institute, University of Chicago, Chicago, IL, USA
| | - Christoph Bostedt
- Argonne National Laboratory, Lemont, IL, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Sendai, Japan
| | - Tatiana Marchenko
- Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, CNRS, Sorbonne Université, Paris, France
| | - Marc Simon
- Laboratoire de Chimie Physique-Matière et Rayonnement, LCPMR, CNRS, Sorbonne Université, Paris, France
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
- Department of Physics, University of Hamburg, Hamburg, Germany
| | - Artem Rudenko
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY, Hamburg, Germany
| | - Daniel Rolles
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA.
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30
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Kumagai Y, Jurek Z, Xu W, Fukuzawa H, Motomura K, Iablonskyi D, Nagaya K, Wada SI, Mondal S, Tachibana T, Ito Y, Sakai T, Matsunami K, Nishiyama T, Umemoto T, Nicolas C, Miron C, Togashi T, Ogawa K, Owada S, Tono K, Yabashi M, Son SK, Ziaja B, Santra R, Ueda K. Radiation-Induced Chemical Dynamics in Ar Clusters Exposed to Strong X-Ray Pulses. PHYSICAL REVIEW LETTERS 2018; 120:223201. [PMID: 29906148 DOI: 10.1103/physrevlett.120.223201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/30/2018] [Indexed: 06/08/2023]
Abstract
We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.
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Affiliation(s)
- Yoshiaki Kumagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
| | - Weiqing Xu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hironobu Fukuzawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Koji Motomura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Denys Iablonskyi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Kiyonobu Nagaya
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - Shin-Ichi Wada
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
- Department of Physical Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Subhendu Mondal
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Tetsuya Tachibana
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Yuta Ito
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Tsukasa Sakai
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | - Kenji Matsunami
- Department of Physics, Kyoto University, Kyoto 606-8502, Japan
| | | | - Takayuki Umemoto
- Department of Physical Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Christophe Nicolas
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex, France
| | - Catalin Miron
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex, France
- Extreme Light Infrastructure-Nuclear Physiscs (ELI-NP), "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125 Mǎgurele, Jud. Ilfov, Romania
- LIDYL, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Tadashi Togashi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | - Kanade Ogawa
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo 679-5198, Japan
| | | | - Sang-Kil Son
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
| | - Beata Ziaja
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
- Institute of Nuclear Physics, PAS, Radzikowskiego 152, 31-342, Krakow, Poland
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22671 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
- RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
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31
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Osipov T, Bostedt C, Castagna JC, Ferguson KR, Bucher M, Montero SC, Swiggers ML, Obaid R, Rolles D, Rudenko A, Bozek JD, Berrah N. The LAMP instrument at the Linac Coherent Light Source free-electron laser. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:035112. [PMID: 29604777 DOI: 10.1063/1.5017727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The Laser Applications in Materials Processing (LAMP) instrument is a new end-station for soft X-ray imaging, high-field physics, and ultrafast X-ray science experiments that is available to users at the Linac Coherent Light Source (LCLS) free-electron laser. While the instrument resides in the Atomic, Molecular and Optical science hutch, its components can be used at any LCLS beamline. The end-station has a modular design that provides high flexibility in order to meet user-defined experimental requirements and specifications. The ultra-high-vacuum environment supports different sample delivery systems, including pulsed and continuous atomic, molecular, and cluster jets; liquid and aerosols jets; and effusive metal vapor beams. It also houses movable, large-format, high-speed pnCCD X-ray detectors for detecting scattered and fluorescent photons. Multiple charged-particle spectrometer options are compatible with the LAMP chamber, including a double-sided spectrometer for simultaneous and even coincident measurements of electrons, ions, and photons produced by the interaction of the high-intensity X-ray beam with the various samples. Here we describe the design and capabilities of the spectrometers along with some general aspects of the LAMP chamber and show some results from the initial instrument commissioning.
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Affiliation(s)
- Timur Osipov
- Physics Department, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J-C Castagna
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ken R Ferguson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Maximilian Bucher
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sebastian C Montero
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Michele L Swiggers
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Razib Obaid
- Physics Department, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Daniel Rolles
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Artem Rudenko
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nora Berrah
- Physics Department, University of Connecticut, Storrs, Connecticut 06269, USA
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Bolognesi P, Bañares L, Alcamí M. XUV/X-ray light and fast ions for ultrafast chemistry. Phys Chem Chem Phys 2018; 19:19533-19535. [PMID: 28744548 DOI: 10.1039/c7cp90137b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The deposition of large amounts of energy in a molecule by XUV/X-ray photon absorption or fast-ion collision, triggers a set of complex ultrafast electronic and nuclear dynamics that allow a deep understanding and control of chemical reactivity. This themed issue showcases the research performed in the understanding, monitoring and control of these processes.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo Scalo, Italy.
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33
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Fortmann-Grote C, Buzmakov A, Jurek Z, Loh NTD, Samoylova L, Santra R, Schneidmiller EA, Tschentscher T, Yakubov S, Yoon CH, Yurkov MV, Ziaja-Motyka B, Mancuso AP. 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. [PMID: 28989713 PMCID: PMC5619849 DOI: 10.1107/s2052252517009496] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/26/2017] [Indexed: 05/23/2023]
Abstract
Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.
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Affiliation(s)
| | - Alexey Buzmakov
- FSRC ‘Crystallography and Photonics’, Russian Academy of Sciences, Moscow, Russian Federation
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ne-Te Duane Loh
- Centre for Bio-Imaging Sciences, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Physics, National University of Singapore, Singapore
| | | | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | | | | | | | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park CA 94025, USA
| | | | - Beata Ziaja-Motyka
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
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34
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Abdullah MM, Jurek Z, Son SK, Santra R. Molecular-dynamics approach for studying the nonequilibrium behavior of x-ray-heated solid-density matter. Phys Rev E 2017; 96:023205. [PMID: 28950476 DOI: 10.1103/physreve.96.023205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Indexed: 06/07/2023]
Abstract
When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on subpicosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate nonequilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and three-dimensional spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above-mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven nonequilibrium dynamics in solids. To illustrate the potential of XMDYN for treating complex systems, we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.
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Affiliation(s)
- Malik Muhammad Abdullah
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
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35
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Amini K, Boll R, Lauer A, Burt M, Lee JWL, Christensen L, Brauβe F, Mullins T, Savelyev E, Ablikim U, Berrah N, Bomme C, Düsterer S, Erk B, Höppner H, Johnsson P, Kierspel T, Krecinic F, Küpper J, Müller M, Müller E, Redlin H, Rouzée A, Schirmel N, Thøgersen J, Techert S, Toleikis S, Treusch R, Trippel S, Ulmer A, Wiese J, Vallance C, Rudenko A, Stapelfeldt H, Brouard M, Rolles D. Alignment, orientation, and Coulomb explosion of difluoroiodobenzene studied with the pixel imaging mass spectrometry (PImMS) camera. J Chem Phys 2017; 147:013933. [DOI: 10.1063/1.4982220] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kasra Amini
- The Chemistry Research Laboratory, Department of Chemistry,
University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Rebecca Boll
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Alexandra Lauer
- The Chemistry Research Laboratory, Department of Chemistry,
University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Michael Burt
- The Chemistry Research Laboratory, Department of Chemistry,
University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Jason W. L. Lee
- The Chemistry Research Laboratory, Department of Chemistry,
University of Oxford, Oxford OX1 3TA, United Kingdom
| | | | - Felix Brauβe
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Terence Mullins
- Center for Free-Electron Laser Science (CFEL),
Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg,
Germany
| | - Evgeny Savelyev
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Utuq Ablikim
- J. R. Macdonald Laboratory, Department of Physics,
Kansas State University, Manhattan, Kansas 66506,
USA
| | - Nora Berrah
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Cédric Bomme
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Stefan Düsterer
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Benjamin Erk
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Hauke Höppner
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Institut für Physik, Carl von Ossietzky Universität, 26111 Oldenburg, Germany
| | - Per Johnsson
- Department of Physics, Lund University, 22100 Lund, Sweden
| | - Thomas Kierspel
- Center for Free-Electron Laser Science (CFEL),
Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg,
Germany
- Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Faruk Krecinic
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science (CFEL),
Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg,
Germany
- Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - Maria Müller
- Institut für Optik und Atomare Physik,
Technische Universität Berlin, 10623 Berlin,
Germany
| | - Erland Müller
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Harald Redlin
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Arnaud Rouzée
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Nora Schirmel
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Jan Thøgersen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Simone Techert
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Max Planck Institute for Biophysical Chemistry, 33077 Göttingen, Germany
- Institute for X-ray Physics, Göttingen University, 33077 Göttingen, Germany
| | - Sven Toleikis
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Rolf Treusch
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Sebastian Trippel
- Center for Free-Electron Laser Science (CFEL),
Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg,
Germany
- Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Anatoli Ulmer
- Institut für Optik und Atomare Physik,
Technische Universität Berlin, 10623 Berlin,
Germany
| | - Joss Wiese
- Center for Free-Electron Laser Science (CFEL),
Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg,
Germany
| | - Claire Vallance
- The Chemistry Research Laboratory, Department of Chemistry,
University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Department of Physics,
Kansas State University, Manhattan, Kansas 66506,
USA
| | | | - Mark Brouard
- The Chemistry Research Laboratory, Department of Chemistry,
University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Daniel Rolles
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- J. R. Macdonald Laboratory, Department of Physics,
Kansas State University, Manhattan, Kansas 66506,
USA
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36
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Femtosecond response of polyatomic molecules to ultra-intense hard X-rays. Nature 2017; 546:129-132. [DOI: 10.1038/nature22373] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/03/2017] [Indexed: 11/08/2022]
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37
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Molecular Dynamics of XFEL-Induced Photo-Dissociation, Revealed by Ion-Ion Coincidence Measurements. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7050531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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X-ray Pump–Probe Investigation of Charge and Dissociation Dynamics in Methyl Iodine Molecule. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7050529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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39
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Berrah N. A perspective for investigating photo-induced molecular dynamics from within with femtosecond free electron lasers. Phys Chem Chem Phys 2017; 19:19536-19544. [DOI: 10.1039/c7cp01996c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photo-induced molecular dynamics can now be investigated using free electron lasers (FELs) whose attributes are unprecedented brightness, few femtosecond pulses duration and in the near future few hundreds of attosecond pulse duration.
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Affiliation(s)
- Nora Berrah
- University of Connecticut
- Physics Department
- Storrs
- USA
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40
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Landau A, Moiseyev N. Molecular resonances by removing complex absorbing potentials via Padé; Application to CO− and N2−. J Chem Phys 2016; 145:164111. [DOI: 10.1063/1.4965887] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Arie Landau
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimrod Moiseyev
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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41
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Abdullah MM, Jurek Z, Son SK, Santra R. Calculation of x-ray scattering patterns from nanocrystals at high x-ray intensity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:054101. [PMID: 27478859 PMCID: PMC4947047 DOI: 10.1063/1.4958887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/01/2016] [Indexed: 06/06/2023]
Abstract
We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution, we have used two different spatial beam profiles, Gaussian and flattop.
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42
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Ziaja B, Saxena V, Son SK, Medvedev N, Barbrel B, Woloncewicz B, Stransky M. Kinetic Boltzmann approach adapted for modeling highly ionized matter created by x-ray irradiation of a solid. Phys Rev E 2016; 93:053210. [PMID: 27300998 DOI: 10.1103/physreve.93.053210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 11/07/2022]
Abstract
We report on the kinetic Boltzmann approach adapted for simulations of highly ionized matter created from a solid by its x-ray irradiation. X rays can excite inner-shell electrons, which leads to the creation of deeply lying core holes. Their relaxation, especially in heavier elements, can take complicated paths, leading to a large number of active configurations. Their number can be so large that solving the set of respective evolution equations becomes computationally inefficient and another modeling approach should be used instead. To circumvent this complexity, the commonly used continuum models employ a superconfiguration scheme. Here, we propose an alternative approach which still uses "true" atomic configurations but limits their number by restricting the sample relaxation to the predominant relaxation paths. We test its reliability, performing respective calculations for a bulk material consisting of light atoms and comparing the results with a full calculation including all relaxation paths. Prospective application for heavy elements is discussed.
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Affiliation(s)
- Beata Ziaja
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.,Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
| | - Vikrant Saxena
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nikita Medvedev
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Benjamin Barbrel
- Center for Intense Lasers and Applications (CELIA), University of Bordeaux 1, 351 Cours de la Liberation, F-33405 Talence, France
| | - Bianca Woloncewicz
- Institute of Experimental Physics, University of Gdansk, ulica Wita Stwosza 57, 80-952 Gdansk, Poland
| | - Michal Stransky
- Department of Radiation and Chemical Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague, Czech Republic
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43
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Yoon CH, Yurkov MV, Schneidmiller EA, Samoylova L, Buzmakov A, Jurek Z, Ziaja B, Santra R, Loh ND, Tschentscher T, Mancuso AP. A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser. Sci Rep 2016; 6:24791. [PMID: 27109208 PMCID: PMC4842992 DOI: 10.1038/srep24791] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/01/2016] [Indexed: 12/04/2022] Open
Abstract
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.
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Affiliation(s)
- Chun Hong Yoon
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.,Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Liubov Samoylova
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Alexey Buzmakov
- Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow 119333, Russia
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Beata Ziaja
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.,Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Krakow, Poland
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - N Duane Loh
- Centre for Bio-Imaging Sciences, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physics, National University of Singapore, Singapore
| | | | - Adrian P Mancuso
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
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44
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Jurek Z, Son SK, Ziaja B, Santra R. XMDYNandXATOM: versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716006014] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Rapid development of X-ray free-electron laser (XFEL) science has taken place in recent years owing to the consecutive launch of large-scale XFEL instruments around the world. Research areas such as warm dense matter physics and coherent X-ray imaging take advantage of the unprecedentedly high intensities of XFELs. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization. Owing to this complexity, theoretical modeling revealing details of the excitation and relaxation of irradiated matter is important for the correct interpretation of the measurements and for proposing new experiments.XMDYNis a computer simulation tool developed for modeling dynamics of matter induced by high-intensity X-rays. It utilizes atomic data calculated by theab initio XATOMtoolkit. Here these tools are discussed in detail.
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45
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Galli L, Son SK, Barends TRM, White TA, Barty A, Botha S, Boutet S, Caleman C, Doak RB, Nanao MH, Nass K, Shoeman RL, Timneanu N, Santra R, Schlichting I, Chapman HN. Towards phasing using high X-ray intensity. IUCRJ 2015; 2:627-34. [PMID: 26594370 PMCID: PMC4645107 DOI: 10.1107/s2052252515014049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 07/24/2015] [Indexed: 05/11/2023]
Abstract
X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential 'bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.
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Affiliation(s)
- Lorenzo Galli
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Thomas R. M. Barends
- Biomolecular Mechanisms, MPI for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Sabine Botha
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025, USA
| | - Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Max H. Nanao
- EMBL, Grenoble Outstation, Rue Jules Horowitz 6, Grenoble, 38042, France
| | - Karol Nass
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Robert L. Shoeman
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala, 75124, Sweden
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
- Department of Physics, University of Hamburg, Juniungstrasse 6, Hamburg, 20355, Germany
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, 22607, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22761, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
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Liekhus-Schmaltz CE, Tenney I, Osipov T, Sanchez-Gonzalez A, Berrah N, Boll R, Bomme C, Bostedt C, Bozek JD, Carron S, Coffee R, Devin J, Erk B, Ferguson KR, Field RW, Foucar L, Frasinski LJ, Glownia JM, Gühr M, Kamalov A, Krzywinski J, Li H, Marangos JP, Martinez TJ, McFarland BK, Miyabe S, Murphy B, Natan A, Rolles D, Rudenko A, Siano M, Simpson ER, Spector L, Swiggers M, Walke D, Wang S, Weber T, Bucksbaum PH, Petrovic VS. Ultrafast isomerization initiated by X-ray core ionization. Nat Commun 2015; 6:8199. [DOI: 10.1038/ncomms9199] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 07/28/2015] [Indexed: 11/09/2022] Open
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Dao EH, Sierra RG, Laksmono H, Lemke HT, Alonso-Mori R, Coey A, Larsen K, Baxter EL, Cohen AE, Soltis SM, DeMirci H. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041706. [PMID: 26798805 PMCID: PMC4711619 DOI: 10.1063/1.4919407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 06/05/2023]
Abstract
In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.
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Affiliation(s)
- E Han Dao
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Henrik T Lemke
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aaron Coey
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Kevin Larsen
- Biophysics Program, Stanford University School of Medicine , Stanford, California 94305, USA
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
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Hao Y, Inhester L, Hanasaki K, Son SK, Santra R. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041707. [PMID: 26798806 PMCID: PMC4711638 DOI: 10.1063/1.4919794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/24/2015] [Indexed: 05/16/2023]
Abstract
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
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49
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Nanoplasma Formation by High Intensity Hard X-rays. Sci Rep 2015; 5:10977. [PMID: 26077863 PMCID: PMC4468420 DOI: 10.1038/srep10977] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/07/2015] [Indexed: 11/14/2022] Open
Abstract
Using electron spectroscopy, we have investigated nanoplasma formation from noble gas clusters exposed to high-intensity hard-x-ray pulses at ~5 keV. Our experiment was carried out at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility in Japan. Dedicated theoretical simulations were performed with the molecular dynamics tool XMDYN. We found that in this unprecedented wavelength regime nanoplasma formation is a highly indirect process. In the argon clusters investigated, nanoplasma is mainly formed through secondary electron cascading initiated by slow Auger electrons. Energy is distributed within the sample entirely through Auger processes and secondary electron cascading following photoabsorption, as in the hard x-ray regime there is no direct energy transfer from the field to the plasma. This plasma formation mechanism is specific to the hard-x-ray regime and may, thus, also be important for XFEL-based molecular imaging studies. In xenon clusters, photo- and Auger electrons contribute more significantly to the nanoplasma formation. Good agreement between experiment and simulations validates our modelling approach. This has wide-ranging implications for our ability to quantitatively predict the behavior of complex molecular systems irradiated by high-intensity hard x-rays.
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50
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Schütte B, Lahl J, Oelze T, Krikunova M, Vrakking MJJ, Rouzée A. Efficient autoionization following intense laser-cluster interactions. PHYSICAL REVIEW LETTERS 2015; 114:123002. [PMID: 25860738 DOI: 10.1103/physrevlett.114.123002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 06/04/2023]
Abstract
Electron emission as a result of the interaction of clusters with intense laser pulses is commonly understood in terms of direct and evaporative ionization processes. In contrast, we provide evidence here of an important role played by autoionization in intense field ionization of molecular oxygen clusters. Superexcited states are populated during the cluster expansion, and their autoionization is observed on a ns time scale. Decay processes on fs to ps time scales are obscured by energy exchange of the emitted electrons with the environment.
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Affiliation(s)
- B Schütte
- Max-Born-Institut, Max-Born-Strasse 2A, 12489 Berlin, Germany
- Department of Physics, Imperial College London, South Kensington Campus, SW7 2AZ London, United Kingdom
| | - J Lahl
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr 36, ER 1-1, 10623 Berlin, Germany
| | - T Oelze
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr 36, ER 1-1, 10623 Berlin, Germany
| | - M Krikunova
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr 36, ER 1-1, 10623 Berlin, Germany
| | - M J J Vrakking
- Max-Born-Institut, Max-Born-Strasse 2A, 12489 Berlin, Germany
| | - A Rouzée
- Max-Born-Institut, Max-Born-Strasse 2A, 12489 Berlin, Germany
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