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  • 1.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca Stella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobicrajski, R.
    Tolcikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, no 1, p. 016403-Article in journal (Refereed)
    Abstract [en]

    Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 1017 W/cm2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 1016 W/cm2. This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.

  • 2.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Liang, Meng
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Wang, Fenglin
    Iwan, Bianca
    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
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    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.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Hartmann, Robert
    Erk, Benjamin
    Rudek, Benedikt
    Chapman, Henry N.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Automated identification and classification of single particle serial femtosecond X-ray diffraction data2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 3, p. 2497-2510Article in journal (Refereed)
    Abstract [en]

    The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of America

  • 3.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    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.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Chapman, Henry N.
    Bielecki, Johan
    Abergel, C.
    Seltzer, V.
    Claverie, J.-M.
    Svenda, M.
    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.
    Time of Flight Mass Spectrometry to Monitor Sample Expansion in Flash Diffraction Studies on Single Virus ParticlesManuscript (preprint) (Other academic)
  • 4. Aquila, Andrew
    et al.
    Hunter, Mark S.
    Doak, R. Bruce
    Kirian, Richard A.
    Fromme, Petra
    White, Thomas A.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Arnlund, David
    Bajt, Saša
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bottin, Hervé
    Bozek, John D.
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Frank, Matthias
    Fromme, Raimund
    Graafsma, Heinz
    Grotjohann, Ingo
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Andreas
    Hartmann, Robert
    Hau-Riege, Stefan
    Hauser, Günter
    Hirsemann, Helmut
    Holl, Peter
    Holton, James M.
    Hömke, André
    Johansson, Linda
    Kimmel, Nils
    Kassemeyer, Stephan
    Krasniqi, Faton
    Kühnel, Kai-Uwe
    Liang, Mengning
    Lomb, Lukas
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Messerschmidt, Marc
    Nass, Karol
    Reich, Christian
    Neutze, Richard
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schmidt, Carlo
    Schmidt, Kevin E.
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Soltau, Heike
    Shoeman, Robert L.
    Sierra, Raymond
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Strüder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wang, Xiaoyu
    Williams, Garth J.
    Weidenspointner, Georg
    Weierstall, Uwe
    Wunderer, Cornelia
    Barty, Anton
    Spence, John C. H.
    Chapman, Henry N.
    Time-resolved protein nanocrystallography using an X-ray free-electron laser2012In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 3, p. 2706-2716Article in journal (Refereed)
    Abstract [en]

    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.

  • 5. Barty, Anton
    et al.
    Caleman, Carl
    Aquila, Andrew
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lomb, Lukas
    White, Thomas A.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Arnlund, David
    Bajt, Sasa
    Barends, Thomas R. M.
    Barthelmess, Miriam
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John D.
    Coffee, Ryan
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    DePonte, Daniel P.
    Doak, R. Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Elser, Veit
    Epp, Sascha W.
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Fromme, Petra
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y.
    Hartmann, Robert
    Hartmann, Andreas
    Hauser, Guenter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S.
    Johansson, Linda
    Kassemeyer, Stephan
    Kimmel, Nils
    Kirian, Richard A.
    Liang, Mengning
    Maia, Filipe R. N. C.
    Malmerberg, Erik
    Marchesini, Stefano
    Martin, Andrew V.
    Nass, Karol
    Neutze, Richard
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Scott, Howard
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shoeman, Robert L.
    Sierra, Raymond G.
    Soltau, Heike
    Spence, John C. H.
    Stellato, Francesco
    Stern, Stephan
    Strueder, Lothar
    Ullrich, Joachim
    Wang, X.
    Weidenspointner, Georg
    Weierstall, Uwe
    Wunderer, Cornelia B.
    Chapman, Henry N.
    Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements2012In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 6, no 1, p. 35-40Article in journal (Refereed)
    Abstract [en]

    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 analysis(1). 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 information(1-4). 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 technology(5) should enable structural determination from submicrometre protein crystals with atomic resolution.

  • 6.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    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.
    Feasibility of imaging living cells at subnanometer resolutions by ultrafast X-ray diffraction2008In: Quarterly reviews of biophysics (Print), ISSN 0033-5835, E-ISSN 1469-8994, Vol. 41, no 3-4, p. 181-204Article, review/survey (Refereed)
    Abstract [en]

    Detailed structural investigations on living cells are problematic because existing structural methods cannot reach high resolutions on non-reproducible objects. Illumination with an ultrashort and extremely bright X-ray pulse can outrun key damage processes over a very short period. This can be exploited to extend the diffraction signal to the highest possible resolution in flash diffraction experiments. Here we present an analysis or the interaction of a very intense and very short X-ray pulse with a living cell, using a non-equilibrium population kinetics plasma code with radiation transfer. Each element in the evolving plasma is modeled by numerous states to monitor changes in the atomic populations as a function of pulse length, wavelength, and fluence. The model treats photoionization, impact ionization, Auger decay, recombination, and inverse bremsstrahlung by solving rate equations in a self-consistent manner and describes hydrodynamic expansion through the ion sound speed, The results show that subnanometer resolutions could be reached on micron-sized cells in a diffraction-limited geometry at wavelengths between 0.75 and 1.5 nm and at fluences of 10(11)-10(12) photonS mu M (2) in less than 10 fs. Subnanometer resolutions could also be achieved with harder X-rays at higher fluences. We discuss experimental and computational strategies to obtain depth information about the object in flash diffraction experiments.

  • 7.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S. P.
    Scott, H. A.
    Interaction of Ultrashort X-ray Pulses with B4C, SiC and Si2008In: 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. 77, no 2, p. 026404-1-026404-8Article in journal (Refereed)
    Abstract [en]

    The interaction of 32.5 and 6 nm ultrashort x-ray pulses with the solid materials B4C, SiC, and Si is simulated with a nonlocal thermodynamic equilibrium radiation transfer code. We study the ionization dynamics as a function of depth in the material and modifications of the opacity during irradiation, and estimate the crater depth. Furthermore, we compare the estimated crater depth with experimental data, for fluences up to 2.2 J/cm(2). Our results show that, at 32.5 nm irradiation, the opacity changes by less than a factor of 2 for B4C and Si and by a factor of 3 for SiC, for fluences up to 200 J/cm(2). At a laser wavelength of 6 nm, the model predicts a dramatic decrease in opacity due to the weak inverse bremsstrahlung, increasing the crater depth for high fluences.

  • 8.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Model for the Dynamics of a Water Cluster in an X-ray Free Electron Laser Beam2004In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 70, no 5:1, p. 051904-Article in journal (Refereed)
    Abstract [en]

    A microscopic sample placed into a focused x-ray free electron laser beam will explode due to strong ionization on a femtosecond time scale. The dynamics of this Coulomb explosion has been modeled by Neutze et al. [Nature (London) 406, 752 (2000)] for a protein, using computer simulations. The results suggest that by using ultrashort exposures, structural information may be collected before the sample is destroyed due to radiation damage. In this paper a method is presented to include the effect of screening by free electrons in the sample in a molecular dynamics simulation. The electrons are approximated by a classical gas, and the electron distribution is calculated iteratively from the Poisson-Boltzmann equation. Test simulations of water clusters reveal the details of the explosion dynamics, as well as the evolution of the free electron gas during the beam exposure. We find that inclusion of the electron gas in the model slows down the Coulomb explosion. The hydrogen atoms leave the sample faster than the oxygen atoms, leading to a double layer of positive ions. A considerable electron density is located between these two layers. The fact that the hydrogens are found to explode much faster than the oxygens means that the diffracting part of the sample stays intact somewhat longer than the sample as a whole.

  • 9.
    Beyerlein, Kenneth
    et al.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Alonso-Mori, Roberto
    SLAC National Accelerator Laboratory, USA.
    Aquila, Andrew
    SLAC National Accelerator Laboratory, USA.
    Bajt, Sasa
    Photon Science, DESY, Hamburg, Germany.
    Barty, Anton
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Bean, Richard
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Koglin, Jason E.
    SLAC National Accelerator Laboratory, USA.
    Messerschmidt, Marc
    SLAC National Accelerator Laboratory, USA.
    Ragazzon, Davide
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Soklaras, Dimosthenis
    SLAC National Accelerator Laboratory, USA.
    Williams, Garth J.
    SLAC National Accelerator Laboratory, USA.
    Hau-Riege, Stefan
    Lawrence Livermore National Laboratory, USA.
    Boutet, Sebastien
    SLAC National Accelerator Laboratory, USA.
    Chapman, Henry N.
    Center for Free-Electron Laser Science,Deutsches Elektronen-Synchrotron, Hamburg, Germany; Department of Physics, University of Hamburg, Hamburg, Germany; Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany .
    Timneanu, Nicusor
    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, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science,Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Ultrafast non-thermal heating of water initiated by an X-ray laser2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 22, p. 5652-5657Article in journal (Refereed)
    Abstract [en]

    X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction region. We have observed structural changes in the carrying water during X-ray exposure, showing how it transforms from the liquid phase to a plasma. This ultrafast phase transition observed in water provides evidence that any biological structure exposed to these X-ray pulses is destroyed during the X-ray exposure.The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

  • 10.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    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.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gunn, Laura H.
    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.
    Munke, Anna
    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.
    Flueckiger, Leonie
    Pietrini, Alberto
    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.
    Lundholm, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    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.
    Kulyk, Olena
    Higashiura, Akifumi
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Ne-Te Duane
    Wysong, Taylor E.
    Bostedt, Christoph
    Gorkhover, Tais
    Iwan, Bianca
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Osipov, Timur
    Walter, Peter
    Hart, Philip
    Bucher, Maximilian
    Ulmer, Anatoli
    Ray, Dipanwita
    Carini, Gabriella
    Ferguson, Ken R.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Electrospray sample injection for single-particle imaging with x-ray lasers2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed)
  • 11. Bogan, M. J.
    et al.
    Boutet, S.
    Barty, A.
    Benner, W. H.
    Frank, M.
    Lomb, L.
    Shoeman, R.
    Starodub, D.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S. P.
    Woods, B.
    Decorwin-Martin, P.
    Bajt, S.
    Schulz, J.
    Rohner, U.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S.
    Schlichting, I.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, H. N.
    Single-shot femtosecond x-ray diffraction from randomly oriented ellipsoidal nanoparticles2010In: Physical Review Special Topics. Accelerators and Beams, ISSN 1098-4402, E-ISSN 1098-4402, Vol. 13, no 9, p. 094701-Article in journal (Refereed)
    Abstract [en]

    Coherent diffractive imaging of single particles using the single-shot "diffract and destroy" approach with an x-ray free electron laser (FEL) was recently demonstrated. A high-resolution low-noise coherent diffraction pattern, representative of the object before it turns into a plasma and explodes, results from the interaction of the FEL with the particle. Iterative phase retrieval algorithms are used to reconstruct two-dimensional projection images of the object from the recorded intensities alone. Here we describe the first single-shot diffraction data set that mimics the data proposed for obtaining 3D structure from identical particles. Ellipsoidal iron oxide nanoparticles (250 nm x 50 nm) were aerosolized and injected through an aerodynamic lens stack into a soft x-ray FEL. Particle orientation was not controlled with this injection method. We observed that, at the instant the x-ray pulse interacts with the particle, a snapshot of the particle's orientation is encoded in the diffraction pattern. The results give credence to one of the technical concepts of imaging individual nanometer and subnanometer-sized objects such as single molecules or larger clusters of molecules using hard x-ray FELs and will be used to help develop robust algorithms for determining particle orientations and 3D structure.

  • 12. Bogan, Michael J.
    et al.
    Boutet, Sebastien
    Chapman, Henry N.
    Marchesini, Stefano
    Barty, Anton
    Benner, W. Henry
    Rohner, Urs
    Frank, Matthias
    Hau-Riege, Stefan P.
    Bajt, Sasa
    Woods, Bruce
    Seibert, M. Marvin
    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.
    Timneanu, Nicusor
    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.
    Schulz, Joachim
    Aerosol Imaging with a Soft X-Ray Free Electron Laser2010In: Aerosol Science and Technology, ISSN 0278-6826, E-ISSN 1521-7388, Vol. 44, no 3, p. I-VIArticle in journal (Refereed)
    Abstract [en]

    Lasers have long played a critical role in the advancement of aerosol science. A new regime of ultrafast laser technology has recently be realized, the world's first soft x-ray free electron laser. The Free electron LASer in Hamburg, FLASH, user facility produces a steady source of 10 femtosecond pulses of 7–32 nm x-rays with 1012 photons per pulse. The high brightness, short wavelength, and high repetition rate (> 500 pulses per second) of this laser offers unique capabilities for aerosol characterization. Here we use FLASH to perform the highest resolution imaging of single PM2.5 aerosol particles in flight to date. We resolve to 35 nm the morphology of fibrous and aggregated spherical carbonaceous nanoparticles that existed for less than two milliseconds in vacuum. Our result opens the possibility for high spatial- and time-resolved single particle aerosol dynamics studies, filling a critical technological need in aerosol science.

  • 13. Boutet, Sébastien
    et al.
    Lomb, Lukas
    Williams, Garth J
    Barends, Thomas R M
    Aquila, Andrew
    Doak, R Bruce
    Weierstall, Uwe
    DePonte, Daniel P
    Steinbrener, Jan
    Shoeman, Robert L
    Messerschmidt, Marc
    Barty, Anton
    White, Thomas A
    Kassemeyer, Stephan
    Kirian, Richard A
    Seibert, M Marvin
    Montanez, Paul A
    Kenney, Chris
    Herbst, Ryan
    Hart, Philip
    Pines, Jack
    Haller, Gunther
    Gruner, Sol M
    Philipp, Hugh T
    Tate, Mark W
    Hromalik, Marianne
    Koerner, Lucas J
    van Bakel, Niels
    Morse, John
    Ghonsalves, Wilfred
    Arnlund, David
    Bogan, Michael J
    Caleman, Carl
    Fromme, Raimund
    Hampton, Christina Y
    Hunter, Mark S
    Johansson, Linda C
    Katona, Gergely
    Kupitz, Christopher
    Liang, Mengning
    Martin, Andrew V
    Nass, Karol
    Redecke, Lars
    Stellato, Francesco
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Dingjie
    Zatsepin, Nadia A
    Schafer, Donald
    Defever, James
    Neutze, Richard
    Fromme, Petra
    Spence, John C H
    Chapman, Henry N
    Schlichting, Ilme
    High-resolution protein structure determination by serial femtosecond crystallography2012In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 337, no 6092, p. 362-364Article in journal (Refereed)
    Abstract [en]

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  • 14. Caleman, Carl
    et al.
    Bergh, Magnus
    Scott, Howard A.
    Spence, John C. H.
    Chapman, Henry N.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses2011In: Journal of Modern Optics, ISSN 0950-0340, E-ISSN 1362-3044, Vol. 58, no 16, p. 1486-1497Article in journal (Refereed)
    Abstract [en]

    The Linac Coherent Light Source (LCLS) is the first X-ray free electron laser to achieve lasing at subnanometer wavelengths (6 angstrom). LCLS is poised to reach even shorter wavelengths (1.5 angstrom) and thus holds the promise of single molecular imaging at atomic resolution. The initial operation at a photon energy of 2 keV provides the possibility to perform the first experiments on damage to biological particles, and to assess the limitations to coherent imaging of biological samples, which are directly relevant at atomic resolution. In this paper we theoretically investigate the damage formation and detection possibilities for a biological crystal, by employing and comparing two different damage models with complementary strengths. Molecular dynamics provides a discrete approach which investigates structural details at the atomic level by tracking all atoms in the real space. Our continuum model is based on a non-local thermodynamics equilibrium code with atomic kinetics and radiation transfer and can treat hydrodynamic expansion of the entire system. The latter approach captures the essential features of atomic displacements, without taking into account structural information and intrinsic atomic movements. This proves to be a powerful computational tool for many samples, including biological crystals, which will be studied with X-ray free electron lasers.

  • 15. Caleman, Carl
    et al.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ortiz, Carlos
    Parak, Fritz G.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Chapman, Henry N.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses2011In: ACS Nano, ISSN 1936-0851, Vol. 5, no 1, p. 139-146Article in journal (Refereed)
    Abstract [en]

    Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses Such pulses may allow the imaging of single molecules, clusters; Or nanoparticles: Coherent flash Imaging Will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain Inaccessible using conventional X-ray sources.

  • 16.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Ortiz, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Parak, Fritz G.
    van der Spool, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nanocrystal imaging using intense and ultrashort X-ray pulsesManuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

    Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters or nanoparticles, but coherent flash imaging will also open up new avenues for structural studies on nano- and micro-crystalline substances. This paper addresses the potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances, and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals.

  • 17.
    Caleman, Carl
    et al.
    Physik Department E17, Technische Universität München.
    Ortiz, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bultmark, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Gabrysch, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Parak, F. G.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Klintenberg, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Radiation damage in biological material: electronic properties and electron impact ionization in urea2009In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 85, no 1, p. 18005-Article in journal (Refereed)
    Abstract [en]

    Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-rays. In crystallography this process can be limited through damage distribution in a crystal, while for single molecular imaging it can be outrun by employing short intense pulses. Secondary electron generation is crucial during damage formation and we present a study of urea, as model for biomaterial. From first principles we calculate the band structure and energy loss function, and subsequently the inelastic electron cross-section in urea. Using Molecular Dynamics simulations, we quantify the damage and study the magnitude and spatial extent of the electron cloud coming from an incident electron, as well as the dependence with initial energy.

  • 18.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Aquila, Andrew
    Barty, Anton
    Scott, Howard A.
    White, Thomas A.
    Chapman, Henry N.
    Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser2015In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 23, no 2, p. 1213-1231Article in journal (Refereed)
    Abstract [en]

    In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

  • 19.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Tîmneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, A. V.
    White, T. A.
    Scott, H. A.
    Barty, A.
    Aquila, A.
    Chapman, H. N.
    Modeling of XFEL induced ionization and atomic displacement in protein nanocrystals2012In: Proceedings of SPIE: The International Society for Optical Engineering, 2012, p. 85040H-Conference paper (Refereed)
    Abstract [en]

    X-ray free-electron lasers enable high-resolution imaging of biological materials by using short enough pulses to outrun many of the effects of radiation damage. Experiments conducted at the LCLS have obtained diffraction data from single particles and protein nanocrystals at doses to the sample over 3 GGy. The details of the interaction of the X-ray FEL pulse with the sample determine the limits of this new paradigm for imaging. Recent studies suggest that in the case of crystalline samples, such as protein nanocrystals, the atomic displacements and loss of bound electrons in the crystal (due to the high X- ray intensity) has the effect of gating the diffraction signal, and hence making the experiment less radiation sensitive. Only the incident photon intensity in the first part of the pulse, before the Bragg diffraction has died out, is relevant to acquiring signal and the rest of the pulse will mainly contribute to a diffuse background. In this work we use a plasma based non-local thermodynamic equilibrium code to explore the displacement and the ionization of a protein nanocrystal at various X-ray wavelengths and intensities.

  • 20. Cavalieri, A L
    et al.
    Fritz, D M
    Lee, S H
    Bucksbaum, P H
    Reis, D A
    Rudati, J
    Mills, D M
    Fuoss, P H
    Stephenson, G B
    Kao, C C
    Siddons, D P
    Lowney, D P
    Macphee, A G
    Weinstein, D
    Falcone, R W
    Pahl, R
    Als-Nielsen, J
    Blome, C
    Düsterer, S
    Ischebeck, R
    Schlarb, H
    Schulte-Schrepping, H
    Tschentscher, Th
    Schneider, J
    Hignette, O
    Sette, F
    Sokolowski-Tinten, K
    Chapman, H N
    Lee, R W
    Hansen, T N
    Synnergren, O
    Larsson, J
    Techert, S
    Sheppard, J
    Wark, J S
    Bergh, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Caleman, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Huldt, G
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Timneanu, N
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Akre, R A
    Bong, E
    Emma, P
    Krejcik, P
    Arthur, J
    Brennan, S
    Gaffney, K J
    Lindenberg, A M
    Luening, K
    Hastings, J B
    Clocking femtosecond X rays.2005In: Phys Rev Lett, ISSN 0031-9007, Vol. 94, no 11, p. 114801-Article in journal (Refereed)
    Abstract [en]

    Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.

  • 21. Chapman, H N
    et al.
    Bajt, S
    Barty, A
    Benner, W H
    Bogan, M J
    Boutet, S
    Cavalleri, A
    Duesterer, S
    Frank, M
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S P
    Iwan, B
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S
    Sakdinawat, A
    Sokolowski-Tinten, K
    Seibert, Marvin M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Treusch, R
    Woods, B W
    Coherent imaging at FLASH2009In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 186, no 1, p. 012051-Article in journal (Refereed)
    Abstract [en]

    We have carried out high-resolution single-pulse coherent diffractive imaging at the FLASH free-electron laser. The intense focused FEL pulse gives a high-resolution low-noise coherent diffraction pattern of an object before that object turns into a plasma and explodes. In particular we are developing imaging of biological specimens beyond conventional radiation damage resolution limits, developing imaging of ultrafast processes, and testing methods to characterize and perform single-particle imaging.

  • 22. Chapman, Henry N.
    et al.
    Barty, Anton
    Bogan, Michael J.
    Boutet, Sebastien
    Frank, Matthias
    Hau-Riege, Stefan P.
    Marchesini, Stefano
    Woods, Bruce W.
    Bajt, Sasa
    Benner, Henry
    London, Richard A.
    Ploenjes, Elke
    Kuhlmann, Marion
    Treusch, Rolf
    Duesterer, Stefan
    Tschentscher, Thomas
    Schneider, Jochen R.
    Spiller, Eberhard
    Moeller, Thomas
    Bostedt, Christoph
    Hoener, Matthias
    Shapiro, David A.
    Hodgson, Keith O.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Huldt, Gösta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lee, Richard W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Szöke, Abraham
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär Biofysik.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär Biofysik.
    Femtosecond diffractive imaging with a soft-X-ray free-electron laser2006In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 2, no 12, p. 839-843Article in journal (Refereed)
    Abstract [en]

    Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).

  • 23. Chapman, Henry N.
    et al.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Diffraction before destruction2014In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1647, p. 20130313-Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.

  • 24. Chapman, Henry N.
    et al.
    Fromme, Petra
    Barty, Anton
    White, Thomas A.
    Kirian, Richard A.
    Aquila, Andrew
    Hunter, Mark S.
    Schulz, Joachim
    DePonte, Daniel P.
    Weierstall, Uwe
    Doak, R. Bruce
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Schlichting, Ilme
    Lomb, Lukas
    Coppola, Nicola
    Shoeman, Robert L.
    Epp, Sascha W.
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Holl, Peter
    Liang, Mengning
    Barthelmess, Miriam
    Caleman, Carl
    Boutet, Sebastien
    Bogan, Michael J.
    Krzywinski, Jacek
    Bostedt, Christoph
    Bajt, Sasa
    Gumprecht, Lars
    Rudek, Benedikt
    Erk, Benjamin
    Schmidt, Carlo
    Hoemke, Andre
    Reich, Christian
    Pietschner, Daniel
    Strueder, Lothar
    Hauser, Guenter
    Gorke, Hubert
    Ullrich, Joachim
    Herrmann, Sven
    Schaller, Gerhard
    Schopper, Florian
    Soltau, Heike
    Kuehnel, Kai-Uwe
    Messerschmidt, Marc
    Bozek, John D.
    Hau-Riege, Stefan P.
    Frank, Matthias
    Hampton, Christina Y.
    Sierra, Raymond G.
    Starodub, Dmitri
    Williams, Garth J.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    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.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rocker, Andrea
    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, 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.
    Stern, Stephan
    Nass, Karol
    Andritschke, Robert
    Schroeter, Claus-Dieter
    Krasniqi, Faton
    Bott, Mario
    Schmidt, Kevin E.
    Wang, Xiaoyu
    Grotjohann, Ingo
    Holton, James M.
    Barends, Thomas R. M.
    Neutze, Richard
    Marchesini, Stefano
    Fromme, Raimund
    Schorb, Sebastian
    Rupp, Daniela
    Adolph, Marcus
    Gorkhover, Tais
    Andersson, Inger
    SLU.
    Hirsemann, Helmut
    Potdevin, Guillaume
    Graafsma, Heinz
    Nilsson, Björn
    Spence, John C. H.
    Femtosecond X-ray protein nanocrystallography2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, p. 73-77Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  • 25.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    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.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    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.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Benner, W. Henry
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tîmneanu, Nicuşor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Loh, N. Duane
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Awel, Salah
    Wiedorn, Max O.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    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.
    Barty, Anton
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastian
    Williams, Garth
    Koglin, Jason
    Andersson, Inger
    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.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed)
  • 26.
    Enberg, Rikard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Ingelman, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Kissavos, A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Diffractive Higgs Boson Production at the Fermilab Tevatron and the CERN Large Hadron Collider2002In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 89, no 8, p. 081801-Article in journal (Refereed)
    Abstract [en]

    Improved possibilities to find the Higgs boson in diffractive events, having less hadronic activity, depend on whether the cross section is large enough. Based on the soft color interaction models that successfully describe diffractive hard scattering at DESY HERA and the Fermilab Tevatron, we find that only a few diffractive Higgs events may be produced at the Tevatron, but we predict a substantial rate at the CERN Large Hadron Collider.

  • 27.
    Enberg, Rikard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Ingelman, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Diffractive Higgs bosons and prompt photons at hadron colliders2003In: Physical Review D, ISSN 1550-7998, E-ISSN 1550-2368, Vol. 67, p. 011301-Article in journal (Refereed)
    Abstract [en]

    Models for soft color interactions have been successful in describing and predicting diffractive hard scattering processes in ep collisions at DESY HERA and pp̅ at the Fermilab Tevatron. Here we present new comparisons of the model to recent diffractive dijet data, also showing good agreement. The topical issue of diffractive Higgs boson production at the Tevatron and CERN LHC hadron colliders is further investigated. For H⃗γγ the irreducible background of prompt photon pairs from qq̅ →γγ and gg⃗γγ is always dominating, implying that higher branching ratio decay modes of the Higgs boson have to be used. However, such prompt photons can be used to test the basic prediction for Higgs boson production since gg⃗γγ involves a quark loop diagram similar to gg⃗H.

  • 28.
    Enberg, Rikard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Ingelman, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Rapidity gaps at HERA and the Tevatron from soft colour exchanges2000In: Journal of Physics G: Nuclear and Particle Physics, ISSN 0954-3899, E-ISSN 1361-6471, Vol. 26, p. 712-715Article in journal (Refereed)
    Abstract [en]

    Models based on soft colour exchanges to rearrange colour strings in the final state provide a general framework for both diffractive and non-diffractive events in ep and hadron-hadron collisions. We study two such models and find that they can reproduce rapidity gap data from both HERA and the Tevatron. We also discuss the influence of parton cascades and multiple interactions on the results.

  • 29.
    Enberg, Rikard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Ingelman, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Soft color interactions and diffractive hard scattering at the Fermilab Tevatron2001In: Physical Review D, ISSN 1550-7998, E-ISSN 1550-2368, Vol. 64, no 11, p. 114015-Article in journal (Refereed)
    Abstract [en]

    An improved understanding of nonperturbative QCD can be obtained by the recently developed soft color interaction models. Their essence is the variation of color string-field topologies, giving a unified description of final states in high energy interactions, e.g., diffractive and nondiffractive events in ep and pp̅ . Here we present a detailed study of such models (the soft color interaction model and the generalized area law model) applied to pp̅ , considering also the general problem of the underlying event including beam particle remnants. With models tuned to DESY HERA ep data, we find a good description also of Fermilab Tevatron data on production of W, beauty and jets in diffractive events defined either by leading antiprotons or by one or two rapidity gaps in the forward or backward regions. We also give predictions for diffractive J/ψ production where the soft exchange mechanism produces both a gap and a color singlet cc̅ state in the same event. This soft color interaction approach is also compared with Pomeron-based models for diffraction, and some possibilities to experimentally discriminate between these different approaches are discussed.

  • 30.
    Enberg, Rikard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Ingelman, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics, High Energy Physics.
    Soft colour interactions and diffractive Higgs production2004In: European Physical Journal C, ISSN 1434-6044, E-ISSN 1434-6052, Vol. 33, no Suppl. 1, p. 542-544Article in journal (Refereed)
    Abstract [en]

    The topical subject of Higgs production in diffractive hard scattering events at the Tevatron and LHC is discussed. This has been proposed as a Higgs discovery channel with appealing experimental features. Predictions are obtained from the Soft Colour Interaction model, where rapidity gaps are created by a new soft interaction added to the normal hard scattering processes, implemented in the Monte Carlo event generator PYTHIA. A brief review of the successful application of the model to describe all CDF and DØ data on diffractive hard scattering, such as production of W/Z, dijets, beauty and $J/\psi$ is also given.

  • 31. Gaffney, K J
    et al.
    Lindenberg, A M
    Larsson, J
    Sokolowski-Tinten, K
    Blome, C
    Synnergren, O
    Sheppard, J
    Caleman, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    MacPhee, A G
    Weinstein, D
    Lowney, D P
    Allison, T
    Matthews, T
    Falcone, R W
    Cavalieri, A L
    Fritz, D M
    Lee, S H
    Bucksbaum, P H
    Reis, D A
    Rudati, J
    Macrander, A T
    Fuoss, P H
    Kao, C C
    Siddons, D P
    Pahl, R
    Moffat, K
    Als-Nielsen, J
    Duesterer, S
    Ischebeck, R
    Schlarb, H
    Schulte-Schrepping, H
    Schneider, J
    von der Linde, D
    Hignette, O
    Sette, F
    Chapman, H N
    Lee, R W
    Hansen, T N
    Wark, J S
    Bergh, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Huldt, G
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Timneanu, N
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Akre, R A
    Bong, E
    Krejcik, P
    Arthur, J
    Brennan, S
    Luening, K
    Hastings, J B
    Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb.2005In: Phys Rev Lett, ISSN 0031-9007, Vol. 95, no 12, p. 125701-Article in journal (Other scientific)
  • 32. 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.

  • 33. 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
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bostedt, Christoph
    Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles2018In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal (Refereed)
  • 34.
    Gunnar, Ingelman
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics and Astronomy.
    Timneanu, Nicusor
    Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Soft remnant interactions and rapidity gaps2000Conference paper (Other scientific)
    Abstract [en]

    Soft colour exchange models give a unified description of both diffractive and non-diffractive events, such that e-p and p-pbar collider data with and without rapidity gaps are well reproduced. We show that these models also describe the new Tevatron data

  • 35. Hajkova, V.
    et al.
    Juha, L.
    Bohacek, P.
    Burian, T.
    Chalupsky, J.
    Vysin, L.
    Gaudin, J.
    Heimann, P. A.
    Hau-Riege, S. P.
    Jurek, M.
    Klinger, D.
    Pelka, J.
    Sobierajski, R.
    Krzywinski, J.
    Messerschmidt, M.
    Moeller, S. P.
    Nagler, B.
    Rowen, M.
    Schlotter, W. F.
    Swiggers, M. L.
    Turner, J. J.
    Vinko, S. M.
    Whitcher, T.
    Wark, J.
    Matuchova, M.
    Bajt, S.
    Chapman, H.
    Dzelzainis, T.
    Riley, D.
    Andreasson, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Saksl, K.
    Faeustlin, R.
    Singer, A.
    Tiedtke, K.
    Toleikis, S.
    Vartaniants, I.
    Wabnitz, H.
    X-ray laser-induced ablation of lead compounds2011In: DAMAGE TO VUV, EUV, AND X-RAY OPTICS III, 2011, Vol. 8077Conference paper (Refereed)
    Abstract [en]

    The recent commissioning of a X-ray free-electron laser triggered an extensive research in the area of X-ray ablation of high-Z, high-density materials. Such compounds should be used to shorten an effective attenuation length for obtaining clean ablation imprints required for the focused beam analysis. Compounds of lead (Z=82) represent the materials of first choice. In this contribution, single-shot ablation thresholds are reported for PbWO(4) and PbI(2) exposed to ultra-short pulses of extreme ultraviolet radiation and X-rays at FLASH and LCLS facilities, respectively. Interestingly, the threshold reaches only 0.11 J/cm(2) at 1.55 nm in lead tungstate although a value of 0.4 J/cm(2) is expected according to the wavelength dependence of an attenuation length and the threshold value determined in the XUV spectral region, i.e., 79 mJ/cm(2) at a FEL wavelength of 13.5 nm. Mechanisms of ablation processes are discussed to explain this discrepancy. Lead iodide shows at 1.55 nm significantly lower ablation threshold than tungstate although an attenuation length of the radiation is in both materials quite the same. Lower thermal and radiation stability of PbI(2) is responsible for this finding.

  • 36.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    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.
    Loh, Duane
    Martin, Andrew V.
    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.
    Larsson, Daniel S.D.
    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.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    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.
    Uetrecht, Charlotte
    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.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Bari, Sadia
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Epp, Sascha W.
    Chapman, Henry N.
    Barty, Anton
    Andersson, Inger
    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.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A data set from flash X-ray imaging of carboxysomes2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed)
    Abstract [en]

    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.

  • 37.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    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.
    Loh, N. Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gijs, van der Schot
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha
    Chapman, Henry N.
    Barty, Anton
    Hajdu, Janos
    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.
    High-throughput imaging of heterogeneous cell organelles with an X-ray laser2014In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 8, no 12, p. 943-949Article in journal (Refereed)
    Abstract [en]

    We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.

  • 38. Hau-Riege, S. P.
    et al.
    London, R. A.
    Bionta, R. M.
    Ryutov, D.
    Soufli, R.
    Bajt, S.
    McKernan, M. A.
    Baker, S. L.
    Krzywinski, J.
    Sobierajski, R.
    Nietubyc, R.
    Klinger, D.
    Pelka, J. B.
    Jurek, M.
    Juha, L.
    Chalupsky, J.
    Cihelka, J.
    Hajkova, V.
    Velyhan, A.
    Krasa, J.
    Tiedtke, K.
    Toleikis, S.
    Wabnitz, H.
    Bergh, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wavelength dependence of the damage threshold of inorganic materials under extreme-ultraviolet free-electron-laser irradiation2009In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 95, no 11, p. 111104-111104-3Article in journal (Refereed)
    Abstract [en]

    We exposed bulk SiC and films of SiC and B4C to single 25 fs long free-electron-laser pulses with wavelengths between 13.5 and 32 nm. The materials are candidates for x-ray free-electron laser optics. We found that the threshold for surface-damage of the bulk SiC samples exceeds the fluence required for thermal melting at all wavelengths. The damage threshold of the film sample shows a strong wavelength dependence. For wavelengths of 13.5 and 21.7 nm, the damage threshold is equal to or exceeds the melting threshold, whereas at 32 nm the damage threshold falls below the melting threshold.

  • 39. Hau-Riege, Stefan P.
    et al.
    London, Richard A.
    Chapman, Henry N.
    Szöke, Abraham
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Encapsulation and diffraction-pattern-correction methods to reduce the effect of damage in x-ray diffraction imaging of single biological molecules2007In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 98, no 19, p. 198302-Article in journal (Refereed)
    Abstract [en]

    Short and intense x-ray pulses may be used for atomic-resolution diffraction imaging of single biological molecules. Radiation damage and a low signal-to-noise ratio impose stringent pulse requirements. In this Letter, we describe methods for decreasing the damage and improving the signal by encapsulating the molecule in a sacrificial layer (tamper) that reduces atomic motion and by postprocessing the pulse-averaged diffraction pattern to correct for ionization damage. Simulations show that these methods greatly improve the image quality.

  • 40.
    Ingelman, Gunnar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Edin, Anders
    Enberg, Rikard
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Rathsman, Johan
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Rapidity gaps from colour string topologies1999In: Nuclear physics B, Proceedings supplements, ISSN 0920-5632, E-ISSN 1873-3832, Vol. 79, no 1-3, p. 386-388Article in journal (Refereed)
    Abstract [en]

    Diffractive deep inelastic scattering at HERA and diffractive W and jet production at the Tevatron are well described by soft colour exchange models. Their essence is the variation of colour string-field topologies giving both gap and no-gap events, with a smooth transition and thereby a unified description of all final states.

  • 41.
    Ingelman, Gunnar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Edin, Anders
    Enberg, Rikard
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Rathsman, Johan
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Nuclear and Particle Physics.
    Soft Colour Interactions in Non-perturbative QCD2000In: Nuclear Physics A, ISSN 0375-9474, E-ISSN 1873-1554, Vol. 663-664, p. 1007c-1010cArticle in journal (Refereed)
  • 42.
    Iwan, B.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Hajdu, J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Modeling of soft X-ray induced ablation in solids2011In: DAMAGE TO VUV, EUV, AND X-RAY OPTICS III, 2011, Vol. 8077Conference paper (Refereed)
    Abstract [en]

    Powerful free electron lasers (FELs) operating in the soft X-ray regime are offering new possibilities for creating and probing materials under extreme conditions. We describe here simulations to model the interaction of a focused FEL pulse with metallic solids (niobium, vanadium, and their deuterides) at 13.5 nm wavelength (92 eV) with peak intensities between 10(15) to 10(18) W/cm(2) and a fixed pulse length of 15 femtoseconds (full width at half maximum). The interaction of the pulse with the metallic solids was modeled with a non-local thermodynamic equilibrium code that included radiation transfer. The calculations also made use of a self-similar isothermal fluid model for plasma expansion into vacuum. We find that the time-evolution of the simulated critical charge density in the sample results in a critical depth that approaches the observed crater depths in an earlier experiment performed at the FLASH free electron laser in Hamburg. The results show saturation in the ablation process at intensities exceeding 10(16) W/cm(2). Furthermore, protons and deuterons with kinetic energies of several keV have been measured, and these concur with predictions from the plasma expansion model. The results indicate that the temperature of the plasma reached almost 5 million K after the pulse has passed.

  • 43.
    Iwan, Bianca
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Thomas, Heiko
    Rupp, Daniela
    Gorkhover, Tais
    Adolph, Markus
    Bostedt, Christoph
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Explosion, ion acceleration and molecular fragmentation of methane clusters in the pulsed beam of a free-electron laser2012In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 86, no 3, p. 033201-Article in journal (Refereed)
    Abstract [en]

    X-ray lasers offer new possibilities for creating and probing extreme states of matter. We used intense and short x-ray pulses from the FLASH soft x-ray laser to trigger the explosions of CH4 and CD4 molecules and their clusters. The results show that the explosion dynamics depends on cluster size and indicate a transition from Coulomb explosion to hydrodynamic expansion in larger clusters. The explosion of CH4 and CD4 clusters shows a strong isotope effect: The heavier deuterons acquire higher kinetic energies than the lighter protons. This may be due to an extended inertial confinement of deuterons vs. protons near a rapidly charging cluster core during exposure.

  • 44.
    Iwan, Bianca S
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobierajski, R.
    Toleikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    TOF-OFF: A method for determining focal positions in tightly focused free-electron laser experiments by measurement of ejected ions2011In: High Energy Density Physics, ISSN 1574-1818, Vol. 7, no 4, p. 336-342Article in journal (Refereed)
    Abstract [en]

    Pulse intensities greater than 1017 Watt/cm2 were reached at the FLASH soft X-ray laser in Hamburg, Germany, using an off-axis parabolic mirror to focus 15 fs pulses of 5–70 μJ energy at 13.5 nm wavelength to a micron-sized spot. We describe the interaction of such pulses with niobium and vanadium targets and their deuterides. The beam produced craters in the solid targets, and we measured the kinetic energy of ions ejected from these craters. Ions with several keV kinetic energy were observed from craters approaching 5 μm in depth when the sample was at best focus. We also observed the onset of saturation in both ion acceleration and ablation with pulse intensities exceeding 1016 W/cm2, when the highest detected ion energies and the crater depths tend to saturate with increasing intensity.

    A general difficulty in working with micron and sub-micron focusing optics is finding the exact focus of the beam inside a vacuum chamber. Here we propose a direct method to measure the focal position to a resolution better than the Rayleigh length. The method is based on the correlation between the energies of ejected ions and the physical dimensions of the craters. We find that the focus position can be quickly determined from the ion time-of-flight (TOF) data as the target is scanned through the expected focal region. The method does not require external access to the sample or venting the vacuum chamber. Profile fitting employed to analyze the TOF data can extend resolution beyond the actual scanning step size.

  • 45. Johansson, Linda C
    et al.
    Arnlund, David
    White, Thomas A
    Katona, Gergely
    DePonte, Daniel P
    Weierstall, Uwe
    Doak, R Bruce
    Shoeman, Robert L
    Lomb, Lukas
    Malmerberg, Erik
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Nass, Karol
    Liang, Mengning
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Bozek, John D
    Caleman, Carl
    Coffee, Ryan
    Coppola, Nicola
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y
    Hartmann, Robert
    Hartmann, Andreas
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kimmel, Nils
    Kirian, Richard A
    Maia, Filipe R N C
    Marchesini, Stefano
    Martin, Andrew V
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sierra, Raymond G
    Soltau, Heike
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wahlgren, Weixiao Y
    Wang, Xiaoyu
    Weidenspointner, Georg
    Wunderer, Cornelia
    Fromme, Petra
    Chapman, Henry N
    Spence, John C H
    Neutze, Richard
    Lipidic phase membrane protein serial femtosecond crystallography2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 263-265Article in journal (Refereed)
    Abstract [en]

    X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.

  • 46.
    Jönsson, H. Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free- Electron Laser Science, Deutsches Elektronen-Synchrotron.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Czech Academy of Science, Chalmers University of Technology.
    Timneanu, Nicusor
    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, Molecular biophysics.
    Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, no 6, p. 778-784Article in journal (Refereed)
    Abstract [en]

    Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

  • 47.
    Jönsson, H. Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Scott, Howard A.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography2015In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, p. 256-266Article in journal (Refereed)
    Abstract [en]

    Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.

  • 48.
    Jönsson, Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala university.
    Scott, Howard A.
    Lawrence Livermore National Laboratory, Livermore, California, USA.
    Chapman, Henry
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science, DESY, Hamburg, Germany.
    Aplin, Steve J.
    Center for Free-Electron Laser Science, DESY, Hamburg, Germany.
    Timneanu, Nicusor
    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, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography2018In: High Energy Density Physics, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed)
    Abstract [en]

    Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

  • 49.
    Jönsson, Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Scott, Howard A.
    Lawrence Livermore Natl Lab, Livermore, CA 94550 USA.
    Chapman, Henry
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany;Univ Hamburg, Dept Phys, Luruper Chaussee 149, DE-22761 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luruper Chaussee 149, DE-22761 Hamburg, Germany.
    Aplin, Steve J.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    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.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    FreeDam: A webtool for free-electron laser-induced damage in femtosecond X-ray crystallography2018In: HIGH ENERGY DENSITY PHYSICS, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed)
    Abstract [en]

    Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

  • 50. Koopmann, Rudolf
    et al.
    Cupelli, Karolina
    Redecke, Lars
    Nass, Karol
    DePonte, Daniel P
    White, Thomas A
    Stellato, Francesco
    Rehders, Dirk
    Liang, Mengning
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Boutet, Sebastien
    Bozek, John D
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Doak, R Bruce
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hampton, Christina Y
    Hartmann, Andreas
    Hartmann, Robert
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kirian, Richard A
    Lomb, Lukas
    Maia, Filipe R N C
    Kimmel, Nils
    Martin, Andrew V
    Messerschmidt, Marc
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ullrich, Joachim
    Wang, Xiaoyu
    Weidenspointner, Georg
    Weierstall, Uwe
    Williams, Garth J
    Wunderer, Cornelia B
    Fromme, Petra
    Spence, John C H
    Stehle, Thilo
    Chapman, Henry N
    Betzel, Christian
    Duszenko, Michael
    In vivo protein crystallization opens new routes in structural biology2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 3, p. 259-262Article in journal (Refereed)
    Abstract [en]

    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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