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  • 51.
    Daurer, Benedikt J
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Simone, Sala
    University College London.
    Hantke, Max
    Oxford University.
    Reddy, Hemanth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    DESY Hamburg.
    Carini, Gabriella
    SLAC Stanford.
    Hart, Philip
    SLAC Stanford.
    Aquila, Andrew
    SLAC Stanford.
    Loh, Duane
    National University of Singapore.
    Thibault, Pierre
    University of Southampton.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wavefront sensing of individual XFEL pulses using ptychographyManuscript (preprint) (Other academic)
    Abstract [en]

    The characterization of the wavefront dynamics is important for many X-ray free-electron laser (XFEL) experiments, in particular for coherent diffractive imaging (CDI), as the reconstructed image is always the product of the incoming wavefront with the object. An accurate understanding of the wavefront is also important for any experiment wishing to achieve peak power densities, making use of the tightest possible focal spots. With the use of ptychography we demonstrate high-resolution imaging of the Linac Coherent Light Source (LCLS) beam focused at the endstation for Atomic, Molecular and Optical (AMO) experiments, including its phase and intensity at every plane along its propagation axis, for each individual pulse. Using a mixed-state approach, we have reconstructed the most dominant beam components that constitute an ensemble of pulses, and from the reconstructed components determined their respective contribution in each of the individual pulses. This enabled us to obtain complete wavefront information about each individual pulse. We hope that our findings aid interpretation of data from past and future LCLS experiments and we propose this method to be used routinely for XFEL beam diagnostics. 

  • 52.
    Dicke, B.
    et al.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Hoffmann, A.
    Rhein Westfal TH Aachen, Inst Inorgan Chem, D-52074 Aachen, Germany..
    Stanek, J.
    Rhein Westfal TH Aachen, Inst Inorgan Chem, D-52074 Aachen, Germany..
    Rampp, M. S.
    Ludwig Maximilians Univ Munchen, Inst Biomol Opt, Oettingenstr 67, D-80538 Munich, Germany.;Ludwig Maximilians Univ Munchen, Ctr Integrated Prot Sci CIPSM, Oettingenstr 67, D-80538 Munich, Germany..
    Grimm-Lebsanft, B.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Biebl, F.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Rukser, D.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Maerz, B.
    Ludwig Maximilians Univ Munchen, Inst Biomol Opt, Oettingenstr 67, D-80538 Munich, Germany.;Ludwig Maximilians Univ Munchen, Ctr Integrated Prot Sci CIPSM, Oettingenstr 67, D-80538 Munich, Germany..
    Goeries, D.
    Deutsch Elektronensynchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Naumova, M.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Univ Paderborn, Dept Chem, D-33098 Paderborn, Germany..
    Biednov, M.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Neuber, G.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Wetzel, A.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Hofmann, S. M.
    Ludwig Maximilians Univ Munchen, Inst Biomol Opt, Oettingenstr 67, D-80538 Munich, Germany.;Ludwig Maximilians Univ Munchen, Ctr Integrated Prot Sci CIPSM, Oettingenstr 67, D-80538 Munich, Germany..
    Roedig, P.
    Deutsch Elektronensynchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Meents, A.
    Deutsch Elektronensynchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Czech Acad Sci, ELI Beamlines, Inst Phys, Na Slovance 2, Prague 18221, Czech Republic.;Chalmers Univ Technol, Dept Phys, Condensed Matter Phys, Gothenburg, Sweden..
    Beyerlein, K. R.
    Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Chapman, H. N.
    Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Deutsch Elektronensynchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Bressler, C.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.;Tech Univ Denmark, Dept Phys, Fysikvej 307, DK-2800 Lyngby, Denmark.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Zinth, W.
    Ludwig Maximilians Univ Munchen, Inst Biomol Opt, Oettingenstr 67, D-80538 Munich, Germany.;Ludwig Maximilians Univ Munchen, Ctr Integrated Prot Sci CIPSM, Oettingenstr 67, D-80538 Munich, Germany..
    Rübhausen, M.
    Univ Hamburg, Inst Nanostruct & Solid State Phys, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci CFEL, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Herres-Pawlis, S.
    Rhein Westfal TH Aachen, Inst Inorgan Chem, D-52074 Aachen, Germany..
    Transferring the entatic-state principle to copper photochemistry2018In: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 10, no 3, p. 355-362Article in journal (Refereed)
    Abstract [en]

    The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored. Here we study a copper complex-with a specifically designed constraining ligand geometry-that exhibits metal-to-ligand charge-transfer state lifetimes that are very short. The guanidine-quinoline ligand used here acts on the bis(chelated) copper(I) centre, allowing only small structural changes after photoexcitation that result in very fast structural dynamics. The data were collected using a multimethod approach that featured time-resolved ultraviolet-visible, infrared and X-ray absorption and optical emission spectroscopy. Through supporting density functional calculations, we deliver a detailed picture of the structural dynamics in the picosecond-to-nanosecond time range.

  • 53. Duane Loh, N.
    et al.
    Starodub, D.
    Lomb, L.
    Hampton, C. Y.
    Martin, A. V.
    Sierra, R. G.
    Barty, A.
    Aquila, A.
    Schulz, J.
    Steinbrener, J.
    Shoeman, R. L.
    Kassemeyer, S.
    Bostedt, C.
    Bozek, J.
    Epp, S. W.
    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, M. S.
    Gumprecht, L.
    Coppola, N.
    Wunderer, C.
    Graafsma, H.
    Maia, F. R. N. C.
    Ekeberg, T.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, H.
    Hirsemann, H.
    Nass, K.
    White, T. A.
    Tobias, H. J.
    Farquar, G. R.
    Henry Benner, W.
    Hau-Riege, S.
    Reich, C.
    Hartmann, A.
    Soltau, H.
    Marchesini, S.
    Bajt, S.
    Barthelmess, M.
    Strueder, L.
    Ullrich, J.
    Bucksbaum, P.
    Hodgson, K. O.
    Frank, M.
    Schlichting, I.
    Chapman, H. N.
    Bogan, M. J.
    Profiling structured beams using injected aerosols2012In: Proceedings of SPIE: The International Society for Optical Engineering, 2012, p. 850403-Conference paper (Refereed)
    Abstract [en]

    Profiling structured beams produced by X-ray free-electron lasers (FELs) is crucial to both maximizing signal intensity for weakly scattering targets and interpreting their scattering patterns. Earlier ablative imprint studies describe how to infer the X-ray beam profile from the damage that an attenuated beam inflicts on a substrate. However, the beams in-situ profile is not directly accessible with imprint studies because the damage profile could be different from the actual beam profile. On the other hand, although a Shack-Hartmann sensor is capable of in-situ profiling, its lenses may be quickly damaged at the intense focus of hard X-ray FEL beams. We describe a new approach that probes the in-situ morphology of the intense FEL focus. By studying the translations in diffraction patterns from an ensemble of randomly injected sub-micron latex spheres, we were able to determine the non-Gaussian nature of the intense FEL beam at the Linac Coherent Light Source (SLAC National Laboratory) near the FEL focus. We discuss an experimental application of such a beam-profiling technique, and the limitations we need to overcome before it can be widely applied.

  • 54.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flash Diffractive Imaging in Three Dimensions2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During the last years we have seen the birth of free-electron lasers, a new type of light source ten billion times brighter than syncrotrons and able to produce pulses only a few femtoseconds long. One of the main motivations for building these multi-million dollar machines was the prospect of imaging biological samples such as proteins and viruses in 3D without the need for crystallization or staining. This thesis contains some of the first biological results from free-electron lasers.

    These results include 2D images, both of whole cells and of the giant mimivirus and also con- tains a 3D density map of the mimivirus assembled from diffraction patterns from many virus particles. These are important proof-of-concept experiments but they also mark the point where free-electron lasers start to produce biologically relevant results. The most noteworthy of these results is the unexpectedly non-uniform density distribution of the internals of the mimivirus.

    We also present Hawk, the only open-source software toolkit for analysing single particle diffraction data. The Uppsala-developed program suite supports a wide range fo algorithms and takes advantage of Graphics Processing Units which makes it very computationally efficient.

    Last, the problem introduced by structural variability in samples is discussed. This includes a description of the problem and how it can be overcome, and also how it could be turned into an advantage that allows us to image samples in all of their conformational states.

    List of papers
    1. Three-dimensional structure determination with an X-ray laser
    Open this publication in new window or tab >>Three-dimensional structure determination with an X-ray laser
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus. 

    Keywords
    Mimivirus, flash diffraction, three dimensional, imaging, CXI
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-179597 (URN)
    Funder
    EU, European Research Council
    Available from: 2012-08-20 Created: 2012-08-20 Last updated: 2014-09-26
    2. Single mimivirus particles intercepted and imaged with an X-ray laser
    Open this publication in new window or tab >>Single mimivirus particles intercepted and imaged with an X-ray laser
    Show others...
    2011 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, p. 78-81Article in journal (Refereed) Published
    Abstract [en]

    X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-146069 (URN)10.1038/nature09748 (DOI)000286886400037 ()21293374 (PubMedID)
    Available from: 2011-02-15 Created: 2011-02-15 Last updated: 2017-12-11
    3. Data requirements for single-particle diffractive imaging
    Open this publication in new window or tab >>Data requirements for single-particle diffractive imaging
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Single-shot diffractive imaging with ultra-short and very intense coherent X-ray pulses has become a routine experimental technique at new free-electron-laser facilities. Extension to three-dimensional imaging requires many diffraction pat- terns from identical objects captured in different orientations. These can then be combined into a full three-dimensional Fourier transform of the object. The ori- entation of the particle intercepted by the pulsed X-ray beam is usually unknown. This makes it hard to predict the number of patterns required to fully cover the Fourier space. In this paper we provide formulae to estimate the number of expo- sures required to achieve a given coverage of Fourier space as a function of parti- cle size, resolution and shot noise. 

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-179594 (URN)
    Funder
    EU, European Research Council
    Available from: 2012-08-20 Created: 2012-08-20 Last updated: 2014-09-26
    4. Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Open this publication in new window or tab >>Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Show others...
    2009 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 3, p. 031905-Article in journal (Refereed) Published
    Abstract [en]

    X-ray lasers may allow structural studies on single particles and biomolecules without crystalline periodicity in the samples. We examine here the effect of sample dynamics as a source of structural heterogeneity on the resolution of the reconstructed image of a small protein molecule. Structures from molecular-dynamics simulations of lysozyme were sampled and aligned. These structures were then used to calculate diffraction patterns corresponding to different dynamic states. The patterns were incoherently summed and the resulting data set was phased using the oversampling method. Reconstructed images of hydrated and dehydrated lysozyme gave resolutions of 3.7 angstrom and 7.6 angstrom, respectively. These are significantly worse than the root-mean-square deviation of the hydrated (2.7 angstrom for all atoms and 1.45 angstrom for C-alpha positions) or dehydrated (3.7 angstrom for all atoms and 2.5 angstrom for C-alpha positions) structures. The noise introduced by structural dynamics and incoherent addition of dissimilar structures restricts the maximum resolution to be expected from direct image reconstruction of dynamic systems. A way of potentially reducing this effect is by grouping dynamic structures into distinct structural substates and solving them separately.

    Keywords
    x-ray-diffraction, electron cascades, proteins, crystallography, resolution, pulses
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-111993 (URN)10.1103/PhysRevE.80.031905 (DOI)000270383400104 ()1539-3755 (ISBN)
    Note

    Part 1 501LM Times Cited:0 Cited References Count:32

    Available from: 2010-01-05 Created: 2010-01-05 Last updated: 2017-12-12Bibliographically approved
    5. Hawk: the image reconstruction package for coherent X-ray diffractive imaging
    Open this publication in new window or tab >>Hawk: the image reconstruction package for coherent X-ray diffractive imaging
    2010 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 43, no 6, p. 1535-1539Article in journal (Other academic) Published
    Abstract [en]

    The past few years have seen a tremendous growth in the field of coherent X-ray diffractive imaging, in large part due to X-ray free-electron lasers which provide a peak brilliance billions of times higher than that of synchrotrons. However, this rapid development in terms of hardware has not been matched on the software side. The release of Hawk is intended to close this gap. To the authors knowledge Hawk is the first publicly available and fully open source software program for reconstructing images from continuous diffraction patterns. The software handles all steps leading from a raw diffraction pattern to a reconstructed two-dimensional image including geometry determination, background correction, masking and phasing. It also includes preliminary three-dimensional support and support for graphics processing units using the Compute Unified Device Architecture, which speeds up processing by orders of magnitude compared to a single central processing unit. Hawk implements numerous algorithms and is easily extended. This, in combination with its open-source licence, provides a platform for other groups to test, develop and distribute their own algorithms.

    Keywords
    computer programs, diffractive imaging, free-electron lasers, Hawk, open-source software, phasing, reconstruction
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121927 (URN)10.1107/S0021889810036083 (DOI)000284550900033 ()
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
    6. Femtosecond diffractive imaging of biological cells
    Open this publication in new window or tab >>Femtosecond diffractive imaging of biological cells
    Show others...
    2010 (English)In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 43, no 19, p. 194015-Article in journal (Refereed) Published
    Abstract [en]

    In a flash diffraction experiment, a short and extremely intense x-ray pulse illuminates the sample to obtain a diffraction pattern before the onset of significant radiation damage. The over-sampled diffraction pattern permits phase retrieval by iterative phasing methods. Flash diffractive imaging was first demonstrated on an inorganic test object (Chapman et al 2006 Nat. Phys. 2 839-43). We report here experiments on biological systems where individual cells were imaged, using single, 10-15 fs soft x-ray pulses at 13.5 nm wavelength from the FLASH free-electron laser in Hamburg. Simulations show that the pulse heated the sample to about 160 000 K but not before an interpretable diffraction pattern could be obtained. The reconstructed projection images return the structures of the intact cells. The simulations suggest that the average displacement of ions and atoms in the hottest surface layers remained below 3 angstrom during the pulse.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-147259 (URN)10.1088/0953-4075/43/19/194015 (DOI)000281958100016 ()
    Available from: 2011-02-25 Created: 2011-02-24 Last updated: 2017-12-11Bibliographically approved
  • 55.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Engblom, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Liu, Jing
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters2015In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 29, p. 233-243Article in journal (Refereed)
  • 56.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Data requirements for single-particle diffractive imagingManuscript (preprint) (Other academic)
    Abstract [en]

    Single-shot diffractive imaging with ultra-short and very intense coherent X-ray pulses has become a routine experimental technique at new free-electron-laser facilities. Extension to three-dimensional imaging requires many diffraction pat- terns from identical objects captured in different orientations. These can then be combined into a full three-dimensional Fourier transform of the object. The ori- entation of the particle intercepted by the pulsed X-ray beam is usually unknown. This makes it hard to predict the number of patterns required to fully cover the Fourier space. In this paper we provide formulae to estimate the number of expo- sures required to achieve a given coverage of Fourier space as a function of parti- cle size, resolution and shot noise. 

  • 57.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
  • 58.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Abergel, Chantal
    Maia, Filipe
    Seltzer, Virginie
    Hantke, Max
    De Ponte, Daniel
    Aquila, Andrew
    Schulz, Joachim
    Andreasson, Jakob
    Iwan, Bianca
    Jönsson, Olof
    Westphal, Daniel
    Odić, Duško
    Andersson, Inger
    Barty, Anton
    Liang, Meng
    Seiberg, Marvin
    Martin, Andrew
    Nass, Karol
    Wang, Fenglin
    White, Thomas
    Gumprecht, Lars
    Fleckenstein, Holger
    Bajt, Saša
    Barthelmess, Miriam
    Claverie, Jean-Michel
    Tegze, Miklos
    Bortel, Gabor
    Faigel, Gyula
    Loh, Ne-Te Duane
    Coppola, Nicola
    Bostedt, Christoph
    Bozek, John
    Krzywinski, Jacek
    Messerschmidt, Marc
    Hodgson, Keith
    Treusch, Rolf
    Toleikis, Sven
    Dusterer, Stefan
    Feldhaus, Josef
    Weckert, Edgar
    Bogan, Michael
    Hampton, Christina
    Sierra, Raymond
    Doak, Bruce
    Weierstall, Uwe
    Spence, John
    Frank, Matthias
    Shoeman, Robert
    Lomb, Lukas
    Foucar, Lutz
    Epp, Sascha
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Hartmann, Andreas
    Kimmel, Nils
    Holl, Peter
    Rudek, Benedikt
    Erk, Benjamin
    Kassemeyer, Stephan
    Schlichting, Ilme
    Strüder, Lothar
    Ullrich, Joachim
    Schmidt, Carlo
    Krasniqi, Faton
    Hauser, Günter
    Reich, Christian
    Soltau, Heike
    Schorb, Sebastian
    Hirsemann, Helmut
    Wunderer, Cornelia
    Graafsma, Heinz
    Chapman, Henry
    Hajdu, Janos
    Three-dimensional structure determination with an X-ray laserManuscript (preprint) (Other academic)
    Abstract [en]

    Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus. 

  • 59.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Aquila, Andrew
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Ctr Etud Saclay, Commissariat Energie Atom & Energies Alternat, F-91191 Gif Sur Yvette, France..
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Liang, Meng
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Martin, Andrew V.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Melbourne, 161 Barry St, Melbourne, Vic 3010, Australia..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Bajt, Sasa
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barthelmess, Miriam
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Coppola, Nicola
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Claverie, Jean-Michel
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Loh, N. Duane
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;Natl Univ Singapore, Ctr BioImaging Sci, 14 Sci Dr 4 Blk S1 A, Singapore 117546, Singapore..
    Bostedt, Christoph
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bozek, John D.
    Synchrotron SOLEIL, Lorme Merisiers Roundabout St Aubin, F-91190 St Aubin, France..
    Krzywinski, Jacek
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bogan, Michael J.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Hampton, Christina Y.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Sierra, Raymond G.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Frank, Matthias
    Lawrence Livermore Natl Lab, 7000 East Ave,Mail Stop L-211, Livermore, CA 94551 USA..
    Shoeman, Robert L.
    Lomb, Lukas
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Foucar, Lutz
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Epp, Sascha W.
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Rolles, Daniel
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Rudenko, Artem
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Hartmann, Robert
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Hartmann, Andreas
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Kimmel, Nils
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Holl, Peter
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Weidenspointner, Georg
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Rudek, Benedikt
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Erk, Benjamin
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Kassemeyer, Stephan
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Schlichting, Ilme
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Strueder, Lothar
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany.;Univ Siegen, Emmy Noether Campus,Walter Flex Str 3, D-57068 Siegen, Germany..
    Ullrich, Joachim
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Phys Tech Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany..
    Schmidt, Carlo
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Krasniqi, Faton
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Hauser, Guenter
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Reich, Christian
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Soltau, Heike
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Schorb, Sebastian
    Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany..
    Hirsemann, Helmut
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Wunderer, Cornelia
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Graafsma, Heinz
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Notkestr 85, D-22607 Hamburg, Germany..
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed)
    Abstract [en]

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

  • 60.
    Ekholm, Victor
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Walz, Marie-Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Werner, Josephina
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Öhrwall, Gunnar
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Björneholm, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Surface propensity of atmospherically relevant carboxylates and alkyl ammonium ions studied by XPS: towards a building-block model of surface propensity based on Langmuir adsorptionManuscript (preprint) (Other academic)
  • 61.
    Espinoza, Shirly
    et al.
    Czech Acad Sci, Inst Phys, ELI Beamlines, Na Slovance 2, Prague 18221, Czech Republic..
    Neuber, Gerd
    Univ Hamburg, Inst Nanostruct & Solid State Phys, Ctr Free Electron Laser Sci, Adv Study Grp APOG, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Brooks, Christopher D.
    Czech Acad Sci, Inst Phys, ELI Beamlines, Na Slovance 2, Prague 18221, Czech Republic..
    Besner, Bastian
    Univ Hamburg, Inst Nanostruct & Solid State Phys, Ctr Free Electron Laser Sci, Adv Study Grp APOG, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Hashemi, Maryam
    4 DOS GmbH, Wehmerweg 26, D-22529 Hamburg, Germany..
    Ruebhausen, Michael
    Univ Hamburg, Inst Nanostruct & Solid State Phys, Ctr Free Electron Laser Sci, Adv Study Grp APOG, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Czech Acad Sci, Inst Phys, ELI Beamlines, Na Slovance 2, Prague 18221, Czech Republic.; Chalmers, Dept Phys, Condensed Matter Phys, Kemigarden 1, SE-41296 Gothenburg, Sweden..
    User oriented end-station on VUV pump-probe magneto-optical ellipsometry at ELI beamlines2017In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 421, no Part B, p. 378-382Article in journal (Refereed)
    Abstract [en]

    A state of the art ellipsometer for user operations is being implemented at ELI Beamlines in Prague, Czech Republic. It combines three of the most promising and exotic forms of ellipsometry: VUV, pump-probe and magneto-optical ellipsometry. This new ellipsometer covers a spectral operational range from the NIR up to the VUV, with high through-put between 1 and 40 eV. The ellipsometer also allows measurements of magneto-optical spectra with a 1 kHz switchable magnetic field of up to 1.5 T across the sample combining ellipsometry and Kerr spectroscopy measurements in an unprecedented spectral range. This form of generalized ellipsometry enables users to address diagonal and off-diagonal components of the dielectric tensor within one measurement. Pump-probe measurements enable users to study the dynamic behaviour of the dielectric tensor in order to resolve the time-domain phenomena in the femto to 100 ns range.

  • 62.
    Farmand, Maryam
    et al.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Celestre, Richard
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Denes, Peter
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Kilcoyne, A. L. David
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Marchesini, Stefano
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Padmore, Howard
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Tyliszczak, Tolek
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Warwick, Tony
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Shi, Xiaowen
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.;Univ Oregon, Dept Phys, Eugene, OR 97401 USA..
    Lee, James
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.;Univ Oregon, Dept Phys, Eugene, OR 97401 USA..
    Yu, Young-Sang
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.;Univ Illinois, Dept Chem, Chicago, IL 60607 USA..
    Cabana, Jordi
    Univ Illinois, Dept Chem, Chicago, IL 60607 USA..
    Joseph, John
    Lawrence Berkeley Natl Lab, Div Engn, Berkeley, CA 94720 USA..
    Krishnan, Harinarayan
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Perciano, Talita
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shapiro, David A.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Near-edge X-ray refraction fine structure microscopy2017In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 110, no 6, article id 063101Article in journal (Refereed)
    Abstract [en]

    We demonstrate a method for obtaining increased spatial resolution and specificity in nanoscale chemical composition maps through the use of full refractive reference spectra in soft x-ray spectro- microscopy. Using soft x-ray ptychography, we measure both the absorption and refraction of x-rays through pristine reference materials as a function of photon energy and use these reference spectra as the basis for decomposing spatially resolved spectra from a heterogeneous sample, thereby quantifying the composition at high resolution. While conventional instruments are limited to absorption contrast, our novel refraction based method takes advantage of the strongly energy dependent scattering cross-section and can see nearly five-fold improved spatial resolution on resonance.

  • 63.
    Ferreira, Ricardo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Lisbon, Fac Pharm, iMed ULisboa Res Inst Med, Ave Prof Gama Pinto, P-1649003 Lisbon, Portugal.
    Kincses, Annamaria
    Univ Szeged, Fac Med, Dept Med Microbiol & Immunobiol, Dom Ter 10, H-6720 Szeged, Hungary.
    Gajdacs, Mario
    Univ Szeged, Fac Med, Dept Med Microbiol & Immunobiol, Dom Ter 10, H-6720 Szeged, Hungary.
    Spengler, Gabriella
    Univ Szeged, Fac Med, Dept Med Microbiol & Immunobiol, Dom Ter 10, H-6720 Szeged, Hungary.
    dos Santos, Daniel J. V. A.
    Univ Lisbon, Fac Pharm, iMed ULisboa Res Inst Med, Ave Prof Gama Pinto, P-1649003 Lisbon, Portugal;Univ Porto, Dept Chem & Biochem, Fac Sci, LAQV REQUIMTE, Rua Campo Alegre, P-4169007 Porto, Portugal.
    Molnar, Joseph
    Univ Szeged, Fac Med, Dept Med Microbiol & Immunobiol, Dom Ter 10, H-6720 Szeged, Hungary.
    Ferreira, Maria-Jose U.
    Univ Lisbon, Fac Pharm, iMed ULisboa Res Inst Med, Ave Prof Gama Pinto, P-1649003 Lisbon, Portugal.
    Terpenoids from Euphorbia pedroi as Multidrug-Resistance Reversers2018In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 81, no 9, p. 2032-2040Article in journal (Refereed)
    Abstract [en]

    The phytochemical study of Euphorbia pedroi led to the isolation of a new tetracyclic triterpenoid with an unusual spiro scaffold, spiropedroxodiol (1), along with seven known terpenoids (2-8). Aiming at obtaining compounds with improved multidrug-resistance (MDR) reversal activity, compound 8, an ent-abietane diterpene, was derivatized by introducing nitrogen-containing and aromatic moieties, yielding compounds 9-14. The structures of compounds were characterized by detailed spectroscopic analysis, including 2D NMR experiments (COSY, HMQC/HSQC, HMBC, and NOESY). Compounds 1-14 were evaluated for their MDR-reversing activity on human ABCB1 gene transfected mouse lymphoma cells (L5178Y-MDR) through a combination of functional and chemosensitivity assays. The natural compounds 1-8 were further evaluated on resistant human colon adenocarcinoma cells (Colo320), and, additionally, their cytotoxicity was assessed on noncancerous mouse (NIH/3T3) and human (MRC-5) embryonic fibroblast cell lines. While spiropedroxodiol (1) was found to be a very strong MDR reversal agent in both L5178Y-MDR and Colo320 cells, the chemical modifications of helioscopinolide E (8) at C-3 positively contributed to increase the MDR reversal activity of compounds 10, 12, and 13. Furthermore, in combination assays, compounds 1 and 7-14 enhanced synergistically the cytotoxicity of doxorubicin. Finally, by means of molecular docking, the key residues and binding modes by which compounds 1-14 may interact with a murine P-glycoprotein model were identified, allowing additional insights on the efflux modulation mechanism of these compounds.

  • 64. Fuchs, M.a b
    et al.
    Trigo, M.b c
    Chen, J.b
    Ghimire, S.b
    Shwartz, S.d
    Kozina, M.b
    Jiang, M.b
    Henighan, T.b
    Bray, C.b
    Ndabashimiye, G.b
    Feng, Y.e
    Herrmann, S.f
    Carini, G.f
    Pines, J.f
    Hart, P.f
    Kenney, C.f
    Guillet, S.e
    Boutete, Sébastien
    Williams, G.e
    Messerschmidt, M.e
    Seibert, M. M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Möllere, Stefan
    Hastings, J.B.e
    Reis, D.A.b g
    Nonlinear X-ray compton scattering2014Conference paper (Other academic)
    Abstract [en]

    We use XFEL pulses to observe the most fundamental nonlinear X-ray-matter interaction: nonlinear Compton scattering. In contrast to theoretical predictions, we measure an anonymous and yet to be explained red-shift in the observed photon energy.

  • 65.
    Gabrysch, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Twitchen, D. J.
    Element Six Ltd, Ascot SL5 8BP, Berks, England.
    Rudati, J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Lindenberg, A. M.
    Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, USA; PULSE Center, Stanford Linear Accelerator Center, Menlo Park, California 94025, USA.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Falcone, R. W.
    Department of Physics, University of California, Berkeley, California 94720, USA.
    Tschentscher, T.
    Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.
    Moffat, K.
    Consortium for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA.
    Bucksbaum, P. H.
    PULSE Center, Stanford Linear Accelerator Center, Menlo Park, California 94025, USA.
    Als-Nielsen, J.
    Niels Bohr Institute, Copenhagen University, 2100 Copenhagen Ø, Denmark.
    Nelson, A. J.
    Lawrence Livermore National Laboratory, Livermore, California 94550, USA.
    Siddons, D. P.
    National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973, USA.
    Emma, P. J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Krejcik, P.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Schlarb, H.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Arthur, J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Brennan, S.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Hastings, J.
    Stanford Linear Accelerator Ctr, PULSE Ctr, Menlo Pk, CA 94025 USA.
    Isberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses2008In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 103, no 6, article id 064909Article in journal (Refereed)
    Abstract [en]

    Secondary electron cascades were measured in high purity single-crystalline chemical vapor deposition (CVD) diamond, following exposure to ultrashort hard x-ray pulses (140 fs full width at half maximum, 8.9 keV energy) from the Sub-Picosecond Pulse Source at the Stanford Linear Accelerator Center. We report measurements of the pair creation energy and of drift mobility of carriers in two CVD diamond crystals. This was done for the first time using femtosecond x-ray excitation. Values for the average pair creation energy were found to be 12.17 +/- 0.57 and 11.81 +/- 0.59 eV for the two crystals, respectively. These values are in good agreement with recent theoretical predictions. The average drift mobility of carriers, obtained by the best fit to device simulations, was mu(h)= 2750 cm(2)/V s for holes and was mu(e)= 2760 cm(2) / V s for electrons. These mobility values represent lower bounds for charge mobilities due to possible polarization of the samples. The results demonstrate outstanding electric properties and the enormous potential of diamond in ultrafast x-ray detectors.

  • 66. Galli, Lorenzo
    et al.
    Son, Sang-Kil
    Barends, Thomas R. M.
    White, Thomas A.
    Barty, Anton
    Botha, Sabine
    Boutet, Sébastien
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Doak, R. Bruce
    Nanao, Max H.
    Nass, Karol
    Shoeman, Robert L.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Santra, Robin
    Schlichting, Ilme
    Chapman, Henry N.
    Towards phasing using high X-ray intensity2015In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 2, p. 627-634Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential ‘bleaching’ of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

  • 67. Ge, X.
    et al.
    Boutu, W.
    Gauthier, D.
    Wang, F.
    Borta, A.
    Barbrel, B.
    Ducousso, M.
    Gonzalez, A. I.
    Carre, B.
    Guillaumet, D.
    Perdrix, M.
    Gobert, O.
    Gautier, J.
    Lambert, G.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zeitoun, P.
    Merdji, H.
    Impact of wave front and coherence optimization in coherent diffractive imaging2013In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, no 9, p. 11441-11447Article in journal (Refereed)
    Abstract [en]

    We present single shot nanoscale imaging using a table-top femtosecond soft X-ray laser harmonic source at a wavelength of 32 nm. We show that the phase retrieval process in coherent diffractive imaging critically depends on beam quality. Coherence and image fidelity are measured from single-shot coherent diffraction patterns of isolated nano-patterned slits. Impact of flux, wave front and coherence of the soft X-ray beam on the phase retrieval process and the image quality are discussed. After beam improvements, a final image reconstruction is presented with a spatial resolution of 78 nm (half period) in a single 20 fs laser harmonic shot. 

  • 68.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hutchison, Geoffrey R.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed)
  • 69.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ditz, Jonas C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145Article in journal (Refereed)
  • 70.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Efficient Physics-Based Polarizable Charges: from Organic Compounds to ProteinsManuscript (preprint) (Other academic)
  • 71.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    The Alexandria library, a quantum-chemical database of molecular properties for force field development2018In: Scientific Data, E-ISSN 2052-4463Article in journal (Refereed)
  • 72. Glownia, James M.
    et al.
    Cryan, J.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Belkacem, A.
    Berrah, N.
    Blaga, C. I.
    Bostedt, C.
    Bozek, J.
    DiMauro, L. F.
    Fang, L.
    Frisch, J.
    Gessner, O.
    Guehr, M.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hertlein, M. P.
    Hoener, M.
    Huang, G.
    Kornilov, O.
    Marangos, J. P.
    March, A. M.
    McFarland, B. K.
    Merdji, H.
    Petrovic, V. S.
    Raman, C.
    Ray, D.
    Reis, D. A.
    Trigo, M.
    White, J. L.
    White, W.
    Wilcox, R.
    Young, L.
    Coffee, R. N.
    Bucksbaum, P. H.
    Time-resolved pump-probe experiments at the LCLS2010In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 18, no 17, p. 17620-17630Article in journal (Refereed)
    Abstract [en]

    The first time-resolved x-ray/optical pump-probe experiments at the SLAC Linac Coherent Light Source (LCLS) used a combination of feedback methods and post-analysis binning techniques to synchronize an ultrafast optical laser to the linac-based x-ray laser. Transient molecular nitrogen alignment revival features were resolved in time-dependent x-ray-induced fragmentation spectra. These alignment features were used to find the temporal overlap of the pump and probe pulses. The strong-field dissociation of x-ray generated quasi-bound molecular dications was used to establish the residual timing jitter. This analysis shows that the relative arrival time of the Ti:Sapphire laser and the x-ray pulses had a distribution with a standard deviation of approximately 120 fs. The largest contribution to the jitter noise spectrum was the locking of the laser oscillator to the reference RF of the accelerator, which suggests that simple technical improvements could reduce the jitter to better than 50 fs.

  • 73. Gorkhover, Tais
    et al.
    Ulmer, Anatoli
    Ferguson, Ken
    Bucher, Max
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bruza, Petr
    Carron, Sebastian
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rupp, Daniela
    Sauppe, Mario
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N.
    Faigel, Gyula
    Möller, Thomas