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

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

  • 3. 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.

  • 4. 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.

  • 5. Barty, Anton
    et al.
    Kirian, Richard A.
    Maia, Filipe R. N. C.
    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.
    Yoon, Chun Hong
    White, Thomas A.
    Chapman, Henry
    Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data2014In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 47, p. 1118-1131Article in journal (Refereed)
    Abstract [en]

    The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.

  • 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. Bogan, Michael J
    et al.
    Benner, W Henry
    Boutet, Sébastien
    Rohner, Urs
    Frank, Matthias
    Barty, Anton
    Seibert, M Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Bajt, Sasa
    Woods, Bruce
    Riot, Vincent
    Hau-Riege, Stefan P
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Spiller, Eberhard
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N
    Single particle X-ray diffractive imaging2008In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 8, no 1, p. 310-6Article in journal (Refereed)
    Abstract [en]

    In nanotechnology, strategies for the creation and manipulation of nanoparticles in the gas phase are critically important for surface modification and substrate-free characterization. Recent coherent diffractive imaging with intense femtosecond X-ray pulses has verified the capability of single-shot imaging of nanoscale objects at suboptical resolutions beyond the radiation-induced damage threshold. By intercepting electrospray-generated particles with a single 15 femtosecond soft-X-ray pulse, we demonstrate diffractive imaging of a nanoscale specimen in free flight for the first time, an important step toward imaging uncrystallized biomolecules.

  • 8. 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.

  • 9.
    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.

  • 10. 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).

  • 11. 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.

  • 12. Commer, Michael
    et al.
    Maia, Filipe R. N. C.
    National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, USA .
    Newman, Gregory A.
    Iterative Krylov solution methods for geophysical electromagnetic simulations on throughput-oriented processing units2012In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 26, no 4, p. 378-385Article in journal (Refereed)
    Abstract [en]

    Many geo-scientific applications involve boundary value problems arising in simulating electrostatic and electromagnetic fields for geophysical prospecting and subsurface imaging of electrical resistivity. Modeling complex geological media with three-dimensional finite-difference grids gives rise to large sparse linear systems of equations. For such systems, we have implemented three common iterative Krylov solution methods on graphics processing units and compared their performance with parallel host-based versions. The benchmarks show that the device efficiency improves with increasing grid sizes. Limitations are currently given by the device memory resources.

  • 13.
    Daurer, Benedikt J.
    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.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time2016In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1042-1047Article in journal (Refereed)
  • 14. Duane Loh, N.
    et al.
    Starodub, D.
    Lomb, L.
    Hampton, C. Y.
    Martin, A. V.
    Sierra, R. G.
    Barty, A.
    Aquila, A.
    Schulz, J.
    Steinbrener, J.
    Shoeman, R. L.
    Kassemeyer, S.
    Bostedt, C.
    Bozek, J.
    Epp, S. W.
    Erk, B.
    Hartmann, R.
    Rolles, D.
    Rudenko, A.
    Rudek, B.
    Foucar, L.
    Kimmel, N.
    Weidenspointner, G.
    Hauser, G.
    Holl, P.
    Pedersoli, E.
    Liang, M.
    Hunter, M. S.
    Gumprecht, L.
    Coppola, N.
    Wunderer, C.
    Graafsma, H.
    Maia, F. R. N. C.
    Ekeberg, T.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, H.
    Hirsemann, H.
    Nass, K.
    White, T. A.
    Tobias, H. J.
    Farquar, G. R.
    Henry Benner, W.
    Hau-Riege, S.
    Reich, C.
    Hartmann, A.
    Soltau, H.
    Marchesini, S.
    Bajt, S.
    Barthelmess, M.
    Strueder, L.
    Ullrich, J.
    Bucksbaum, P.
    Hodgson, K. O.
    Frank, M.
    Schlichting, I.
    Chapman, H. N.
    Bogan, M. J.
    Profiling structured beams using injected aerosols2012In: Proceedings of SPIE: The International Society for Optical Engineering, 2012, p. 850403-Conference paper (Refereed)
    Abstract [en]

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

  • 15.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Data requirements for single-particle diffractive imagingManuscript (preprint) (Other academic)
    Abstract [en]

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

  • 16.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
  • 17.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Abergel, Chantal
    Maia, Filipe
    Seltzer, Virginie
    Hantke, Max
    De Ponte, Daniel
    Aquila, Andrew
    Schulz, Joachim
    Andreasson, Jakob
    Iwan, Bianca
    Jönsson, Olof
    Westphal, Daniel
    Odić, Duško
    Andersson, Inger
    Barty, Anton
    Liang, Meng
    Seiberg, Marvin
    Martin, Andrew
    Nass, Karol
    Wang, Fenglin
    White, Thomas
    Gumprecht, Lars
    Fleckenstein, Holger
    Bajt, Saša
    Barthelmess, Miriam
    Claverie, Jean-Michel
    Tegze, Miklos
    Bortel, Gabor
    Faigel, Gyula
    Loh, Ne-Te Duane
    Coppola, Nicola
    Bostedt, Christoph
    Bozek, John
    Krzywinski, Jacek
    Messerschmidt, Marc
    Hodgson, Keith
    Treusch, Rolf
    Toleikis, Sven
    Dusterer, Stefan
    Feldhaus, Josef
    Weckert, Edgar
    Bogan, Michael
    Hampton, Christina
    Sierra, Raymond
    Doak, Bruce
    Weierstall, Uwe
    Spence, John
    Frank, Matthias
    Shoeman, Robert
    Lomb, Lukas
    Foucar, Lutz
    Epp, Sascha
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Hartmann, Andreas
    Kimmel, Nils
    Holl, Peter
    Rudek, Benedikt
    Erk, Benjamin
    Kassemeyer, Stephan
    Schlichting, Ilme
    Strüder, Lothar
    Ullrich, Joachim
    Schmidt, Carlo
    Krasniqi, Faton
    Hauser, Günter
    Reich, Christian
    Soltau, Heike
    Schorb, Sebastian
    Hirsemann, Helmut
    Wunderer, Cornelia
    Graafsma, Heinz
    Chapman, Henry
    Hajdu, Janos
    Three-dimensional structure determination with an X-ray laserManuscript (preprint) (Other academic)
    Abstract [en]

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

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

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

  • 19. Gomez, L. F.
    et al.
    Ferguson, K. R.
    Cryan, J. P.
    Bacellar, C.
    Tanyag, R. M. P.
    Jones, C.
    Schorb, S.
    Anielski, D.
    Belkacem, A.
    Bernando, C.
    Boll, R.
    Bozek, J.
    Carron, S.
    Chen, G.
    Delmas, T.
    Englert, L.
    Epp, S. W.
    Erk, B.
    Foucar, L.
    Hartmann, R.
    Hexemer, A.
    Huth, M.
    Kwok, J.
    Leone, S. R.
    Ma, J. H. S.
    Maia, F. R. N. C.
    National Energy Research Scientific Computing Center, LBNL, Berkeley, CA 94720, USA. .
    Malmerberg, E.
    Marchesini, S.
    Neumark, D. M.
    Poon, B.
    Prell, J.
    Rolles, D.
    Rudek, B.
    Rudenko, A.
    Seifrid, M.
    Siefermann, K. R.
    Sturm, F. P.
    Swiggers, M.
    Ullrich, J.
    Weise, F.
    Zwart, P.
    Bostedt, C.
    Gessner, O.
    Vilesov, A. F.
    Shapes and vorticities of superfluid helium nanodroplets2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 345, no 6199, p. 906-909Article in journal (Refereed)
    Abstract [en]

    Helium nanodroplets are considered ideal model systems to explore quantum hydrodynamics in self-contained, isolated superfluids. However, exploring the dynamic properties of individual droplets is experimentally challenging. In this work, we used single-shot femtosecond x-ray coherent diffractive imaging to investigate the rotation of single, isolated superfluid helium-4 droplets containing ~108 to 1011 atoms. The formation of quantum vortex lattices inside the droplets is confirmed by observing characteristic Bragg patterns from xenon clusters trapped in the vortex cores. The vortex densities are up to five orders of magnitude larger than those observed in bulk liquid helium. The droplets exhibit large centrifugal deformations but retain axially symmetric shapes at angular velocities well beyond the stability range of viscous classical droplets.

  • 20.
    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.

  • 21.
    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.

  • 22. 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.

  • 23. Kassemeyer, Stephan
    et al.
    Steinbrener, Jan
    Lomb, Lukas
    Hartmann, Elisabeth
    Aquila, Andrew
    Barty, Anton
    Martin, Andrew V
    Hampton, Christina Y
    Bajt, Saša
    Barthelmess, Miriam
    Barends, Thomas R M
    Bostedt, Christoph
    Bott, Mario
    Bozek, John D
    Coppola, Nicola
    Cryle, Max
    Deponte, Daniel P
    Doak, R Bruce
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hartmann, Andreas
    Hartmann, Robert
    Hauser, Günter
    Hirsemann, Helmut
    Hömke, André
    Holl, Peter
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kimmel, Nils
    Krasniqi, Faton
    Liang, Mengning
    Maia, Filipe R N C
    Marchesini, Stefano
    Nass, Karol
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schmidt, Carlo
    Schulz, Joachim
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Spence, John C H
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Stier, Gunter
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Weidenspointner, Georg
    Weierstall, Uwe
    White, Thomas A
    Wunderer, Cornelia
    Frank, Matthias
    Chapman, Henry N
    Ullrich, Joachim
    Strüder, Lothar
    Bogan, Michael J
    Schlichting, Ilme
    Femtosecond free-electron laser x-ray diffraction data sets for algorithm development2012In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 4, p. 4149-4158Article in journal (Refereed)
    Abstract [en]

    We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.

  • 24. Kirian, Richard A.
    et al.
    White, Thomas A.
    Holton, James M.
    Chapman, Henry N.
    Fromme, Petra
    Barty, Anton
    Lomb, Lukas
    Aquila, Andrew
    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.
    Fromme, Raimund
    Wang, Xiaoyu
    Hunter, Mark S.
    Schmidt, Kevin E.
    Spence, John C. H.
    Structure-factor analysis of femtosecond micro-diffraction patterns from protein nanocrystals2011In: Acta Crystallographica Section A: Foundations of Crystallography, ISSN 0108-7673, E-ISSN 1600-5724, Vol. 67, no 2, p. 131-140Article in journal (Refereed)
    Abstract [en]

    A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single 'still' diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 mu m, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.

  • 25. 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.

  • 26. Kurta, Ruslan P.
    et al.
    Donatelli, Jeffrey J.
    Yoon, Chun Hong
    Berntsen, Peter
    Bielecki, Johan
    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.
    DeMirci, Hasan
    Fromme, Petra
    Hantke, Max Felix
    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.
    Munke, Anna
    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, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pande, Kanupriya
    Reddy, Hemanth K. N.
    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.
    Sierra, Raymond G.
    Svenda, Martin
    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.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Aquila, Andrew
    Zwart, Peter H.
    Mancuso, Adrian P.
    Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses2017In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 119, no 15, p. 158102:1-7, article id 158102Article in journal (Refereed)
  • 27. Loh, N. D.
    et al.
    Bogan, M. J.
    Elser, V.
    Barty, A.
    Boutet, S.
    Bajt, S.
    Hajdu, Janos
    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.
    Schulz, J.
    Seibert, Marvin 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.
    Marchesini, S.
    Schlichting, I.
    Shoeman, R. L.
    Lomb, L.
    Frank, M.
    Liang, M.
    Chapman, H. N.
    Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns2010In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 104, no 22, p. 225501-1-225501-5Article in journal (Refereed)
    Abstract [en]

    We reconstructed the 3D Fourier intensity distribution of monodisperse prolate nanoparticles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast x-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the expansion-maximization-compression framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.

  • 28. Loh, N. D.
    et al.
    Hampton, C. Y.
    Martin, A. V.
    Starodub, D.
    Sierra, R. G.
    Barty, A.
    Aquila, A.
    Schulz, J.
    Lomb, L.
    Steinbrener, J.
    Shoeman, R. L.
    Kassemeyer, S.
    Bostedt, C.
    Bozek, J.
    Epp, S. W.
    Erk, B.
    Hartmann, R.
    Rolles, D.
    Rudenko, A.
    Rudek, B.
    Foucar, L.
    Kimmel, N.
    Weidenspointner, G.
    Hauser, G.
    Holl, P.
    Pedersoli, E.
    Liang, M.
    Hunter, M. M.
    Gumprecht, L.
    Coppola, N.
    Wunderer, C.
    Graafsma, H.
    Maia, F. R. N. C.
    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.
    Fleckenstein, H.
    Hirsemann, H.
    Nass, K.
    White, T. A.
    Tobias, H. J.
    Farquar, G. R.
    Benner, W. H.
    Hau-Riege, S. P.
    Reich, C.
    Hartmann, A.
    Soltau, H.
    Marchesini, S.
    Bajt, S.
    Barthelmess, M.
    Bucksbaum, P.
    Hodgson, K. O.
    Strueder, L.
    Ullrich, J.
    Frank, M.
    Schlichting, I.
    Chapman, H. N.
    Bogan, M. J.
    Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 486, no 7404, p. 513-517Article in journal (Refereed)
    Abstract [en]

    The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology(1) to climate science(2), yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate(3); visible light scattering provides insufficient resolution(4); and X-ray synchrotron studies have been limited to ensembles of particles(5). Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source(6) free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins(7), vibrational energy transfer by the hydrodynamic interaction of amino acids(8), and large-scale production of nanoscale structures by flame synthesis(9).

  • 29. Loh, N. Duane
    et al.
    Starodub, Dmitri
    Lomb, Lukas
    Hampton, Christina Y.
    Martin, Andrew V.
    Sierra, Raymond G.
    Barty, Anton
    Aquila, Andrew
    Schulz, Joachim
    Steinbrener, Jan
    Shoeman, Robert L.
    Kassemeyer, Stephan
    Bostedt, Christoph
    Bozek, John
    Epp, Sascha W.
    Erk, Benjamin
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Rudek, Benedikt
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Hauser, Guenter
    Holl, Peter
    Pedersoli, Emanuele
    Liang, Mengning
    Hunter, Mark S.
    Gumprecht, Lars
    Coppola, Nicola
    Wunderer, Cornelia
    Graafsma, Heinz
    Maia, Filipe R. N. C.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Hirsemann, Helmut
    Nass, Karol
    White, Thomas A.
    Tobias, Herbert J.
    Farquar, George R.
    Benner, W. Henry
    Hau-Riege, Stefan
    Reich, Christian
    Hartmann, Andreas
    Soltau, Heike
    Marchesini, Stefano
    Bajt, Sasa
    Barthelmess, Miriam
    Strueder, Lothar
    Ullrich, Joachim
    Bucksbaum, Philip
    Frank, Matthias
    Schlichting, Ilme
    Chapman, Henry N.
    Bogan, Michael J.
    Sensing the wavefront of x-ray free-electron lasers using aerosol spheres2013In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, no 10, p. 12385-12394Article in journal (Refereed)
    Abstract [en]

    Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 1021 W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.

  • 30. Lomb, Lukas
    et al.
    Barends, Thomas R. M.
    Kassemeyer, Stephan
    Aquila, Andrew
    Epp, Sascha W.
    Erk, Benjamin
    Foucar, Lutz
    Hartmann, Robert
    Rudek, Benedikt
    Rolles, Daniel
    Rudenko, Artem
    Shoeman, Robert L.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John D.
    Caleman, Carl
    Coffee, Ryan
    Coppola, Nicola
    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.
    Fleckenstein, Holger
    Fromme, Petra
    Gebhardt, Maike
    Graafsma, Heinz
    Gumprecht, Lars
    Hampton, Christina Y.
    Hartmann, Andreas
    Hauser, Guenter
    Hirsemann, Helmut
    Holl, Peter
    Holton, James M.
    Hunter, Mark S.
    Kabsch, Wolfgang
    Kimmel, Nils
    Kirian, Richard A.
    Liang, Mengning
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Meinhart, Anton
    Marchesini, Stefano
    Martin, Andrew V.
    Nass, Karol
    Reich, Christian
    Schulz, Joachim
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sierra, Raymond
    Soltau, Heike
    Spence, John C. H.
    Steinbrener, Jan
    Stellato, Francesco
    Stern, Stephan
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, Xiaoyu
    Weidenspointner, Georg
    Weierstall, Uwe
    White, Thomas A.
    Wunderer, Cornelia
    Chapman, Henry N.
    Ullrich, Joachim
    Strüder, Lothar
    Schlichting, Ilme
    Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 84, no 21, p. 214111-1-214111-6Article in journal (Refereed)
    Abstract [en]

    X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.

  • 31.
    Maia, Filipe R N C
    NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
    The Coherent X-ray Imaging Data Bank2012In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, no 9, p. 854-855Article in journal (Refereed)
  • 32.
    Maia, Filipe R. N. C.
    et al.
    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.
    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.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structural variability and the incoherent addition of scattered intensities in single-particle diffraction2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 3, p. 031905-Article in journal (Refereed)
    Abstract [en]

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

  • 33.
    Maia, Filipe R. N. C.
    et al.
    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.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hawk: the image reconstruction package for coherent X-ray diffractive imaging2010In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 43, no 6, p. 1535-1539Article in journal (Other academic)
    Abstract [en]

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

  • 34.
    Maia, Filipe R.N.C.
    et al.
    Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
    Yang, Chao
    Marchesini, Stefano
    Compressive auto-indexing in femtosecond nanocrystallography2011In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 111, no 7, p. 807-811Article in journal (Refereed)
    Abstract [en]

    Ultrafast nanocrystallography has the potential to revolutionize biology by enabling structural elucidation of proteins for which it is possible to grow crystals with 10 or fewer unit cells on the side. The success of nanocrystallography depends on robust orientation-determination procedures that allow us to average diffraction data from multiple nanocrystals to produce a three-dimensional (3D) diffraction data volume with a high signal-to-noise ratio. Such a 3D diffraction volume can then be phased using standard crystallographic techniques. “Indexing” algorithms used in crystallography enable orientation determination of diffraction data from a single crystal when a relatively large number of reflections are recorded. Here we show that it is possible to obtain the exact lattice geometry from a smaller number of measurements than standard approaches using a basis pursuit solver.

  • 35.
    Maia, Filipe
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Szoke, Abraham
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    DeLano, Warren
    van der Spoel, David
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Interactive visualization of electron density slices2005In: J. Appl. Cryst., ISSN 0021-8898, Vol. 38, p. 563-565Article in journal (Other (popular scientific, debate etc.))
    Abstract [en]

    A new tool has been developed to aid in the visualization of electron density in crystals or from quantum chemistry calculations. It displays the fine details of the electron density on a plane and the three-dimensional model of the molecule at the same time. The program enables the user to examine the details of weak or irregular features. Such features frequently occur in low-resolution maps, where they determine the correct tracing of a protein backbone. In high-resolution maps, solvent regions are difficult or impossible to observe using isosurfaces. The tool has been integrated into an existing molecular visualization package (PyMol) making it possible to observe and interact both with a structure model and the electron density slices freely, simultaneously and independently. This visualization model fills a gap in the visualization methods available to crystallographers and others who work with electron density maps.

  • 36. Marchesini, Stefano
    et al.
    Schirotzek, Andre
    Yang, Chao
    Wu, Hau-tieng
    Maia, Filipe
    NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA .
    Augmented projections for ptychographic imaging2013In: Inverse Problems, ISSN 0266-5611, E-ISSN 1361-6420, Vol. 29, no 11, p. 115009-Article in journal (Refereed)
    Abstract [en]

    Ptychography is a popular technique to achieve diffraction limited resolution images of a two- or three-dimensional sample using high frame rate detectors. We introduce a relaxation of common projection algorithms to account for instabilities given by intensity and background fluctuations, position errors, or poor calibration using multiplexing illumination. This relaxation introduces an additional phasing optimization at every step that enhances the convergence rate of common projection algorithms. Numerical tests exhibit the exact recovery of the object and the perturbations when there is high redundancy in the data.

  • 37. Martin, A. V.
    et al.
    Loh, N. D.
    Hampton, C. Y.
    Sierra, R. G.
    Wang, F.
    Aquila, A.
    Bajt, S.
    Barthelmess, M.
    Bostedt, C.
    Bozek, J. D.
    Coppola, N.
    Epp, S. W.
    Erk, B.
    Fleckenstein, H.
    Foucar, L.
    Frank, M.
    Graafsma, H.
    Gumprecht, L.
    Hartmann, A.
    Hartmann, R.
    Hauser, G.
    Hirsemann, H.
    Holl, P.
    Kassemeyer, S.
    Kimmel, N.
    Liang, M.
    Lomb, L.
    Maia, F. R. N. C.
    NERSC, Lawrence Berkeley National Laboratory, Berkeley,California 94720, USA .
    Marchesini, S.
    Nass, K.
    Pedersoli, E.
    Reich, C.
    Rolles, D.
    Rudek, B.
    Rudenko, A.
    Schulz, J.
    Shoeman, R. L.
    Soltau, H.
    Starodub, D.
    Steinbrener, J.
    Stellato, F.
    Strüder, L.
    Ullrich, J.
    Weidenspointner, G.
    White, T. A.
    Wunderer, C. B.
    Barty, A.
    Schlichting, I.
    Bogan, M. J.
    Chapman, H. N.
    Femtosecond dark-field imaging with an X-ray free electron laser2012In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 12, p. 13501-13512Article in journal (Refereed)
    Abstract [en]

    The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.

  • 38. Martin, A. V.
    et al.
    Morgan, A. J.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. D.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wang, F.
    Spence, J. C. H.
    Chapman, H. N.
    The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern2013In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, no 13, p. 15102-15112Article in journal (Refereed)
    Abstract [en]

    The structures of biological molecules may soon be determined with X-ray free-electron lasers without crystallization by recording the coherent diffraction patterns of many identical copies of a molecule. Most analysis methods require a measurement of each molecule individually. However, current injection methods deliver particles to the X-ray beam stochastically and the maximum yield of single particle measurements is 37% at optimal concentration. The remaining 63% of pulses intercept no particles or multiple particles. We demonstrate that in the latter case single particle diffraction patterns can be extracted provided the particles are sufficiently separated. The technique has the potential to greatly increase the amount of data available for three-dimensional imaging of identical particles with X-ray lasers.

  • 39. Martin, A. V.
    et al.
    Wang, F.
    Loh, N. D.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, F. R. N. C.
    Hantke, Max Felix
    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.
    Hampton, C. Y.
    Sierra, R. G.
    Aquila, A.
    Bajt, S.
    Barthelmess, M.
    Bostedt, C.
    Bozek, J. D.
    Coppola, N.
    Epp, S. W.
    Erk, B.
    Fleckenstein, H.
    Foucar, L.
    Frank, M.
    Graafsma, H.
    Gumprecht, L.
    Hartmann, A.
    Hartmann, R.
    Hauser, G.
    Hirsemann, H.
    Holl, P.
    Kassemeyer, S.
    Kimmel, N.
    Liang, M.
    Lomb, L.
    Marchesini, S.
    Nass, K.
    Pedersoli, E.
    Reich, C.
    Rolles, D.
    Rudek, B.
    Rudenko, A.
    Schulz, J.
    Shoeman, R. L.
    Soltau, H.
    Starodub, D.
    Steinbrener, J.
    Stellato, F.
    Strueder, L.
    Ullrich, J.
    Weidenspointner, G.
    White, T. A.
    Wunderer, C. B.
    Barty, A.
    Schlichting, I.
    Bogan, M. J.
    Chapman, H. N.
    Noise-robust coherent diffractive imaging with a single diffraction pattern2012In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 15, p. 16650-16661Article in journal (Refereed)
    Abstract [en]

    The resolution of single-shot coherent diffractive imaging at X-ray free-electron laser facilities is limited by the low signal-to-noise level of diffraction data at high scattering angles. The iterative reconstruction methods, which phase a continuous diffraction pattern to produce an image, must be able to extract information from these weak signals to obtain the best quality images. Here we show how to modify iterative reconstruction methods to improve tolerance to noise. The method is demonstrated with the hybrid input-output method on both simulated data and single-shot diffraction patterns taken at the Linac Coherent Light Source. (C) 2012 Optical Society of America

  • 40.
    Meyer, Peter A.
    et al.
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Socias, Stephanie
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Key, Jason
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Ransey, Elizabeth
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Tjon, Emily C.
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Buschiazzo, Alejandro
    Inst Pasteur Montevideo, Lab Mol & Struct Microbiol, Montevideo 11400, Uruguay.;Inst Pasteur, Dept Biol Struct & Chem, F-75015 Paris, France..
    Lei, Ming
    Chinese Acad Sci, Inst Biochem & Cell Biol, Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China..
    Botka, Chris
    Harvard Univ, Sch Med, Boston, MA 02115 USA..
    Withrow, James
    Cornell Univ, Argonne Natl Lab, NE CAT, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA.;Cornell Univ, Argonne Natl Lab, Dept Chem & Chem Biol, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA..
    Neau, David
    Cornell Univ, Argonne Natl Lab, NE CAT, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA.;Cornell Univ, Argonne Natl Lab, Dept Chem & Chem Biol, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA..
    Rajashankar, Kanagalaghatta
    Cornell Univ, Argonne Natl Lab, NE CAT, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA.;Cornell Univ, Argonne Natl Lab, Dept Chem & Chem Biol, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA..
    Anderson, Karen S.
    Yale Univ, Sch Med, Dept Pharmacol, 333 Cedar St, New Haven, CT 06520 USA.;Yale Univ, Sch Med, Dept Mol Biophys & Biochem, 333 Cedar St, New Haven, CT 06520 USA..
    Baxter, Richard H.
    Yale Univ, Sch Med, Dept Mol Biophys & Biochem, 333 Cedar St, New Haven, CT 06520 USA.;Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA..
    Blacklow, Stephen C.
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Boggon, Titus J.
    Yale Univ, Sch Med, Dept Pharmacol, 333 Cedar St, New Haven, CT 06520 USA.;Yale Univ, Sch Med, Dept Mol Biophys & Biochem, 333 Cedar St, New Haven, CT 06520 USA..
    Bonvin, Alexandre M. J. J.
    Univ Utrecht, Bijvoet Ctr, Fac Sci, NL-3584 CH Utrecht, Netherlands..
    Borek, Dominika
    Univ Texas SW Med Ctr Dallas, Dept Biophys & Biochem, Dallas, TX 75390 USA..
    Brett, Tom J.
    Washington Univ, Sch Med, Dept Internal Med, St Louis, MO 63110 USA..
    Caflisch, Amedeo
    Univ Zurich, Dept Biochem, CH-8057 Zurich, Switzerland..
    Chang, Chung-I
    Acad Sinica, Inst Biol Chem, Taipei 11529, Taiwan..
    Chazin, Walter J.
    Vanderbilt Univ, Dept Biochem, Struct Biol Ctr, Nashville, TN 37232 USA.;Vanderbilt Univ, Dept Chem, Struct Biol Ctr, Nashville, TN 37232 USA..
    Corbett, Kevin D.
    Ludwig Inst Canc Res, San Diego Branch, La Jolla, CA 92093 USA.;Univ Calif San Diego, Dept Cellular & Mol Med, La Jolla, CA 92093 USA..
    Cosgrove, Michael S.
    SUNY Upstate Med Univ, Dept Biochem & Mol Biol, Syracuse, NY 13210 USA..
    Crosson, Sean
    Univ Chicago, Dept Biochem & Mol Biol, 920 E 58Th St, Chicago, IL 60637 USA..
    Dhe-Paganon, Sirano
    Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02115 USA..
    Di Cera, Enrico
    St Louis Univ, Sch Med, Edward A Doisy Dept Biochem & Mol Biol, St Louis, MO 63104 USA..
    Drennan, Catherine L.
    MIT, Dept Chem, Cambridge, MA 02139 USA.;MIT, Dept Biol, Cambridge, MA 02139 USA. MIT, Howard Hughes Med Inst, Cambridge, MA 02139 USA..
    Eck, Michael J.
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA.;Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02115 USA..
    Eichman, Brandt F.
    Vanderbilt Univ, Dept Biol, Nashville, TN 37235 USA.;Vanderbilt Univ, Struct Biol Ctr, 221 Kirkland Hall, Nashville, TN 37235 USA..
    Fan, Qing R.
    Columbia Univ, Dept Pharmacol, New York, NY 10032 USA.;Columbia Univ, Dept Pathol & Cell Biol, New York, NY 10032 USA..
    Ferre-D'Amare, Adrian R.
    NHLBI, Lab RNA Biophys, NIH, Bldg 10, Bethesda, MD 20892 USA..
    Fromme, J. Christopher
    Cornell Univ, Dept Mol Biol & Genet, Weill Inst Cell & Mol Biol, Ithaca, NY 14853 USA..
    Garcia, K. Christopher
    Stanford Univ, Howard Hughes Med Inst, Sch Med, Stanford, CA 94305 USA.;Stanford Univ, Dept Mol & Cellular Physiol, Sch Med, Stanford, CA 94305 USA.;Stanford Univ, Dept Biol Struct, Sch Med, Stanford, CA 94305 USA..
    Gaudet, Rachelle
    Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA..
    Gong, Peng
    Chinese Acad Sci, Key Lab Special Pathogens & Biosafety, Wuhan Inst Virol, Wuhan 430071, Peoples R China..
    Harrison, Stephen C.
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA.;Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA.;Harvard Univ, Mol Med Lab, Boston Childrens Hosp, Sch Med, Boston, MA 02115 USA..
    Heldwein, Ekaterina E.
    Tufts Univ, Sch Med, Dept Mol Biol & Microbiol, Boston, MA 02111 USA..
    Jia, Zongchao
    Queens Univ, Dept Biomed & Mol Sci, Kingston, ON K7M 3G5, Canada..
    Keenan, Robert J.
    Univ Chicago, Dept Biochem & Mol Biol, 920 E 58Th St, Chicago, IL 60637 USA..
    Kruse, Andrew C.
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Kvansakul, Marc
    La Trobe Univ, Dept Biochem & Genet, Melbourne, Vic, Australia..
    McLellan, Jason S.
    Geisel Sch Med Dartmouth, Dept Biochem, Hanover, NH 03755 USA..
    Modis, Yorgo
    Univ Cambridge, Dept Med, MRC Lab Mol Biol, Francis Crick Ave, Cambridge CB2 0QH, England..
    Nam, Yunsun
    Univ Texas SW Med Ctr Dallas, Dallas, TX 75390 USA..
    Otwinowski, Zbyszek
    Univ Texas SW Med Ctr Dallas, Dept Biophys & Biochem, Dallas, TX 75390 USA..
    Pai, Emil F.
    Univ Toronto, Dept Biochem, Toronto, ON M5S 1A8, Canada.;Univ Toronto, Dept Med Biophys, Toronto, ON M5S 1A8, Canada.;Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada.;Univ Hlth Network, Ontario Canc Inst, Campbell Family Inst Canc Res, Toronto, ON M5G 2M9, Canada..
    Barbosa Pereira, Pedro Jose
    Univ Porto, Inst Biol Mol & Celular, P-4150 Oporto, Portugal.;Univ Porto, Inst Invest & Inovacao Saude, P-4150 Oporto, Portugal..
    Petosa, Carlo
    Univ Grenoble Alpes, CNRS, CFA, Inst Biol Struct, F-38027 Grenoble, France..
    Raman, S.
    Univ Maryland, Dept Pharmaceut Sci, Baltimore, MD 21201 USA..
    Rapoport, Tom A.
    Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA.;Harvard Univ, Sch Med, Dept Cell Biol, Boston, MA 02115 USA..
    Roll-Mecak, Antonina
    Natl Inst Neurol Disorders & Stroke, Cell Biol & Biophys Unit, Porter Neurosci Res Ctr, Bethesda, MD 20892 USA.;NHLBI, Bethesda, MD 20892 USA..
    Rosen, Michael K.
    Univ Texas SW Med Ctr Dallas, Dept Biophys, Dallas, TX 75390 USA.;Univ Texas SW Med Ctr Dallas, Howard Hughes Med Inst, Dallas, TX 75390 USA..
    Rudenko, Gabby
    Univ Texas Med Branch, Dept Pharmacol & Toxicol, Sealy Ctr Struct Biol & Mol Biophys, Galveston, TX 77555 USA..
    Schlessinger, Joseph
    Yale Univ, Sch Med, Dept Pharmacol, New Haven, CT 06520 USA..
    Schwartz, Thomas U.
    MIT, Dept Biol, Cambridge, MA 02139 USA..
    Shamoo, Yousif
    Rice Univ, Dept Biosci, Houston, TX 77005 USA..
    Sondermann, Holger
    Cornell Univ, Dept Mol Med, Coll Vet Med, Ithaca, NY 14853 USA..
    Tao, Yizhi J.
    Rice Univ, Dept Biosci, Houston, TX 77005 USA..
    Tolia, Niraj H.
    Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA..
    Tsodikov, Oleg V.
    Univ Kentucky, Dept Pharmaceut Sci, Coll Pharm, Lexington, KY 40536 USA..
    Westover, Kenneth D.
    Univ Texas SW Med Ctr Dallas, Dept Biochem, Dallas, TX 75390 USA.;Univ Texas SW Med Ctr Dallas, Dept Radiat Oncol, Dallas, TX 75390 USA..
    Wu, Hao
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA.;Boston Childrens Hosp, Program Cellular & Mol Med, Boston, MA 02115 USA..
    Foster, Ian
    Argonne Natl Lab, Math & Comp Sci Div, 9700 S Cass Ave, Argonne, IL 60439 USA.;Univ Chicago, Dept Comp Sci, Chicago, IL 60637 USA..
    Fraser, James S.
    Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94158 USA..
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Lawrence Berkeley Natl Lab, NERSC, Berkeley, CA 94720 USA..
    Gonen, Tamir
    Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA 20147 USA..
    Kirchhausen, Tom
    Boston Childrens Hosp, Program Cellular & Mol Med, Boston, MA 02115 USA.;Boston Childrens Hosp, Dept Pediat, Boston, MA 02115 USA.;Harvard Univ, Sch Med, Dept Cell Biol, Boston, MA 02115 USA.;Harvard Univ, Sch Med, Dept Pediat, Boston, MA 02115 USA..
    Diederichs, Kay
    Univ Konstanz, Dept Biol, D-78457 Constance, Germany..
    Crosas, Merce
    Harvard Univ, Inst Quantitat Social Sci, Cambridge, MA 02138 USA..
    Sliz, Piotr
    Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Data publication with the structural biology data grid supports live analysis2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 10882Article in journal (Refereed)
    Abstract [en]

    Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data. sbgrid. org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

  • 41.
    Munke, Anna
    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.
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Bean, Richard J.
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    Bucher, Maximilian
    Chapman, Henry N.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Elser, Veit
    Fromme, Petra
    Hajdu, Janos
    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.
    Higashiura, Akifumi
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lan, Ti-Yen
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liu, Haiguang
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nakagawa, Atsushi
    Nam, Daewoong
    Nelson, Garrett
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ourmazd, Abbas
    Rose, Max
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schwander, Peter
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Sierra, Raymond G.
    Song, Changyong
    Svenda, Martin
    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.
    Vartanyants, Ivan A.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Wiedorn, Max O.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Yoon, Chun Hong
    Zook, James
    Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, p. 160064:1-12, article id 160064Article in journal (Refereed)
  • 42.
    Okamoto, Kenta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Miyazaki, Naoyuki
    NIPS, Okazaki, Aichi 4448585, Japan..
    Song, Chihong
    NIPS, Okazaki, Aichi 4448585, Japan..
    Maia, Filipe
    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.
    Abergel, Chantal
    CNRS, UMR 7256, IMM FR 3479, Struct & Genom Informat Lab, F-13288 Marseille, France..
    Claverie, Jean-Michel
    CNRS, UMR 7256, IMM FR 3479, Struct & Genom Informat Lab, F-13288 Marseille, France.;Aix Marseille Univ, F-13288 Marseille, France.;AP HM, F-13005 Marseille, France..
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic..
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Murata, Kazuyoshi
    NIPS, Okazaki, Aichi 4448585, Japan..
    Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 13291Article in journal (Refereed)
    Abstract [en]

    The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 mu m in length and 0.9 mu m in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.

  • 43. Park, Hyung Joo
    et al.
    Loh, N. Duane
    Sierra, Raymond G.
    Hampton, Christina Y.
    Starodub, Dmitri
    Martin, Andrew V.
    Barty, Anton
    Aquila, Andrew
    Schulz, Joachim
    Steinbrener, Jan
    Shoeman, Robert L.
    Lomb, Lukas
    Kassemeyer, Stephan
    Bostedt, Christoph
    Bozek, John
    Epp, Sascha W.
    Erk, Benjamin
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Rudek, Benedikt
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Hauser, Guenter
    Holl, Peter
    Pedersoli, Emanuele
    Liang, Mengning
    Hunter, Mark S.
    Gumprecht, Lars
    Coppola, Nicola
    Wunderer, Cornelia
    Graafsma, Heinz
    Maia, Filipe R. N. C.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Hirsemann, Helmut
    Nass, Karol
    Tobias, Herbert J.
    Farquar, George R.
    Benner, W. Henry
    Hau-Riege, Stefan
    Reich, Christian
    Hartmann, Andreas
    Soltau, Heike
    Marchesini, Stefano
    Bajt, Sasa
    Barthelmess, Miriam
    Strueder, Lothar
    Ullrich, Joachim
    Bucksbaum, Philip
    Frank, Matthias
    Schlichting, Ilme
    Chapman, Henry N.
    Bogan, Michael J.
    Elser, Veit
    Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers2013In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, no 23, p. 28729-28742Article in journal (Refereed)
    Abstract [en]

    Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

  • 44. Pedersoli, E.
    et al.
    Loh, N. D.
    Capotondi, F.
    Hampton, C. Y.
    Sierra, R. G.
    Starodub, D.
    Bostedt, C.
    Bozek, J.
    Nelson, A. J.
    Aslam, M.
    Li, S.
    Dravid, V. P.
    Martin, A. V.
    Aquila, A.
    Barty, A.
    Fleckenstein, H.
    Gumprecht, L.
    Liang, M.
    Nass, K.
    Schulz, J.
    White, T. A.
    Coppola, N.
    Bajt, S.
    Barthelmess, M.
    Graafsma, H.
    Hirsemann, H.
    Wunderer, C.
    Epp, S. W.
    Erk, B.
    Rudek, B.
    Rudenko, A.
    Foucar, L.
    Kassemeyer, S.
    Lomb, L.
    Rolles, D.
    Shoeman, R. L.
    Steinbrener, J.
    Hartmann, R.
    Hartmann, A.
    Hauser, G.
    Holl, P.
    Kimmel, N.
    Reich, C.
    Soltau, H.
    Weidenspointner, G.
    Benner, W. H.
    Farquar, G. R.
    Hau-Riege, S. P.
    Hunter, M. S.
    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.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tobias, H. J.
    Marchesini, S.
    Frank, M.
    Strueder, L.
    Schlichting, I.
    Ullrich, J.
    Chapman, H. N.
    Bucksbaum, P. H.
    Kiskinova, M.
    Bogan, M. J.
    Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging2013In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 46, no 16 SI, p. 164033-Article in journal (Refereed)
    Abstract [en]

    Unraveling the complex morphology of functional materials like core-shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core-shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with similar to 10 nm core diameter and similar to 30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core-shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.

  • 45.
    R. N. C. Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ultrafast Coherent X-ray Diffractive Nanoimaging2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    X-ray lasers are creating unprecedented research opportunities in physics,chemistry and biology. The peak brightness of these lasers exceeds presentsynchrotrons by 1010, the coherence degeneracy parameters exceedsynchrotrons by 109, and the time resolution is 105 times better. In theduration of a single flash, the beam focused to a micron-sized spot has the samepower density as all the sunlight hitting the Earth, focused to a millimetresquare. Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploitsthese unique properties of X-ray lasers to obtain high-resolution structures fornon-crystalline biological (and other) objects. In such an experiment, thesample is quickly vaporised, but not before sufficient scattered light can berecorded. The continuous diffraction pattern can then be phased and thestructure of a more or less undamaged sample recovered% (speed of light vs. speed of a shock wave).This thesis presents results from the first ultrafast X-ray diffractive imagingexperiments with linear accelerator-driven free-electron lasers and fromoptically-driven table-top X-ray lasers. It also explores the possibility ofinvestigating phase transitions in crystals by X-ray lasers. An important problem with ultrafast CXDI of small samples such as single proteinmolecules is that the signal from a single measurement will be small, requiringsignal enhancement by averaging over multiple equivalent samples. We present anumerical investigation of the problems, including the case where samplemolecules are not exactly identical, and propose tentative solutions. A new software package (Hawk) has been developed for data processing and imagereconstruction. Hawk is the first publicly available software package in thisarea, and it is released as an open source software with the aspiration offostering the development of this field.

    List of papers
    1. Femtosecond diffractive imaging with a soft-X-ray free-electron laser
    Open this publication in new window or tab >>Femtosecond diffractive imaging with a soft-X-ray free-electron laser
    Show others...
    2006 (English)In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 2, no 12, p. 839-843Article in journal (Refereed) Published
    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).

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-24416 (URN)10.1038/nphys461 (DOI)000242478000021 ()
    Available from: 2007-02-05 Created: 2007-02-05 Last updated: 2017-12-07Bibliographically approved
    2. Structural studies of melting on the picosecond time scale
    Open this publication in new window or tab >>Structural studies of melting on the picosecond time scale
    2008 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 42, p. 6344-6349Article, review/survey (Refereed) Published
    Abstract [en]

    Ultrafast structural studies of laser-induced melting have demonstrated that the solid-liquid phase transition can take place on a picosecond time scale in a variety of materials. Experimental studies using ångström wavelength X-rays from the sub-picosecond pulse source at Stanford (now retired) on non-thermal melting of semi-conductors, such as indium antimonide, employed the decay of a single Bragg-peak to measure the time component of the phase transition. These materials were found to start melting within one picosecond after the laser pulse. Recent computer simulations have described the thermal melting of ice induced by an infrared laser pulse. Here it was shown that melting can happen within a few picoseconds, somewhat slower than non-thermal melting in semi-conductors. These computer simulations are compatible with spectroscopy experiments on ice-melting, demonstrating that simulations form a very powerful complement to experiments targeting the process of phase-transitions. Here we present an overview of recent experimental and theoretical studies of melting, as well as new simulations of ice-melting where the effect of the size of the crystal on scattering is studied. Based on simulations of a near-macroscopic crystal, we predict the decay of the most intense Bragg peaks of ice following heating by laser pulse, by modeling the scattering from the melting sample in the simulations.

    National Category
    Physical Sciences Chemical Sciences Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121924 (URN)10.1039/b807550f (DOI)000260485600001 ()18972022 (PubMedID)
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
    3. Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source
    Open this publication in new window or tab >>Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source
    Show others...
    2009 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 103, no 2, p. 028104-Article in journal (Refereed) Published
    Abstract [en]

    Coherent x-ray diffractive imaging is a powerful method for studies on   nonperiodic structures on the nanoscale. Access to femtosecond dynamics   in major physical, chemical, and biological processes requires   single-shot diffraction data. Up to now, this has been limited to   intense coherent pulses from a free electron laser. Here we show that   laser-driven ultrashort x-ray sources offer a comparatively inexpensive  alternative. We present measurements of single-shot diffraction patterns from isolated nano-objects with a single 20 fs pulse from a   table-top high-harmonic x-ray laser. Images were reconstructed with a   resolution of 119 nm from the single shot and 62 nm from multiple shots.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-121910 (URN)10.1103/PhysRevLett.103.028104 (DOI)000267887800065 ()
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
    4. Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Open this publication in new window or tab >>Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Show others...
    2009 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 3, p. 031905-Article in journal (Refereed) Published
    Abstract [en]

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

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

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

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

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

    Keyword
    computer programs, diffractive imaging, free-electron lasers, Hawk, open-source software, phasing, reconstruction
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121927 (URN)10.1107/S0021889810036083 (DOI)000284550900033 ()
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
  • 46.
    Rath, Asawari D.
    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.
    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.
    Fleckenstein, Holger
    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.
    Hasse, Dirk
    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.
    Westphal, Daniel
    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.
    Hantke, Max
    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.
    Seibert, M. Marvin
    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.
    Liang, Mengning
    Stellato, Francesco
    Kirian, Richard
    Bean, Richard
    Barty, Anton
    Galli, Lorenzo
    Nass, Karol
    Barthelmess, Miriam
    Aquila, Andrew
    Toleikis, Sven
    Treusch, Rolf
    Roling, Sebastian
    Wöstmann, Michael
    Zacharias, Helmut
    Chapman, Henry N.
    Bajt, Saša
    DePonte, Daniel
    Hajdu, Janos
    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.
    Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 23, p. 28914-28925Article in journal (Refereed)
    Abstract [en]

    We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 1016 W/cm2 with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.

  • 47. Ravasio, A
    et al.
    Gauthier, D
    Maia, F. R. N. C.
    Billon, M
    Caumes, J
    Garzella, D
    Geleoc, M
    Gobert, O
    Hergott, J
    Pena, A
    Perez, H
    Carre, B
    Bourhis, E
    Gierak, J
    Madouri, A
    Mailly, D
    Schiedt, B
    Fajardo, M
    Gautier, J
    Zeitoun, P
    Bucksbaum, P
    Hajdu, J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Merdji, H
    Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source2009In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 103, no 2, p. 028104-Article in journal (Refereed)
    Abstract [en]

    Coherent x-ray diffractive imaging is a powerful method for studies on   nonperiodic structures on the nanoscale. Access to femtosecond dynamics   in major physical, chemical, and biological processes requires   single-shot diffraction data. Up to now, this has been limited to   intense coherent pulses from a free electron laser. Here we show that   laser-driven ultrashort x-ray sources offer a comparatively inexpensive  alternative. We present measurements of single-shot diffraction patterns from isolated nano-objects with a single 20 fs pulse from a   table-top high-harmonic x-ray laser. Images were reconstructed with a   resolution of 119 nm from the single shot and 62 nm from multiple shots.

  • 48.
    Reddy, Hemanth K. N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Yoon, Chun Hong
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bobkov, Sergey
    Bucher, Maximilian
    Carini, Gabriella A.
    Carron, Sebastian
    Chapman, Henry
    Daurer, Benedikt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fromme, Petra
    Hajdu, Janos
    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.
    Hart, Philip
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Kurta, Ruslan P.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    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.
    Nam, Daewoong
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ourmazd, Abbas
    Rose, Max
    Schwander, Peter
    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. KTH Royal Inst Technol, AlbaNova Univ Ctr, Dept Appl Phys, Biomed & Xray Phys, SE-10691 Stockholm, Sweden.
    Song, Changyong
    Spence, John C. H.
    Svenda, Martin
    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.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed)
    Abstract [en]

    Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported similar to 600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

  • 49.
    Sala, S.
    et al.
    UCL, London, England; Univ Southampton, Southampton, England.
    Daurer, B. J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, M. F.
    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.
    Loh, N. D.
    Natl Univ Singapore, Singapore, Singapore.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Thibault, P.
    Univ Southampton, Southampton, England.
    Ptychographic imaging for the characterization of X-ray free-electron laser beams2017In: X-RAY MICROSCOPY CONFERENCE 2016 (XRM 2016) / [ed] Rau, C, 2017, article id 012032Conference paper (Refereed)
    Abstract [en]

    We present some preliminary results from a study aimed at the characterization of the wavefront of X-ray free electron laser (XFEL) beams in the same operation conditions as for single particle imaging (or flash X-ray imaging) experiments. The varying illumination produced by wavefront fluctuations between several pulses leads to a partially coherent average beam which can be decomposed into several coherent modes using ptychographic reconstruction algorithms. Such a decomposition can give insight into pulse-to-pulse variations of the wavefront. We discuss data collected at the Linac Coherent Light Source (LCLS) and FERMI.

  • 50.
    Seibert, M. Marvin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastien
    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.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bogan, Michael J.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Hau-Riege, Stefan
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Frank, Matthias
    Benner, Henry
    Lee, Joanna Y.
    Marchesini, Stefano
    Shaevitz, Joshua W.
    Fletcher, Daniel A.
    Bajt, Sasa
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Femtosecond diffractive imaging of biological cells2010In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 43, no 19, p. 194015-Article in journal (Refereed)
    Abstract [en]

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

12 1 - 50 of 55
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