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63 results on '"Linac Coherent Light Source (LCLS)"'

1. Ultrafast X-ray Diffraction Study of a Shock-Compressed Iron Meteorite above 100 GPa

Author

Roberto A. Colina-Ruiz, Hae Ja Lee, Sovanndara Hok, Wendy L. Mao, Kyle J. Ramos, Dylan R. Rittman, Sébastien Merkel, Richard Walroth, Akel Hashim, Eduardo Granados, Benjamin M. Morrow, Sabrina Tecklenburg, Cynthia Bolme, Bob Nagler, Arianna Gleason, Eric Galtier, Université de Lille, CNRS, INRA, ENSCL, Stanford EARTH, Stanford Synchrotron Radiation Lightsource [SSRL SLAC], Los Alamos National Laboratory [LANL], Linac Coherent Light Source [LCLS], Unité Matériaux et Transformations - UMR 8207 [UMET], Stanford University, Stanford Synchrotron Radiation Lightsource (SSRL SLAC), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Los Alamos National Laboratory (LANL), Linac Coherent Light Source (LCLS), Unité Matériaux et Transformations - UMR 8207 (UMET), Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centrale Lille Institut (CLIL)

Subjects
Materials science, 010504 meteorology & atmospheric sciences, Analytical chemistry, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Geology, iron meteorite, Mineralogy, 010502 geochemistry & geophysics, Geotechnical Engineering and Engineering Geology, 01 natural sciences, Iron meteorite, Shock (mechanics), [PHYS.MECA.MEMA]Physics [physics]/Mechanics [physics]/Mechanics of materials [physics.class-ph], Kamacite, Crystal, Meteorite, Phase (matter), X-ray crystallography, Crystallite, ultrafast X-ray diffraction, laser shock compression, QE351-399.2, 0105 earth and related environmental sciences
Abstract

Natural kamacite samples (Fe92.5Ni7.5) from a fragment of the Gibeon meteorite were studied as a proxy material for terrestrial cores to examine phase transition kinetics under shock compression for a range of different pressures up to 140 GPa. In situ time-resolved X-ray diffraction (XRD) data were collected of a body-centered cubic (bcc) kamacite section that transforms to the high-pressure hexagonal close-packed (hcp) phase with sub-nanosecond temporal resolution. The coarse-grained crystal of kamacite rapidly transformed to highly oriented crystallites of the hcp phase at maximum compression. The hcp phase persisted for as long as 9.5 ns following shock release. Comparing the c/a ratio with previous static and dynamic work on Fe and Fe-rich Fe-Ni alloys, it was found that some shots exhibit a larger than ideal c/a ratio, up to nearly 1.65. This work represents the first time-resolved laser shock compression structural study of a natural iron meteorite, relevant for understanding the dynamic material properties of metallic planetary bodies during impact events and Earth’s core elasticity.

Published
2021
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2. Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade

Author

Martin Rosenthal, Maria Bacia, Maria Teresa Fernandez-Luna, Luca Signor, Guillaume Tetreau, Jayesh Arun Bafna, Enrico Gratton, Anne-Sophie Banneville, Iris D. Young, Mathias Winterhalter, Frederic Laporte, Aaron S. Brewster, Raymond G. Sierra, Manfred Burghammer, Mark S. Hunter, Sébastien Boutet, Elisabetta Boeri-Erba, Elena A. Andreeva, Ninon Zala, Jacques-Philippe Colletier, Tilman A. Grünewald, Irina Gutsche, Nicolas Coquelle, Niamh Burke, Duilio Cascio, Laurence Després, Irina Snigireva, Daphna Fenel, Alister Burt, Jean-Marie Teulon, Rabia Sadir, Nicholas K. Sauter, Jean-Luc Pellequer, Martin Weik, Brian A. Federici, Joël Beaudouin, Hyun-Woo Park, Michael R. Sawaya, Groupe Dynamique et Cinétique des processus moléculaires (IBS-DYNAMOP), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, European Synchrotron Radiation Facility (ESRF), Department of Entomology [Riverside], University of California [Riverside] (UCR), University of California-University of California, California Baptist University (CBU), Jacobs University [Bremen], Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut Laue-Langevin (ILL), ILL, UCLA/DOE Institute for Genomics and Proteomics, University of California [Los Angeles] (UCLA), Laboratory for Fluorescence Dynamics [Irvine], University of California [Irvine] (UCI), AFM platform, Grenoble Instruct-ERIC center (ISBG, UMS 3518 CNRS-CEA-UGAEMBL), ANR-17-CE11-0018,X-in-vivo,Cristallisation in vivo: une nouvelle stratégie pour étudier la structure et la dynamique des protéines dans les lasers à électrons libres et les synchrotrons.(2017), ANR-18-CE11-0005,DynOCP,Investigation du mécanisme de photo-activation de l'OCP par spectroscopie optique ultrarapide et cristallographie sérielle temps-résolue.(2018), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Université Grenoble Alpes (UGA), University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), and University of California [Irvine] (UC Irvine)

Subjects
0301 basic medicine, Insecticides, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Protein Conformation, General Physics and Astronomy, Crystallography, X-Ray, Microscopy, Atomic Force, Atomic force microscopy, Hemolysin Proteins, Mice, 0302 clinical medicine, Sf9 Cells, Disulfides, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Microscopy, Crystallography, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Nanocrystallography, Chemistry, Atomic Force, Limiting, Hydrogen-Ion Concentration, Bacillus thuringiensis israelensis, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Femtosecond, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Science, Mechanism of action, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Bacterial Proteins, In vivo, parasitic diseases, Animals, Humans, Bacillus thuringiensis Toxins, Cell Membrane, fungi, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Chemistry, Endotoxins, HEK293 Cells, 030104 developmental biology, Yield (chemistry), X-Ray, NIH 3T3 Cells, lcsh:Q, 030217 neurology & neurosurgery
Abstract

Cyt1Aa is the one of four crystalline protoxins produced by mosquitocidal bacterium Bacillus thuringiensis israelensis (Bti) that has been shown to delay the evolution of insect resistance in the field. Limiting our understanding of Bti efficacy and the path to improved toxicity and spectrum has been ignorance of how Cyt1Aa crystallizes in vivo and of its mechanism of toxicity. Here, we use serial femtosecond crystallography to determine the Cyt1Aa protoxin structure from sub-micron-sized crystals produced in Bti. Structures determined under various pH/redox conditions illuminate the role played by previously uncharacterized disulfide-bridge and domain-swapped interfaces from crystal formation in Bti to dissolution in the larval mosquito midgut. Biochemical, toxicological and biophysical methods enable the deconvolution of key steps in the Cyt1Aa bioactivation cascade. We additionally show that the size, shape, production yield, pH sensitivity and toxicity of Cyt1Aa crystals grown in Bti can be controlled by single atom substitution., Bacillus thuringiensis israelensis (Bti) produces the naturally-crystalline proteinaceous toxin Cyt1Aa that is toxic to mosquito larvae. Here the authors grow recombinant nanocrystals of the Cyt1Aa protoxin in vivo and use serial femtosecond crystallography to determine its structure at different redox and pH conditions and by combining their structural data with further biochemical, toxicological and biophysical analyses provide mechanistic insights into the Cyt1Aa bioactivation cascade.

Published
2020
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7. Rational control of off‐state heterogeneity in a photoswitchable fluorescent protein provides switching contrast enhancement

Author

Angela Mantovanelli, A. Gorel, Dominique Bourgeois, M. Hilpert, Gabriela Nass Kovacs, Mark S. Hunter, Sébastien Boutet, Ninon Zala, Kiyoshi Ueda, Jason E. Koglin, Andrew Aquila, Michel Sliwa, Ilme Schlichting, M. Stricker, Stefan Jakobs, Kensuke Tono, Martin Weik, Virgile Adam, Anne-Sophie Banneville, Lucas Martinez Uriarte, T. Domratcheva, Michel Thépaut, Mengning Liang, Oleksandr Glushonkov, Martin Byrdin, Giorgio Schirò, Marie Luise Grünbein, Robert L. Shoeman, Kyprianos Hadjidemetriou, Thomas R. M. Barends, Sergio Carbajo, Nina Eleni Christou, Thomas J. Lane, Victor Bezchastnov, Daehyun You, Tadeo Moreno Chicano, Lutz Foucar, Marco Cammarata, Nickels A. Jensen, C.M. Roome, Jacques-Philippe Colletier, Marco Kloos, Franck Fieschi, Eugenio de la Mora, Mariam El Khatib, Nicolas Coquelle, Shigeki Owada, Matthew Seaberg, R. Bruce Doak, Karol Nass, Joyce Woodhouse, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Department of NanoBiophotonics [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Max-Planck-Institut für Medizinische Forschung, Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), RIKEN SPring-8 Center [Hyogo] (RIKEN RSC), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Japan Synchrotron Radiation Research Institute [Hyogo] (JASRI), Tohoku University [Sendai], Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry, Lomonosov Moscow State University, Lomonosov Moscow State University (MSU), The XFEL experiments were carried out at BL2-EH3 of SACLA with the approval of the Japan Synchrotron Radiation Research Institute (JASRI, Proposal No. 2018 A8026, 27–29 July 2018) and at the CXI beamline at the LCLS (Proposal No. LM47 (23–27 June 2016) and LR38 (22–26 February 2018). We warmly thank the SACLA and LCLS staff for assistance. Use of the LCLS, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract no. DE-AC02-76SF00515. Part of the sample injector used at LCLS for this research was funded by the National Institutes of Health, P41 GM103393, formerly P41RR001209. We acknowledge support from the Max Planck Society. The study was supported by travel grants from the CNRS (GoToXFEL) to MW, an ANR grant to MW, MC, MSl (BioXFEL), a PhD fellowship from Lille University to LMU and an MENESR – Univ. Grenoble Alpes fellowship to KH. This work was partially carried out at the platforms of the Grenoble Instruct-ERIC center (IBS and ISBG, UMS 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB)., ANR-17-CE11-0047,Cryo-PALM,Microscopie super-résolution par localisation de molécules uniques à température cryogénique.(2017), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Physico-Chimie Curie [Institut Curie] (PCC), Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Publica

Subjects
serial femtosecond crystallography, [SDV]Life Sciences [q-bio], RESOLFT, Green Fluorescent Proteins, nanoscopy, Atomic, quantum chemistry, Particle and Plasma Physics, Theoretical and Computational Chemistry, Microscopy, Side chain, switching contrast, Escherichia coli, Nuclear, Physical and Theoretical Chemistry, [PHYS]Physics [physics], Chemical Physics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, photoswitchable fluorescent proteins, Resolution (electron density), Molecular, Chromophore, Fluorescence, Atomic and Molecular Physics, and Optics, Luminescent Proteins, Femtosecond, Biophysics, Generic health relevance, Biological imaging, Physical Chemistry (incl. Structural)
Abstract

Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, a key parameter that largely dictates the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

Published
2022
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8. De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Author

Guillaume Tetreau, Michael R. Sawaya, Elke De Zitter, Elena A. Andreeva, Anne-Sophie Banneville, Natalie A. Schibrowsky, Nicolas Coquelle, Aaron S. Brewster, Marie Luise Grünbein, Gabriela Nass Kovacs, Mark S. Hunter, Marco Kloos, Raymond G. Sierra, Giorgio Schiro, Pei Qiao, Myriam Stricker, Dennis Bideshi, Iris D. Young, Ninon Zala, Sylvain Engilberge, Alexander Gorel, Luca Signor, Jean-Marie Teulon, Mario Hilpert, Lutz Foucar, Johan Bielecki, Richard Bean, Raphael de Wijn, Tokushi Sato, Henry Kirkwood, Romain Letrun, Alexander Batyuk, Irina Snigireva, Daphna Fenel, Robin Schubert, Ethan J. Canfield, Mario M. Alba, Frédéric Laporte, Laurence Després, Maria Bacia, Amandine Roux, Christian Chapelle, François Riobé, Olivier Maury, Wai Li Ling, Sébastien Boutet, Adrian Mancuso, Irina Gutsche, Eric Girard, Thomas R. M. Barends, Jean-Luc Pellequer, Hyun-Woo Park, Arthur D. Laganowsky, Jose Rodriguez, Manfred Burghammer, Robert L. Shoeman, R. Bruce Doak, Martin Weik, Nicholas K. Sauter, Brian Federici, Duilio Cascio, Ilme Schlichting, Jacques-Philippe Colletier, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), UCLA/DOE Institute for Genomics and Proteomics, University of California [Los Angeles] (UCLA), University of California (UC)-University of California (UC), Groupe Dynamique et Cinétique des processus moléculaires (IBS-DYNAMOP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Max-Planck-Institut für Medizinische Forschung, Max-Planck-Gesellschaft, Max Planck Institute for Medical Research [Heidelberg], Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, California Baptist University (CBU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), European Synchroton Radiation Facility [Grenoble] (ESRF), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire de Chimie - UMR5182 (LC), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Stanford University, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), and ANR-17-CE11-0018,X-in-vivo,Cristallisation in vivo: une nouvelle stratégie pour étudier la structure et la dynamique des protéines dans les lasers à électrons libres et les synchrotrons.(2017)

Subjects
Mosquito Control, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Bacillus thuringiensis, General Physics and Astronomy, General Chemistry, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, General Biochemistry, Genetics and Molecular Biology, Endotoxins, Hemolysin Proteins, Bacterial Proteins, Larva, [CHIM.CRIS]Chemical Sciences/Cristallography, Animals, Nanoparticles, [CHIM]Chemical Sciences
Abstract

Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

Published
2022
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9. Ultrafast structural changes within a photosynthetic reaction centre

Author

Rebecka Andersson, Gisela Brändén, Gergely Katona, Michał Maj, Antoine Royant, David Arnlund, Hoi Ling Luk, Oleksandr Yefanov, Despina Milathianaki, Sergio Carbajo, Robert Bosman, Greger Hammarin, Linda C. Johansson, Adams Vallejos, Elin Claesson, Joseph Robinson, Cecilia Wickstrand, Erik Malmerberg, Cecilia Safari, Garth J. Williams, Chelsie E. Conrad, Kenneth R. Beyerlein, Richard Neutze, Anton Barty, Chufeng Li, Rajiv Harimoorthy, Daniel P. DePonte, Amit Sharma, Mark S. Hunter, Sébastien Boutet, Viktor Ahlberg Gagnér, Garrett Nelson, Dmitry Morozov, Stella Lisova, Jan Davidsson, Joachim Kübel, Petra Båth, Robert Dods, Mengning Liang, Sebastian Westenhoff, Peter Dahl, Peter Berntsen, Gerrit Groenhof, Department of Chemistry and Molecular Biology [Gothenburg], University of Gothenburg (GU), Department of Chemistry [Jyväskylä Univ] (JYU), University of Jyväskylä (JYU), Nanoscience Center [Jyväskylä Univ] (NSC@JYU), Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron [Hamburg] (DESY), Department of Physics, Arizona State University (ASU), Arizona State University [Tempe] (ASU), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Australian Research Council Centre of Excellence in Advanced Molecular Imaging [Victoria, Australia], Molecular Biophysics and Integrated Bioimaging Division [Berkeley, CA, USA], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of Southern California (USC), Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85282, U.S.A., Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), European Synchrotron Radiation Facility (ESRF), Department of Chemistry – Ångström Laboratory, UPPSALA University, Box 538, 75120, Uppsala, Sweden, and Uppsala University

Subjects
0301 basic medicine, Photosynthetic reaction centre, Chlorophyll, Models, Molecular, klorofylli, Cytoplasm, Ubiquinone, Photosynthetic Reaction Center Complex Proteins, Electrons, 02 engineering and technology, Photochemistry, medicine.disease_cause, yhteyttäminen, bakteerit, Electron Transport, 03 medical and health sciences, Electron transfer, medicine, Molecule, ddc:530, Bacteriochlorophylls, bioenergetiikka, ComputingMilieux_MISCELLANEOUS, Hyphomicrobiaceae, Multidisciplinary, Binding Sites, Crystallography, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Blastochloris viridis, Lasers, kalvot (biologia), Pheophytins, Biological membrane, Vitamin K 2, 021001 nanoscience & nanotechnology, Acceptor, 030104 developmental biology, Picosecond, Femtosecond, sense organs, Protons, 0210 nano-technology, Oxidation-Reduction, röntgenkristallografia
Abstract

Nature / Physical science 589, 310 - 314 (2021). doi:10.1038/s41586-020-3000-7, Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions., Published by Macmillan Publishers Limited, part of Springer Nature, London

Published
2021
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10. Charge-transfer driven by ultrafast spin-transition in a CoFe Prussian blue analogue

Author

Matilde Cardoso Trabuco, Laure Catala, Serhane Zerdane, Lodovico Balducci, Cécile Exertier, Sanghoon Song, Samir F. Matar, Matteo Levantino, Marco Cammarata, Sandra Mazerat, James M. Glownia, Roberto Alonso-Mori, Talal Mallah, Eric Collet, Giovanni Azzolina, Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), European Synchrotron Radiation Facility (ESRF), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Lebanese German University (LGU), Rennes Métropole, Centre National de la Recherche Scientifique (CNRS, PEPS SASLELX), Fonds Européen de Développement Régional (FEDER), Région Bretagne (ARED 8925/XFELMAT), ANR-13-BS04-0002,FEMTOMAT,Etude femtoseconde rayons X et optique de la dynamique ultrarapide de photocommutation de matériaux moléculaires magnétiques(2013), ANR-15-CE32-0004,BioXFEL,Caractérisation d'états intermédiaires de protéines fluorescentes en utilisant des lasers à électrons libres X et les spectroscopies UV-visible et infrarouge ultra-rapides(2015), European Project: 637295,H2020,H2020-MSCA-ITN-2014,X-probe(2015), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Cammarata M., Zerdane S., Balducci L., Azzolina G., Mazerat S., Exertier C., Trabuco M., Levantino M., Alonso-Mori R., Glownia J.M., Song S., Catala L., Mallah T., Matar S.F., and Collet E.

Subjects
[PHYS]Physics [physics], Prussian blue, 010405 organic chemistry, General Chemical Engineering, Spin transition, Intermetallic, General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, Photomagnetism, 01 natural sciences, 0104 chemical sciences, ultrafast dynamics, chemistry.chemical_compound, chemistry, Chemical physics, Femtosecond, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [CHIM]Chemical Sciences, [CHIM.COOR]Chemical Sciences/Coordination chemistry, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Absorption (electromagnetic radiation), Ultrashort pulse, Bimetallic strip, ComputingMilieux_MISCELLANEOUS
Abstract

Photoinduced charge-transfer is an important process in nature and technology and is responsible for the emergence of exotic functionalities, such as magnetic order for cyanide-bridged bimetallic coordination networks. Despite its broad interest and intensive developments in chemistry and material sciences, the atomic-scale description of the initial photoinduced process, which couples intermetallic charge-transfer and spin transition, has been debated for decades; it has been beyond reach due to its extreme speed. Here we study this process in a prototype cyanide-bridged CoFe system by femtosecond X-ray and optical absorption spectroscopies, enabling the disentanglement of ultrafast electronic and structural dynamics. Our results demonstrate that it is the spin transition that occurs first on the Co site within ~50 fs, and it is this that drives the subsequent Fe-to-Co charge-transfer within ~200 fs. This study represents a step towards understanding and controlling charge-transfer-based functions using light. Cyanide-bridged CoFe coordination networks exhibit photomagnetism because of coupled charge-transfer and spin transition. Now, femtosecond X-ray and optical absorption spectroscopies have enabled the electronic and structural dynamics of this light-induced process to be disentangled and show that it is the spin transition on the cobalt atom, occurring within ~50 fs, that induces the Fe-to-Co charge-transfer within ~200 fs.

Published
2021
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11. Single-shot X-ray Absorption Spectroscopy at X-ray Free Electron Lasers

Author

Harmand, M., Krygier, A.G., Cammarata, Marco, Chollet, M., Lemke, H.T., Zhu, D., Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Lawrence Livermore National Laboratory (LLNL), European Synchrotron Radiation Facility (ESRF), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University [Stanford]-Stanford University [Stanford], Paul Scherrer Institute (PSI), Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Stanford University-Stanford University, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS)

Subjects
X-ray Absorption Spectroscopy, Free Electron Lasers, [PHYS]Physics [physics], Condensed Matter - Materials Science, EXAFS, Physics - Instrumentation and Detectors, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, Instrumentation and Detectors (physics.ins-det), [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], [PHYS.PHYS.PHYS-GEN-PH]Physics [physics]/Physics [physics]/General Physics [physics.gen-ph], XANES
Abstract

X-ray Absorption Spectroscopy (XAS) is a widely used X-ray diagnostic method. While synchrotrons have large communities of XAS users, its use on X-Ray Free Electron Lasers (XFEL) facilities has been rather limited. At a first glance, the relatively narrow bandwidth and the highly fluctuating spectral structure of XFEL sources seem to prevent high-quality XAS measurements without accumulating over many shots. Here, we demonstrate for the first time the collection of single-shot XAS spectra on an XFEL, with error bars of only a few percent, over tens of eV. We show how this technique can be extended over wider spectral ranges towards Extended X-ray Absorption Fine Structure (EXAFS) measurements, by concatenating a few tens of single-shot measurements. Such results open indisputable perspectives for future femtosecond time resolved XAS studies, especially for transient processes that can be initiated at low repetition rate., 11 pages, 5 figures

Published
2020

12. Relativistic and resonant effects in the ionization of heavy atoms by ultra-intense hard X-rays

Author

Bertold Krässig, Sébastien Boutet, Sebastian Carron, Tais Gorkhover, Robin Santra, Kiyoshi Ueda, Benjamin Erk, Benedikt Rudek, Christoph Bostedt, J. Correa, Stephen H. Southworth, Lutz Foucar, Marc Simon, Maximilian Bucher, C. S. Lehmann, Roberto Alonso-Mori, Daniel Rolles, Sang-Kil Son, Tatiana Marchenko, Cédric Bomme, Rebecca Boll, Ken R. Ferguson, Zoltan Jurek, Garth J. Williams, Koudai Toyota, Jason E. Koglin, Linda Young, Artem Rudenko, Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, Deutsches Elektronen-Synchrotron [Hamburg] (DESY), SLAC National Accelerator Laboratory (SLAC), Stanford University, Linac Coherent Light Source (LCLS), Stanford University-Stanford University, School of Science and Technology, University of Camerino, Argonne National Laboratory [Lemont] (ANL), Graduate school of science, Hiroshima International University, Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Center for Free-Electron Laser Science (CFEL), and Kansas State University

Subjects
Photon, Science, Astrophysics::High Energy Astrophysical Phenomena, General Physics and Astronomy, chemistry.chemical_element, 02 engineering and technology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Ion, Xenon, Ionization, 0103 physical sciences, 010306 general physics, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Physics, Range (particle radiation), Multidisciplinary, [PHYS.PHYS]Physics [physics]/Physics [physics], General Chemistry, 021001 nanoscience & nanotechnology, 3. Good health, chemistry, Femtosecond, lcsh:Q, ddc:500, Electron configuration, Atomic physics, 0210 nano-technology, Relativistic quantum chemistry
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., Availability of intense hard X-ray pulses allows exploration of multiple ionization effects in heavier elements. Here, the authors measure the complex charge state distributions of xenon and found a reasonable agreement by comparing with the model including the relativistic and resonance effects.

Published
2018
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13. Analysis of XFEL serial diffraction data from individual crystalline fibrils

Author

Carolin Seuring, Kartik Ayyer, Kenneth R. Beyerlein, Holger Fleckenstein, Sébastien Boutet, Anton Barty, Estelle Mossou, Dominik Oberthuer, Oleksandr Yefanov, V. Trevor Forsyth, Mengning Liang, P. Lourdu Xavier, Richard Bean, David H. Wojtas, Saša Bajt, Andrew Aquila, Wai Li Ling, Anna Mitraki, Michael Heymann, Filippo Romoli, Rick P. Millane, Eirini Ornithopoulou, Henry N. Chapman, Miriam Barthelmess, Thomas A. White, Chun Hong Yoon, Andrew J. Morgan, Cornelius Gati, Matthias Frank, Lorenzo Galli, Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Keele Univ, Fac Nat Sci, Keele ST5 5BG, Staffs, England, Ctr Ultrafast Imaging, D-22607 Hamburg, Germany, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Lawrence Livermore National Laboratory (LLNL), DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany, Department of Materials Science and Technology, University of Crete [Heraklion] (UOC), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
0301 basic medicine, Diffraction, molecular orientation determination, 02 engineering and technology, Crystal structure, macromolecular substances, Neurodegenerative, Atomic, Biochemistry, 03 medical and health sciences, Particle and Plasma Physics, Optics, coherent X-ray diffractive imaging, Nuclear, ddc:530, General Materials Science, serial crystallography, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Jet (fluid), Quantitative Biology::Biomolecules, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], crystalline fibrils, Orientation (computer vision), Scattering, business.industry, Free-electron laser, Molecular, amyloid, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, coherent X-ray diffractive imaging (CXDI), Research Papers, Brain Disorders, QR, 3. Good health, Reciprocal lattice, 030104 developmental biology, single particles, X-ray crystallography, lcsh:Q, 0210 nano-technology, business, Physical Chemistry (incl. Structural)
Abstract

Methods are described for processing XFEL data from individual crystalline fibrils. The methods are applied to data collected at the Linac Coherent Light Source from an amyloid-forming oligopeptide from the adenovirus shaft., Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

Published
2017
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14. Magnetic Switching in Granular FePt Layers Promoted by Near-Field Laser Enhancement

Author

Emmanuelle Jal, Tianmin Liu, Sebastian Carron, Zhao Chen, Joachim Stöhr, P. W. Granitzka, Padraic Shafer, Elke Arenholz, Eric E. Fullerton, Alexander X. Gray, L. Le Guyader, Alexander H. Reid, Hermann A. Dürr, Daniel J. Higley, Olav Hellwig, T. Chase, Georgi L. Dakovski, Yukiko Takahashi, Virat Mehta, Matthias C. Hoffman, William F. Schlotter, Jian Wang, Hendrik Ohldag, Matteo Savoini, Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, Fudan University [Shanghai], Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Stanford University, Advanced Light Source [LBNL Berkeley] (ALS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), HGST San Jose Research Center, Hard Condensed Matter (WZI, IoP, FNWI), IoP (FNWI), Quantum Matter and Quantum Information, and Faculty of Science

Subjects
Materials science, Physics::Optics, FOS: Physical sciences, Bioengineering, Nanotechnology, Near and far field, 02 engineering and technology, 01 natural sciences, law.invention, Magnetization, law, ultrafast magnetism, 0103 physical sciences, pump−probe, General Materials Science, Nanoscience & Nanotechnology, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, ComputingMilieux_MISCELLANEOUS, Condensed Matter - Materials Science, Condensed matter physics, Mechanical Engineering, Materials Science (cond-mat.mtrl-sci), General Chemistry, Coercivity, X-ray scattering, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Magnetostatics, Laser, magnetic switching, cond-mat.mtrl-sci, Magnetic anisotropy, pump-probe, Femtosecond, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0210 nano-technology, Excitation, FePt
Abstract

© 2017 American Chemical Society. Light-matter interaction at the nanoscale in magnetic materials is a topic of intense research in view of potential applications in next-generation high-density magnetic recording. Laser-assisted switching provides a pathway for overcoming the material constraints of high-anisotropy and high-packing density media, though much about the dynamics of the switching process remains unexplored. We use ultrafast small-angle X-ray scattering at an X-ray free-electron laser to probe the magnetic switching dynamics of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse. We observe that the combination of laser excitation and applied static magnetic field, 1 order of magnitude smaller than the coercive field, can overcome the magnetic anisotropy barrier between "up" and "down" magnetization, enabling magnetization switching. This magnetic switching is found to be inhomogeneous throughout the material with some individual FePt nanoparticles neither switching nor demagnetizing. The origin of this behavior is identified as the near-field modification of the incident laser radiation around FePt nanoparticles. The fraction of not-switching nanoparticles is influenced by the heat flow between FePt and a heat-sink layer.

Published
2017
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15. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin

Author

Gabriela Nass Kovacs, Yang Yang, Lutz Foucar, Tatiana Domratcheva, A. Gorel, Ramona Schlesinger, Ilme Schlichting, Robert L. Shoeman, C.M. Roome, Stefan Haacke, Marco Kloos, Jason E. Koglin, Marie Luise Grünbein, Jacques-Philippe Colletier, M. Stricker, Sébastien Boutet, Karsten Heyne, Sergio Carbajo, Till Stensitzki, D. Ehrenberg, Alexander Batyuk, Raphael Gasper, M. Hilpert, R.B. Doak, Jochen Reinstein, Thomas R. M. Barends, Joachim Heberle, Matthew Seaberg, Max-Planck-Institut für Medizinische Forschung, Max-Planck-Gesellschaft, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), SLAC National Accelerator Laboratory (SLAC), Stanford University, Max-Planck-Institut für Molekulare Physiologie, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE11-0018,X-in-vivo,Cristallisation in vivo: une nouvelle stratégie pour étudier la structure et la dynamique des protéines dans les lasers à électrons libres et les synchrotrons.(2017), Max Planck Institute for Medical Research [Heidelberg], Freie Universität Berlin, Linac Coherent Light Source (LCLS), Stanford University-Stanford University, Fachbereich Physik [Freie Univeristät Berlin] | Department of Physics [Freie Univeristät Berlin], Max Planck Institute of Molecular Physiology, Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Fachbereich Physik, Freie Universität Berlin, Fachbereich Physik [Berlin], Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), and Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique

Subjects
photon absorption, 0301 basic medicine, Science, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [SDV]Life Sciences [q-bio], FOS: Physical sciences, General Physics and Astronomy, 02 engineering and technology, Photochemistry, Quantum chemistry, Article, General Biochemistry, Genetics and Molecular Biology, quantum chemistry, 03 medical and health sciences, chemistry.chemical_compound, Molecule, [CHIM]Chemical Sciences, Physics - Biological Physics, Spectroscopy, lcsh:Science, Photons, Multidisciplinary, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], bacteriorhodopsin, Nanocrystallography, Hydrogen bond, Biomolecules (q-bio.BM), Retinal, Bacteriorhodopsin, General Chemistry, 021001 nanoscience & nanotechnology, Photobiology, 3. Good health, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, 030104 developmental biology, chemistry, Quantitative Biology - Biomolecules, Biological Physics (physics.bio-ph), FOS: Biological sciences, Bacteriorhodopsins, Excited state, Picosecond, Retinaldehyde, biology.protein, lcsh:Q, 0210 nano-technology
Abstract

Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins., Bacteriorhodopsin (bR) is a light-driven proton pump. Here the authors combine time-resolved crystallography at a free-electron laser, ultrafast spectroscopy and quantum chemistry to study the structural changes following multiphoton photoexcitation of bR and find that they occur within 300 fs not only in the light-absorbing chromophore but also in the surrounding protein.

Published
2019
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16. Ultrafast Structural Dynamics along the β − γ Phase Transition Path in MnAs

Author

Mahmoud Eddrief, Carlo Spezzani, Hailong Wang, Roberto Alonso-Mori, Jialin Ma, L. N. Coelho, Lounès Lounis, Matthieu Chollet, Horia Popescu, Alessandra Ciavardini, Y. Zheng, Claire Laulhé, Enrico Allaria, Eugenio Ferrari, James M. Glownia, Franck Vidal, Jianhua Zhao, Matthew Seaberg, Maurizio Sacchi, Croissance et propriétés de systèmes hybrides en couches minces (INSP-E8), Institut des Nanosciences de Paris (INSP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Universidade de Brasilia [Brasília] (UnB), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique des Solides (LPS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Elettra Sincrotrone Trieste, Ecole Polytechnique Fédérale de Lausanne (EPFL), State Key Laboratory for Superlattices and Microstructures Institute of Semiconductors, Chinese Academy of Sciences, State Key Laboratory, State Key Laboratory for Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Chinese Academy of Sciences [Beijing] (CAS), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), and Stanford University-Stanford University

Subjects
Diffraction, Phase transition, Materials science, Condensed matter physics, Phonon, Phase (waves), General Physics and Astronomy, Physics::Optics, Epitaxy, 01 natural sciences, Condensed Matter::Materials Science, Distortion, 0103 physical sciences, Orthorhombic crystal system, Condensed Matter::Strongly Correlated Electrons, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, Softening
Abstract

International audience; We investigate the orthorhombic distortion and the structural dynamics of epitaxial MnAs layers on GaAs(001) using static and time-resolved x-ray diffraction. Laser-induced intensity oscillations of Bragg reflections allow us to identify the optical phonon associated with orthorhombic distortion and to follow its softening along the path towards an undistorted phase of hexagonal symmetry. The frequency of this mode falls in the THz range, in agreement with recent calculations. Incomplete softening suggests that the $\beta-\gamma$ transformation deviates from a purely second-order displacive transition.

Published
2019
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17. Editorial: Lasers in Accelerator Science and Secondary Emission Light Source Technology

Author

Sergio Carbajo, Arya Fallahi, Jerome Faure, Liang Jie Wong, SLAC National Accelerator Laboratory (SLAC), Stanford University, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Nanyang Technological University [Singapour], Linac Coherent Light Source (LCLS), and Stanford University-Stanford University

Subjects
Laser accelerated particles, X-ray emission, Free electron laser (FEL), Ultrafast optics, Secondary emission and photoemission, Non-linear optics, Materials Science (miscellaneous), Biophysics, General Physics and Astronomy, 02 engineering and technology, 01 natural sciences, law.invention, Optics, Light source, law, [PHYS.PHYS.PHYS-PLASM-PH]Physics [physics]/Physics [physics]/Plasma Physics [physics.plasm-ph], 0103 physical sciences, Physical and Theoretical Chemistry, 010306 general physics, Mathematical Physics, ComputingMilieux_MISCELLANEOUS, Physics, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], business.industry, Nonlinear optics, 021001 nanoscience & nanotechnology, Laser, lcsh:QC1-999, Secondary emission, 0210 nano-technology, business, lcsh:Physics
Abstract

Frontiers in Physics, 7, ISSN:2296-424X

Published
2019
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18. Observing Solvation Dynamics with Simultaneous Femtosecond X-ray Emission Spectroscopy and X-ray Scattering

Author

Klaus Braagaard Møller, Rafael Abela, Kasper S. Kjær, Mátyás Pápai, Villy Sundström, Uwe Bergmann, Sophie E. Canton, Tim Brandt van Driel, Pieter Glatzel, Asmus Ougaard Dohn, Martin Nielsen, Jens Uhlig, Diling Zhu, György Vankó, Kristoffer Haldrup, M. Cammarata, Roberto Alonso-Mori, Christian Bressler, Andreas Galler, Henrik T. Lemke, Zoltán Németh, David M. Fritz, Norbert Sas, Amélie Bordage, Tobias Harlang, Wojciech Gawelda, Technical University of Denmark [Lyngby] (DTU), European XFEL, Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland, Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Stanford Synchrotron Radiation Lightsource (SSRL SLAC), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Stanford University, European Synchrotron Radiation Facility (ESRF), Department of Chemistry, Department of Nuclear Chemistry [Budapest], Eötvös Loránd University (ELTE), and Lund University [Lund]

Subjects
[PHYS]Physics [physics], Physics, Quantitative Biology::Biomolecules, Scattering, Intermolecular force, Solvation, 02 engineering and technology, Chromophore, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Surfaces, Coatings and Films, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Nuclear magnetic resonance, Chemical physics, Intramolecular force, Femtosecond, Materials Chemistry, Emission spectrum, Physics::Chemical Physics, Physical and Theoretical Chemistry, 0210 nano-technology, Ultrashort pulse, ComputingMilieux_MISCELLANEOUS
Abstract

In liquid phase chemistry dynamic solute-solvent interactions often govern the path, ultimate outcome, and efficiency of chemical reactions. These steps involve many-body movements on subpicosecond time scales and thus ultrafast structural tools capable of capturing both intramolecular electronic and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3](2+), with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering patterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited solute. By simultaneous combination of both methods only, we can extract new information about the solvation dynamic processes unfolding during the first picosecond (ps). The measured bulk solvent density increase of 0.2% indicates a dramatic change of the solvation shell around each photoexcited solute, confirming previous ab initio molecular dynamics simulations. Structural changes in the aqueous solvent associated with density and temperature changes occur with ∼1 ps time constants, characteristic for structural dynamics in water. This slower time scale of the solvent response allows us to directly observe the structure of the excited solute molecules well before the solvent contributions become dominant.

Published
2016
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19. Ultrafast terahertz field control of electronic and structural interactions in vanadium dioxide

Author

Jaewoo Jeong, Stefano Bonetti, Daniel J. Higley, Roopali Kukreja, D. Sokaras, N. C. Brandt, Elsa Abreu, Mengkun Liu, Diling Zhu, John W. Freeland, Alexander H. Reid, Harold Y. Hwang, Emmanuelle Jal, Haidan Wen, Mariano Trigo, P. Granitzka, Hendrik Ohldag, Catherine Graves, Hermann A. Dürr, T. Chase, Jamal Berakdar, Roberto Alonso-Mori, Alexander X. Gray, Henrik T. Lemke, A. J. Sternbach, S. S. P. Parkin, Richard D. Averitt, Zhao Chen, M. C. Hoffmann, Keith A. Nelson, Dennis Nordlund, Tianhan Wang, Mahesh Govind Samant, T.-C. Weng, M. Chollet, N. P. Aetukuri, James M. Glownia, Y. Zhu, Department of Chemistry, Inha University - Incheon, Nanjing University (NJU), Center for High Pressure Science & Technology Advanced Research (HPSTAR), GKSS Research Center Geesthacht, Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), and Stanford University-Stanford University

Subjects
FOS: Physical sciences, Field (mathematics), 02 engineering and technology, Electronic structure, Space (mathematics), 01 natural sciences, Settore FIS/03 - Fisica della Materia, symbols.namesake, Condensed Matter - Strongly Correlated Electrons, 0103 physical sciences, Electronic, Optical and Magnetic Materials, Metal–insulator transition, 010306 general physics, ComputingMilieux_MISCELLANEOUS, Electronic, Optical and Magnetic Materials, Condensed Matter Physics, Condensed Matter::Quantum Gases, Physics, [PHYS]Physics [physics], Strongly Correlated Electrons (cond-mat.str-el), Degenerate energy levels, Fermi level, Fermion, 021001 nanoscience & nanotechnology, symbols, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Atomic physics, 0210 nano-technology, Group theory
Abstract

As a type of fermions without counterpart in high energy physics, triply degenerate fermions show exotic physical properties, which are represented by triply degenerate nodal points in topological semimetals. Here, based on the space group theory analysis, we propose a practical guidance for seeking a topological semimetal with triply degenerate nodal points located at a symmetric axis, which is applicable to both symmorphic and nonsymmorphic crystals. By using this guidance in combination with the first-principles electronic structure calculations, we predict a class of triply degenerate topological semimetals $R{\mathrm{Rh}}_{6}{\mathrm{Ge}}_{4}\phantom{\rule{4pt}{0ex}}(R=\text{Y},\text{La},\text{Lu})$. In these compounds, the triply degenerate nodal points are located at the $\mathrm{\ensuremath{\Gamma}}\text{\ensuremath{-}}A$ axis and not far from the Fermi level. Especially, ${\mathrm{LaRh}}_{6}{\mathrm{Ge}}_{4}$ has a pair of triply degenerate nodal points located at just $\ensuremath{\sim}3$ meV below the Fermi level. Considering the fact that the single crystals of $R{\mathrm{Rh}}_{6}{\mathrm{Ge}}_{4}$ have been synthesized experimentally, the $R{\mathrm{Rh}}_{6}{\mathrm{Ge}}_{4}$ class of compounds will be an appropriate platform for studying exotic physical properties of triply degenerate topological semimetals.

Published
2018
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20. Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography

Author

Martin J. Field, Jacqueline Ridard, Stefan Jakobs, Dominique Bourgeois, Giorgio Schirò, Martin Weik, Virgile Adam, C.M. Roome, Lutz Foucar, Jacques-Philippe Colletier, R. Bruce Doak, M. Hilpert, Franck Fieschi, Karol Nass, Andrew Aquila, Martin Byrdin, Thomas R. M. Barends, Thomas J. Lane, Joyce Woodhouse, Michel Sliwa, Mengning Liang, Virginia Guillon, Isabelle Demachy, Eugenio de la Mora, Bernard I. Levy, Robert L. Shoeman, Mark S. Hunter, Sébastien Boutet, Marco Cammarata, Nicolas Coquelle, Jason E. Koglin, Sergio Carbajo, Matthew Seaberg, Ilme Schlichting, Michel Thépaut, Mikolaj Feliks, Gabriela Kovacsova, Joseph Robinson, Cyril Ruckebusch, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, Department of NanoBiophotonics [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Medizinische Forschung, ANR-15-CE32-0004,BioXFEL,Caractérisation d'états intermédiaires de protéines fluorescentes en utilisant des lasers à électrons libres X et les spectroscopies UV-visible et infrarouge ultra-rapides(2015), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), European Project: 317079,EC:FP7:PEOPLE,FP7-PEOPLE-2012-ITN,NANOMEM(2013), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, General Chemical Engineering, Quantum yield, General Chemistry, Chromophore, Laser, law.invention, 03 medical and health sciences, Molecular dynamics, Crystallography, 030104 developmental biology, law, Picosecond, Excited state, Femtosecond, Physics::Chemical Physics, Ultrashort pulse
Abstract

International audience; Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

Published
2018
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21. Femtosecond electron-phonon lock-in by photoemission and x-ray free-electron laser

Author

Gerber, S., Yang, S., Zhu, D., Soifer, H., Sobota, J., Rebec, S., Lee, J., Jia, T., Moritz, B., Jia, C., Gauthier, A., Li, Y., Leuenberger, D., Zhang, Y., Laura Chaix, Li, W., Jang, H., Yi, M., Dakovski, L., Song, S., Glownia, J., Nelson, S., Kim, W., Chuang, D., Hussain, Z., Moore, G., Devereaux, T., S Lee, W., Kirchmann, S., X Shen, Z., Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, International Center for Quantum Materials, Peking University, Stanford Synchrotron Radiation Lightsource (SSRL SLAC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Physics, Chungbuk National University, and Advanced Light Source [LBNL Berkeley] (ALS)

Subjects
[PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

22. Ultrafast evolution and transient phases of a prototype out-of-equilibrium Mott-Hubbard material

Author

Lantz, G., Mansart, B., Grieger, D., Boschetto, D., Nilforoushan, N., Papalazarou, E., Moisan, N., Perfetti, L., Jacques, V. L. R., Le Bolloc'h, D., Laulhé, C., Ravy, S., Rueff, J-P, Glover, T. E., Hertlein, M. P., Hussain, Z., Song, S., Chollet, M., Fabrizio, M., Marsi, M., Laboratoire de Physique des Solides (LPS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institute for Quantum Electronics, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Advanced Light Source [LBNL Berkeley] (ALS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-11-EQPX-0005,ATTOLAB,Plateforme pour la dynamique attoseconde(2011), European Project: 280555,EC:FP7:NMP,FP7-NMP-2011-SMALL-5,GO FAST(2012), European Project: 692670,H2020,ERC-2015-AdG,FIRSTORM(2016), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)

Subjects
Materials science, Phonon, Science, General Physics and Astronomy, 02 engineering and technology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, VIBRATIONS, Settore FIS/03 - Fisica della Materia, Condensed Matter::Materials Science, VO2, CR-DOPED V2O3, 0103 physical sciences, Physics::Chemical Physics, 010306 general physics, Phase diagram, [PHYS]Physics [physics], Multidisciplinary, Condensed matter physics, General Chemistry, 021001 nanoscience & nanotechnology, STATE, TRANSITION, TIME, SPIN, Photoexcitation, Picosecond, Femtosecond, Strongly correlated material, Condensed Matter::Strongly Correlated Electrons, Atomic physics, 0210 nano-technology, Ultrashort pulse, Excitation
Abstract

The study of photoexcited strongly correlated materials is attracting growing interest since their rich phase diagram often translates into an equally rich out-of-equilibrium behaviour. With femtosecond optical pulses, electronic and lattice degrees of freedom can be transiently decoupled, giving the opportunity of stabilizing new states inaccessible by quasi-adiabatic pathways. Here we show that the prototype Mott–Hubbard material V2O3 presents a transient non-thermal phase developing immediately after ultrafast photoexcitation and lasting few picoseconds. For both the insulating and the metallic phase, the formation of the transient configuration is triggered by the excitation of electrons into the bonding a1g orbital, and is then stabilized by a lattice distortion characterized by a hardening of the A1g coherent phonon, in stark contrast with the softening observed upon heating. Our results show the importance of selective electron–lattice interplay for the ultrafast control of material parameters, and are relevant for the optical manipulation of strongly correlated systems., Nature Communications, 8, ISSN:2041-1723

Published
2017
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23. Indirect excitation of ultrafast demagnetization

Author

Boris Vodungbo, Emmanuelle Jal, Jan Lüning, Sebastian Carron, Alexander H. Reid, Gregory Malinowski, Stefan Moeller, Bastian Pfau, Nicolas Jaouen, Patrick W. Granitzka, Michael Schneider, Christian Gutt, Philippe Zeitoun, Gerhard Grübel, Jonathan Perron, Julien Gautier, Clemens von Korff Schmising, Leonard Müller, Ankush Mitra, Christian Weier, Georgi L. Dakovski, M. H. Berntsen, Bharati Tudu, Guillaume Lambert, Michael P. Minitti, Renaud Delaunay, Stefan Eisebitt, Hard Condensed Matter (WZI, IoP, FNWI), Laboratoire de Chimie Physique - Matière et Rayonnement (LCPMR), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Deutsches Elektronen-Synchrotron [Hamburg] (DESY), Institut Jean Lamour (IJL), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Laboratoire d'optique appliquée (LOA), École Nationale Supérieure de Techniques Avancées (ENSTA Paris)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Universität Siegen [Siegen], Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, University of Amsterdam Van der Waals-Zeeman Institute (VAN DER WAALS-ZEEMAN INSTITUTE), University of Amsterdam [Amsterdam] (UvA), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Lund University [Lund], Institut fur Optik und Atomare Physik, Technische Universität Berlin (TU), IMPACT N4S, ANR-15-IDEX-0004,LUE,Isite LUE(2015), and Université de Lorraine (UL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Materials science, Physics::Optics, 02 engineering and technology, 01 natural sciences, Molecular physics, Article, Optical pumping, Condensed Matter::Materials Science, Magnetization, Condensed Matter::Superconductivity, 0103 physical sciences, Physics::Atomic and Molecular Clusters, ddc:530, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, Magnetization dynamics, Multidisciplinary, Demagnetizing field, 021001 nanoscience & nanotechnology, Corrigenda, Ferromagnetism, Excited state, ddc:000, 0210 nano-technology, Ultrashort pulse, Excitation
Abstract

International audience; Does the excitation of ultrafast magnetization require direct interaction between the photons of the optical pump pulse and the magnetic layer? Here, we demonstrate unambiguously that this is not the case. For this we have studied the magnetization dynamics of a ferromagnetic cobalt/palladium multilayer capped by an IR-opaque aluminum layer. Upon excitation with an intense femtosecond-short IR laser pulse, the film exhibits the classical ultrafast demagnetization phenomenon although only a negligible number of IR photons penetrate the aluminum layer. In comparison with an uncapped cobalt/ palladium reference film, the initial demagnetization of the capped film occurs with a delayed onset and at a slower rate. Both observations are qualitatively in line with energy transport from the aluminum layer into the underlying magnetic film by the excited, hot electrons of the aluminum film. Our data thus confirm recent theoretical predictions. Ultrafast demagnetization is a very intriguing phenomenon. The existence and origin of this rapid loss of a thin film's magnetization on the femtosecond timescale has been controversially debated ever since its discovery in 1996 1. Recently, it has been proposed that the origin of this magnetization loss could be due to spin-dependent motion of the optically excited hot valence electrons causing a spatial redistribution of the magnetization, either to an adjacent metallic layer 2,3 or within the magnetic layer itself 4. Strong experimental evidence for this so-called superdiffusive spin transport has been found lately 5-8. However, the experiment of Eschenlohr and co-workers 8 , similar to our study reported here, has been challenged recently. Khorsand and co-workers 9 showed that the Au cap layer employed in that experiment does not yield the postulated, and for the interpretation of the data crucial, attenuation of the incident IR pump pulse. Implementing a truly IR-opaque capping layer, we evade the limitation affecting the interpretation of the results of Eschenlohr and co-workers 8. Proper characterization of the number of photons reaching the magnetic layer demonstrates that the transmitted intensity is by orders of magnitude too small to excite the ultrafast demagnet-ization process.

Published
2016
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24. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Author

Christoph Bostedt, Marc Messerschmidt, Anton Barty, M. Marvin Seibert, Christina Y. Hampton, Henry N. Chapman, Jakob Andreasson, N. Duane Loh, Michael J. Bogan, Sebastian Schorb, Dusko Odic, Holger Fleckenstein, Nicola Coppola, Benjamin Erk, Bianca Iwan, Robert L. Shoeman, Meng Liang, Georg Weidenspointner, Stephan Kassemeyer, Raymond G. Sierra, Christian Reich, Tomas Ekeberg, Lars Gumprecht, Günter Hauser, Ilme Schlichting, Faton Krasniqi, Janos Hajdu, Carlo Schmidt, Filipe R. N. C. Maia, Sascha W. Epp, Olof Jönsson, Lothar Strüder, Miriam Barthelmess, Inger Andersson, Andrew V. Martin, Benedikt Rudek, Cornelia B. Wunderer, Nils Kimmel, Martin Svenda, Saša Bajt, John D. Bozek, Virginie Seltzer, Lukas Lomb, Heike Soltau, Daniel Rolles, Matthias Frank, Chantal Abergel, Helmut Hirsemann, Heinz Graafsma, Jacek Krzywinski, Daniel P. DePonte, Daniel Westphal, Joachim Ullrich, Peter Holl, Robert Hartmann, Andreas Hartmann, Artem Rudenko, Andrew Aquila, Jean-Michel Claverie, Lutz Foucar, Department of Cell and Molecular Biology [Uppsala], Uppsala University, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Centre for Quantum Engineering and Space-time Research (QUEST), Leibniz Universität Hannover=Leibniz University Hannover, Department of Molecular Biology, Swedish University of Agricultural Sciences (SLU), Lawrence Livermore National Laboratory (LLNL), Brain imaging (LIAMA), Laboratoire Franco-Chinois d'Informatique, d'Automatique et de Mathématiques Appliquées (LIAMA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Chinese Academy of Sciences [Changchun Branch] (CAS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institute of Automation - Chinese Academy of Sciences-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Chinese Academy of Sciences [Changchun Branch] (CAS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institute of Automation - Chinese Academy of Sciences-Centre National de la Recherche Scientifique (CNRS), University of Oxford, Public Medicine Infectious Diseases Section, SUN, Argonne National Laboratory [Lemont] (ANL), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Stanford University, National Science Foundation [Arlington] (NSF), Max Planck Institute for Medical Research [Heidelberg], Max-Planck-Gesellschaft, Deutsches Elektronen-Synchrotron [Hamburg] (DESY), Kansas State University, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre d'étude spatiale des rayonnements (CESR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Department of Biomolecular Mechanisms, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Institut für Kernphysik (MPIK), Space Sciences Laboratory [Berkeley] (SSL), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany, Department of Cell and Molecular Biology [Sweden] (DCMB), Uppsala University-Medical Nobel Institute, Linac Coherent Light Source, SLAC - National Accelerator Laboratory, Leibniz Universität Hannover [Hannover] (LUH), University of Oxford [Oxford], Stanford Linear Accelerator Center (SLAC), Stanford University [Stanford], Centre de Référence National 'Syndrome Gilles de la Tourette', Pôle des Maladies du Système Nerveux, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley], University of California-University of California, Institute of Automation - Chinese Academy of Sciences-Institut National de Recherche en Informatique et en Automatique (Inria)-Chinese Academy of Sciences [Changchun Branch] (CAS)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institute of Automation - Chinese Academy of Sciences-Institut National de Recherche en Informatique et en Automatique (Inria)-Chinese Academy of Sciences [Changchun Branch] (CAS)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées

Subjects
0301 basic medicine, Data Descriptor, Computer science, Image Processing, 02 engineering and technology, Bioinformatics, law.invention, Imaging, Scattering, Computer-Assisted, Theoretical, X-Ray Diffraction, law, Models, Crystallography, Radiation, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Data Collection, 3D reconstruction, Free-electron laser, Virus structures, 021001 nanoscience & nanotechnology, Computer Science Applications, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Benchmark (computing), Biomedical Imaging, Statistics, Probability and Uncertainty, 0210 nano-technology, Mimiviridae, Algorithms, Information Systems, Statistics and Probability, Atom and Molecular Physics and Optics, Image processing, Electrons, Library and Information Sciences, Education, 03 medical and health sciences, Optics, Imaging, Three-Dimensional, X-rays, Medical imaging, Computer Simulation, ddc:610, Particle Size, Mimivirus, business.industry, X-Rays, Lasers, Laser, biology.organism_classification, 030104 developmental biology, Three-Dimensional, X-Ray, Atom- och molekylfysik och optik, business, Biological physics
Abstract

Scientific data 3, 160060 (2016). doi:10.1038/sdata.2016.60, Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms., Published by Nature Publ. Group, London

Published
2016
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25. Observing heme doming in myoglobin with femtosecond X-ray absorption spectroscopy

Author

Matteo Levantino, Antonio Cupane, M. Glownia, Marco Cammarata, Henrik T. Lemke, Giorgio Schirò, Department of Physics - University of Palermo, Università degli studi di Palermo - University of Palermo, SLAC National Accelerator Laboratory (SLAC), Stanford University, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Portions of this research were carried out at the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory. LCLS is an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Stanford University. M.C. acknowledges the PEPS project 'SASLELX' of the CNRS and the University of Rennes 1 for financial support. M.L. acknowledges the financial support of the University of Palermo (FFR program 2012/2013 and CoRI program 2013)., Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Levantino, M, Lemke, HT., Schirò, G, Glownia, M, Cupane, A, and Cammarata, M

Subjects
Photodissociation, Absorption spectroscopy, Time resolved spectroscopy, Invited Articles, Photochemistry, SPECIAL TOPIC: BIOLOGY WITH X-RAY LASERS 2, chemistry.chemical_compound, X-ray absorption spectra, lcsh:QD901-999, X-ray absorption near edge structure, Spectroscopy, Instrumentation, Heme, [PHYS]Physics [physics], Radiation, X-ray optics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Relaxation (NMR), Chromophore, Condensed Matter Physics, Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin), Myoglobin, Biofisica, Dinamica delle proteine, Spettroscopia risolta in tempo, X-ray free-electron laser, Assorbimento di raggi X, lcsh:Crystallography, Time-resolved spectroscopy
Abstract

International audience; We report time-resolved X-ray absorption measurements after photolysis of carbonmonoxy myoglobin performed at the LCLS X-ray free electron laser with nearly 100 fs (FWHM) time resolution. Data at the Fe K-edge reveal that the photoinduced structural changes at the heme occur in two steps, with a faster (∼70 fs) relaxation preceding a slower (∼400 fs) one. We tentatively attribute the first relaxation to a structural rearrangement induced by photolysis involving essentially only the heme chromophore and the second relaxation to a residual Fe motion out of the heme plane that is coupled to the displacement of myoglobin F-helix

Published
2015
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26. Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser

Author

N. Duane Loh, M. Marvin Seibert, Mengning Liang, Martin Svenda, Nils Kimmel, Daniel P. DePonte, Jean-Michel Claverie, John D. Bozek, Bianca Iwan, Filipe R. N. C. Maia, Tomas Ekeberg, Robert Hartmann, Ken R. Ferguson, Artem Rudenko, Olof Jönsson, Virginie Seltzer, Inger Andersson, Daniel Rolles, Chantal Abergel, Andrew V. Martin, Christoph Bostedt, Gijs van der Schot, Jacek Krzywinski, Anton Barty, Max F. Hantke, Carl Nettelblad, Henry N. Chapman, Janos Hajdu, Sascha W. Epp, Department of Cell and Molecular Biology [Uppsala], Uppsala University, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Lawrence Livermore National Laboratory (LLNL), Centre for Quantum Engineering and Space-time Research (QUEST), Leibniz Universität Hannover=Leibniz University Hannover, Department of Molecular Biology, Swedish University of Agricultural Sciences (SLU), University of Oxford, DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany, Argonne National Laboratory [Lemont] (ANL), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Stanford University, Deutsches Elektronen-Synchrotron [Hamburg] (DESY), Kansas State University, Leibniz Universität Hannover [Hannover] (LUH), and University of Oxford [Oxford]

Subjects
Diffraction, Mimivirus, Materials science, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], business.industry, Free-electron laser, Biophysics, General Physics and Astronomy, Nanotechnology, Electron, biology.organism_classification, Laser, Biofysik, law.invention, symbols.namesake, Fourier transform, Optics, law, ddc:550, symbols, Particle, business, Compress Algorithm
Abstract

International audience; We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.

Published
2015
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27. Sequential Activation of Molecular Breathing and Bending during Spin-Crossover Photoswitching Revealed by Femtosecond Optical and X-Ray Absorption Spectroscopy

Author

Maciej Lorenc, Claire Laulhé, Matthieu Chollet, Eric Collet, Hervé Cailleau, Marco Cammarata, Sylvain Ravy, Jean-François Létard, Samir F. Matar, Henrik T. Lemke, Roman Bertoni, Sergio Di Matteo, Cindy Mauriac, Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Université de Bordeaux (UB), SLAC National Accelerator Laboratory (SLAC), Stanford University, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France, Rennes Métropole, Région Bretagne (CREATE 4146), Centre National de la Recherche Scientifique (CNRS) (PEPS SASLELX), and Fonds Européen de Développement Régional (FEDER).Portions of this research were carried out at the Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory. LCLS is an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Stanford University., ANR-13-BS04-0002,FEMTOMAT,Etude femtoseconde rayons X et optique de la dynamique ultrarapide de photocommutation de matériaux moléculaires magnétiques(2013), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), and Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
X-ray absorption spectroscopy, Materials science, Photoswitch, business.industry, General Physics and Astronomy, 02 engineering and technology, Bending, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Molecular physics, 0104 chemical sciences, Optics, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], Spin crossover, Potential energy surface, Femtosecond, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], [CHIM.COOR]Chemical Sciences/Coordination chemistry, 0210 nano-technology, Spectroscopy, business, Absorption (electromagnetic radiation)
Abstract

International audience; We study the basic mechanisms allowing light to photoswitch at molecular scale a spin-crossover material from low-to high-spin state. Combined femtosecond x-ray absorption performed at LCLS X-FEL and optical spectroscopy reveal that the structural stabilization of the photoinduced HS state results from a two step structural trapping. Molecular breathing vibrations are first activated and rapidly damped as part of the energy is sequentially transferred to molecular bending vibrations. During the photoswitching, the system follows a curved trajectory on the potential energy surface.

Published
2014
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28. Activation of coherent lattice phonon following ultrafast molecular spin-state photo-switching: A molecule-to-lattice energy transfer

Author

Eric Collet, Marco Cammarata, Jean-François Létard, Matthieu Chollet, Andrea Marino, James M. Glownia, Henrik T. Lemke, Guillaume Chastanet, Samir F. Matar, Institut de Physique de Rennes (IPR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Université de Bordeaux (UB), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, ANR-13-BS04-0002,FEMTOMAT,Etude femtoseconde rayons X et optique de la dynamique ultrarapide de photocommutation de matériaux moléculaires magnétiques(2013), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), and Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Spin states, Phonon, Invited Articles, 010402 general chemistry, SPECIAL TOPIC: SELECTED PAPERS FROM THE 3RD INTERNATIONAL CONFERENCE ON ULTRAFAST STRUCTURAL DYNAMICS, 01 natural sciences, Molecular solid, 0103 physical sciences, lcsh:QD901-999, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Physics::Chemical Physics, 010306 general physics, Coherent spectroscopy, Spectroscopy, Instrumentation, [PHYS]Physics [physics], Lattice energy, Radiation, Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, Condensed Matter Physics, 0104 chemical sciences, Molecular vibration, Excited state, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], lcsh:Crystallography, Atomic physics
Abstract

International audience; We combine ultrafast optical spectroscopy with femtosecond X-ray absorption to study the photo-switching dynamics of the [Fe(PM-AzA)2(NCS)2] spin-crossover molecular solid. The light-induced excited spin-state trapping process switches the molecules from low spin to high spin (HS) states on the sub-picosecond timescale. The change of the electronic state (

Published
2016
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29. Femtosecond X-ray magnetic circular dichroism absorption spectroscopy at an X-ray free electron laser

Author

Giacomo Coslovich, Padraic Shafer, Matthias C. Hoffmann, L. Le Guyader, Peter Denes, Patrick W. Granitzka, Emmanuelle Jal, Tianmin Liu, Zhao Chen, Edwin Yuan, Hermann A. Dürr, Heinz-Dieter Nuhn, William F. Schlotter, John Joseph, Matthew Seaberg, Elke Arenholz, Arata Tsukamoto, Georgi L. Dakovski, Ankush Mitra, Alexander H. Reid, Hendrik Ohldag, Alberto Lutman, Daniel J. Higley, K. Hirsch, Joachim Stöhr, Philip Hart, James P. MacArthur, Stefan Moeller, Hard Condensed Matter (WZI, IoP, FNWI), IoP (FNWI), Quantum Matter and Quantum Information, Other Research IHEF (IoP, FNWI), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Advanced Light Source [LBNL Berkeley] (ALS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Fudan University [Shanghai], Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory and Stanford University, and Stanford University

Subjects
Materials science, Absorption spectroscopy, Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, Physics::Optics, 02 engineering and technology, 01 natural sciences, Molecular physics, Magnetization, 0103 physical sciences, ddc:530, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 010306 general physics, Spectroscopy, Instrumentation, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], Condensed Matter - Materials Science, Magnetic circular dichroism, Demagnetizing field, Free-electron laser, Materials Science (cond-mat.mtrl-sci), 021001 nanoscience & nanotechnology, 3. Good health, X-ray magnetic circular dichroism, Femtosecond, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], 0210 nano-technology
Abstract

X-ray magnetic circular dichroism spectroscopy using an X-ray free electron laser is demonstrated with spectra over the Fe L$_{3,2}$-edges. This new ultrafast time-resolved capability is then applied to a fluence-dependent study of all-optical magnetic switching dynamics of Fe and Gd magnetic sublattices in a GdFeCo thin film above its magnetization compensation temperature. At the magnetic switching fuence, we corroborate the existence of a transient ferromagnetic-like state. The timescales of the dynamics, however, are longer than previously observed below the magnetization compensation temperature. Above and below the switching fluence range, we observe secondary demagnetization with about 5 ps timescales. This indicates that the spin thermalization takes longer than 5 ps., 5 pages, 4 figures

Published
2016
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30. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam.

Author

Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN Jr, Pollack L, and Schmidt M

Subjects
Humans, Ligands, Sulbactam pharmacology, beta-Lactamases, Mycobacterium tuberculosis, Tuberculosis
Abstract

For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction., (© 2023. Springer Nature Limited.)

Published
2023
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31. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme.

Author

Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, and Ros A

Subjects
Humans, Crystallography, X-Ray, Injections, NAD(P)H Dehydrogenase (Quinone), Proteins chemistry, Lasers
Abstract

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

Published
2023
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32. Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement.

Author

Adam V, Hadjidemetriou K, Jensen N, Shoeman RL, Woodhouse J, Aquila A, Banneville AS, Barends TRM, Bezchastnov V, Boutet S, Byrdin M, Cammarata M, Carbajo S, Eleni Christou N, Coquelle N, De la Mora E, El Khatib M, Moreno Chicano T, Bruce Doak R, Fieschi F, Foucar L, Glushonkov O, Gorel A, Grünbein ML, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Liang M, Mantovanelli A, Nass K, Nass Kovacs G, Owada S, Roome CM, Schirò G, Seaberg M, Stricker M, Thépaut M, Tono K, Ueda K, Uriarte LM, You D, Zala N, Domratcheva T, Jakobs S, Sliwa M, Schlichting I, Colletier JP, Bourgeois D, and Weik M

Subjects
Green Fluorescent Proteins, Luminescent Proteins chemistry, Escherichia coli metabolism, Microscopy
Abstract

Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications., (© 2022 The Authors. ChemPhysChem published by Wiley-VCH GmbH.)

Published
2022
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33. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography.

Author

Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, and Ros A

Abstract

With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time., Competing Interests: A.E.G., J.C.V., and A.R. hold a patent on electrical droplet stimulation in a 3D-printed device., (© 2022 The Authors.)

Published
2022
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34. Anisotropic Surface Broadening and Core Depletion during the Evolution of a Strong-Field Induced Nanoplasma.

Author

Bacellar C, Chatterley AS, Lackner F, Pemmaraju CD, Tanyag RMP, Verma D, Bernando C, O'Connell SMO, Bucher M, Ferguson KR, Gorkhover T, Coffee RN, Coslovich G, Ray D, Osipov T, Neumark DM, Bostedt C, Vilesov AF, and Gessner O

Abstract

Strong-field ionization of nanoscale clusters provides excellent opportunities to study the complex correlated electronic and nuclear dynamics of near-solid density plasmas. Yet, monitoring ultrafast, nanoscopic dynamics in real-time is challenging, which often complicates a direct comparison between theory and experiment. Here, near-infrared laser-induced plasma dynamics in ∼600  nm diameter helium droplets are studied by femtosecond time-resolved x-ray coherent diffractive imaging. An anisotropic, ∼20  nm wide surface region, defined as the range where the density lies between 10% and 90% of the core value, is established within ∼100  fs, in qualitative agreement with theoretical predictions. At longer timescales, however, the width of this region remains largely constant while the radius of the dense plasma core shrinks at average rates of ≈71  nm/ps along and ≈33  nm/ps perpendicular to the laser polarization. These dynamics are not captured by previous plasma expansion models. The observations are phenomenologically described within a numerical simulation; details of the underlying physics, however, remain to be explored.

Published
2022
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35. Mechanism and dynamics of fatty acid photodecarboxylase.

Author

Sorigué D, Hadjidemetriou K, Blangy S, Gotthard G, Bonvalet A, Coquelle N, Samire P, Aleksandrov A, Antonucci L, Benachir A, Boutet S, Byrdin M, Cammarata M, Carbajo S, Cuiné S, Doak RB, Foucar L, Gorel A, Grünbein M, Hartmann E, Hienerwadel R, Hilpert M, Kloos M, Lane TJ, Légeret B, Legrand P, Li-Beisson Y, Moulin SLY, Nurizzo D, Peltier G, Schirò G, Shoeman RL, Sliwa M, Solinas X, Zhuang B, Barends TRM, Colletier JP, Joffre M, Royant A, Berthomieu C, Weik M, Domratcheva T, Brettel K, Vos MH, Schlichting I, Arnoux P, Müller P, and Beisson F

Subjects
Algal Proteins chemistry, Algal Proteins metabolism, Alkanes metabolism, Amino Acid Substitution, Amino Acids metabolism, Bicarbonates metabolism, Biocatalysis, Carbon Dioxide metabolism, Catalytic Domain, Crystallography, X-Ray, Decarboxylation, Electron Transport, Flavin-Adenine Dinucleotide chemistry, Hydrogen Bonding, Light, Models, Molecular, Mutant Proteins chemistry, Mutant Proteins metabolism, Oxidation-Reduction, Photons, Protein Conformation, Temperature, Carboxy-Lyases chemistry, Carboxy-Lyases metabolism, Chlorella enzymology, Fatty Acids metabolism
Abstract

Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Published
2021
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36. Time-resolved RIXS experiment with pulse-by-pulse parallel readout data collection using X-ray free electron laser.

Author

Lu H, Gauthier A, Hepting M, Tremsin AS, Reid AH, Kirchmann PS, Shen ZX, Devereaux TP, Shao YC, Feng X, Coslovich G, Hussain Z, Dakovski GL, Chuang YD, and Lee WS

Abstract

Time-resolved resonant inelastic X-ray scattering (RIXS) is one of the developing techniques enabled by the advent of X-ray free electron laser (FEL). It is important to evaluate how the FEL jitter, which is inherent in the self-amplified spontaneous emission process, influences the RIXS measurement. Here, we use a microchannel plate (MCP) based Timepix soft X-ray detector to conduct a time-resolved RIXS measurement at the Ti L 3 -edge on a charge-density-wave material TiSe 2 . The fast parallel Timepix readout and single photon sensitivity enable pulse-by-pulse data acquisition and analysis. Due to the FEL jitter, low detection efficiency of spectrometer, and low quantum yield of RIXS process, we find that less than 2% of the X-ray FEL pulses produce signals, preventing acquiring sufficient data statistics while maintaining temporal and energy resolution in this measurement. These limitations can be mitigated by using future X-ray FELs with high repetition rates, approaching MHz such as the European XFEL in Germany and LCLS-II in the USA, as well as by utilizing advanced detectors, such as the prototype used in this study.

Published
2020
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37. Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses.

Author

Kayser Y, Milne C, Juranić P, Sala L, Czapla-Masztafiak J, Follath R, Kavčič M, Knopp G, Rehanek J, Błachucki W, Delcey MG, Lundberg M, Tyrała K, Zhu D, Alonso-Mori R, Abela R, Sá J, and Szlachetko J

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.

Published
2019
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38. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.

Author

Nass Kovacs G, Colletier JP, Grünbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, and Schlichting I

Subjects
Crystallography, Isomerism, Light, Photons, Protein Conformation, Spectrum Analysis, Water chemistry, Bacteriorhodopsins chemistry, Halobacterium salinarum metabolism, Retinaldehyde chemistry
Abstract

Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.

Published
2019
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39. Identification of Phase Transitions and Metastability in Dynamically Compressed Antimony Using Ultrafast X-Ray Diffraction.

Author

Coleman AL, Gorman MG, Briggs R, McWilliams RS, McGonegle D, Bolme CA, Gleason AE, Fratanduono DE, Smith RF, Galtier E, Lee HJ, Nagler B, Granados E, Collins GW, Eggert JH, Wark JS, and McMahon MI

Abstract

Ultrafast x-ray diffraction at the LCLS x-ray free electron laser has been used to resolve the structural behavior of antimony under shock compression to 59 GPa. Antimony is seen to transform to the incommensurate, host-guest phase Sb-II at ∼11  GPa, which forms on nanosecond timescales with ordered guest-atom chains. The high-pressure bcc phase Sb-III is observed above ∼15  GPa, some 8 GPa lower than in static compression studies, and mixed Sb-III/liquid diffraction are obtained between 38 and 59 GPa. An additional phase which does not exist under static compression, Sb-I^{'}, is also observed between 8 and 12 GPa, beyond the normal stability field of Sb-I, and resembles Sb-I with a resolved Peierls distortion. The incommensurate Sb-II high-pressure phase can be recovered metastably on release to ambient pressure, where it is stable for more than 10 ns.

Published
2019
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40. Ultrafast Structural Dynamics along the β-γ Phase Transition Path in MnAs.

Author

Vidal F, Zheng Y, Lounis L, Coelho L, Laulhé C, Spezzani C, Ciavardini A, Popescu H, Ferrari E, Allaria E, Ma J, Wang H, Zhao J, Chollet M, Seaberg M, Alonso-Mori R, Glownia JM, Eddrief M, and Sacchi M

Abstract

We investigate the orthorhombic distortion and the structural dynamics of epitaxial MnAs layers on GaAs(001) using static and time-resolved x-ray diffraction. Laser-induced intensity oscillations of Bragg reflections allow us to identify the optical phonon associated with orthorhombic distortion and to follow its softening along the path towards an undistorted phase of hexagonal symmetry. The frequency of this mode falls in the THz range, in agreement with recent calculations. Incomplete softening suggests that the β-γ transformation deviates from a purely second-order displacive transition.

Published
2019
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41. The ultrafast Einstein-de Haas effect.

Author

Dornes C, Acremann Y, Savoini M, Kubli M, Neugebauer MJ, Abreu E, Huber L, Lantz G, Vaz CAF, Lemke H, Bothschafter EM, Porer M, Esposito V, Rettig L, Buzzi M, Alberca A, Windsor YW, Beaud P, Staub U, Zhu D, Song S, Glownia JM, and Johnson SL

Abstract

The Einstein-de Haas effect was originally observed in a landmark experiment 1 demonstrating that the angular momentum associated with aligned electron spins in a ferromagnet can be converted to mechanical angular momentum by reversing the direction of magnetization using an external magnetic field. A related problem concerns the timescale of this angular momentum transfer. Experiments have established that intense photoexcitation in several metallic ferromagnets leads to a drop in magnetization on a timescale shorter than 100 femtoseconds-a phenomenon called ultrafast demagnetization 2-4 . Although the microscopic mechanism for this process has been hotly debated, the key question of where the angular momentum goes on these femtosecond timescales remains unanswered. Here we use femtosecond time-resolved X-ray diffraction to show that most of the angular momentum lost from the spin system upon laser-induced demagnetization of ferromagnetic iron is transferred to the lattice on sub-picosecond timescales, launching a transverse strain wave that propagates from the surface into the bulk. By fitting a simple model of the X-ray data to simulations and optical data, we estimate that the angular momentum transfer occurs on a timescale of 200 femtoseconds and corresponds to 80 per cent of the angular momentum that is lost from the spin system. Our results show that interaction with the lattice has an essential role in the process of ultrafast demagnetization in this system.

Published
2019
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42. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.

Author

Nogly P, Weinert T, James D, Carbajo S, Ozerov D, Furrer A, Gashi D, Borin V, Skopintsev P, Jaeger K, Nass K, Båth P, Bosman R, Koglin J, Seaberg M, Lane T, Kekilli D, Brünle S, Tanaka T, Wu W, Milne C, White T, Barty A, Weierstall U, Panneels V, Nango E, Iwata S, Hunter M, Schapiro I, Schertler G, Neutze R, and Standfuss J

Subjects
Aspartic Acid chemistry, Ion Transport, Isomerism, Protein Conformation, Schiff Bases chemistry, Time Factors, Water chemistry, X-Rays, Bacteriorhodopsins chemistry, Bacteriorhodopsins radiation effects, Retinaldehyde chemistry, Retinaldehyde radiation effects
Abstract

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Published
2018
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43. Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals.

Author

Awel S, Kirian RA, Wiedorn MO, Beyerlein KR, Roth N, Horke DA, Oberthür D, Knoska J, Mariani V, Morgan A, Adriano L, Tolstikova A, Xavier PL, Yefanov O, Aquila A, Barty A, Roy-Chowdhury S, Hunter MS, James D, Robinson JS, Weierstall U, Rode AV, Bajt S, Küpper J, and Chapman HN

Abstract

High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.

Published
2018
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44. Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography.

Author

Coquelle N, Sliwa M, Woodhouse J, Schirò G, Adam V, Aquila A, Barends TRM, Boutet S, Byrdin M, Carbajo S, De la Mora E, Doak RB, Feliks M, Fieschi F, Foucar L, Guillon V, Hilpert M, Hunter MS, Jakobs S, Koglin JE, Kovacsova G, Lane TJ, Lévy B, Liang M, Nass K, Ridard J, Robinson JS, Roome CM, Ruckebusch C, Seaberg M, Thepaut M, Cammarata M, Demachy I, Field M, Shoeman RL, Bourgeois D, Colletier JP, Schlichting I, and Weik M

Abstract

Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

Published
2018
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45. Femtosecond electron-phonon lock-in by photoemission and x-ray free-electron laser.

Author

Gerber S, Yang SL, Zhu D, Soifer H, Sobota JA, Rebec S, Lee JJ, Jia T, Moritz B, Jia C, Gauthier A, Li Y, Leuenberger D, Zhang Y, Chaix L, Li W, Jang H, Lee JS, Yi M, Dakovski GL, Song S, Glownia JM, Nelson S, Kim KW, Chuang YD, Hussain Z, Moore RG, Devereaux TP, Lee WS, Kirchmann PS, and Shen ZX

Abstract

The interactions that lead to the emergence of superconductivity in iron-based materials remain a subject of debate. It has been suggested that electron-electron correlations enhance electron-phonon coupling in iron selenide (FeSe) and related pnictides, but direct experimental verification has been lacking. Here we show that the electron-phonon coupling strength in FeSe can be quantified by combining two time-domain experiments into a "coherent lock-in" measurement in the terahertz regime. X-ray diffraction tracks the light-induced femtosecond coherent lattice motion at a single phonon frequency, and photoemission monitors the subsequent coherent changes in the electronic band structure. Comparison with theory reveals a strong enhancement of the coupling strength in FeSe owing to correlation effects. Given that the electron-phonon coupling affects superconductivity exponentially, this enhancement highlights the importance of the cooperative interplay between electron-electron and electron-phonon interactions., (Copyright © 2017, American Association for the Advancement of Science.)

Published
2017
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46. Structure of the full-length glucagon class B G-protein-coupled receptor.

Author

Zhang H, Qiao A, Yang D, Yang L, Dai A, de Graaf C, Reedtz-Runge S, Dharmarajan V, Zhang H, Han GW, Grant TD, Sierra RG, Weierstall U, Nelson G, Liu W, Wu Y, Ma L, Cai X, Lin G, Wu X, Geng Z, Dong Y, Song G, Griffin PR, Lau J, Cherezov V, Yang H, Hanson MA, Stevens RC, Zhao Q, Jiang H, Wang MW, and Wu B

Subjects
Allosteric Site drug effects, Benzamides chemistry, Benzamides metabolism, Benzamides pharmacology, Cell Membrane metabolism, Cross-Linking Reagents chemistry, Crystallography, X-Ray, Deuterium Exchange Measurement, Disulfides chemistry, Humans, Ligands, Models, Molecular, Molecular Dynamics Simulation, Phenylurea Compounds chemistry, Phenylurea Compounds metabolism, Phenylurea Compounds pharmacology, Protein Domains, Protein Stability, Receptors, Glucagon agonists, Receptors, Glucagon metabolism, Receptors, Glucagon chemistry, Receptors, Glucagon classification
Abstract

The human glucagon receptor, GCGR, belongs to the class B G-protein-coupled receptor family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both the extracellular domain and transmembrane domain in an inactive conformation. The two domains are connected by a 12-residue segment termed the stalk, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of the GCGR transmembrane domain. The first extracellular loop exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen-deuterium exchange, disulfide crosslinking and molecular dynamics studies suggest that the stalk and the first extracellular loop have critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding of the signalling mechanisms of class B G-protein-coupled receptors.

Published
2017
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47. Femtosecond response of polyatomic molecules to ultra-intense hard X-rays.

Author

Rudenko A, Inhester L, Hanasaki K, Li X, Robatjazi SJ, Erk B, Boll R, Toyota K, Hao Y, Vendrell O, Bomme C, Savelyev E, Rudek B, Foucar L, Southworth SH, Lehmann CS, Kraessig B, Marchenko T, Simon M, Ueda K, Ferguson KR, Bucher M, Gorkhover T, Carron S, Alonso-Mori R, Koglin JE, Correa J, Williams GJ, Boutet S, Young L, Bostedt C, Son SK, Santra R, and Rolles D

Subjects
Iodine chemistry, Kinetics, Photons, Protein Conformation, Static Electricity, Time Factors, Crystallography methods, Electrons, Lasers, Proteins chemistry, X-Rays
Abstract

X-ray free-electron lasers enable the investigation of the structure and dynamics of diverse systems, including atoms, molecules, nanocrystals and single bioparticles, under extreme conditions. Many imaging applications that target biological systems and complex materials use hard X-ray pulses with extremely high peak intensities (exceeding 10 20 watts per square centimetre). However, fundamental investigations have focused mainly on the individual response of atoms and small molecules using soft X-rays with much lower intensities. Studies with intense X-ray pulses have shown that irradiated atoms reach a very high degree of ionization, owing to multiphoton absorption, which in a heteronuclear molecular system occurs predominantly locally on a heavy atom (provided that the absorption cross-section of the heavy atom is considerably larger than those of its neighbours) and is followed by efficient redistribution of the induced charge. In serial femtosecond crystallography of biological objects-an application of X-ray free-electron lasers that greatly enhances our ability to determine protein structure-the ionization of heavy atoms increases the local radiation damage that is seen in the diffraction patterns of these objects and has been suggested as a way of phasing the diffraction data. On the basis of experiments using either soft or less-intense hard X-rays, it is thought that the induced charge and associated radiation damage of atoms in polyatomic molecules can be inferred from the charge that is induced in an isolated atom under otherwise comparable irradiation conditions. Here we show that the femtosecond response of small polyatomic molecules that contain one heavy atom to ultra-intense (with intensities approaching 10 20 watts per square centimetre), hard (with photon energies of 8.3 kiloelectronvolts) X-ray pulses is qualitatively different: our experimental and modelling results establish that, under these conditions, the ionization of a molecule is considerably enhanced compared to that of an individual heavy atom with the same absorption cross-section. This enhancement is driven by ultrafast charge transfer within the molecule, which refills the core holes that are created in the heavy atom, providing further targets for inner-shell ionization and resulting in the emission of more than 50 electrons during the X-ray pulse. Our results demonstrate that efficient modelling of X-ray-driven processes in complex systems at ultrahigh intensities is feasible.

Published
2017
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48. Diffraction data of core-shell nanoparticles from an X-ray free electron laser.

Author

Li X, Chiu CY, Wang HJ, Kassemeyer S, Botha S, Shoeman RL, Lawrence RM, Kupitz C, Kirian R, James D, Wang D, Nelson G, Messerschmidt M, Boutet S, Williams GJ, Hartmann E, Jafarpour A, Foucar LM, Barty A, Chapman H, Liang M, Menzel A, Wang F, Basu S, Fromme R, Doak RB, Fromme P, Weierstall U, Huang MH, Spence JC, Schlichting I, Hogue BG, and Liu H

Abstract

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.

Published
2017
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49. Multiple Supersonic Phase Fronts Launched at a Complex-Oxide Heterointerface.

Author

Först M, Beyerlein KR, Mankowsky R, Hu W, Mattoni G, Catalano S, Gibert M, Yefanov O, Clark JN, Frano A, Glownia JM, Chollet M, Lemke H, Moser B, Collins SP, Dhesi SS, Caviglia AD, Triscone JM, and Cavalleri A

Abstract

Selective optical excitation of a substrate lattice can drive phase changes across heterointerfaces. This phenomenon is a nonequilibrium analogue of static strain control in heterostructures and may lead to new applications in optically controlled phase change devices. Here, we make use of time-resolved nonresonant and resonant x-ray diffraction to clarify the underlying physics and to separate different microscopic degrees of freedom in space and time. We measure the dynamics of the lattice and that of the charge disproportionation in NdNiO_{3}, when an insulator-metal transition is driven by coherent lattice distortions in the LaAlO_{3} substrate. We find that charge redistribution propagates at supersonic speeds from the interface into the NdNiO_{3} film, followed by a sonic lattice wave. When combined with measurements of magnetic disordering and of the metal-insulator transition, these results establish a hierarchy of events for ultrafast control at complex-oxide heterointerfaces.

Published
2017
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50. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.

Author

Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Båth P, Dods R, Harimoorthy R, Beyerlein KR, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams GJ, Hunter MS, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman HN, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, and Standfuss J

Subjects
Crystallography, X-Ray instrumentation, Feasibility Studies, Protein Conformation, Synchrotrons, Time Factors, Viscosity, X-Ray Absorption Spectroscopy instrumentation, X-Ray Absorption Spectroscopy methods, Bacteriorhodopsins chemistry, Crystallography, X-Ray methods, Lasers, Lipids chemistry
Abstract

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

Published
2016
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