1
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Kayanattil M, Huang Z, Gitaric D, Epp SW. Rubber-like elasticity in laser-driven free surface flow of a Newtonian fluid. Proc Natl Acad Sci U S A 2023; 120:e2301956120. [PMID: 37364115 DOI: 10.1073/pnas.2301956120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/21/2023] [Indexed: 06/28/2023] Open
Abstract
The energy needed to deform an elastic solid may be recovered, while in Newtonian fluids, like water and glycerol, deformation energy dissipates on timescales of the intermolecular relaxation time [Formula: see text] . For times considerably longer than [Formula: see text] the existence of shear elasticity requires long-range correlations, which challenge our understanding of the liquid state. We investigated laser-driven free surface bubbles in liquid glycerol by analyzing their expansion and bursting dynamics, in which we found a flow-dominating, rubber-like elasticity unrelated to surface tension forces. In extension to findings of a measurable liquid elasticity at even very low deformation frequencies [L. Noirez, P. Baroni, J. Mol. Struct. 972, 16-21 (2010), A. Zaccone, K. Trachenko, Proc. Natl. Acad. Sci. U.S.A. 117, 19653-19655 (2020)], that is difficult to access under increased strain, we find a robust, strain rate driven elasticity. The recovery of deformation energy allows the bursting bubble to reach Taylor-Culick velocities 20-fold higher than expected. The elasticity is persistent for microseconds, hence four orders of magnitude longer than [Formula: see text] . The dynamic shows that this persistence cannot originate from the far tail of a distribution of relaxation times around [Formula: see text] but must appear by frustrating the short molecular dissipation. The longer time should be interpreted as a relaxation of collective modes of metastable groups of molecules. With strain rates of 106 s-1, we observe a metastable glycerol shell exhibiting a rubber-like solid behavior with similar elasticity values and characteristic tolerance toward large strains, although the molecular interaction is fundamentally different.
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Affiliation(s)
- Meghanad Kayanattil
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Zhipeng Huang
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Djordje Gitaric
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Sascha W Epp
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
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2
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Krutilin A, Epp SW, Alejo GML, Busse F, Gitaric D, Schikora H, Schwoerer H, Tellkamp F. Peptide Mass Spectra from Micrometer-Thick Ice Films Produced with Femtosecond Pulses. Anal Chem 2022; 94:13359-13367. [PMID: 36153751 PMCID: PMC9535622 DOI: 10.1021/acs.analchem.2c01810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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We present a cryogenic
mass spectrometry protocol with the capability
to detect peptides in the attomole dilution range from ice films.
Our approach employs femtosecond laser pulses and implements neither
substrate modification nor proton donor agents in the aqueous solution,
known to facilitate analyte detection in mass spectrometry. In a systematic
study, we investigated the impact of temperature, substrate composition,
and irradiation wavelength (513 and 1026 nm) on the bradykinin signal
onset. Our findings show that substrate choice and irradiation wavelength
have a minor impact on signal intensity once the preparation protocol
is optimized. However, if the temperature is increased from −140
to 0 °C, which is accompanied by ice film thinning, a somehow
complex picture of analyte desorption and ionization is recognizable,
which has not been described in the literature yet. Under cryogenic
conditions (−140 °C), obtaining a signal is only possible
from isolated sweet spots across the film. If the thin ice film is
between −100 and −70 °C of temperature, these sweet
spots appear more frequently. Ice sublimation triggered by temperatures
above −70 °C leads to an intense and robust signal onset
that could be maintained for several hours. In addition to the above
findings, we notice that a vibrant fragmentation pattern produced
is strikingly similar with both wavelengths. Our findings suggest
that while following an optimized protocol, femtosecond mass spectrometry
has excellent potential to analyze small organic molecules and peptides
with a mass range of up to 2.5 kDa in aqueous solution without any
matrix, as employed in matrix-assisted laser desorption/ionization
(MALDI) or any substrate surface modification, found in surface-assisted
laser desorption/ionization (SALDI).
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Affiliation(s)
- Andrey Krutilin
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Sascha W Epp
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Glaynel M L Alejo
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Frederik Busse
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Djordje Gitaric
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Hendrik Schikora
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Heinrich Schwoerer
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Friedjof Tellkamp
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
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3
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Tanyag RMP, Bacellar C, Pang W, Bernando C, Gomez LF, Jones CF, Ferguson KR, Kwok J, Anielski D, Belkacem A, Boll R, Bozek J, Carron S, Chen G, Delmas T, Englert L, Epp SW, Erk B, Foucar L, Hartmann R, Hexemer A, Huth M, Leone SR, Ma JH, Marchesini S, Neumark DM, Poon BK, Prell J, Rolles D, Rudek B, Rudenko A, Seifrid M, Swiggers M, Ullrich J, Weise F, Zwart P, Bostedt C, Gessner O, Vilesov AF. Sizes of pure and doped helium droplets from single shot x-ray imaging. J Chem Phys 2022; 156:041102. [PMID: 35105059 DOI: 10.1063/5.0080342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advancements in x-ray free-electron lasers on producing ultrashort, ultrabright, and coherent x-ray pulses enable single-shot imaging of fragile nanostructures, such as superfluid helium droplets. This imaging technique gives unique access to the sizes and shapes of individual droplets. In the past, such droplet characteristics have only been indirectly inferred by ensemble averaging techniques. Here, we report on the size distributions of both pure and doped droplets collected from single-shot x-ray imaging and produced from the free-jet expansion of helium through a 5 μm diameter nozzle at 20 bars and nozzle temperatures ranging from 4.2 to 9 K. This work extends the measurement of large helium nanodroplets containing 109-1011 atoms, which are shown to follow an exponential size distribution. Additionally, we demonstrate that the size distributions of the doped droplets follow those of the pure droplets at the same stagnation condition but with smaller average sizes.
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Affiliation(s)
- Rico Mayro P Tanyag
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Camila Bacellar
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Weiwu Pang
- Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Charles Bernando
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Luis F Gomez
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Curtis F Jones
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ken R Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Justin Kwok
- Department of Chemical Engineering and Material Science, University of Southern California, Los Angeles, California 90089, USA
| | - Denis Anielski
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Ali Belkacem
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Rebecca Boll
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - John Bozek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sebastian Carron
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gang Chen
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tjark Delmas
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstraße, 85741 Garching, Germany
| | - Sascha W Epp
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | | | - Alexander Hexemer
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Huth
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Stephen R Leone
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jonathan H Ma
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Billy K Poon
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - James Prell
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Daniel Rolles
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benedikt Rudek
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Artem Rudenko
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Martin Seifrid
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Michele Swiggers
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Joachim Ullrich
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Fabian Weise
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Petrus Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Oliver Gessner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Andrey F Vilesov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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4
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Mehrabi P, Müller-Werkmeister HM, Leimkohl JP, Schikora H, Ninkovic J, Krivokuca S, Andriček L, Epp SW, Sherrell D, Owen RL, Pearson AR, Tellkamp F, Schulz EC, Miller RJD. The HARE chip for efficient time-resolved serial synchrotron crystallography. J Synchrotron Radiat 2020; 27:360-370. [PMID: 32153274 PMCID: PMC7064102 DOI: 10.1107/s1600577520000685] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/20/2020] [Indexed: 05/02/2023]
Abstract
Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.
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Affiliation(s)
- Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henrike M. Müller-Werkmeister
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Jan-Philipp Leimkohl
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jelena Ninkovic
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Silvia Krivokuca
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Ladislav Andriček
- Halbleiterlabor der Max-Planck-Gesellschaft, Otto-Hahn-Ring 6, D-81739 Munich, Germany
| | - Sascha W. Epp
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Darren Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Arwen R. Pearson
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Friedjof Tellkamp
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, Ontario M5S 3H6, Canada
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5
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Pande K, Donatelli JJ, Malmerberg E, Foucar L, Poon BK, Sutter M, Botha S, Basu S, Bruce Doak R, Dörner K, Epp SW, Englert L, Fromme R, Hartmann E, Hartmann R, Hauser G, Hattne J, Hosseinizadeh A, Kassemeyer S, Lomb L, Montero SFC, Menzel A, Rolles D, Rudenko A, Seibert MM, Sierra RG, Schwander P, Ourmazd A, Fromme P, Sauter NK, Bogan M, Bozek J, Bostedt C, Schlichting I, Kerfeld CA, Zwart PH. Free-electron laser data for multiple-particle fluctuation scattering analysis. Sci Data 2018; 5:180201. [PMID: 30277481 PMCID: PMC6167951 DOI: 10.1038/sdata.2018.201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/09/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which solution scattering data are collected using X-ray exposures below rotational diffusion times, resulting in angularly anisotropic X-ray snapshots that provide several orders of magnitude more information than traditional solution scattering data. Such experiments can be performed using the ultrashort X-ray pulses provided by a free-electron laser source, allowing one to collect a large number of diffraction patterns in a relatively short time. Here, we describe a test data set for FXS, obtained at the Linac Coherent Light Source, consisting of close to 100 000 multi-particle diffraction patterns originating from approximately 50 to 200 Paramecium Bursaria Chlorella virus particles per snapshot. In addition to the raw data, a selection of high-quality pre-processed diffraction patterns and a reference SAXS profile are provided.
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Affiliation(s)
- Kanupriya Pande
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffrey J Donatelli
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Computational Research Division, Dept. of Mathematics, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Erik Malmerberg
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany.,Max Planck Advanced Study Group, Center for Free Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany
| | - Billy K Poon
- Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Markus Sutter
- Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sabine Botha
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany.,University of Hamburg, Hamburg Germany
| | - Shibom Basu
- Arizona State University, Tempe, AZ, USA.,Macromolecular Crystallography Group, Paul Scherrer Institute, 5232 Villigen - PSI, Switzerland
| | - R Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany.,Arizona State University, Tempe, AZ, USA
| | - Katerina Dörner
- Arizona State University, Tempe, AZ, USA.,European XFEL GmbH, Schenefeld, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, Hamburg, Germany
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany.,Carl von Ossietzky Universität Oldenburg, Department of Physics, Oldenburg, Germany
| | | | - Elisabeth Hartmann
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | | | - Guenter Hauser
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Johan Hattne
- Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Los Angeles, Los Angeles, CA, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, 3135N. Maryland Ave, Milwaukee, WI 53211, USA
| | - Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Lukas Lomb
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Sebastian F Carron Montero
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, CA, USA.,Department of Physics, California Lutheran University, Thousand Oaks, CA, USA
| | - Andreas Menzel
- Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen - PSI, Switzerland
| | - Daniel Rolles
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany.,Max Planck Advanced Study Group, Center for Free Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany.,James R Macdonald Laboratory, Kansas State University, Manhattan, KS, USA
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany.,James R Macdonald Laboratory, Kansas State University, Manhattan, KS, USA
| | - Marvin M Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, CA, USA
| | - Raymond George Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, CA, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, 3135N. Maryland Ave, Milwaukee, WI 53211, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, 3135N. Maryland Ave, Milwaukee, WI 53211, USA
| | - Petra Fromme
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Bogan
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, CA, USA.,Traction on Demand, Burnaby, BC, Canada
| | - John Bozek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, CA, USA.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex, France
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford, CA, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.,Atomic, Molecular and Optical Physics, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany.,Max Planck Advanced Study Group, Center for Free Electron Laser Science (CFEL), Notkestrasse 85, 22607 Hamburg, Germany
| | - Cheryl A Kerfeld
- Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Petrus H Zwart
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Molecular Biophysics and Integrated Bio-imaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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6
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Krasniqi FS, Zhong Y, Epp SW, Foucar L, Trigo M, Chen J, Reis DA, Wang HL, Zhao JH, Lemke HT, Zhu D, Chollet M, Fritz DM, Hartmann R, Englert L, Strüder L, Schlichting I, Ullrich J. Spatial Distortion of Vibration Modes via Magnetic Correlation of Impurities. Phys Rev Lett 2018; 120:105501. [PMID: 29570335 DOI: 10.1103/physrevlett.120.105501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Indexed: 06/08/2023]
Abstract
Long wavelength vibrational modes in the ferromagnetic semiconductor Ga_{0.91}Mn_{0.09}As are investigated using time resolved x-ray diffraction. At room temperature, we measure oscillations in the x-ray diffraction intensity corresponding to coherent vibrational modes with well-defined wavelengths. When the correlation of magnetic impurities sets in, we observe the transition of the lattice into a disordered state that does not support coherent modes at large wavelengths. Our measurements point toward a magnetically induced broadening of long wavelength vibrational modes in momentum space and their quasilocalization in the real space. More specifically, long wavelength vibrational modes cannot be assigned to a single wavelength but rather should be represented as a superposition of plane waves with different wavelengths. Our findings have strong implications for the phonon-related processes, especially carrier-phonon and phonon-phonon scattering, which govern the electrical conductivity and thermal management of semiconductor-based devices.
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Affiliation(s)
- F S Krasniqi
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Y Zhong
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Building 99 (CFEL), 22761 Hamburg, Germany
| | - S W Epp
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Building 99 (CFEL), 22761 Hamburg, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - L Foucar
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - M Trigo
- Stanford PULSE and SIMES Institutes, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - J Chen
- Stanford PULSE and SIMES Institutes, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D A Reis
- Stanford PULSE and SIMES Institutes, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - H L Wang
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, People's Republic of China
| | - J H Zhao
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083, People's Republic of China
| | - H T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - M Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - D M Fritz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - R Hartmann
- PNSensor GmbH, Römerstraße 28, 80803 München, Germany
| | - L Englert
- Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse 1, 85748 Garching, Germany
| | - L Strüder
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- PNSensor GmbH, Römerstraße 28, 80803 München, Germany
- Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse 1, 85748 Garching, Germany
- Max-Planck-Society Semiconductor Laboratory, Otto-Hahn-Ring 6, 81739 München, Germany
| | - I Schlichting
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - J Ullrich
- Max Planck Advanced Study Group at CFEL/DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, 69117 Heidelberg, Germany
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7
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Epp SW, Hada M, Zhong Y, Kumagai Y, Motomura K, Mizote S, Ono T, Owada S, Axford D, Bakhtiarzadeh S, Fukuzawa H, Hayashi Y, Katayama T, Marx A, Müller-Werkmeister HM, Owen RL, Sherrell DA, Tono K, Ueda K, Westermeier F, Miller RJD. Time zero determination for FEL pump-probe studies based on ultrafast melting of bismuth. Struct Dyn 2017; 4:054308. [PMID: 29152535 PMCID: PMC5658228 DOI: 10.1063/1.4999701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/11/2017] [Indexed: 05/18/2023]
Abstract
A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T0)-the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T0 might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T0. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T0 with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV-IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.
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Affiliation(s)
- S W Epp
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - M Hada
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Y Zhong
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Y Kumagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - K Motomura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - S Mizote
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - T Ono
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - S Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - D Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | | | - H Fukuzawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Y Hayashi
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | | | - A Marx
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | | | - R L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - D A Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | | | - K Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - F Westermeier
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
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8
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Zhong Y, Ostach D, Scholz M, Epp SW, Techert S, Schlichting I, Ullrich J, Krasniqi FS. Hot carrier relaxation in CdTe via phonon-plasmon modes. J Phys Condens Matter 2017; 29:095701. [PMID: 27991427 DOI: 10.1088/1361-648x/aa5478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Carrier and lattice dynamics of laser excited CdTe was studied by time-resolved reflectivity for excitation fluences spanning about three orders of magnitude, from 0.064 to 6.14 mJ cm-2. At fluences below 1 mJ cm-2 the transient reflectivity is dominated by the dynamics of hybrid phonon-plasmon modes. At fluences above 1 mJ cm-2 the time-dependent reflectivity curves show a complex interplay between band-gap renormalization, band filling, carrier dynamics and recombination. A framework that accounts for such complex dynamics is presented and used to model the time-dependent reflectivity data. This model suggests that the excess energy of the laser-excited hot carriers is reduced much more efficiently by emitting hybrid phonon-plasmon modes rather than bare longitudinal optical phonons.
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Affiliation(s)
- Y Zhong
- Max Planck Advanced Study Group at CFEL/DESY, Notkestr. 85, 22607 Hamburg, Germany. Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany. Max-Planck-Institut für Struktur und Dynamik der Matterie, Geb. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
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9
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Oghbaey S, Sarracini A, Ginn HM, Pare-Labrosse O, Kuo A, Marx A, Epp SW, Sherrell DA, Eger BT, Zhong Y, Loch R, Mariani V, Alonso-Mori R, Nelson S, Lemke HT, Owen RL, Pearson AR, Stuart DI, Ernst OP, Mueller-Werkmeister HM, Miller RJD. Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography. Acta Crystallogr D Struct Biol 2016; 72:944-55. [PMID: 27487825 PMCID: PMC5937680 DOI: 10.1107/s2059798316010834] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022] Open
Abstract
The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.
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Affiliation(s)
- Saeed Oghbaey
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Antoine Sarracini
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Olivier Pare-Labrosse
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
| | - Anling Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Alexander Marx
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Sascha W. Epp
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Darren A. Sherrell
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Yinpeng Zhong
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Rolf Loch
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Desy, 22607, Hamburg, Germany
| | - Roberto Alonso-Mori
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Silke Nelson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Henrik T. Lemke
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Arwen R. Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN, UK
- Diamond Light Source, Harwell & Innovation Campus, Didcot, Oxfordshire, OX11 ODE, UK
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Henrike M. Mueller-Werkmeister
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics & Chemistry, University of Toronto, 60 St. George Street, Toronto, Ontario, M5S 1A7, Canada
- Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany
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10
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van der Schot G, Svenda M, Maia FRNC, Hantke MF, DePonte DP, Seibert MM, Aquila A, Schulz J, Kirian RA, Liang M, Stellato F, Bari S, Iwan B, Andreasson J, Timneanu N, Bielecki J, Westphal D, Nunes de Almeida F, Odić D, Hasse D, Carlsson GH, Larsson DSD, Barty A, Martin AV, Schorb S, Bostedt C, Bozek JD, Carron S, Ferguson K, Rolles D, Rudenko A, Epp SW, Foucar L, Rudek B, Erk B, Hartmann R, Kimmel N, Holl P, Englert L, Loh ND, Chapman HN, Andersson I, Hajdu J, Ekeberg T. Open data set of live cyanobacterial cells imaged using an X-ray laser. Sci Data 2016; 3:160058. [PMID: 27479514 PMCID: PMC4968219 DOI: 10.1038/sdata.2016.58] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/18/2016] [Indexed: 01/20/2023] Open
Abstract
Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.
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Affiliation(s)
- Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Joachim Schulz
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Richard A Kirian
- Arizona State University, Physics Department, PO Box 871504, Tempe, Arizona 85287-1504, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sadia Bari
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,ELI beamlines, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 18221 Prague, Czech Republic
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, Box 516, SE-751 20 Uppsala, Sweden
| | - Johan Bielecki
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | | | - Duško Odić
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,Center for Technology Transfer and Innovation, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gunilla H Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Daniel S D Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew V Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Victoria 3010, Australia
| | - Sebastian Schorb
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- Synchrotron SOLEIL, L'orme des Merisiers roundabout of St Aubin, 91190 Saint Aubin, France
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Lutz Foucar
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | | | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany.,Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Peter Holl
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 Munich, Germany
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany.,Ultrafast Coherent Dynamics Group, University Oldenburg, Carl-von-Ossietzky Strasse 9-11, 26129 Oldenburg, Germany
| | - N Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4 Blk S1 A, Singapore 117546, Singapore
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.,European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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11
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Hantke MF, Hasse D, Ekeberg T, John K, Svenda M, Loh D, Martin AV, Timneanu N, Larsson DSD, van der Schot G, Carlsson GH, Ingelman M, Andreasson J, Westphal D, Iwan B, Uetrecht C, Bielecki J, Liang M, Stellato F, DePonte DP, Bari S, Hartmann R, Kimmel N, Kirian RA, Seibert MM, Mühlig K, Schorb S, Ferguson K, Bostedt C, Carron S, Bozek JD, Rolles D, Rudenko A, Foucar L, Epp SW, Chapman HN, Barty A, Andersson I, Hajdu J, Maia FRNC. A data set from flash X-ray imaging of carboxysomes. Sci Data 2016; 3:160061. [PMID: 27479842 DOI: 10.1038/nphoton.2014.270] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/01/2016] [Indexed: 05/26/2023] Open
Abstract
Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
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Affiliation(s)
- Max F Hantke
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Dirk Hasse
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Katja John
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Andrew V Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, Victoria 3010, Australia
| | - Nicusor Timneanu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, Box 516, Uppsala SE- 751 20, Sweden
| | - Daniel S D Larsson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Gijs van der Schot
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Gunilla H Carlsson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Margareta Ingelman
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Jakob Andreasson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- ELI beamlines, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, Prague 18221, Czech Republic
| | - Daniel Westphal
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Bianca Iwan
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Charlotte Uetrecht
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Johan Bielecki
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- I.N.F.N. and Physics Department, University of Rome 'Tor Vergata', Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Daniel P DePonte
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sadia Bari
- European XFEL GmbH, Albert-Einstein-Ring 19, Hamburg 22761, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, Hamburg 22607, Germany
| | | | - Nils Kimmel
- Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, Garching 85741, Germany
| | - Richard A Kirian
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - M Marvin Seibert
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Kerstin Mühlig
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Sebastian Schorb
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sebastian Carron
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
- Department of Physics, J.R. Macdonald Laboratory, Kansas State University, Cardwell Hall, Manhattan, Kansas 66506, USA
- Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
| | - Artem Rudenko
- Department of Physics, J.R. Macdonald Laboratory, Kansas State University, Cardwell Hall, Manhattan, Kansas 66506, USA
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, Heidelberg 69117, Germany
| | - Lutz Foucar
- Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg 69120, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
| | - Sascha W Epp
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, Hamburg 22607, Germany
- Max Planck Institute for Nuclear Physics, Saupfercheckweg 1, Heidelberg 69117, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Inger Andersson
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- European XFEL GmbH, Albert-Einstein-Ring 19, Hamburg 22761, Germany
| | - Filipe R N C Maia
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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12
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Müller-Werkmeister HM, Kuo A, Ginn HM, Oghbaey S, Sarracini A, Pare-Labrosse O, Sherrell D, Marx A, Epp SW, Pearson AR, Owen RL, Stuart DI, Ernst OP, Dwayne Miller R. Capturing Functionally Relevant Protein Motions at the Atomic Level: Femtosecond Time Resolved Serial Crystallography of Ligand Dissociation of Carboxy-Myoglobin. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Manz S, Casandruc A, Zhang D, Zhong Y, Loch RA, Marx A, Hasegawa T, Liu LC, Bayesteh S, Delsim-Hashemi H, Hoffmann M, Felber M, Hachmann M, Mayet F, Hirscht J, Keskin S, Hada M, Epp SW, Flöttmann K, Miller RJD. Mapping atomic motions with ultrabright electrons: towards fundamental limits in space-time resolution. Faraday Discuss 2015; 177:467-91. [PMID: 25631530 DOI: 10.1039/c4fd00204k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The long held objective of directly observing atomic motions during the defining moments of chemistry has been achieved based on ultrabright electron sources that have given rise to a new field of atomically resolved structural dynamics. This class of experiments requires not only simultaneous sub-atomic spatial resolution with temporal resolution on the 100 femtosecond time scale but also has brightness requirements approaching single shot atomic resolution conditions. The brightness condition is in recognition that chemistry leads generally to irreversible changes in structure during the experimental conditions and that the nanoscale thin samples needed for electron structural probes pose upper limits to the available sample or "film" for atomic movies. Even in the case of reversible systems, the degree of excitation and thermal effects require the brightest sources possible for a given space-time resolution to observe the structural changes above background. Further progress in the field, particularly to the study of biological systems and solution reaction chemistry, requires increased brightness and spatial coherence, as well as an ability to tune the electron scattering cross-section to meet sample constraints. The electron bunch density or intensity depends directly on the magnitude of the extraction field for photoemitted electron sources and electron energy distribution in the transverse and longitudinal planes of electron propagation. This work examines the fundamental limits to optimizing these parameters based on relativistic electron sources using re-bunching cavity concepts that are now capable of achieving 10 femtosecond time scale resolution to capture the fastest nuclear motions. This analysis is given for both diffraction and real space imaging of structural dynamics in which there are several orders of magnitude higher space-time resolution with diffraction methods. The first experimental results from the Relativistic Electron Gun for Atomic Exploration (REGAE) are given that show the significantly reduced multiple electron scattering problem in this regime, which opens up micron scale systems, notably solution phase chemistry, to atomically resolved structural dynamics.
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Affiliation(s)
- Stephanie Manz
- The Max Planck Institute for the Structure and Dynamics of Matter, Center for Free Electron Laser Science, Luruper Chaussee 149, Hamburg 22761, Germany.
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14
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Tanyag RMP, Bernando C, Jones CF, Bacellar C, Ferguson KR, Anielski D, Boll R, Carron S, Cryan JP, Englert L, Epp SW, Erk B, Foucar L, Gomez LF, Hartmann R, Neumark DM, Rolles D, Rudek B, Rudenko A, Siefermann KR, Ullrich J, Weise F, Bostedt C, Gessner O, Vilesov AF. Communication: X-ray coherent diffractive imaging by immersion in nanodroplets. Struct Dyn 2015; 2:051102. [PMID: 26798821 PMCID: PMC4711653 DOI: 10.1063/1.4933297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/05/2015] [Indexed: 05/12/2023]
Abstract
Lensless x-ray microscopy requires the recovery of the phase of the radiation scattered from a specimen. Here, we demonstrate a de novo phase retrieval technique by encapsulating an object in a superfluid helium nanodroplet, which provides both a physical support and an approximate scattering phase for the iterative image reconstruction. The technique is robust, fast-converging, and yields the complex density of the immersed object. Images of xenon clusters embedded in superfluid helium droplets reveal transient configurations of quantum vortices in this fragile system.
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Affiliation(s)
- Rico Mayro P Tanyag
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, USA
| | - Charles Bernando
- Department of Physics and Astronomy, University of Southern California , Los Angeles, California 90089, USA
| | - Curtis F Jones
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, USA
| | | | - Ken R Ferguson
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Sebastian Carron
- Linac Coherent Light Source, LCLS, SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - James P Cryan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik , Giessenbachstraße, 85741 Garching, Germany
| | | | | | | | - Luis F Gomez
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, USA
| | | | | | | | | | | | - Katrin R Siefermann
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
| | | | - Fabian Weise
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
| | | | - Oliver Gessner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, USA
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15
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Mueller C, Marx A, Epp SW, Zhong Y, Kuo A, Balo AR, Soman J, Schotte F, Lemke HT, Owen RL, Pai EF, Pearson AR, Olson JS, Anfinrud PA, Ernst OP, Dwayne Miller RJ. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography. Struct Dyn 2015; 2:054302. [PMID: 26798825 PMCID: PMC4711646 DOI: 10.1063/1.4928706] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/06/2015] [Indexed: 05/18/2023]
Abstract
We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.
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Affiliation(s)
- C Mueller
- Departments of Chemistry and Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Marx
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - S W Epp
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Y Zhong
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - A R Balo
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - J Soman
- Department of BioSciences, Rice University , Houston, Texas 77251-1892, USA
| | - F Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA
| | - H T Lemke
- LCLS, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - R L Owen
- Diamond Light Source , Harwell Campus for Science and Innovation, Didcot OX11 0DE, United Kingdom
| | | | - A R Pearson
- Hamburg Centre for Ultrafast Imaging, University of Hamburg , CFEL, Building 99, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - J S Olson
- Department of BioSciences, Rice University , Houston, Texas 77251-1892, USA
| | - P A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA
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16
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Ekeberg T, Svenda M, Abergel C, Maia FRNC, Seltzer V, Claverie JM, Hantke M, Jönsson O, Nettelblad C, van der Schot G, Liang M, DePonte DP, Barty A, Seibert MM, Iwan B, Andersson I, Loh ND, Martin AV, Chapman H, Bostedt C, Bozek JD, Ferguson KR, Krzywinski J, Epp SW, Rolles D, Rudenko A, Hartmann R, Kimmel N, Hajdu J. Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser. Phys Rev Lett 2015; 114:098102. [PMID: 25793853 DOI: 10.1103/physrevlett.114.098102] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Indexed: 05/19/2023]
Abstract
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.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Chantal Abergel
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Virginie Seltzer
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Jean-Michel Claverie
- Génomique & Structurale - IGS - UMR 7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Case 934, 13288 Marseille Cedex 9, France
| | - Max Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Olof Jönsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel P DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Bianca Iwan
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- Attophysics Group, CEA-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - N Duane Loh
- Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4 Blk S1 A, Singapore 117546, Singapore
| | - Andrew V Martin
- The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Henry Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ken R Ferguson
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Jacek Krzywinski
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Sascha W Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel Rolles
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, 116 Cardwell Hall, Manhattan, Kansas 66506, USA
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, 116 Cardwell Hall, Manhattan, Kansas 66506, USA
| | | | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
- European XFEL, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
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17
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Gomez LF, Ferguson KR, Cryan JP, Bacellar C, Tanyag RMP, Jones C, Schorb S, Anielski D, Belkacem A, Bernando C, Boll R, Bozek J, Carron S, Chen G, Delmas T, Englert L, Epp SW, Erk B, Foucar L, Hartmann R, Hexemer A, Huth M, Kwok J, Leone SR, Ma JHS, Maia FRNC, Malmerberg E, Marchesini S, Neumark DM, Poon B, Prell J, Rolles D, Rudek B, Rudenko A, Seifrid M, Siefermann KR, Sturm FP, Swiggers M, Ullrich J, Weise F, Zwart P, Bostedt C, Gessner O, Vilesov AF. Shapes and vorticities of superfluid helium nanodroplets. Science 2014; 345:906-9. [DOI: 10.1126/science.1252395] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Luis F. Gomez
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Ken R. Ferguson
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James P. Cryan
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Camila Bacellar
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rico Mayro P. Tanyag
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Curtis Jones
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Sebastian Schorb
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Denis Anielski
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Ali Belkacem
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Charles Bernando
- Department of Physics and Astronomy, USC, Los Angeles, CA 90089, USA
| | - Rebecca Boll
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - John Bozek
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sebastian Carron
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gang Chen
- Advanced Light Source, LBNL, Berkeley, CA 94720, USA
| | - Tjark Delmas
- CFEL, DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Lars Englert
- Max-Planck-Institut für Extraterrestrische Physik, Giessenbachstraße, 85741 Garching, Germany
| | - Sascha W. Epp
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Benjamin Erk
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | | | | | - Martin Huth
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Justin Kwok
- Mork Family Department of Chemical Engineering and Materials Science, USC, Los Angeles, CA 90089, USA
| | - Stephen R. Leone
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan H. S. Ma
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China
| | - Filipe R. N. C. Maia
- National Energy Research Scientific Computing Center, LBNL, Berkeley, CA 94720, USA
| | - Erik Malmerberg
- Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of Calfornia Berkeley, Berkeley, CA 94720, USA
| | - Stefano Marchesini
- Advanced Light Source, LBNL, Berkeley, CA 94720, USA
- Department of Physics, University of California Davis, Davis, CA 95616, USA
| | - Daniel M. Neumark
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Billy Poon
- Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
| | - James Prell
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Daniel Rolles
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Artem Rudenko
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- James R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Martin Seifrid
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Katrin R. Siefermann
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Felix P. Sturm
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Michele Swiggers
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Joachim Ullrich
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Fabian Weise
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Petrus Zwart
- Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
| | - Christoph Bostedt
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- PULSE Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Oliver Gessner
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Andrey F. Vilesov
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, USC, Los Angeles, CA 90089, USA
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18
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Boll R, Rouzée A, Adolph M, Anielski D, Aquila A, Bari S, Bomme C, Bostedt C, Bozek JD, Chapman HN, Christensen L, Coffee R, Coppola N, De S, Decleva P, Epp SW, Erk B, Filsinger F, Foucar L, Gorkhover T, Gumprecht L, Hömke A, Holmegaard L, Johnsson P, Kienitz JS, Kierspel T, Krasniqi F, Kühnel KU, Maurer J, Messerschmidt M, Moshammer R, Müller NLM, Rudek B, Savelyev E, Schlichting I, Schmidt C, Scholz F, Schorb S, Schulz J, Seltmann J, Stener M, Stern S, Techert S, Thøgersen J, Trippel S, Viefhaus J, Vrakking M, Stapelfeldt H, Küpper J, Ullrich J, Rudenko A, Rolles D. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules. Faraday Discuss 2014; 171:57-80. [PMID: 25290160 DOI: 10.1039/c4fd00037d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.
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Affiliation(s)
- Rebecca Boll
- Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany.
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19
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Erk B, Boll R, Trippel S, Anielski D, Foucar L, Rudek B, Epp SW, Coffee R, Carron S, Schorb S, Ferguson KR, Swiggers M, Bozek JD, Simon M, Marchenko T, Küpper J, Schlichting I, Ullrich J, Bostedt C, Rolles D, Rudenko A. Imaging charge transfer in iodomethane upon x-ray photoabsorption. Science 2014; 345:288-91. [DOI: 10.1126/science.1253607] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Benjamin Erk
- Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - Rebecca Boll
- Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - Sebastian Trippel
- Center for Free-Electron Laser Science (CFEL), DESY, 22607 Hamburg, Germany
| | - Denis Anielski
- Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - Lutz Foucar
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
- Physikalisch-Technische Bundesanstalt, 38116 Braunschweig, Germany
| | - Sascha W. Epp
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
| | - Ryan Coffee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - Sebastian Carron
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - Sebastian Schorb
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - Ken R. Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - Michele Swiggers
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - John D. Bozek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - Marc Simon
- Sorbonne Universités, UPMC Université Paris 06, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005, Paris, France
- CNRS, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005, Paris, France
| | - Tatiana Marchenko
- Sorbonne Universités, UPMC Université Paris 06, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005, Paris, France
- CNRS, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005, Paris, France
| | - Jochen Küpper
- Center for Free-Electron Laser Science (CFEL), DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Center for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Ilme Schlichting
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, 69120 Heidelberg, Germany
| | - Joachim Ullrich
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
- Physikalisch-Technische Bundesanstalt, 38116 Braunschweig, Germany
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 94025 Menlo Park, CA, USA
| | - Daniel Rolles
- Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, 69120 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group at CFEL, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS 66506, USA
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20
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Park HJ, Loh ND, Sierra RG, Hampton CY, Starodub D, Martin AV, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Lomb L, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ, Elser V. Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers. Opt Express 2013; 21:28729-42. [PMID: 24514385 DOI: 10.1364/oe.21.028729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
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21
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Rudolph JK, Bernitt S, Epp SW, Steinbrügge R, Beilmann C, Brown GV, Eberle S, Graf A, Harman Z, Hell N, Leutenegger M, Müller A, Schlage K, Wille HC, Yavaş H, Ullrich J, Crespo López-Urrutia JR. X-ray resonant photoexcitation: linewidths and energies of Kα transitions in highly charged Fe ions. Phys Rev Lett 2013; 111:103002. [PMID: 25166661 DOI: 10.1103/physrevlett.111.103002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Indexed: 06/03/2023]
Abstract
Photoabsorption by and fluorescence of the Kα transitions in highly charged iron ions are essential mechanisms for x-ray radiation transfer in astrophysical environments. We study photoabsorption due to the main Kα transitions in highly charged iron ions from heliumlike to fluorinelike (Fe24+ to Fe17+) using monochromatic x rays around 6.6 keV at the PETRA III synchrotron photon source. Natural linewidths were determined with hitherto unattained accuracy. The observed transitions are of particular interest for the understanding of photoexcited plasmas found in x-ray binary stars and active galactic nuclei.
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Affiliation(s)
- J K Rudolph
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany and Institut für Atom- und Molekülphysik, Justus-Liebig-Universität Gießen, Leihgesterner Weg 217, 35392 Gießen, Germany
| | - S Bernitt
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - S W Epp
- Max Planck Advanced Study Group, CFEL, Notkestraße 85, 22607 Hamburg, Germany
| | - R Steinbrügge
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - C Beilmann
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany and Physikalisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 226, 69120 Heidelberg, Germany
| | - G V Brown
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - S Eberle
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - A Graf
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - Z Harman
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany and ExtreMe Matter Institute (EMMI), Planckstraße 1, 64291 Darmstadt, Germany
| | - N Hell
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA and Dr. Karl Remeis-Observatory and ECAP, Universität Erlangen Nürnberg, Sternwartstraße 7, 96049 Bamberg, Germany
| | - M Leutenegger
- NASA/Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, Maryland 20771, USA and Center for Space Sciences and Technology, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
| | - A Müller
- Institut für Atom- und Molekülphysik, Justus-Liebig-Universität Gießen, Leihgesterner Weg 217, 35392 Gießen, Germany
| | - K Schlage
- Deutsches Elektronen-Synchrotron (PETRA III), Notkestraße 85, 22607 Hamburg, Germany
| | - H-C Wille
- Deutsches Elektronen-Synchrotron (PETRA III), Notkestraße 85, 22607 Hamburg, Germany
| | - H Yavaş
- Deutsches Elektronen-Synchrotron (PETRA III), Notkestraße 85, 22607 Hamburg, Germany
| | - J Ullrich
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
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22
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Starodub D, Aquila A, Bajt S, Barthelmess M, Barty A, Bostedt C, Bozek JD, Coppola N, Doak RB, Epp SW, Erk B, Foucar L, Gumprecht L, Hampton CY, Hartmann A, Hartmann R, Holl P, Kassemeyer S, Kimmel N, Laksmono H, Liang M, Loh ND, Lomb L, Martin AV, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Sierra RG, Soltau H, Steinbrener J, Stellato F, Stern S, Weidenspointner G, Frank M, Ullrich J, Strüder L, Schlichting I, Chapman HN, Spence JCH, Bogan MJ. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns. Nat Commun 2013; 3:1276. [PMID: 23232406 DOI: 10.1038/ncomms2288] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 11/14/2012] [Indexed: 11/09/2022] Open
Abstract
Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.
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Affiliation(s)
- D Starodub
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.
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23
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Loh ND, Starodub D, Lomb L, Hampton CY, Martin AV, Sierra RG, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres. Opt Express 2013; 21:12385-12394. [PMID: 23736456 DOI: 10.1364/oe.21.012385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
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Affiliation(s)
- N Duane Loh
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
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24
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Epp SW. Comment on "Testing three-body quantum electrodynamics with trapped Ti20+ ions: evidence for a Z-dependent divergence between experiment and calculation". Phys Rev Lett 2013; 110:159301. [PMID: 25167321 DOI: 10.1103/physrevlett.110.159301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Indexed: 06/03/2023]
Affiliation(s)
- S W Epp
- Max Planck Advanced Study Group, Center for Free-Electron Laser Science, 22607 Hamburg, Germany and Max-Planck-Institut für Kernphysik, 69117 Heidelberg, Germany
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25
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Barends TRM, Foucar L, Shoeman RL, Bari S, Epp SW, Hartmann R, Hauser G, Huth M, Kieser C, Lomb L, Motomura K, Nagaya K, Schmidt C, Strecker R, Anielski D, Boll R, Erk B, Fukuzawa H, Hartmann E, Hatsui T, Holl P, Inubushi Y, Ishikawa T, Kassemeyer S, Kaiser C, Koeck F, Kunishima N, Kurka M, Rolles D, Rudek B, Rudenko A, Sato T, Schroeter CD, Soltau H, Strueder L, Tanaka T, Togashi T, Tono K, Ullrich J, Yase S, Wada SI, Yao M, Yabashi M, Ueda K, Schlichting I. Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. Acta Crystallogr D Biol Crystallogr 2013; 69:838-42. [PMID: 23633593 DOI: 10.1107/s0907444913002448] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/24/2013] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (FELs) enable crystallographic data collection using extremely bright femtosecond pulses from microscopic crystals beyond the limitations of conventional radiation damage. This diffraction-before-destruction approach requires a new crystal for each FEL shot and, since the crystals cannot be rotated during the X-ray pulse, data collection requires averaging over many different crystals and a Monte Carlo integration of the diffraction intensities, making the accurate determination of structure factors challenging. To investigate whether sufficient accuracy can be attained for the measurement of anomalous signal, a large data set was collected from lysozyme microcrystals at the newly established `multi-purpose spectroscopy/imaging instrument' of the SPring-8 Ångstrom Compact Free-Electron Laser (SACLA) at RIKEN Harima. Anomalous difference density maps calculated from these data demonstrate that serial femtosecond crystallography using a free-electron laser is sufficiently accurate to measure even the very weak anomalous signal of naturally occurring S atoms in a protein at a photon energy of 7.3 keV.
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Affiliation(s)
- Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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26
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Graves CE, Reid AH, Wang T, Wu B, de Jong S, Vahaplar K, Radu I, Bernstein DP, Messerschmidt M, Müller L, Coffee R, Bionta M, Epp SW, Hartmann R, Kimmel N, Hauser G, Hartmann A, Holl P, Gorke H, Mentink JH, Tsukamoto A, Fognini A, Turner JJ, Schlotter WF, Rolles D, Soltau H, Strüder L, Acremann Y, Kimel AV, Kirilyuk A, Rasing T, Stöhr J, Scherz AO, Dürr HA. Nanoscale spin reversal by non-local angular momentum transfer following ultrafast laser excitation in ferrimagnetic GdFeCo. Nat Mater 2013; 12:293-8. [PMID: 23503010 DOI: 10.1038/nmat3597] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 02/07/2012] [Indexed: 05/19/2023]
Abstract
Ultrafast laser techniques have revealed extraordinary spin dynamics in magnetic materials that equilibrium descriptions of magnetism cannot explain. Particularly important for future applications is understanding non-equilibrium spin dynamics following laser excitation on the nanoscale, yet the limited spatial resolution of optical laser techniques has impeded such nanoscale studies. Here we present ultrafast diffraction experiments with an X-ray laser that probes the nanoscale spin dynamics following optical laser excitation in the ferrimagnetic alloy GdFeCo, which exhibits macroscopic all-optical switching. Our study reveals that GdFeCo displays nanoscale chemical and magnetic inhomogeneities that affect the spin dynamics. In particular, we observe Gd spin reversal in Gd-rich nanoregions within the first picosecond driven by the non-local transfer of angular momentum from larger adjacent Fe-rich nanoregions. These results suggest that a magnetic material's microstructure can be engineered to control transient laser-excited spins, potentially allowing faster (~ 1 ps) spin reversal than in present technologies.
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Affiliation(s)
- C E Graves
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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27
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Erk B, Rolles D, Foucar L, Rudek B, Epp SW, Cryle M, Bostedt C, Schorb S, Bozek J, Rouzee A, Hundertmark A, Marchenko T, Simon M, Filsinger F, Christensen L, De S, Trippel S, Küpper J, Stapelfeldt H, Wada S, Ueda K, Swiggers M, Messerschmidt M, Schröter CD, Moshammer R, Schlichting I, Ullrich J, Rudenko A. Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. Phys Rev Lett 2013; 110:053003. [PMID: 23414017 DOI: 10.1088/0953-4075/46/16/164031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 05/23/2023]
Abstract
Ionization and fragmentation of methylselenol (CH(3)SeH) molecules by intense (>10(17) W/cm(2)) 5 fs x-ray pulses (ħω=2 keV) are studied by coincident ion momentum spectroscopy. We contrast the measured charge state distribution with data on atomic Kr, determine kinetic energies of resulting ionic fragments, and compare them to the outcome of a Coulomb explosion model. We find signatures of ultrafast charge redistribution from the inner-shell ionized Se atom to its molecular partners, and observe significant displacement of the atomic constituents in the course of multiple ionization.
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Affiliation(s)
- B Erk
- Max Planck Advanced Study Group (ASG) at CFEL, 22761 Hamburg, Germany
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28
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Erk B, Rolles D, Foucar L, Rudek B, Epp SW, Cryle M, Bostedt C, Schorb S, Bozek J, Rouzee A, Hundertmark A, Marchenko T, Simon M, Filsinger F, Christensen L, De S, Trippel S, Küpper J, Stapelfeldt H, Wada S, Ueda K, Swiggers M, Messerschmidt M, Schröter CD, Moshammer R, Schlichting I, Ullrich J, Rudenko A. Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. Phys Rev Lett 2013; 110:053003. [PMID: 23414017 DOI: 10.1103/physrevlett.110.053003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 05/11/2023]
Abstract
Ionization and fragmentation of methylselenol (CH(3)SeH) molecules by intense (>10(17) W/cm(2)) 5 fs x-ray pulses (ħω=2 keV) are studied by coincident ion momentum spectroscopy. We contrast the measured charge state distribution with data on atomic Kr, determine kinetic energies of resulting ionic fragments, and compare them to the outcome of a Coulomb explosion model. We find signatures of ultrafast charge redistribution from the inner-shell ionized Se atom to its molecular partners, and observe significant displacement of the atomic constituents in the course of multiple ionization.
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Affiliation(s)
- B Erk
- Max Planck Advanced Study Group (ASG) at CFEL, 22761 Hamburg, Germany
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29
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Loh ND, Hampton CY, Martin AV, Starodub D, Sierra RG, Barty A, Aquila A, Schulz J, Lomb L, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Hunter MM, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege SP, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Bucksbaum P, Hodgson KO, Strüder L, Ullrich J, Frank M, Schlichting I, Chapman HN, Bogan MJ. Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 2012; 486:513-7. [PMID: 22739316 DOI: 10.1038/nature11222] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 05/09/2012] [Indexed: 11/09/2022]
Abstract
The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.
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Affiliation(s)
- N D Loh
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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Gorkhover T, Adolph M, Rupp D, Schorb S, Epp SW, Erk B, Foucar L, Hartmann R, Kimmel N, Kühnel KU, Rolles D, Rudek B, Rudenko A, Andritschke R, Aquila A, Bozek JD, Coppola N, Erke T, Filsinger F, Gorke H, Graafsma H, Gumprecht L, Hauser G, Herrmann S, Hirsemann H, Hömke A, Holl P, Kaiser C, Krasniqi F, Meyer JH, Matysek M, Messerschmidt M, Miessner D, Nilsson B, Pietschner D, Potdevin G, Reich C, Schaller G, Schmidt C, Schopper F, Schröter CD, Schulz J, Soltau H, Weidenspointner G, Schlichting I, Strüder L, Ullrich J, Möller T, Bostedt C. Nanoplasma dynamics of single large xenon clusters irradiated with superintense x-ray pulses from the linac coherent light source free-electron laser. Phys Rev Lett 2012; 108:245005. [PMID: 23004284 DOI: 10.1103/physrevlett.108.245005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Indexed: 05/09/2023]
Abstract
The plasma dynamics of single mesoscopic Xe particles irradiated with intense femtosecond x-ray pulses exceeding 10(16) W/cm2 from the Linac Coherent Light Source free-electron laser are investigated. Simultaneous recording of diffraction patterns and ion spectra allows eliminating the influence of the laser focal volume intensity and particle size distribution. The data show that for clusters illuminated with intense x-ray pulses, highly charged ionization fragments in a narrow distribution are created and that the nanoplasma recombination is efficiently suppressed.
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Affiliation(s)
- T Gorkhover
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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Martin AV, Loh ND, Hampton CY, Sierra RG, Wang F, Aquila A, Bajt S, Barthelmess M, Bostedt C, Bozek JD, Coppola N, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Liang M, Lomb L, Maia FRNC, Marchesini S, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Soltau H, Starodub D, Steinbrener J, Stellato F, Strüder L, Ullrich J, Weidenspointner G, White TA, Wunderer CB, Barty A, Schlichting I, Bogan MJ, Chapman HN. Femtosecond dark-field imaging with an X-ray free electron laser. Opt Express 2012; 20:13501-12. [PMID: 22714377 DOI: 10.1364/oe.20.013501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.
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Affiliation(s)
- A V Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
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32
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Kassemeyer S, Steinbrener J, Lomb L, Hartmann E, Aquila A, Barty A, Martin AV, Hampton CY, Bajt S, Barthelmess M, Barends TRM, Bostedt C, Bott M, Bozek JD, Coppola N, Cryle M, DePonte DP, Doak RB, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Hömke A, Holl P, Jönsson O, Kimmel N, Krasniqi F, Liang M, Maia FRNC, Marchesini S, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schmidt C, Schulz J, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Starodub D, Stellato F, Stern S, Stier G, Svenda M, Weidenspointner G, Weierstall U, White TA, Wunderer C, Frank M, Chapman HN, Ullrich J, Strüder L, Bogan MJ, Schlichting I. Femtosecond free-electron laser x-ray diffraction data sets for algorithm development. Opt Express 2012; 20:4149-58. [PMID: 22418172 DOI: 10.1364/oe.20.004149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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Affiliation(s)
- Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
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Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, Caleman C, Coppola N, Davidsson J, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel KU, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FRNC, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JCH, Chapman HN. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express 2012; 20:2706-16. [PMID: 22330507 PMCID: PMC3413412 DOI: 10.1364/oe.20.002706] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/16/2011] [Accepted: 12/18/2011] [Indexed: 05/17/2023]
Abstract
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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Affiliation(s)
- Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, 22607 Hamburg, Germany.
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34
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Koopmann R, Cupelli K, Redecke L, Nass K, Deponte DP, White TA, Stellato F, Rehders D, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Boutet S, Bozek JD, Caleman C, Coppola N, Davidsson J, Doak RB, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kirian RA, Lomb L, Maia FRNC, Kimmel N, Martin AV, Messerschmidt M, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Williams GJ, Wunderer CB, Fromme P, Spence JCH, Stehle T, Chapman HN, Betzel C, Duszenko M. In vivo protein crystallization opens new routes in structural biology. Nat Methods 2012; 9:259-62. [PMID: 22286384 PMCID: PMC3429599 DOI: 10.1038/nmeth.1859] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 12/21/2011] [Indexed: 11/08/2022]
Abstract
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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Affiliation(s)
- Rudolf Koopmann
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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35
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Barty A, Caleman C, Aquila A, Timneanu N, Lomb L, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bozek JD, Coffee R, Coppola N, Davidsson J, DePonte DP, Doak RB, Ekeberg T, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Fromme P, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Johansson L, Kassemeyer S, Kimmel N, Kirian RA, Liang M, Maia FRNC, Malmerberg E, Marchesini S, Martin AV, Nass K, Neutze R, Reich C, Rolles D, Rudek B, Rudenko A, Scott H, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Stellato F, Stern S, Strüder L, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Wunderer CB, Chapman HN. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat Photonics 2012; 6:35-40. [PMID: 24078834 PMCID: PMC3783007 DOI: 10.1038/nphoton.2011.297] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1-4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
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Affiliation(s)
- Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence and requests for materials should be addressed to A.B. and H.N.C., ;
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Lukas Lomb
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - David Arnlund
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Saša Bajt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas R. M. Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D. Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ryan Coffee
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Nicola Coppola
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Davidsson
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Daniel P. DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - R. Bruce Doak
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Veit Elser
- Department of Physics, Cornell University, Ithaca, New York 14853, USA
| | - Sascha W. Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Heinz Graafsma
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Günter Hauser
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | | | - Peter Holl
- PN Sensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Mark S. Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Linda Johansson
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Erik Malmerberg
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Andrew V. Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Karol Nass
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Richard Neutze
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Daniel Rolles
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Howard Scott
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joachim Schulz
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Robert L. Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Heike Soltau
- PN Sensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stephan Stern
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lothar Strüder
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Joachim Ullrich
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - X. Wang
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Georg Weidenspointner
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | | | - Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence and requests for materials should be addressed to A.B. and H.N.C., ;
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Lomb L, Barends TRM, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L, Hartmann R, Rudek B, Rolles D, Rudenko A, Shoeman RL, Andreasson J, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Deponte DP, Doak RB, Ekeberg T, Fleckenstein H, Fromme P, Gebhardt M, Graafsma H, Gumprecht L, Hampton CY, Hartmann A, Hauser G, Hirsemann H, Holl P, Holton JM, Hunter MS, Kabsch W, Kimmel N, Kirian RA, Liang M, Maia FRNC, Meinhart A, Marchesini S, Martin AV, Nass K, Reich C, Schulz J, Seibert MM, Sierra R, Soltau H, Spence JCH, Steinbrener J, Stellato F, Stern S, Timneanu N, Wang X, Weidenspointner G, Weierstall U, White TA, Wunderer C, Chapman HN, Ullrich J, Strüder L, Schlichting I. Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B Condens Matter Mater Phys 2011; 84:214111. [PMID: 24089594 PMCID: PMC3786679 DOI: 10.1103/physrevb.84.214111] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
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Affiliation(s)
- Lukas Lomb
- Max-Planck Institut für medizinische Forschung, Jahnstrasse 29, DE-69120 Heidelberg, Germany ; Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, DE-22607 Hamburg, Germany
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37
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Yoon CH, Schwander P, Abergel C, Andersson I, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek J, Chapman HN, Claverie JM, Coppola N, DePonte DP, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann E, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Kiskinova M, Liang M, Loh NTD, Lomb L, Maia FRNC, Martin AV, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert M, Seltzer V, Shoeman RL, Sierra RG, Soltau H, Starodub D, Steinbrener J, Stier G, Strüder L, Svenda M, Ullrich J, Weidenspointner G, White TA, Wunderer C, Ourmazd A. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. Opt Express 2011; 19:16542-9. [PMID: 21935018 DOI: 10.1364/oe.19.016542] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.
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Affiliation(s)
- Chun Hong Yoon
- Department of Physics, University of Wisconsin-Milwaukee, 1900 East Kenwood Blvd, Milwaukee, Wisconsin 53211, USA
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Simon MC, López-Urrutia JRC, Beilmann C, Schwarz M, Harman Z, Epp SW, Schmitt BL, Baumann TM, Behar E, Bernitt S, Follath R, Ginzel R, Keitel CH, Klawitter R, Kubiček K, Mäckel V, Mokler PH, Reichardt G, Schwarzkopf O, Ullrich J. Resonant and near-threshold photoionization cross sections of Fe14+. Phys Rev Lett 2010; 105:183001. [PMID: 21231102 DOI: 10.1103/physrevlett.105.183001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 11/05/2009] [Indexed: 05/30/2023]
Abstract
Photoionization (PI) of Fe14+ in the range from 450 to 1100 eV was measured at the BESSY II storage ring using an electron beam ion trap achieving high target-ion area densities of 10(10) cm(-2). Photoabsorption by this ion is observed in astrophysical spectra and plasmas, but until now cross sections and resonance energies could only be provided by calculations. We reach a resolving power E/ΔE of at least 6500, outstanding in the present energy range, which enables benchmarking and improving the most advanced theories for PI of ions in high charge states.
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Affiliation(s)
- M C Simon
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany.
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Lapierre A, Crespo López-Urrutia JR, Baumann TM, Epp SW, Gonchar A, González Martínez AJ, Liang G, Rohr A, Soria Orts R, Simon MC, Tawara H, Versteegen R, Ullrich J. Compact soft x-ray spectrometer for plasma diagnostics at the Heidelberg Electron Beam Ion Trap. Rev Sci Instrum 2007; 78:123105. [PMID: 18163718 DOI: 10.1063/1.2818808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A compact flat-field soft x-ray grazing-incidence grating spectrometer equipped with a cryogenically cooled back-illuminated charge-coupled device camera was built and implemented at the Heidelberg Electron Beam Ion Trap. The instrument spans the spectral region from 1 to 37 nm using two different gratings. In slitless operation mode, it directly images a radiation source, in this case ions confined in an electron beam ion trap, with high efficiency and reaching hereby a resolving power of lambda/Deltalambda approximately =130 at 2 nm and of lambda/Deltalambda approximately =600 at 28 nm. Capable of automatized operation, its low noise and excellent stability make it an ideal instrument not only for spectroscopic diagnostics requiring wide spectral coverage but also for precision wavelength measurements.
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Affiliation(s)
- A Lapierre
- Max-Planck Institut für Kernphysik, Saupfercheckweg 1, D-69117 Heidelberg, Germany
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Epp SW, López-Urrutia JRC, Brenner G, Mäckel V, Mokler PH, Treusch R, Kuhlmann M, Yurkov MV, Feldhaus J, Schneider JR, Wellhöfer M, Martins M, Wurth W, Ullrich J. Soft x-ray laser spectroscopy on trapped highly charged ions at FLASH. Phys Rev Lett 2007; 98:183001. [PMID: 17501569 DOI: 10.1103/physrevlett.98.183001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Indexed: 05/15/2023]
Abstract
In a proof-of-principle experiment, we demonstrate high-resolution resonant laser excitation in the soft x-ray region at 48.6 eV of the 2 (2)S(1/2) to 2 (2)P(1/2) transition of Li-like Fe23+ ions trapped in an electron beam ion trap by using ultrabrilliant light from Free Electron Laser in Hamburg (FLASH). High precision spectroscopic studies of highly charged ions at this and upcoming x-ray lasers with an expected accuracy gain up to a factor of a thousand, become possible with our technique, thus potentially yielding fundamental insights, e.g., into basic aspects of QED.
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Affiliation(s)
- S W Epp
- Max-Planck-Institut für Kernphysik, D-69117 Heidelberg, Germany.
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