1
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Grieco A, Boneta S, Gavira JA, Pey AL, Basu S, Orlans J, de Sanctis D, Medina M, Martin‐Garcia JM. Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations. Protein Sci 2024; 33:e4957. [PMID: 38501509 PMCID: PMC10949395 DOI: 10.1002/pro.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/20/2024]
Abstract
The human NQO1 (hNQO1) is a flavin adenine nucleotide (FAD)-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics. Moreover, it is overexpressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of our knowledge, the first structure of the hNQO1 in complex with NADH. We have also performed molecular dynamics simulations of free hNQO1 and in complex with NADH. This is the first structural evidence that the hNQO1 functional cooperativity is driven by structural communication between the active sites through long-range propagation of cooperative effects across the hNQO1 structure. Both structural results and MD simulations have supported that the binding of NADH significantly decreases protein dynamics and stabilizes hNQO1 especially at the dimer core and interface. Altogether, these results pave the way for future time-resolved studies, both at x-ray free-electron lasers and synchrotrons, of the dynamics of hNQO1 upon binding to NADH as well as during the FAD cofactor reductive half-reaction. This knowledge will allow us to reveal unprecedented structural information of the relevance of the dynamics during the catalytic function of hNQO1.
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Grants
- P18-RT-2413 Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía
- RTI2018-096246-B-I00 ERDF/Spanish Ministry of Science, Innovation and Universities-State Research Agency
- E35-23R Gobierno de Aragón
- B-BIO-84-UGR20 ERDF/Counseling of Economic Transformation, Industry, Knowledge and Universities
- CNS2022-135713 The European Union NextGenerationEU/PRTR
- 2019-T1/BMD-15552 Comunidad de Madrid
- MCIN/AEI/PID2022-136369NB-I00 MCIN/AEI/10.13039/501100011033/ERDF
- Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía
- ERDF/Spanish Ministry of Science, Innovation and Universities‐State Research Agency
- Gobierno de Aragón
- ERDF/Counseling of Economic Transformation, Industry, Knowledge and Universities
- Comunidad de Madrid
- MCIN/AEI/10.13039/501100011033/ERDF
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Affiliation(s)
- Alice Grieco
- Department of Crystallography and Structural BiologyInstitute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC)MadridSpain
| | - Sergio Boneta
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)Universidad de ZaragozaZaragozaSpain
| | - José A. Gavira
- Laboratory of Crystallographic StudiesIACT (CSIC‐UGR)ArmillaSpain
| | - Angel L. Pey
- Departamento de Química FísicaUnidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de GranadaGranadaSpain
| | - Shibom Basu
- European Molecular Biology LaboratoryGrenobleFrance
| | | | | | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)Universidad de ZaragozaZaragozaSpain
| | - Jose Manuel Martin‐Garcia
- Department of Crystallography and Structural BiologyInstitute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC)MadridSpain
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2
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Stubbs J, Hornsey T, Hanrahan N, Esteban LB, Bolton R, Malý M, Basu S, Orlans J, de Sanctis D, Shim JU, Shaw Stewart PD, Orville AM, Tews I, West J. Droplet microfluidics for time-resolved serial crystallography. IUCRJ 2024; 11:237-248. [PMID: 38446456 PMCID: PMC10916287 DOI: 10.1107/s2052252524001799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
Serial crystallography requires large numbers of microcrystals and robust strategies to rapidly apply substrates to initiate reactions in time-resolved studies. Here, we report the use of droplet miniaturization for the controlled production of uniform crystals, providing an avenue for controlled substrate addition and synchronous reaction initiation. The approach was evaluated using two enzymatic systems, yielding 3 µm crystals of lysozyme and 2 µm crystals of Pdx1, an Arabidopsis enzyme involved in vitamin B6 biosynthesis. A seeding strategy was used to overcome the improbability of Pdx1 nucleation occurring with diminishing droplet volumes. Convection within droplets was exploited for rapid crystal mixing with ligands. Mixing times of <2 ms were achieved. Droplet microfluidics for crystal size engineering and rapid micromixing can be utilized to advance time-resolved serial crystallography.
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Affiliation(s)
- Jack Stubbs
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Theo Hornsey
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Niall Hanrahan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Luis Blay Esteban
- Universitat Carlemany, Avenida Verge de Canolich, 47, Sant Julia de Loria, Principat d’Andorra AD600, Spain
| | - Rachel Bolton
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Martin Malý
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble 38042, Cedex 9, France
| | - Julien Orlans
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38042, Cedex 9, France
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38042, Cedex 9, France
| | - Jung-uk Shim
- Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Allen M. Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Ivo Tews
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Jonathan West
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, United Kingdom
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3
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Galchenkova M, Tolstikova A, Klopprogge B, Sprenger J, Oberthuer D, Brehm W, White TA, Barty A, Chapman HN, Yefanov O. Data reduction in protein serial crystallography. IUCRJ 2024; 11:190-201. [PMID: 38327201 PMCID: PMC10916297 DOI: 10.1107/s205225252400054x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Serial crystallography (SX) has become an established technique for protein structure determination, especially when dealing with small or radiation-sensitive crystals and investigating fast or irreversible protein dynamics. The advent of newly developed multi-megapixel X-ray area detectors, capable of capturing over 1000 images per second, has brought about substantial benefits. However, this advancement also entails a notable increase in the volume of collected data. Today, up to 2 PB of data per experiment could be easily obtained under efficient operating conditions. The combined costs associated with storing data from multiple experiments provide a compelling incentive to develop strategies that effectively reduce the amount of data stored on disk while maintaining the quality of scientific outcomes. Lossless data-compression methods are designed to preserve the information content of the data but often struggle to achieve a high compression ratio when applied to experimental data that contain noise. Conversely, lossy compression methods offer the potential to greatly reduce the data volume. Nonetheless, it is vital to thoroughly assess the impact of data quality and scientific outcomes when employing lossy compression, as it inherently involves discarding information. The evaluation of lossy compression effects on data requires proper data quality metrics. In our research, we assess various approaches for both lossless and lossy compression techniques applied to SX data, and equally importantly, we describe metrics suitable for evaluating SX data quality.
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Affiliation(s)
- Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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4
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Banerjee A, Jay RM, Leitner T, Wang RP, Harich J, Stefanuik R, Coates MR, Beale EV, Kabanova V, Kahraman A, Wach A, Ozerov D, Arrell C, Milne C, Johnson PJM, Cirelli C, Bacellar C, Huse N, Odelius M, Wernet P. Accessing metal-specific orbital interactions in C-H activation with resonant inelastic X-ray scattering. Chem Sci 2024; 15:2398-2409. [PMID: 38362433 PMCID: PMC10866335 DOI: 10.1039/d3sc04388f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/01/2024] [Indexed: 02/17/2024] Open
Abstract
Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C-H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C-H group and the transition metal is the decisive interaction in the C-H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal-alkane interactions during transition-metal mediated C-H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C-H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C-H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO)2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C-H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.
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Affiliation(s)
- Ambar Banerjee
- Department of Physics and Astronomy, Uppsala University 751 20 Uppsala Sweden
| | - Raphael M Jay
- Department of Physics and Astronomy, Uppsala University 751 20 Uppsala Sweden
| | - Torsten Leitner
- Department of Physics and Astronomy, Uppsala University 751 20 Uppsala Sweden
| | - Ru-Pan Wang
- Center for Free-Electron Laser Science, Department of Physics, University of Hamburg 22761 Hamburg Germany
| | - Jessica Harich
- Center for Free-Electron Laser Science, Department of Physics, University of Hamburg 22761 Hamburg Germany
| | - Robert Stefanuik
- Department of Physics and Astronomy, Uppsala University 751 20 Uppsala Sweden
| | - Michael R Coates
- Department of Physics, Stockholm University, AlbaNova University Center 106 91 Stockholm Sweden
| | - Emma V Beale
- Paul Scherrer Institute CH-5232 Villigen PSI Switzerland
| | | | | | - Anna Wach
- Paul Scherrer Institute CH-5232 Villigen PSI Switzerland
- Institute of Nuclear Physics, Polish Academy of Sciences PL-31342 Krakow Poland
| | - Dmitry Ozerov
- Paul Scherrer Institute CH-5232 Villigen PSI Switzerland
| | | | | | | | | | | | - Nils Huse
- Center for Free-Electron Laser Science, Department of Physics, University of Hamburg 22761 Hamburg Germany
| | - Michael Odelius
- Department of Physics, Stockholm University, AlbaNova University Center 106 91 Stockholm Sweden
| | - Philippe Wernet
- Department of Physics and Astronomy, Uppsala University 751 20 Uppsala Sweden
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5
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Leonarski F, Nan J, Matej Z, Bertrand Q, Furrer A, Gorgisyan I, Bjelčić M, Kepa M, Glover H, Hinger V, Eriksson T, Cehovin A, Eguiraun M, Gasparotto P, Mozzanica A, Weinert T, Gonzalez A, Standfuss J, Wang M, Ursby T, Dworkowski F. Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source. IUCRJ 2023; 10:729-737. [PMID: 37830774 PMCID: PMC10619449 DOI: 10.1107/s2052252523008618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Serial and time-resolved macromolecular crystallography are on the rise. However, beam time at X-ray free-electron lasers is limited and most third-generation synchrotron-based macromolecular crystallography beamlines do not offer the necessary infrastructure yet. Here, a new setup is demonstrated, based on the JUNGFRAU detector and Jungfraujoch data-acquisition system, that enables collection of kilohertz serial crystallography data at fourth-generation synchrotrons. More importantly, it is shown that this setup is capable of collecting multiple-time-point time-resolved protein dynamics at kilohertz rates, allowing the probing of microsecond to second dynamics at synchrotrons in a fraction of the time needed previously. A high-quality complete X-ray dataset was obtained within 1 min from lysozyme microcrystals, and the dynamics of the light-driven sodium-pump membrane protein KR2 with a time resolution of 1 ms could be demonstrated. To make the setup more accessible for researchers, downstream data handling and analysis will be automated to allow on-the-fly spot finding and indexing, as well as data processing.
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Affiliation(s)
- Filip Leonarski
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Jie Nan
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Quentin Bertrand
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | | | - Monika Bjelčić
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Michal Kepa
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Hannah Glover
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Viktoria Hinger
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Thomas Eriksson
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | | | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Piero Gasparotto
- Scientific Computing, Theory and Data, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Ana Gonzalez
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
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6
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Grimes M, Pauwels K, Schülli TU, Martin T, Fajardo P, Douissard PA, Kocsis M, Nishino H, Ozaki K, Honjo Y, Nishiyama Hiraki T, Joti Y, Hatsui T, Levi M, Rabkin E, Leake SJ, Richard MI. Bragg coherent diffraction imaging with the CITIUS charge-integrating detector. J Appl Crystallogr 2023; 56:1032-1037. [PMID: 37555222 PMCID: PMC10405578 DOI: 10.1107/s1600576723004314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/17/2023] [Indexed: 08/10/2023] Open
Abstract
The CITIUS detector is a next-generation high-speed X-ray imaging detector. It has integrating-type pixels and is designed to show a consistent linear response at a frame rate of 17.4 kHz, which results in a saturation count rate of over 30 Mcps pixel-1 when operating at an acquisition duty cycle close to 100%, and up to 20 times higher with special extended acquisition modes. Here, its application for Bragg coherent diffraction imaging is demonstrated by taking advantage of the fourth-generation Extremely Brilliant Source of the European Synchrotron (ESRF-EBS, Grenoble, France). The CITIUS detector outperformed a photon-counting detector, similar spatial resolution being achieved (20 ± 6 nm versus 22 ± 9 nm) with greatly reduced acquisition times (23 s versus 200 s). It is also shown how the CITIUS detector can be expected to perform during dynamic Bragg coherent diffraction imaging measurements. Finally, the current limitations of the CITIUS detector and further optimizations for coherent imaging techniques are discussed.
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Affiliation(s)
- Michael Grimes
- Université Grenoble Alpes, CEA Grenoble, IRIG, MEM, NRS, 17 rue des Martyrs, F-38000 Grenoble, France
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Kristof Pauwels
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Tobias U. Schülli
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Thierry Martin
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Pablo Fajardo
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | | | - Menyhert Kocsis
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Haruki Nishino
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kyosuke Ozaki
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiaki Honjo
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | | | - Yasumasa Joti
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, RIKEN, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mor Levi
- Department of Materials Science and Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Eugen Rabkin
- Department of Materials Science and Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Steven J. Leake
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Marie-Ingrid Richard
- Université Grenoble Alpes, CEA Grenoble, IRIG, MEM, NRS, 17 rue des Martyrs, F-38000 Grenoble, France
- ESRF – The European Synchrotron, 71 avenue des Martyrs, F-38000 Grenoble, France
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7
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Doblas A, Flores D, Hidalgo S, Moffat N, Pellegrini G, Quirion D, Villegas J, Maneuski D, Ruat M, Fajardo P. Inverse LGAD (iLGAD) Periphery Optimization for Surface Damage Irradiation. SENSORS (BASEL, SWITZERLAND) 2023; 23:3450. [PMID: 37050510 PMCID: PMC10098583 DOI: 10.3390/s23073450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Pixelated LGADs have been established as the baseline technology for timing detectors for the High Granularity Timing Detector (HGTD) and the Endcap Timing Layer (ETL) of the ATLAS and CMS experiments, respectively. The drawback of segmenting an LGAD is the non-gain area present between pixels and the consequent reduction in the fill factor. To overcome this issue, the inverse LGAD (iLGAD) technology has been proposed by IMB-CNM to enhance the fill factor and provide excellent tracking capabilities. In this work, we explore the use of iLGAD sensors for surface damage irradiation by developing a new generation of iLGADs, the periphery of which is optimized to improve the performance of irradiated sensors. The fabricated iLGAD sensors exhibit good electrical performances before and after X-ray irradiation.
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Affiliation(s)
- Albert Doblas
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - David Flores
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - Salvador Hidalgo
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - Neil Moffat
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - Giulio Pellegrini
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - David Quirion
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - Jairo Villegas
- Centro Nacional de Microelectrónica, IMB-CNM-CSIC, 08193 Barcelona, Spain
| | - Dzmitry Maneuski
- School of Physics and Astronomy, University of Glasgow, Glasgow G12 0YN, UK
| | - Marie Ruat
- European Synchrotron Radiation Facility, ESRF, 38000 Grenoble, France
| | - Pablo Fajardo
- European Synchrotron Radiation Facility, ESRF, 38000 Grenoble, France
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8
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Tahir NA, Bagnoud V, Neumayer P, Piriz AR, Piriz SA. Production of diamond using intense heavy ion beams at the FAIR facility and application to planetary physics. Sci Rep 2023; 13:1459. [PMID: 36702850 PMCID: PMC9879936 DOI: 10.1038/s41598-023-28709-7] [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: 10/27/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Diamonds are supposedly abundantly present in different objects in the Universe including meteorites, carbon-rich stars as well as carbon-rich extrasolar planets. Moreover, the prediction that in deep layers of Uranus and Neptune, methane may undergo a process of phase separation into diamond and hydrogen, has been experimentally verified. In particular, high power lasers have been used to study this problem. It is therefore important from the point of view of astrophysics and planetary physics, to further study the production processes of diamond in the laboratory. In the present paper, we present numerical simulations of implosion of a solid carbon sample using an intense uranium beam that is to be delivered by the heavy ion synchrotron, SIS100, that is under construction at the Facility for Antiprotons and Ion Research (FAIR), at Darmstadt. These calculations show that using our proposed experimental scheme, one can generate the extreme pressure and temperature conditions, necessary to produce diamonds of mm3 dimensions.
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Affiliation(s)
- Naeem Ahmad Tahir
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291, Darmstadt, Germany.
| | - Vincent Bagnoud
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291, Darmstadt, Germany
| | - Paul Neumayer
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, 64291, Darmstadt, Germany
| | | | - Sofia Ayelen Piriz
- E.T.S.I. Industriales, Universidad de Castilla-La Mancha, 13071, Ciudad Real, Spain
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9
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Leonarski F, Brückner M, Lopez-Cuenca C, Mozzanica A, Stadler HC, Matěj Z, Castellane A, Mesnet B, Wojdyla JA, Schmitt B, Wang M. Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:227-234. [PMID: 36601941 PMCID: PMC9814052 DOI: 10.1107/s1600577522010268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
The JUNGFRAU 4-megapixel (4M) charge-integrating pixel-array detector, when operated at a full 2 kHz frame rate, streams data at a rate of 17 GB s-1. To operate this detector for macromolecular crystallography beamlines, a data-acquisition system called Jungfraujoch was developed. The system, running on a single server with field-programmable gate arrays and general-purpose graphics processing units, is capable of handling data produced by the JUNGFRAU 4M detector, including conversion of raw pixel readout to photon counts, compression and on-the-fly spot finding. It was also demonstrated that 30 GB s-1 can be handled in performance tests, indicating that the operation of even larger and faster detectors will be achievable in the future. The source code is available from a public repository.
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Affiliation(s)
- Filip Leonarski
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Martin Brückner
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Carlos Lopez-Cuenca
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Hans-Christian Stadler
- Scientific Computing, Theory and Data Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Zdeněk Matěj
- MAX IV Laboratory, Lund University, Fotongatan 2, 221 00 Lund, Sweden
| | | | - Bruno Mesnet
- IBM France, 21 av Simone Veil, 06206 Nice, France
| | | | - Bernd Schmitt
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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10
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He Z, Rödel M, Lütgert J, Bergermann A, Bethkenhagen M, Chekrygina D, Cowan TE, Descamps A, French M, Galtier E, Gleason AE, Glenn GD, Glenzer SH, Inubushi Y, Hartley NJ, Hernandez JA, Heuser B, Humphries OS, Kamimura N, Katagiri K, Khaghani D, Lee HJ, McBride EE, Miyanishi K, Nagler B, Ofori-Okai B, Ozaki N, Pandolfi S, Qu C, Ranjan D, Redmer R, Schoenwaelder C, Schuster AK, Stevenson MG, Sueda K, Togashi T, Vinci T, Voigt K, Vorberger J, Yabashi M, Yabuuchi T, Zinta LMV, Ravasio A, Kraus D. Diamond formation kinetics in shock-compressed C─H─O samples recorded by small-angle x-ray scattering and x-ray diffraction. SCIENCE ADVANCES 2022; 8:eabo0617. [PMID: 36054354 PMCID: PMC10848955 DOI: 10.1126/sciadv.abo0617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Extreme conditions inside ice giants such as Uranus and Neptune can result in peculiar chemistry and structural transitions, e.g., the precipitation of diamonds or superionic water, as so far experimentally observed only for pure C─H and H2O systems, respectively. Here, we investigate a stoichiometric mixture of C and H2O by shock-compressing polyethylene terephthalate (PET) plastics and performing in situ x-ray probing. We observe diamond formation at pressures between 72 ± 7 and 125 ± 13 GPa at temperatures ranging from ~3500 to ~6000 K. Combining x-ray diffraction and small-angle x-ray scattering, we access the kinetics of this exotic reaction. The observed demixing of C and H2O suggests that diamond precipitation inside the ice giants is enhanced by oxygen, which can lead to isolated water and thus the formation of superionic structures relevant to the planets' magnetic fields. Moreover, our measurements indicate a way of producing nanodiamonds by simple laser-driven shock compression of cheap PET plastics.
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Affiliation(s)
- Zhiyu He
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
- Shanghai Institute of Laser Plasma, 201800 Shanghai, China
| | - Melanie Rödel
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Technische Universität Dresden, 01069 Dresden, Germany
| | - Julian Lütgert
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
- Technische Universität Dresden, 01069 Dresden, Germany
| | - Armin Bergermann
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Mandy Bethkenhagen
- École Normale Supérieure de Lyon, Laboratoire de Géologie de Lyon, LGLTPE UMR 5276, Centre Blaise Pascal, 46 allée d’Italie, Lyon 69364, France
| | - Deniza Chekrygina
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Thomas E. Cowan
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Technische Universität Dresden, 01069 Dresden, Germany
| | - Adrien Descamps
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Martin French
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Eric Galtier
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Griffin D. Glenn
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Stanford University, Stanford, CA 94305, USA
| | | | - Yuichi Inubushi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | | | - Jean-Alexis Hernandez
- Centre for Earth Evolution and Dynamics, University of Oslo, N-0315 Oslo, Norway
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Benjamin Heuser
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Oliver S. Humphries
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Nobuki Kamimura
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kento Katagiri
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | | | - Hae Ja Lee
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Emma E. McBride
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Kohei Miyanishi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Bob Nagler
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Norimasa Ozaki
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Institute of Laser Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Silvia Pandolfi
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Chongbing Qu
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Divyanshu Ranjan
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Ronald Redmer
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Christopher Schoenwaelder
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Erlangen Centre for Astroparticle Physics, Friedrich-Alexander-Universität Erlangen Nürnberg, Erwin-Rommel-Str 1, 91058 Erlangen, Germany
| | - Anja K. Schuster
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Technische Universität Dresden, 01069 Dresden, Germany
| | - Michael G. Stevenson
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Keiichi Sueda
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tadashi Togashi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tommaso Vinci
- LULI, CNRS, CEA, Sorbonne Université, Ecole Polytechnique–Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Katja Voigt
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Technische Universität Dresden, 01069 Dresden, Germany
| | - Jan Vorberger
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Toshinori Yabuuchi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Lisa M. V. Zinta
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Alessandra Ravasio
- LULI, CNRS, CEA, Sorbonne Université, Ecole Polytechnique–Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Dominik Kraus
- Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
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11
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Vakili M, Bielecki J, Knoška J, Otte F, Han H, Kloos M, Schubert R, Delmas E, Mills G, de Wijn R, Letrun R, Dold S, Bean R, Round A, Kim Y, Lima FA, Dörner K, Valerio J, Heymann M, Mancuso AP, Schulz J. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:331-346. [PMID: 35254295 PMCID: PMC8900844 DOI: 10.1107/s1600577521013370] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.
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Affiliation(s)
| | | | - Juraj Knoška
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Florian Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Physics, TU Dortmund, Otto-Hahn-Straße 4, 44221 Dortmund, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Elisa Delmas
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Simon Dold
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5AZ, United Kingdom
| | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Heymann
- Institute for Biomaterials and Biomolecular Systems (IBBS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia
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12
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Terrill NJ, Dent AJ, Dobson B, Beale AM, Allen L, Bras W. Past, present and future-sample environments for materials research studies in scattering and spectroscopy; a UK perspective. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:483002. [PMID: 34479225 DOI: 10.1088/1361-648x/ac2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Small angle x-ray scattering and x-ray absorption fine structure are two techniques that have been employed at synchrotron sources ever since their inception. Over the course of the development of the techniques, the introduction of sample environments for added value experiments has grown dramatically. This article reviews past successes, current developments and an exploration of future possibilities for these two x-ray techniques with an emphasis on the developments in the United Kingdom between 1980-2020.
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Affiliation(s)
| | - Andrew J Dent
- Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Barry Dobson
- Sagentia Ltd, Harston Mill, Harston Mill, CB22 7GG, United Kingdom
| | - Andrew M Beale
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
- The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, United Kingdom
| | - Lisa Allen
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
- The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, United Kingdom
| | - Wim Bras
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, One Bethel Valley Road TN 37831, United States of America
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13
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Zastrau U, Appel K, Baehtz C, Baehr O, Batchelor L, Berghäuser A, Banjafar M, Brambrink E, Cerantola V, Cowan TE, Damker H, Dietrich S, Di Dio Cafiso S, Dreyer J, Engel HO, Feldmann T, Findeisen S, Foese M, Fulla-Marsa D, Göde S, Hassan M, Hauser J, Herrmannsdörfer T, Höppner H, Kaa J, Kaever P, Knöfel K, Konôpková Z, Laso García A, Liermann HP, Mainberger J, Makita M, Martens EC, McBride EE, Möller D, Nakatsutsumi M, Pelka A, Plueckthun C, Prescher C, Preston TR, Röper M, Schmidt A, Seidel W, Schwinkendorf JP, Schoelmerich MO, Schramm U, Schropp A, Strohm C, Sukharnikov K, Talkovski P, Thorpe I, Toncian M, Toncian T, Wollenweber L, Yamamoto S, Tschentscher T. The High Energy Density Scientific Instrument at the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1393-1416. [PMID: 34475288 PMCID: PMC8415338 DOI: 10.1107/s1600577521007335] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
The European XFEL delivers up to 27000 intense (>1012 photons) pulses per second, of ultrashort (≤50 fs) and transversely coherent X-ray radiation, at a maximum repetition rate of 4.5 MHz. Its unique X-ray beam parameters enable groundbreaking experiments in matter at extreme conditions at the High Energy Density (HED) scientific instrument. The performance of the HED instrument during its first two years of operation, its scientific remit, as well as ongoing installations towards full operation are presented. Scientific goals of HED include the investigation of extreme states of matter created by intense laser pulses, diamond anvil cells, or pulsed magnets, and ultrafast X-ray methods that allow their diagnosis using self-amplified spontaneous emission between 5 and 25 keV, coupled with X-ray monochromators and optional seeded beam operation. The HED instrument provides two target chambers, X-ray spectrometers for emission and scattering, X-ray detectors, and a timing tool to correct for residual timing jitter between laser and X-ray pulses.
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Affiliation(s)
- Ulf Zastrau
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Karen Appel
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Carsten Baehtz
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Oliver Baehr
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | | | - Mohammadreza Banjafar
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | | | - Thomas E. Cowan
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Horst Damker
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | | | - Jörn Dreyer
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Hans-Olaf Engel
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | | | - Manon Foese
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | | | - Mohammed Hassan
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Jens Hauser
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | - Hauke Höppner
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Johannes Kaa
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Peter Kaever
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Klaus Knöfel
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | | | | | - Jona Mainberger
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Mikako Makita
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Emma E. McBride
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Dominik Möller
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | - Alexander Pelka
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | | | | | - Michael Röper
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | - Wolfgang Seidel
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | | | - Ulrich Schramm
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Andreas Schropp
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | | | - Peter Talkovski
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Ian Thorpe
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Monika Toncian
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | - Toma Toncian
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
| | | | - Shingo Yamamoto
- Helmholtz-Zentrum Dresden-Rossendorf eV, 01328 Dresden, Germany
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14
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Cerantola V, Rosa AD, Konôpková Z, Torchio R, Brambrink E, Rack A, Zastrau U, Pascarelli S. New frontiers in extreme conditions science at synchrotrons and free electron lasers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:274003. [PMID: 33930892 DOI: 10.1088/1361-648x/abfd50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Synchrotrons and free electron lasers are unique facilities to probe the atomic structure and electronic properties of matter at extreme thermodynamical conditions. In this context, 'matter at extreme pressures and temperatures' was one of the science drivers for the construction of low emittance 4th generation synchrotron sources such as the Extremely Brilliant Source of the European Synchrotron Radiation Facility and hard x-ray free electron lasers, such as the European x-ray free electron laser. These new user facilities combine static high pressure and dynamic shock compression experiments to outstanding high brilliance and submicron beams. This combination not only increases the data-quality but also enlarges tremendously the accessible pressure, temperature and density space. At the same time, the large spectrum of available complementary x-ray diagnostics for static and shock compression studies opens unprecedented insights into the state of matter at extremes. The article aims at highlighting a new horizon of scientific opportunities based on the synergy between extremely brilliant synchrotrons and hard x-ray free electron lasers.
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Affiliation(s)
- Valerio Cerantola
- European X-ray Free-Electron Laser, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Zuzana Konôpková
- European X-ray Free-Electron Laser, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Raffaella Torchio
- ESRF-The European Synchrotron, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Erik Brambrink
- European X-ray Free-Electron Laser, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alexander Rack
- ESRF-The European Synchrotron, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Ulf Zastrau
- European X-ray Free-Electron Laser, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Sakura Pascarelli
- European X-ray Free-Electron Laser, Holzkoppel 4, 22869 Schenefeld, Germany
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15
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Greiffenberg D, Andrä M, Barten R, Bergamaschi A, Brückner M, Busca P, Chiriotti S, Chsherbakov I, Dinapoli R, Fajardo P, Fröjdh E, Hasanaj S, Kozlowski P, Lopez Cuenca C, Lozinskaya A, Meyer M, Mezza D, Mozzanica A, Redford S, Ruat M, Ruder C, Schmitt B, Thattil D, Tinti G, Tolbanov O, Tyazhev A, Vetter S, Zarubin A, Zhang J. Characterization of Chromium Compensated GaAs Sensors with the Charge-Integrating JUNGFRAU Readout Chip by Means of a Highly Collimated Pencil Beam. SENSORS (BASEL, SWITZERLAND) 2021; 21:1550. [PMID: 33672262 PMCID: PMC7926367 DOI: 10.3390/s21041550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
Chromium compensated GaAs or GaAs:Cr sensors provided by the Tomsk State University (Russia) were characterized using the low noise, charge integrating readout chip JUNGFRAU with a pixel pitch of 75 × 75 µm2 regarding its application as an X-ray detector at synchrotrons sources or FELs. Sensor properties such as dark current, resistivity, noise performance, spectral resolution capability and charge transport properties were measured and compared with results from a previous batch of GaAs:Cr sensors which were produced from wafers obtained from a different supplier. The properties of the sample from the later batch of sensors from 2017 show a resistivity of 1.69 × 109 Ω/cm, which is 47% higher compared to the previous batch from 2016. Moreover, its noise performance is 14% lower with a value of (101.65 ± 0.04) e- ENC and the resolution of a monochromatic 60 keV photo peak is significantly improved by 38% to a FWHM of 4.3%. Likely, this is due to improvements in charge collection, lower noise, and more homogeneous effective pixel size. In a previous work, a hole lifetime of 1.4 ns for GaAs:Cr sensors was determined for the sensors of the 2016 sensor batch, explaining the so-called "crater effect" which describes the occurrence of negative signals in the pixels around a pixel with a photon hit due to the missing hole contribution to the overall signal causing an incomplete signal induction. In this publication, the "crater effect" is further elaborated by measuring GaAs:Cr sensors using the sensors from 2017. The hole lifetime of these sensors was 2.5 ns. A focused photon beam was used to illuminate well defined positions along the pixels in order to corroborate the findings from the previous work and to further characterize the consequences of the "crater effect" on the detector operation.
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Affiliation(s)
- Dominic Greiffenberg
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Marie Andrä
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Rebecca Barten
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Anna Bergamaschi
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Martin Brückner
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Paolo Busca
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, F-38043 Grenoble, France; (P.B.); (P.F.); (M.R.)
| | - Sabina Chiriotti
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Ivan Chsherbakov
- R&D Center “Advanced Electronic Technologies”, Tomsk State University (TSU), Lenin Ave 36, RUS-634050 Tomsk, Russia; (I.C.); (A.L.); (O.T.); (A.T.); (A.Z.)
| | - Roberto Dinapoli
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Pablo Fajardo
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, F-38043 Grenoble, France; (P.B.); (P.F.); (M.R.)
| | - Erik Fröjdh
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Shqipe Hasanaj
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Pawel Kozlowski
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Carlos Lopez Cuenca
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Anastassiya Lozinskaya
- R&D Center “Advanced Electronic Technologies”, Tomsk State University (TSU), Lenin Ave 36, RUS-634050 Tomsk, Russia; (I.C.); (A.L.); (O.T.); (A.T.); (A.Z.)
| | - Markus Meyer
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Davide Mezza
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Aldo Mozzanica
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Sophie Redford
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Marie Ruat
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, F-38043 Grenoble, France; (P.B.); (P.F.); (M.R.)
| | - Christian Ruder
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Bernd Schmitt
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Dhanya Thattil
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Gemma Tinti
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Oleg Tolbanov
- R&D Center “Advanced Electronic Technologies”, Tomsk State University (TSU), Lenin Ave 36, RUS-634050 Tomsk, Russia; (I.C.); (A.L.); (O.T.); (A.T.); (A.Z.)
| | - Anton Tyazhev
- R&D Center “Advanced Electronic Technologies”, Tomsk State University (TSU), Lenin Ave 36, RUS-634050 Tomsk, Russia; (I.C.); (A.L.); (O.T.); (A.T.); (A.Z.)
| | - Seraphin Vetter
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
| | - Andrei Zarubin
- R&D Center “Advanced Electronic Technologies”, Tomsk State University (TSU), Lenin Ave 36, RUS-634050 Tomsk, Russia; (I.C.); (A.L.); (O.T.); (A.T.); (A.Z.)
| | - Jiaguo Zhang
- PSD Detector Group, Paul Scherrer Institut (PSI), Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland; (M.A.); (R.B.); (A.B.); (M.B.); (S.C.); (R.D.); (E.F.); (S.H.); (P.K.); (C.L.C.); (M.M.); (D.M.); (A.M.); (S.R.); (C.R.); (B.S.); (D.T.); (G.T.); (S.V.); (J.Z.)
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16
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Mariette C, Lorenc M, Cailleau H, Collet E, Guérin L, Volte A, Trzop E, Bertoni R, Dong X, Lépine B, Hernandez O, Janod E, Cario L, Ta Phuoc V, Ohkoshi S, Tokoro H, Patthey L, Babic A, Usov I, Ozerov D, Sala L, Ebner S, Böhler P, Keller A, Oggenfuss A, Zmofing T, Redford S, Vetter S, Follath R, Juranic P, Schreiber A, Beaud P, Esposito V, Deng Y, Ingold G, Chergui M, Mancini GF, Mankowsky R, Svetina C, Zerdane S, Mozzanica A, Bosak A, Wulff M, Levantino M, Lemke H, Cammarata M. Strain wave pathway to semiconductor-to-metal transition revealed by time-resolved X-ray powder diffraction. Nat Commun 2021; 12:1239. [PMID: 33623010 PMCID: PMC7902810 DOI: 10.1038/s41467-021-21316-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 01/13/2021] [Indexed: 11/09/2022] Open
Abstract
One of the main challenges in ultrafast material science is to trigger phase transitions with short pulses of light. Here we show how strain waves, launched by electronic and structural precursor phenomena, determine a coherent macroscopic transformation pathway for the semiconducting-to-metal transition in bistable Ti3O5 nanocrystals. Employing femtosecond powder X-ray diffraction, we measure the lattice deformation in the phase transition as a function of time. We monitor the early intra-cell distortion around the light absorbing metal dimer and the long range deformations governed by acoustic waves propagating from the laser-exposed Ti3O5 surface. We developed a simplified elastic model demonstrating that picosecond switching in nanocrystals happens concomitantly with the propagating acoustic wavefront, several decades faster than thermal processes governed by heat diffusion.
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Affiliation(s)
- C Mariette
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France.
| | - M Lorenc
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France.
| | - H Cailleau
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - E Collet
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - L Guérin
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - A Volte
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - E Trzop
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - R Bertoni
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - X Dong
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - B Lépine
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France
| | - O Hernandez
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Rennes, France
| | - E Janod
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, CNRS, Nantes, France
| | - L Cario
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, CNRS, Nantes, France
| | - V Ta Phuoc
- GREMAN-UMR 7347 CNRS, Université de Tours, Tours, France
| | - S Ohkoshi
- Department of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - H Tokoro
- Department of Chemistry, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - L Patthey
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - A Babic
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - I Usov
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - D Ozerov
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - L Sala
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - S Ebner
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - P Böhler
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - A Keller
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - A Oggenfuss
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - T Zmofing
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - S Redford
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - S Vetter
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - R Follath
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - P Juranic
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - A Schreiber
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - P Beaud
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - V Esposito
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland.,Institute for Materials and Energy Science, Stanford University and SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Y Deng
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - G Ingold
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - M Chergui
- Laboratory of Ultrafast Spectroscopy, Lausanne Center for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - G F Mancini
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland.,Laboratory of Ultrafast Spectroscopy, Lausanne Center for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - R Mankowsky
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - C Svetina
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - S Zerdane
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - A Mozzanica
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - A Bosak
- European Synchrotron Radiation Facility, Grenoble, France
| | - M Wulff
- European Synchrotron Radiation Facility, Grenoble, France
| | - M Levantino
- European Synchrotron Radiation Facility, Grenoble, France
| | - H Lemke
- SwissFEL, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - M Cammarata
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, Rennes, France. .,European Synchrotron Radiation Facility, Grenoble, France.
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17
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Ponsard R, Janvier N, Kieffer J, Houzet D, Fristot V. RDMA data transfer and GPU acceleration methods for high-throughput online processing of serial crystallography images. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1297-1306. [PMID: 32876605 PMCID: PMC7842203 DOI: 10.1107/s1600577520008140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
The continual evolution of photon sources and high-performance detectors drives cutting-edge experiments that can produce very high throughput data streams and generate large data volumes that are challenging to manage and store. In these cases, efficient data transfer and processing architectures that allow online image correction, data reduction or compression become fundamental. This work investigates different technical options and methods for data placement from the detector head to the processing computing infrastructure, taking into account the particularities of modern modular high-performance detectors. In order to compare realistic figures, the future ESRF beamline dedicated to macromolecular X-ray crystallography, EBSL8, is taken as an example, which will use a PSI JUNGFRAU 4M detector generating up to 16 GB of data per second, operating continuously during several minutes. Although such an experiment seems possible at the target speed with the 100 Gb s-1 network cards that are currently available, the simulations generated highlight some potential bottlenecks when using a traditional software stack. An evaluation of solutions is presented that implements remote direct memory access (RDMA) over converged ethernet techniques. A synchronization mechanism is proposed between a RDMA network interface card (RNIC) and a graphics processing unit (GPU) accelerator in charge of the online data processing. The placement of the detector images onto the GPU is made to overlap with the computation carried out, potentially hiding the transfer latencies. As a proof of concept, a detector simulator and a backend GPU receiver with a rejection and compression algorithm suitable for a synchrotron serial crystallography (SSX) experiment are developed. It is concluded that the available transfer throughput from the RNIC to the GPU accelerator is at present the major bottleneck in online processing for SSX experiments.
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Affiliation(s)
- Raphael Ponsard
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
- GIPSALAB, Grenoble Alpes University, 11 Rue des Mathématiques, 38400 Saint-Martin-d’Hères, France
| | - Nicolas Janvier
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jerome Kieffer
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Dominique Houzet
- GIPSALAB, Grenoble Alpes University, 11 Rue des Mathématiques, 38400 Saint-Martin-d’Hères, France
| | - Vincent Fristot
- GIPSALAB, Grenoble Alpes University, 11 Rue des Mathématiques, 38400 Saint-Martin-d’Hères, France
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18
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Smolentsev G, Milne CJ, Guda A, Haldrup K, Szlachetko J, Azzaroli N, Cirelli C, Knopp G, Bohinc R, Menzi S, Pamfilidis G, Gashi D, Beck M, Mozzanica A, James D, Bacellar C, Mancini GF, Tereshchenko A, Shapovalov V, Kwiatek WM, Czapla-Masztafiak J, Cannizzo A, Gazzetto M, Sander M, Levantino M, Kabanova V, Rychagova E, Ketkov S, Olaru M, Beckmann J, Vogt M. Taking a snapshot of the triplet excited state of an OLED organometallic luminophore using X-rays. Nat Commun 2020; 11:2131. [PMID: 32358505 PMCID: PMC7195477 DOI: 10.1038/s41467-020-15998-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/07/2020] [Indexed: 12/21/2022] Open
Abstract
OLED technology beyond small or expensive devices requires light-emitters, luminophores, based on earth-abundant elements. Understanding and experimental verification of charge transfer in luminophores are needed for this development. An organometallic multicore Cu complex comprising Cu–C and Cu–P bonds represents an underexplored type of luminophore. To investigate the charge transfer and structural rearrangements in this material, we apply complementary pump-probe X-ray techniques: absorption, emission, and scattering including pump-probe measurements at the X-ray free-electron laser SwissFEL. We find that the excitation leads to charge movement from C- and P- coordinated Cu sites and from the phosphorus atoms to phenyl rings; the Cu core slightly rearranges with 0.05 Å increase of the shortest Cu–Cu distance. The use of a Cu cluster bonded to the ligands through C and P atoms is an efficient way to keep structural rigidity of luminophores. Obtained data can be used to verify computational methods for the development of luminophores. OLED materials based on thermally activated delayed fluorescence have promising efficiency. Here, the authors investigate an organometallic multicore Cu complex as luminophore, by pump-probe X-ray techniques at three different facilities deriving a complete picture of the charge transfer in the triplet excited state.
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Affiliation(s)
| | | | - Alexander Guda
- The Smart Materials Research Institute, Southern Federal University, 344090, Rostov-on-Don, Russia
| | - Kristoffer Haldrup
- Physics Department, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Kraków, Poland
| | | | | | - Gregor Knopp
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Rok Bohinc
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Samuel Menzi
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | | | - Dardan Gashi
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Martin Beck
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | | | - Daniel James
- Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Laboratory for Ultrafast Spectroscopy, Lausanne Center for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Giulia F Mancini
- Paul Scherrer Institute, 5232, Villigen, Switzerland.,Laboratory for Ultrafast Spectroscopy, Lausanne Center for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Andrei Tereshchenko
- The Smart Materials Research Institute, Southern Federal University, 344090, Rostov-on-Don, Russia
| | - Victor Shapovalov
- The Smart Materials Research Institute, Southern Federal University, 344090, Rostov-on-Don, Russia
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Kraków, Poland
| | | | - Andrea Cannizzo
- Institute of Applied Physics, University of Bern, 3012, Bern, Switzerland
| | - Michela Gazzetto
- Institute of Applied Physics, University of Bern, 3012, Bern, Switzerland
| | - Mathias Sander
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Matteo Levantino
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Victoria Kabanova
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Elena Rychagova
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russia
| | - Sergey Ketkov
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russia
| | - Marian Olaru
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobenerstr. 7, 28359, Bremen, Germany
| | - Jens Beckmann
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobenerstr. 7, 28359, Bremen, Germany
| | - Matthias Vogt
- Institute of Inorganic Chemistry and Crystallography, University of Bremen, Leobenerstr. 7, 28359, Bremen, Germany. .,Martin-Luther-Universität Halle-Wittenberg Naturwissenschaftliche Fakultät II, Institut für Chemie, Anorganische Chemie, D-06120, Halle, Germany.
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19
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Ultrafast X-ray Photochemistry at European XFEL: Capabilities of the Femtosecond X-ray Experiments (FXE) Instrument. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10030995] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Time-resolved X-ray methods are widely used for monitoring transient intermediates over the course of photochemical reactions. Ultrafast X-ray absorption and emission spectroscopies as well as elastic X-ray scattering deliver detailed electronic and structural information on chemical dynamics in the solution phase. In this work, we describe the opportunities at the Femtosecond X-ray Experiments (FXE) instrument of European XFEL. Guided by the idea of combining spectroscopic and scattering techniques in one experiment, the FXE instrument has completed the initial commissioning phase for most of its components and performed first successful experiments within the baseline capabilities. This is demonstrated by its currently 115 fs (FWHM) temporal resolution to acquire ultrafast X-ray emission spectra by simultaneously recording iron Kα and Kβ lines, next to wide angle X-ray scattering patterns on a photoexcited aqueous solution of [Fe(bpy)3]2+, a transition metal model compound.
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20
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Mishin A, Gusach A, Luginina A, Marin E, Borshchevskiy V, Cherezov V. An outlook on using serial femtosecond crystallography in drug discovery. Expert Opin Drug Discov 2019; 14:933-945. [PMID: 31184514 DOI: 10.1080/17460441.2019.1626822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: X-ray crystallography has made important contributions to modern drug development but its application to many important drug targets has been extremely challenging. The recent emergence of X-ray free electron lasers (XFELs) and advancements in serial femtosecond crystallography (SFX) have offered new opportunities to overcome limitations of traditional crystallography to accelerate the structure-based drug discovery (SBDD) process. Areas covered: In this review, the authors describe the general principles of X-ray generation and the main properties of XFEL beams, outline details of SFX data collection and processing, and summarize the progress in the development of associated instrumentation for sample delivery and X-ray detection. An overview of the SFX applications to various important drug targets such as membrane proteins is also provided. Expert opinion: While SFX has already made clear advancements toward the understanding of the structure and dynamics of several major drug targets, its robust application in SBDD still needs further developments of new high-throughput techniques for sample production, automation of crystal delivery and data collection, as well as for processing and storage of large amounts of data. The expansion of the available XFEL beamtime is a key to the success of SFX in SBDD.
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Affiliation(s)
- Alexey Mishin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Anastasiia Gusach
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Aleksandra Luginina
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Egor Marin
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Valentin Borshchevskiy
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia
| | - Vadim Cherezov
- a Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology , Dolgoprudny , Russia.,b Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California , Los Angeles , CA , USA
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21
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Ingold G, Abela R, Arrell C, Beaud P, Böhler P, Cammarata M, Deng Y, Erny C, Esposito V, Flechsig U, Follath R, Hauri C, Johnson S, Juranic P, Mancini GF, Mankowsky R, Mozzanica A, Oggenfuss RA, Patterson BD, Patthey L, Pedrini B, Rittmann J, Sala L, Savoini M, Svetina C, Zamofing T, Zerdane S, Lemke HT. Experimental station Bernina at SwissFEL: condensed matter physics on femtosecond time scales investigated by X-ray diffraction and spectroscopic methods. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:874-886. [PMID: 31074452 PMCID: PMC6510206 DOI: 10.1107/s160057751900331x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/07/2019] [Indexed: 05/22/2023]
Abstract
The Bernina instrument at the SwissFEL Aramis hard X-ray free-electron laser is designed for studying ultrafast phenomena in condensed matter and material science. Ultrashort pulses from an optical laser system covering a large wavelength range can be used to generate specific non-equilibrium states, whose subsequent temporal evolution can be probed by selective X-ray scattering techniques in the range 2-12 keV. For that purpose, the X-ray beamline is equipped with optical elements which tailor the X-ray beam size and energy, as well as with pulse-to-pulse diagnostics that monitor the X-ray pulse intensity, position, as well as its spectral and temporal properties. The experiments can be performed using multiple interchangeable endstations differing in specialization, diffractometer and X-ray analyser configuration and load capacity for specialized sample environment. After testing the instrument in a series of pilot experiments in 2018, regular user operation begins in 2019.
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Affiliation(s)
- Gerhard Ingold
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Rafael Abela
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - Paul Beaud
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Pirmin Böhler
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Marco Cammarata
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Yunpei Deng
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Christian Erny
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Vincent Esposito
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Uwe Flechsig
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Rolf Follath
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Christoph Hauri
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Steven Johnson
- Institute for Quantum Electronics, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zurich, Switzerland
| | - Pavle Juranic
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - Roman Mankowsky
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | | | - Luc Patthey
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Jochen Rittmann
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Matteo Savoini
- Institute for Quantum Electronics, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zurich, Switzerland
| | - Cristian Svetina
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Thierry Zamofing
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Serhane Zerdane
- SwissFEL, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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