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  • 1. Aquila, A.
    et al.
    Barty, A.
    Bostedt, C.
    Boutet, S.
    Carini, G.
    dePonte, D.
    Drell, P.
    Doniach, S.
    Downing, K. H.
    Earnest, T.
    Elmlund, H.
    Elser, V.
    Gühr, M.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hastings, J.
    Hau-Riege, S. P.
    Huang, Z.
    Lattman, E. E.
    Maia, F. R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S.
    Ourmazd, A.
    Pellegrini, C.
    Santra, R.
    Schlichting, I.
    Schroer, C.
    Spence, J. C. H.
    Vartanyants, I. A.
    Wakatsuki, S.
    Weis, W. I.
    Williams, G. J.
    The linac coherent light source single particle imaging road map2015In: Structural Dynamics, E-ISSN 2329-7778, Vol. 2, no 4, article id 041701Article in journal (Refereed)
    Abstract [en]

    Intense femtosecond x-ray pulses from free-electron laser sources allow the imag-ing of individual particles in a single shot. Early experiments at the Linac CoherentLight Source (LCLS) have led to rapid progress in the field and, so far, coherentdiffractive images have been recorded from biological specimens, aerosols, andquantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLSheld a workshop to discuss the scientific and technical challenges for reaching theultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap towardreaching atomic resolution, 3D imaging at free-electron laser sources.

  • 2.
    Bengtsson, A. U. J.
    et al.
    Lund Univ, Dept Phys, POB 118, SE-22100 Lund, Sweden..
    Ekström, J. C.
    Lund Univ, Dept Phys, POB 118, SE-22100 Lund, Sweden..
    Wang, Xiaocui
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, FREIA. Lund Univ, Dept Phys, POB 118, SE-22100 Lund, Sweden.
    Jurgilaitis, A.
    Lund Univ, MAX IV Lab, POB 118, SE-22100 Lund, Sweden..
    Pham, Van-Thai
    Lund Univ, MAX IV Lab, POB 118, SE-22100 Lund, Sweden..
    Kroon, D.
    Lund Univ, MAX IV Lab, POB 118, SE-22100 Lund, Sweden..
    Larsson, J.
    Lund Univ, Dept Phys, POB 118, SE-22100 Lund, Sweden.;Lund Univ, MAX IV Lab, POB 118, SE-22100 Lund, Sweden..
    Repetitive non-thermal melting as a timing monitor for femtosecond pump/probe X-ray experiments2020In: Structural Dynamics, E-ISSN 2329-7778, Vol. 7, no 5, article id 054303Article in journal (Refereed)
    Abstract [en]

    Time-resolved optical pump/X-ray probe experiments are often used to study structural dynamics. To ensure high temporal resolution, it is necessary to monitor the timing between the X-ray pulses and the laser pulses. The transition from a crystalline solid material to a disordered state in a non-thermal melting process can be used as a reliable timing monitor. We have performed a study of the non-thermal melting of InSb in single-shot mode, where we varied the sample temperature in order to determine the conditions required for repetitive melting. We show how experimental conditions affect the feasibility of such a timing tool.

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  • 3.
    Bielecki, Johan
    et al.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.;La Trobe Univ, La Trobe Inst Mol Sci, Dept Chem & Phys, Melbourne, Vic 3086, Australia..
    Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources2020In: Structural Dynamics, E-ISSN 2329-7778, Vol. 7, no 4, article id 040901Article in journal (Refereed)
    Abstract [en]

    X-ray free electron lasers (XFELs) now routinely produce millijoule level pulses of x-ray photons with tens of femtoseconds duration. Such x-ray intensities gave rise to the idea that weakly scattering particles-perhaps single biomolecules or viruses-could be investigated free of radiation damage. Here, we examine elements from the past decade of so-called single particle imaging with hard XFELs. We look at the progress made to date and identify some future possible directions for the field. In particular, we summarize the presently achieved resolutions as well as identifying the bottlenecks and enabling technologies to future resolution improvement, which in turn enables application to samples of scientific interest.

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  • 4.
    Blachucki, W.
    et al.
    Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Kayser, Y.
    Phys Tech Bundesanstalt, D-10587 Berlin, Germany.
    Czapla-Masztafiak, J.
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Juranic, P.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Kavcic, M.
    Jozef Stefan Inst, SI-1000 Ljubljana, Slovenia.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Knopp, G.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Milne, C.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Rehanek, J.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Sá, Jacinto
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Szlachetko, J.
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Inception of electronic damage of matter by photon-driven post-ionization mechanisms2019In: Structural Dynamics, E-ISSN 2329-7778, Vol. 6, no 2, article id 024901Article in journal (Refereed)
    Abstract [en]

    "Probe-before-destroy" methodology permitted diffraction and imaging measurements of intact specimens using ultrabright but highly destructive X-ray free-electron laser (XFEL) pulses. The methodology takes advantage of XFEL pulses ultrashort duration to outrun the destructive nature of the X-rays. Atomic movement, generally on the order of >50 fs, regulates the maximum pulse duration for intact specimen measurements. In this contribution, we report the electronic structure damage of a molecule with ultrashort X-ray pulses under preservation of the atoms' positions. A detailed investigation of the X-ray induced processes revealed that X-ray absorption events in the solvent produce a significant number of solvated electrons within attosecond and femtosecond timescales that are capable of coulombic interactions with the probed molecules. The presented findings show a strong influence on the experimental spectra coming from ionization of the probed atoms' surroundings leading to electronic structure modification much faster than direct absorption of photons. This work calls for consideration of this phenomenon in cases focused on samples embedded in, e.g., solutions or in matrices, which in fact concerns most of the experimental studies.

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  • 5.
    Engel, Robin Y.
    et al.
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany.;Univ Hamburg, Dept Phys, Hamburg, Germany..
    Alexander, Oliver
    Imperial Coll London, Dept Phys, London, England..
    Atak, Kaan
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany..
    Bovensiepen, Uwe
    Univ Duisburg Essen, Fac Phys, Duisburg, Germany.;Univ Duisburg Essen, Ctr Nanointegrat Duisburg Essen CENIDE, Duisburg, Germany.;Univ Tokyo, Inst Solid State Phys, Kashiwa, Chiba 2778581, Japan..
    Buck, Jens
    Deutsch Elektronen Synchrotron DESY, Ruprecht Haensel Lab, Hamburg, Germany.;Christian Albrechts Univ Kiel, Inst Experimentelle & Angew Phys, Kiel, Germany..
    Carley, Robert
    European XFEL, Schenefeld, Germany..
    Cascella, Michele
    Lund Univ, MAX Lab 4, Lund, Sweden..
    Chardonnet, Valentin
    Sorbonne Univ, CNRS, Lab Chim Phys Matiere & Rayonnement LCPMR, Paris, France..
    Chiuzbaian, Gheorghe Sorin
    Sorbonne Univ, CNRS, Lab Chim Phys Matiere & Rayonnement LCPMR, Paris, France..
    David, Christian
    Paul Scherrer Inst, Villigen, Switzerland. Univ Utrecht, Debye Inst Nanomat Sci Inorgan Chem & Catalysis, Utrecht, Netherlands..
    Doring, Florian
    Paul Scherrer Inst, Villigen, Switzerland. Univ Utrecht, Debye Inst Nanomat Sci Inorgan Chem & Catalysis, Utrecht, Netherlands..
    Eschenlohr, Andrea
    Univ Duisburg Essen, Fac Phys, Duisburg, Germany.;Univ Duisburg Essen, Ctr Nanointegrat Duisburg Essen CENIDE, Duisburg, Germany..
    Gerasimova, Natalia
    European XFEL, Schenefeld, Germany..
    de Groot, Frank
    Le Guyader, Loic
    Humphries, Oliver S.
    European XFEL, Schenefeld, Germany..
    Izquierdo, Manuel
    European XFEL, Schenefeld, Germany..
    Jal, Emmanuelle
    Sorbonne Univ, CNRS, Lab Chim Phys Matiere & Rayonnement LCPMR, Paris, France..
    Kubec, Adam
    Paul Scherrer Inst, Villigen, Switzerland. Univ Utrecht, Debye Inst Nanomat Sci Inorgan Chem & Catalysis, Utrecht, Netherlands..
    Laarmann, Tim
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany.;Hamburg Ctr Ultrafast Imaging CUI, Hamburg, Germany..
    Lambert, Charles-Henri
    Swiss Fed Inst Technol, Dept Mat, Zurich, Switzerland..
    Luening, Jan
    Helmholtz Zentrum Berlin Materialien & Energie Gmb, Berlin, Germany..
    Marangos, Jonathan P.
    Imperial Coll London, Dept Phys, London, England..
    Mercadier, Laurent
    European XFEL, Schenefeld, Germany..
    Mercurio, Giuseppe
    European XFEL, Schenefeld, Germany..
    Miedema, Piter S.
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany..
    Ollefs, Katharina
    Univ Duisburg Essen, Fac Phys, Duisburg, Germany.;Univ Duisburg Essen, Ctr Nanointegrat Duisburg Essen CENIDE, Duisburg, Germany..
    Pfau, Bastian
    Max Born Inst Nonlinear Opt & Short Pulse Spect, Berlin, Germany..
    Rosner, Benedikt
    Paul Scherrer Inst, Villigen, Switzerland. Univ Utrecht, Debye Inst Nanomat Sci Inorgan Chem & Catalysis, Utrecht, Netherlands..
    Rossnagel, Kai
    Deutsch Elektronen Synchrotron DESY, Ruprecht Haensel Lab, Hamburg, Germany.;Christian Albrechts Univ Kiel, Inst Experimentelle & Angew Phys, Kiel, Germany..
    Rothenbach, Nico
    Univ Duisburg Essen, Fac Phys, Duisburg, Germany.;Univ Duisburg Essen, Ctr Nanointegrat Duisburg Essen CENIDE, Duisburg, Germany..
    Scherz, Andreas
    European XFEL, Schenefeld, Germany..
    Schlappa, Justine
    European XFEL, Schenefeld, Germany..
    Scholz, Markus
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany..
    Schunck, Jan O.
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany.;Univ Hamburg, Dept Phys, Hamburg, Germany..
    Setoodehnia, Kiana
    European XFEL, Schenefeld, Germany..
    Stamm, Christian
    Swiss Fed Inst Technol, Dept Mat, Zurich, Switzerland.;Univ Appl Sci & Arts Northwestern Switzerland, Inst Elect Power Syst, Windisch, Switzerland..
    Techert, Simone
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany.;Gottingen Univ, Inst X Ray Phys, Gottingen, Germany..
    Vinko, Sam M.
    Univ Oxford, Dept Phys, Clarendon Lab, Oxford, England.;STFC Rutherford Appleton Lab, Cent Laser Facil, Didcot, England..
    Wende, Heiko
    Univ Duisburg Essen, Fac Phys, Duisburg, Germany.;Univ Duisburg Essen, Ctr Nanointegrat Duisburg Essen CENIDE, Duisburg, Germany..
    Yaroslavtsev, Alexander A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, FREIA.
    Yin, Zhong
    Tohoku Univ, Int Ctr Synchrotron Radiat Innovat Smart, Sendai, Japan.;Swiss Fed Inst Technol, Lab Phys Chem, Zurich, Switzerland..
    Beye, Martin
    Deutsch Elektronen Synchrotron DESY, Hamburg, Germany.;Univ Hamburg, Dept Phys, Hamburg, Germany..
    Electron population dynamics in resonant non-linear x-ray absorption in nickel at a free-electron laser2023In: Structural Dynamics, E-ISSN 2329-7778, Vol. 10, no 5, article id 054501Article in journal (Refereed)
    Abstract [en]

    Free-electron lasers provide bright, ultrashort, and monochromatic x-ray pulses, enabling novel spectroscopic measurements not only with femtosecond temporal resolution: The high fluence of their x-ray pulses can also easily enter the regime of the non-linear x-ray-matter interaction. Entering this regime necessitates a rigorous analysis and reliable prediction of the relevant non-linear processes for future experiment designs. Here, we show non-linear changes in the L-3-edge absorption of metallic nickel thin films, measured with fluences up to 60 J/cm(2). We present a simple but predictive rate model that quantitatively describes spectral changes based on the evolution of electronic populations within the pulse duration. Despite its simplicity, the model reaches good agreement with experimental results over more than three orders of magnitude in fluence, while providing a straightforward understanding of the interplay of physical processes driving the non-linear changes. Our findings provide important insights for the design and evaluation of future high-fluence free-electron laser experiments and contribute to the understanding of non-linear electron dynamics in x-ray absorption processes in solids at the femtosecond timescale.

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  • 6.
    Fransson, Thomas
    et al.
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, Stockholm, Sweden..
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Chatterjee, Ruchira
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Cheah, Mun Hon
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Ibrahim, Mohamed
    Humboldt Univ, Dept Biol, D-10099 Berlin, Germany..
    Hussein, Rana
    Humboldt Univ, Dept Biol, D-10099 Berlin, Germany..
    Zhang, Miao
    Humboldt Univ, Dept Biol, D-10099 Berlin, Germany..
    Fuller, Franklin
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Gul, Sheraz
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Kim, In-Sik
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Simon, Philipp S.
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Bogacz, Isabel
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Makita, Hiroki
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    de Lichtenberg, Casper
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Umeå Univ, Dept Chem, SE-90187 Umeå, Sweden.;Univ Copenhagen, Sect Biomol Sci, Dept Biol, DK-2200 Copenhagen N, Denmark..
    Song, Sanghoon
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Batyuk, Alexander
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Sokaras, Dimosthenis
    SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA..
    Massad, Ramzi
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Doyle, Margaret
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Britz, Alexander
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA..
    Weninger, Clemens
    Lund Univ, MAX Lab 4, Lund, Sweden..
    Zouni, Athina
    Humboldt Univ, Dept Biol, D-10099 Berlin, Germany..
    Messinger, Johannes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Umeå Univ, Dept Chem, SE-90187 Umeå, Sweden..
    Yachandra, Vittal K.
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Yano, Junko
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Kern, Jan
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Bergmann, Uwe
    Univ Wisconsin, Dept Phys, Madison, WI 53706 USA..
    Effects of x-ray free-electron laser pulse intensity on the Mn K beta(1,3) x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions2021In: Structural Dynamics, E-ISSN 2329-7778, Vol. 8, no 6, article id 064302Article in journal (Refereed)
    Abstract [en]

    In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and K beta x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the K beta XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn K beta(1,3) XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from & SIM;5 x 10(15) to 5 x 10(17) W/cm(2) at a pulse length of & SIM;35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.

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  • 7.
    Galli, L.
    et al.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-20355 Hamburg, Germany..
    Son, S. -K
    Klinge, M.
    Univ Hamburg, Inst Biochem & Mol Biol, Joint Lab Struct Biol Infect & Inflammat, D-22607 Hamburg, Germany.;Univ Lubeck, Inst Biochem, DESY, D-22607 Hamburg, Germany..
    Bajt, S.
    Deutsch Elektronen Synchrotron DESY, Photon Sci, D-22607 Hamburg, Germany..
    Barty, A.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Bean, R.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Betzel, C.
    Univ Hamburg, DESY, Inst Biochem & Mol Biol, Dept Chem, D-22607 Hamburg, Germany..
    Beyerlein, K. R.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Doak, R. B.
    Max Planck Inst Med Res, Dept Biomol Mech, D-69120 Heidelberg, Germany..
    Duszenko, M.
    Univ Tubingen, Interfac Inst Biochem, D-72076 Tubingen, Germany..
    Fleckenstein, H.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Gati, C.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Hunt, B.
    Brigham Young Univ, Dept Phys & Astron, Provo, UT 84602 USA..
    Kirian, R. A.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Liang, M.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Nanao, M. H.
    EMBL, Grenoble Outstn, F-38042 Grenoble, France..
    Nass, K.
    Max Planck Inst Med Res, Dept Biomol Mech, D-69120 Heidelberg, Germany..
    Oberthuer, D.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Redecke, L.
    Univ Hamburg, Inst Biochem & Mol Biol, Joint Lab Struct Biol Infect & Inflammat, D-22607 Hamburg, Germany.;Univ Lubeck, Inst Biochem, DESY, D-22607 Hamburg, Germany..
    Shoeman, R.
    Max Planck Inst Med Res, Dept Biomol Mech, D-69120 Heidelberg, Germany..
    Stellato, F.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Yoon, C. H.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.;European XFEL GmbH, D-22761 Hamburg, Germany..
    White, T. A.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Yefanov, O.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany..
    Spence, J.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Chapman, H. N.
    Deutsch Elektronen Synchrotron DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-20355 Hamburg, Germany.;Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany..
    Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse2015In: Structural Dynamics, E-ISSN 2329-7778, Vol. 2, no 4, article id 041703Article in journal (Refereed)
    Abstract [en]

    Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.

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  • 8.
    Josefsson, Ida
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Eriksson, Susanna Kaufmann
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Solvation structure around ruthenium(II) tris(bipyridine) in lithium halide solutions2016In: Structural Dynamics, E-ISSN 2329-7778, Vol. 3, no 2, article id 023607Article in journal (Refereed)
    Abstract [en]

    The solvation of the ruthenium(II) tris(bipyridine) ion ([Ru(bpy)(3)](2+)) is investigated with molecular dynamics simulations of lithium halide solutions in polar solvents. The anion distribution around the [Ru(bpy)(3)](2+) complex exhibits a strong solvent dependence. In aqueous solution, the iodide ion forms a solvent shared complex with [Ru(bpy)(3)](2+), but not in the other solvents. Between Cl- and [Ru(bpy)(3)](2+), the strong hydration of the chloride ion results in a solvent separated complex where more than one solvent molecule separates the anion from the metal center. Hence, tailored solvation properties in electrolytes is a route to influence ion-ion interactions and related electron transfer processes.

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  • 9.
    Khubbutdinov, Ruslan
    et al.
    DESY, Notkestr 85, D-22607 Hamburg, Germany.;Natl Res Nucl Univ MEPhI, Moscow Engn Phys Inst, Kashirskoe Shosse 31, Moscow 115409, Russia..
    Gerasimova, Natalia
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Mercurio, Giuseppe
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Assalauova, Dameli
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Carnis, Jerome
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Gelisio, Luca
    DESY, Ctr Free Electron Laser Sci, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Le Guyader, Loic
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Ignatenko, Alexandr
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Kim, Young Yong
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Van Kuiken, Benjamin E.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Kurta, Ruslan P.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Lapkin, Dmitry
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Teichmann, Martin
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Yaroslavtsev, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, FREIA. European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Gorobtsov, Oleg
    Cornell Univ, Dept Mat Sci & Engn, Ithaca, NY 14850 USA..
    Menushenkov, Alexey P.
    Natl Res Nucl Univ MEPhI, Moscow Engn Phys Inst, Kashirskoe Shosse 31, Moscow 115409, Russia..
    Scholz, Matthias
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Scherz, Andreas
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Vartanyants, Ivan A.
    DESY, Notkestr 85, D-22607 Hamburg, Germany.;Natl Res Nucl Univ MEPhI, Moscow Engn Phys Inst, Kashirskoe Shosse 31, Moscow 115409, Russia..
    High spatial coherence and short pulse duration revealed by the Hanbury Brown and Twiss interferometry at the European XFEL2021In: Structural Dynamics, E-ISSN 2329-7778, Vol. 8, no 4, article id 044305Article in journal (Refereed)
    Abstract [en]

    Second-order intensity interferometry was employed to study the spatial and temporal properties of the European X-ray Free-Electron Laser (EuXFEL). Measurements were performed at the soft x-ray Self-Amplified Spontaneous Emission (SASE3) undulator beamline at a photon energy of 1.2 keV in the Self-Amplified Spontaneous Emission (SASE) mode. Two high-power regimes of the SASE3 undulator settings, i.e., linear and quadratic undulator tapering at saturation, were studied in detail and compared with the linear gain regime. The statistical analysis showed an exceptionally high degree of spatial coherence up to 90% for the linear undulator tapering. Analysis of the measured data in spectral and spatial domains provided an average pulse duration of about 10 fs in our measurements. The obtained results will be valuable for the experiments requiring and exploiting short pulse duration and utilizing high coherence properties of the EuXFEL.

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  • 10.
    Kim, Seonmyeong
    et al.
    Seoul Natl Univ, Inst Appl Phys, Ctr THz Driven Biomed Syst, Dept Phys & Astron,Coll Nat Sci, Seoul, South Korea.;Adv Inst Convergence Technol, Ctr Appl Electromagnet Res, Suwon, South Korea..
    Sattorov, Matlabjon
    Seoul Natl Univ, Inst Appl Phys, Ctr THz Driven Biomed Syst, Dept Phys & Astron,Coll Nat Sci, Seoul, South Korea.;Adv Inst Convergence Technol, Ctr Appl Electromagnet Res, Suwon, South Korea..
    Hong, Dongpyo
    Adv Inst Convergence Technol, Ctr Appl Electromagnet Res, Suwon, South Korea..
    Kang, Heon
    Seoul Natl Univ, Res Inst Basic Sci, Dept Chem, 1 Gwanakro, Seoul 08826, South Korea..
    Park, Jaehun
    POSTECH, Pohang Accelerator Lab, Pohang 37673, South Korea..
    Lee, Jae Hyuk
    POSTECH, Pohang Accelerator Lab, Pohang 37673, South Korea.;POSTECH, Photon Sci Ctr, Pohang 37673, South Korea..
    Ma, Rory
    POSTECH, Pohang Accelerator Lab, Pohang 37673, South Korea..
    Martin, Andrew, V
    RMIT Univ, Coll STEM, Sch Sci, 124 La Trobe St, Melbourne, Vic 3000, Australia..
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Sellberg, Jonas A.
    KTH Royal Inst Technol, Dept Appl Phys, S-10691 Stockholm, Sweden..
    Datta, Prasanta Kumar
    Indian Inst Technol Kharagpur, Dept Phys, Kharagpur 721302, W Bengal, India..
    Park, Sang Yoon
    Adv Inst Convergence Technol, Ctr Appl Electromagnet Res, Suwon, South Korea..
    Park, Gun-Sik
    Seoul Natl Univ, Inst Appl Phys, Ctr THz Driven Biomed Syst, Dept Phys & Astron,Coll Nat Sci, Seoul, South Korea.;Adv Inst Convergence Technol, Ctr Appl Electromagnet Res, Suwon, South Korea..
    Observing ice structure of micron-sized vapor-deposited ice with an x-ray free-electron laser2023In: Structural Dynamics, E-ISSN 2329-7778, Vol. 10, no 4, article id 044302Article in journal (Refereed)
    Abstract [en]

    The direct observation of the structure of micrometer-sized vapor-deposited ice is performed at Pohang Accelerator Laboratory x-ray free electron laser (PAL-XFEL). The formation of micrometer-sized ice crystals and their structure is important in various fields, including atmospheric science, cryobiology, and astrophysics, but understanding the structure of micrometer-sized ice crystals remains challenging due to the lack of direct observation. Using intense x-ray diffraction from PAL-XFEL, we could observe the structure of micrometer-sized vapor-deposited ice below 150K with a thickness of 2-50 mu m grown in an ultrahigh vacuum chamber. The structure of the ice grown comprises cubic and hexagonal sequences that are randomly arranged to produce a stacking-disordered ice. We observed that ice with a high cubicity of more than 80% was transformed to partially oriented hexagonal ice when the thickness of the ice deposition grew beyond 5 mu m. This suggests that precise temperature control and clean deposition conditions allow mu m-thick ice films with high cubicity to be grown on hydrophilic Si3N4 membranes. The low influence of impurities could enable in situ diffraction experiments of ice nucleation and growth from interfacial layers to bulk ice.

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  • 11.
    Kubin, Markus
    et al.
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Kern, Jan
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA.;SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Gul, Sheraz
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Kroll, Thomas
    SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA..
    Chatterjee, Ruchira
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Loechel, Heike
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Nanometre Opt & Technol, D-12489 Berlin, Germany..
    Fuller, Franklin D.
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Sierra, Raymond G.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Quevedo, Wilson
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Weniger, Christian
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Rehanek, Jens
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Nanometre Opt & Technol, D-12489 Berlin, Germany.;Paul Scherrer Inst, CH-5232 Villigen, Switzerland..
    Firsov, Anatoly
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Nanometre Opt & Technol, D-12489 Berlin, Germany..
    Laksmono, Hartawan
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA..
    Weninger, Clemens
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA.;SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA..
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Nordlund, Dennis L.
    Lassalle-Kaiser, Benedikt
    Synchrotron SOLEIL, F-91191 Gif Sur Yvette, France..
    Glownia, James M.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Krzywinski, Jacek
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Moeller, Stefan
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Turner, Joshua J.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Minitti, Michael P.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Dakovski, Georgi L.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Koroidov, Sergey
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA.;Umea Univ, Inst Kemi, Kem Biol Ctr, SE-90187 Umea, Sweden..
    Kawde, Anurag
    Umea Univ, Inst Kemi, Kem Biol Ctr, SE-90187 Umea, Sweden..
    Kanady, Jacob S.
    CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA..
    Tsui, Emily Y.
    CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA..
    Suseno, Sandy
    CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA..
    Han, Zhiji
    CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA..
    Hill, Ethan
    Univ Calif Irvine, Dept Chem, 1102 Nat Sci 2, Irvine, CA 92697 USA..
    Taguchi, Taketo
    Univ Calif Irvine, Dept Chem, 1102 Nat Sci 2, Irvine, CA 92697 USA..
    Borovik, Andrew S.
    Univ Calif Irvine, Dept Chem, 1102 Nat Sci 2, Irvine, CA 92697 USA..
    Agapie, Theodor
    CALTECH, Div Chem & Chem Engn, Pasadena, CA 91125 USA..
    Messinger, Johannes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Umea Univ, Inst Kemi, Kem Biol Ctr, SE-90187 Umea, Sweden.;Uppsala Univ, Angstrom Lab, Mol Biomimet, Dept Chem, SE-75237 Uppsala, Sweden..
    Erko, Alexei
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Nanometre Opt & Technol, D-12489 Berlin, Germany..
    Foehlisch, Alexander
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany.;Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany..
    Bergmann, Uwe
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, Menlo Pk, CA 94025 USA..
    Mitzner, Rolf
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Yachandra, Vittal K.
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Yano, Junko
    Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA 94720 USA..
    Wernet, Philippe
    Helmholtz Zentrum Berlin Mat & Energie GmbH, Inst Methods & Instrumentat Synchrotron Radiat Re, D-12489 Berlin, Germany..
    Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers2017In: Structural Dynamics, E-ISSN 2329-7778, Vol. 4, no 5, article id 054307Article in journal (Refereed)
    Abstract [en]

    X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn similar to 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn4CaO5) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions. (C) 2017 Author(s).

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  • 12.
    Milne, Christopher J.
    et al.
    European XFEL, D-22761 Schenefeld, Germany.;Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland..
    Nagornova, Natalia
    Ecole Polytech Fed Lausanne, Lausanne Ctr Ultrafast Sci LACUS, ISIC, FSB, CH-1015 Lausanne, Switzerland..
    Pope, Thomas
    Newcastle Univ, Sch Nat & Environm Sci, Chem, Newcastle Upon Tyne NE1 7RU, England..
    Chen, Hui-Yuan
    Ecole Polytech Fed Lausanne, Lausanne Ctr Ultrafast Sci LACUS, ISIC, FSB, CH-1015 Lausanne, Switzerland..
    Rossi, Thomas
    Ecole Polytech Fed Lausanne, Lausanne Ctr Ultrafast Sci LACUS, ISIC, FSB, CH-1015 Lausanne, Switzerland..
    Szlachetko, Jakub
    Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland.;Adam Mickiewicz Univ, Fac Phys, Uniwersytetu Poznanskiego 2, PL-61614 Poznan, Poland..
    Gawelda, Wojciech
    European XFEL, D-22761 Schenefeld, Germany.;Adam Mickiewicz Univ, Fac Phys, Uniwersytetu Poznanskiego 2, PL-61614 Poznan, Poland.;IMDEA Nanosci Inst, Calle Faraday 9,Campus Cantoblanco, Madrid 28049, Spain.;Univ Autonoma Madrid, Dept Quim, Campus Cantoblanco, Madrid 28047, Spain..
    Britz, Alexander
    European XFEL, D-22761 Schenefeld, Germany.;Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    van Driel, Tim B.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Sala, Leonardo
    Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland..
    Ebner, Simon
    Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland..
    Katayama, Tetsuo
    Japan Synchrotron Radiat Res Inst JASRI, Kouto 1-1-1, Sayo, Hyogo 6795198, Japan.;RIKEN, SPring Ctr 8, Kouto 1-1-1, Sayo, Hyogo 6795148, Japan..
    Southworth, Stephen H.
    Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA..
    Doumy, Gilles
    Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA..
    March, Anne Marie
    Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA..
    Lehmann, C. Stefan
    Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA.;Adv Res Ctr Nanolithog ARCNL, Sci Pk 106, NL-1098 XG Amsterdam, Netherlands..
    Mucke, Melanie
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Iablonskyi, Denys
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai 9808577, Japan..
    Kumagai, Yoshiaki
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai 9808577, Japan..
    Knopp, Gregor
    Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland..
    Motomura, Koji
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai 9808577, Japan..
    Togashi, Tadashi
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Owada, Shigeki
    RIKEN, SPring Ctr 8, Kouto 1-1-1, Sayo, Hyogo 6795148, Japan..
    Yabashi, Makina
    RIKEN, SPring Ctr 8, Kouto 1-1-1, Sayo, Hyogo 6795148, Japan..
    Nielsen, Martin M.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark..
    Pajek, Marek
    Adam Mickiewicz Univ, Fac Phys, Uniwersytetu Poznanskiego 2, PL-61614 Poznan, Poland..
    Ueda, Kiyoshi
    RIKEN, SPring Ctr 8, Kouto 1-1-1, Sayo, Hyogo 6795148, Japan.;Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai 9808577, Japan..
    Abela, Rafael
    Paul Scherrer Inst, SwissFEL, CH-5232 Villigen, Switzerland..
    Penfold, Thomas J.
    Newcastle Univ, Sch Nat & Environm Sci, Chem, Newcastle Upon Tyne NE1 7RU, England..
    Chergui, Majed
    Ecole Polytech Fed Lausanne, Lausanne Ctr Ultrafast Sci LACUS, ISIC, FSB, CH-1015 Lausanne, Switzerland..
    Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles2023In: Structural Dynamics, E-ISSN 2329-7778, Vol. 10, no 6, article id 064501Article in journal (Refereed)
    Abstract [en]

    The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton formation occur in <500 fs, in excellent agreement with theoretical predictions. The x-ray absorption measurements, obtained upon excitation close to the band edge at 3.49 eV, are sensitive to the migration and trapping of holes. They reveal that the 2 ps transient largely reproduces the previously reported transient obtained at 100 ps time delay in synchrotron studies. In addition, the x-ray absorption signal is found to rise in similar to 1.4 ps, which we attribute to the diffusion of holes through the lattice prior to their trapping at singly charged oxygen vacancies. Indeed, the MD simulations show that impulsive trapping of holes induces an ultrafast expansion of the cage of Zn atoms in <200 fs, followed by an oscillatory response at a frequency of similar to 100 cm-1, which corresponds to a phonon mode of the system involving the Zn sub-lattice.

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  • 13.
    Norell, Jesper
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Nantes, CNRS, Lab CEISAM, UMR 6230, F-44300 Nantes, France.
    Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways2020In: Structural Dynamics, E-ISSN 2329-7778, Vol. 7, no 2, article id 024101Article in journal (Refereed)
    Abstract [en]

    Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S-2(pi,pi*) state is found to promptly relax to S-1(n, pi*) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both complex population transfers among all the available states and intersystem crossing predominantly through the "El-Sayed forbidden" S-1(n, pi*) to T-2(n, pi*) channel, through significant mixing of electronic excitation characters. Despite this complexity, the femto- to picosecond triplet population, expected from several spectroscopic measurements, is well described as a simple exponential decay of the singlet state manifold. No proton transfer is found in the reported trajectories, but two mechanisms for its possible mediation in previously reported experiments are proposed based on the observed structural dynamics: (i) ultrafast intra-molecular transfer driven by the initially coherent in-plane motion and (ii) inter-molecular solvent-mediated transfer driven by the out-of-plane modes that dominate the later motion.

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  • 14.
    Szöke, Abraham
    et al.
    Lawrence Livermore Natl Lab, Livermore, CA 94551 USA.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Energy utilization in fluctuating biological energy converters2016In: Structural Dynamics, E-ISSN 2329-7778, Vol. 3, no 3, article id 034701Article in journal (Refereed)
    Abstract [en]

    We have argued previously [Szoke et al., FEBS Lett. 553, 18-20 (2003); Curr. Chem. Biol. 1, 53-57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systems fluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems.

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  • 15.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Nantes, Lab CEISAM, UMR CNRS 6230, F-44300 Nantes, France..
    Kunnus, Kristjan
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA.;Univ Tartu, Inst Phys, W Ostwaldi 1, EE-50411 Tartu, Estonia..
    Delcey, Mickael G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Gaffney, Kelly J.
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA..
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Origin of core-to-core x-ray emission spectroscopy sensitivity to structural dynamics2020In: Structural Dynamics, E-ISSN 2329-7778, Vol. 7, no 4, article id 044102Article in journal (Refereed)
    Abstract [en]

    Recently, coherent structural dynamics in the excited state of an iron photosensitizer was observed through oscillations in the intensity of K alpha x-ray emission spectroscopy (XES). Understanding the origin of the unexpected sensitivity of core-to-core transitions to structural dynamics is important for further development of femtosecond time-resolved XES methods and, we believe, generally necessary for interpretation of XES signals from highly non-equilibrium structures that are ubiquitous in photophysics and photochemistry. Here, we use multiconfigurational wavefunction calculations combined with atomic theory to analyze the emission process in detail. The sensitivity of core-to-core transitions to structural dynamics is due to a shift of the minimum energy metal-ligand bond distance between 1s and 2p core-hole states. A key effect is the additional contraction of the non-bonding 3s and 3p orbitals in 1s core-hole states, which decreases electron-electron repulsion and increases overlap in the metal-ligand bonds. The effect is believed to be general and especially pronounced for systems with strong bonds. The important role of 3s and 3p orbitals is consistent with the analysis of radial charge and spin densities and can be connected to the negative chemical shift observed for many transition metal complexes. The XES sensitivity to structural dynamics can be optimized by tuning the emission energy spectrometer, with oscillations up to +/- 4% of the maximum intensity for the current system. The theoretical predictions can be used to design experiments that separate electronic and nuclear degrees of freedom in ultrafast excited state dynamics.

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  • 16.
    Watson, Luke
    et al.
    Newcastle Univ, Sch Nat & Environm Sci, Chem, Newcastle Upon Tyne NE1 7RU, England..
    Pope, Thomas
    Newcastle Univ, Sch Nat & Environm Sci, Chem, Newcastle Upon Tyne NE1 7RU, England..
    Jay, Raphael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Banerjee, Ambar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Penfold, Thomas J.
    Newcastle Univ, Sch Nat & Environm Sci, Chem, Newcastle Upon Tyne NE1 7RU, England..
    A Δ”-learning strategy for interpretation of spectroscopic observables2023In: Structural Dynamics, E-ISSN 2329-7778, Vol. 10, no 6, article id 064101Article in journal (Refereed)
    Abstract [en]

    Accurate computations of experimental observables are essential for interpreting the high information content held within x-ray spectra. However, for complicated systems this can be difficult, a challenge compounded when dynamics becomes important owing to the large number of calculations required to capture the time-evolving observable. While machine learning architectures have been shown to represent a promising approach for rapidly predicting spectral lineshapes, achieving simultaneously accurate and sufficiently comprehensive training data is challenging. Herein, we introduce Delta-learning for x-ray spectroscopy. Instead of directly learning the structure-spectrum relationship, the Delta-model learns the structure dependent difference between a higher and lower level of theory. Consequently, once developed these models can be used to translate spectral shapes obtained from lower levels of theory to mimic those corresponding to higher levels of theory. Ultimately, this achieves accurate simulations with a much reduced computational burden as only the lower level of theory is computed, while the model can instantaneously transform this to a spectrum equivalent to a higher level of theory. Our present model, demonstrated herein, learns the difference between TDDFT(BLYP) and TDDFT(B3LYP) spectra. Its effectiveness is illustrated using simulations of Rh L-3-edge spectra tracking the C-H activation of octane by a cyclopentadienyl rhodium carbonyl complex.

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  • 17.
    Yefanov, Oleksandr
    et al.
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Oberthuer, Dominik
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Bean, Richard
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Wiedorn, Max O.
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luru Chaussee 149, D-22761 Hamburg, Germany.
    Knoska, Juraj
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Pena, Gisel
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Awel, Salah
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Gumprecht, Lars
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Domaracky, Martin
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Sarrou, Iosifina
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Xavier, P. Lourdu
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Metz, Markus
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Bajt, Sasa
    Deutsch Elekt Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Mariani, Valerio
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Gevorkov, Yaroslav
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Hamburg Univ Technol, Inst Vis Syst, Vis Syst E-2,Harburger Schlossstr 20, D-21079 Hamburg, Germany.
    White, Thomas A.
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Tolstikova, Aleksandra
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Villanueva-Perez, Pablo
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Seuring, Carolin
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Aplin, Steve
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Estillore, Armando D.
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Küpper, Jochen
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luru Chaussee 149, D-22761 Hamburg, Germany;Univ Hamburg, Dept Phys, Luru Chaussee 149, D-22761 Hamburg, Germany.
    Klyuev, Alexander
    Deutsch Elekt Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Kuhn, Manuela
    Deutsch Elekt Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Laurus, Torsten
    Deutsch Elekt Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Graafsma, Heinz
    Deutsch Elekt Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Monteiro, Diana C. F.
    Univ Hamburg, Ctr Ultrafast Imaging, Luru Chaussee 149, D-22761 Hamburg, Germany;Univ Hamburg, Dept Phys, Luru Chaussee 149, D-22761 Hamburg, Germany.
    Trebbin, Martin
    Univ Buffalo, Dept Chem, 359 Nat Sci Complex, Buffalo, NY 14260 USA;Hauptman Woodward Med Res Inst, 700 Ellicott St, Buffalo, NY 14203 USA.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Lawrence Berkeley Natl Lab, NERSC, Berkeley, CA 94720 USA.
    Cruz-Mazo, Francisco
    Univ Seville, ETSI, Dept Ingn Aeroespacial & Mecon Fluidos, Seville 41092, Spain.
    Ganan-Calvo, Alfonso M.
    Univ Seville, ETSI, Dept Ingn Aeroespacial & Mecon Fluidos, Seville 41092, Spain.
    Heymann, Michael
    Univ Stuttgart, Inst Biomat & Biomol Syst, Intelligent Biointegrat Syst Grp, D-70569 Stuttgart, Germany.
    Darmanin, Connie
    La Trobe Univ, La Trobe Inst Mol Sci, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic 3086, Australia.
    Abbey, Brian
    La Trobe Univ, La Trobe Inst Mol Sci, ARC Ctr Excellence Adv Mol Imaging, Melbourne, Vic 3086, Australia.
    Schmidt, Marius
    Univ Wisconsin, Phys Dept, 3135 N Maryland Ave, Milwaukee, WI 53211 USA.
    Fromme, Petra
    Arizona State Univ, Sch Mol Sci, Tempe, AZ 85287 USA;Arizona State Univ, Biodesign Ctr Appl Struct Discovery, Tempe, AZ 85287 USA.
    Giewekemeyer, Klaus
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Sikorski, Marcin
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Graceffa, Rita
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Vagovic, Patrik
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Kluyver, Thomas
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Bergemann, Martin
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Fangohr, Hans
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Sztuk-Dambietz, Jolanta
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Hauf, Steffen
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Raab, Natascha
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Bondar, Valerii
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany;La Trobe Univ, La Trobe Inst Mol Sci, Dept Chem & Phys, Melbourne, Vic 3086, Australia.
    Chapman, Henry
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luru Chaussee 149, D-22761 Hamburg, Germany;Univ Hamburg, Dept Phys, Luru Chaussee 149, D-22761 Hamburg, Germany.
    Barty, Anton
    Deutsch Elekt Synchrotron, Ctr Free Elect Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.
    Evaluation of serial crystallographic structure determination within megahertz pulse trains2019In: Structural Dynamics, E-ISSN 2329-7778, Vol. 6, no 6, article id 064702Article in journal (Refereed)
    Abstract [en]

    The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.

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  • 18.
    Östlin, Christofer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science, DESY, Hamburg, Germany .
    Martin, Andrew
    School of Science, RMIT University, Melbourne, Australia.
    Is Radiation Damage the Limiting Factor in Single Particle Imaging with X-ray Free-Electron Lasers?2019In: Structural Dynamics, E-ISSN 2329-7778, Vol. 6, article id 044103Article in journal (Refereed)
    Abstract [en]

    The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors of coherent diffractive imaging of single particles and that X-ray pulses need to be as short as possible. Based on molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.

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    fulltext
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