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  • 1. Allen, Andrew J.
    et al.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kaysser-Pyzalla, Anke R.
    Beyond the International Year of Crystallography2015In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 48, no P1, p. 1-2Article in journal (Other academic)
  • 2.
    Allen, Andrew J.
    et al.
    NIST, Mat Measurement Sci Div Gaithersburg, MD USA.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. AS CR, European Extreme Light Infrastruct, Inst Phys, Prague, Czech Republic..
    McIntyre, Garry J.
    Australian Nucl Sci & Technol Org, New Illawarra Rd, Lucas Heights, NSW, Australia.
    Journal of Applied Crystallography: the first 50 years and beyond2018In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 51, no Part: 2, p. 233-234Article in journal (Other academic)
    Abstract [en]

    The Editors of Journal of Applied Crystallography mark the journal's 50th anniversary.

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

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

  • 4. 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.

  • 5. 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.

  • 6. Bajt, Sasa
    et al.
    Chapman, Henry N
    Spiller, Eberhard A
    Alameda, Jennifer B
    Woods, Bruce W
    Frank, Matthias
    Bogan, Michael J
    Barty, Anton
    Boutet, Sebastien
    Marchesini, Stefano
    Hau-Riege, Stefan P
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Shapiro, David
    Camera for coherent diffractive imaging and holography with a soft-x-ray free-electron laser2008In: Applied Optics, ISSN 1559-128X, E-ISSN 2155-3165, Vol. 47, no 10, p. 1673-1683Article in journal (Refereed)
    Abstract [en]

    We describe a camera to record coherent scattering patterns with a soft-x-ray free-electron laser (FEL). The camera consists of a laterally graded multilayer mirror, which reflects the diffraction pattern onto a CCD detector. The mirror acts as a bandpass filter for both the wavelength and the angle, which isolates the desired scattering pattern from nonsample scattering or incoherent emission from the sample. The mirror also solves the particular problem of the extreme intensity of the FEL pulses, which are focused to greater than 10(14) W/cm2. The strong undiffracted pulse passes through a hole in the mirror and propagates onto a beam dump at a distance behind the instrument rather than interacting with a beam stop placed near the CCD. The camera concept is extendable for the full range of the fundamental wavelength of the free electron laser in Hamburg (FLASH) FEL (i.e., between 6 and 60 nm) and into the water window. We have fabricated and tested various multilayer mirrors for wavelengths of 32, 16, 13.5, and 4.5 nm. At the shorter wavelengths mirror roughness must be minimized to reduce scattering from the mirror. We have recorded over 30,000 diffraction patterns at the FLASH FEL with no observable mirror damage or degradation of performance.

  • 7. 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.

  • 8.
    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.

  • 9.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gunn, Laura H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flueckiger, Leonie
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lundholm, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kulyk, Olena
    Higashiura, Akifumi
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Ne-Te Duane
    Wysong, Taylor E.
    Bostedt, Christoph
    Gorkhover, Tais
    Iwan, Bianca
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Osipov, Timur
    Walter, Peter
    Hart, Philip
    Bucher, Maximilian
    Ulmer, Anatoli
    Ray, Dipanwita
    Carini, Gabriella
    Ferguson, Ken R.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Electrospray sample injection for single-particle imaging with x-ray lasers2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed)
  • 10. 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.

  • 11.
    Caleman, Carl
    et al.
    Physik Department E17, Technische Universität München.
    Ortiz, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bultmark, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Gabrysch, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Electricity.
    Parak, F. G.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Klintenberg, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Radiation damage in biological material: electronic properties and electron impact ionization in urea2009In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 85, no 1, p. 18005-Article in journal (Refereed)
    Abstract [en]

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

  • 12.
    Carlsson, Gunilla H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Nicholls, Peter
    Svistunenko, Dimitri
    Berglund, Gunnar I.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Complexes of horseradish peroxidase with formate, acetate and carbon monoxide2005In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 44, no 2, p. 635-642Article in journal (Refereed)
    Abstract [en]

    Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. These ligands also bind to catalases, but their interactions are different in the two types of enzymes. Formate (notionally the “hydrated” form of carbon monoxide) is oxidized to carbon dioxide by compound I in catalase, while no such reaction is reported to occur in HRP, and the CO complex of ferrocatalase can only be obtained indirectly. Here we describe high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate, and compare these with the previously determined HRP−acetate structure [Berglund, G. I., et al. (2002) Nature 417, 463−468]. A multicrystal X-ray data collection strategy preserved the correct oxidation state of the iron during the experiments. Absorption spectra of the crystals and electron paramagnetic resonance data for the acetate and formate complexes in solution correlate electronic states with the structural results. Formate in ferric HRP and CO in ferrous HRP bind directly to the heme iron with iron−ligand distances of 2.3 and 1.8 Å, respectively. CO does not bind to the ferric iron in the crystal. Acetate bound to ferric HRP stacks parallel with the heme plane with its carboxylate group 3.6 Å from the heme iron, and without an intervening solvent molecule between the iron and acetate. The positions of the oxygen atoms in the bound ligands outline a potential access route for hydrogen peroxide to the iron. We propose that interactions in this channel ensure deprotonation of the proximal oxygen before binding to the heme iron.

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

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

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

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

  • 15. 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).

  • 16. 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.

  • 17. Chapman, Henry N
    et al.
    Hau-Riege, Stefan P
    Bogan, Michael J
    Bajt, Sasa
    Barty, Anton
    Boutet, Sébastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Frank, Matthias
    Woods, Bruce W
    Benner, W Henry
    London, Richard A
    Rohner, Urs
    Szöke, Abraham
    Spiller, Eberhard
    Möller, Thomas
    Bostedt, Christoph
    Shapiro, David A
    Kuhlmann, Marion
    Treusch, Rolf
    Plönjes, Elke
    Burmeister, Florian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    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.
    Seibert, M. Marvin
    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.
    Femtosecond time-delay X-ray holography2007In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 448, no 7154, p. 676-679Article in journal (Refereed)
    Abstract [en]

    Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment1, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging2, 3 can be used to achieve high resolution, beyond radiation damage limits for biological samples4. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.

  • 18. Cryan, J P
    et al.
    Glownia, J M
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Belkacem, A
    Berrah, N
    Blaga, C I
    Bostedt, C
    Bozek, J
    Cherepkov, N A
    DiMauro, L F
    Fang, L
    Gessner, O
    Guhr, M
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hertlein, M P
    Hoener, M
    Kornilov, O
    Marangos, J P
    March, A M
    McFarland, B K
    Merdji, H
    Messerschmidt, M
    Petrović, V S
    Raman, C
    Ray, D
    Reis, D A
    Semenov, S K
    Trigo, M
    White, J L
    White, W
    Young, L
    Bucksbaum, P H
    Coffee, R N
    Molecular frame Auger electron energy spectrum from N22012In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 45, no 5, p. 055601-Article in journal (Refereed)
    Abstract [en]

    Here we present the first angle-resolved, non-resonant (normal) Auger spectra for impulsively aligned nitrogen molecules. We have measured the angular pattern of Auger electron emission following K -shell photoionization by 1.1 keV photons from the Linac Coherent Light Source (LCLS). Using strong-field-induced molecular alignment to make molecular frame measurements is equally effective for both repulsive and quasi-bound final states. The capability to resolve Auger emission angular distributions in the molecular frame of reference provides a new tool for spectral assignments in congested Auger electron spectra that takes advantage of the symmetries of the final diction states. Based on our experimental results and theoretical predictions, we propose the assignment of the spectral features in the Auger electron spectrum.

  • 19. Cryan, James P.
    et al.
    Glownia, J. M.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Belkacem, A.
    Berrah, N.
    Blaga, C. I.
    Bostedt, C.
    Bozek, J.
    Buth, C.
    DiMauro, L. F.
    Fang, L.
    Gessner, O.
    Guehr, M.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hertlein, M. P.
    Hoener, M.
    Kornilov, O.
    Marangos, J. P.
    March, A. M.
    McFarland, B. K.
    Merdji, H.
    Petrovic, V. S.
    Raman, C.
    Ray, D.
    Reis, D.
    Tarantelli, F.
    Trigo, M.
    White, J. L.
    White, W.
    Young, L.
    Bucksbaum, P. H.
    Coffee, R. N.
    Auger Electron Angular Distribution of Double Core-Hole States in the Molecular Reference Frame2010In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 105, no 8, p. 083004-Article in journal (Refereed)
    Abstract [en]

    The Linac Coherent Light Source free electron laser is a source of high brightness x rays, 2×1011 photons in a ∼5  fs pulse, that can be focused to produce double core vacancies through rapid sequential ionization. This enables double core vacancy Auger electron spectroscopy, an entirely new way to study femtosecond chemical dynamics with Auger electrons that probe the local valence structure of molecules near a specific atomic core. Using 1.1 keV photons for sequential x-ray ionization of impulsively aligned molecular nitrogen, we observed a rich single-site double core vacancy Auger electron spectrum near 413 eV, in good agreement with ab initio calculations, and we measured the corresponding Auger electron angle dependence in the molecular frame.

  • 20.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Benner, W. Henry
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tîmneanu, Nicuşor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Loh, N. Duane
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Awel, Salah
    Wiedorn, Max O.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastian
    Williams, Garth
    Koglin, Jason
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed)
  • 21.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
  • 22.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Aquila, Andrew
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Ctr Etud Saclay, Commissariat Energie Atom & Energies Alternat, F-91191 Gif Sur Yvette, France..
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Liang, Meng
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Martin, Andrew V.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Melbourne, 161 Barry St, Melbourne, Vic 3010, Australia..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Bajt, Sasa
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barthelmess, Miriam
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Coppola, Nicola
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Claverie, Jean-Michel
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Loh, N. Duane
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;Natl Univ Singapore, Ctr BioImaging Sci, 14 Sci Dr 4 Blk S1 A, Singapore 117546, Singapore..
    Bostedt, Christoph
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bozek, John D.
    Synchrotron SOLEIL, Lorme Merisiers Roundabout St Aubin, F-91190 St Aubin, France..
    Krzywinski, Jacek
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bogan, Michael J.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Hampton, Christina Y.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Sierra, Raymond G.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Frank, Matthias
    Lawrence Livermore Natl Lab, 7000 East Ave,Mail Stop L-211, Livermore, CA 94551 USA..
    Shoeman, Robert L.
    Lomb, Lukas
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Foucar, Lutz
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Epp, Sascha W.
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Rolles, Daniel
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Rudenko, Artem
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Hartmann, Robert
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Hartmann, Andreas
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Kimmel, Nils
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Holl, Peter
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Weidenspointner, Georg
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Rudek, Benedikt
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Erk, Benjamin
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Kassemeyer, Stephan
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Schlichting, Ilme
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Strueder, Lothar
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany.;Univ Siegen, Emmy Noether Campus,Walter Flex Str 3, D-57068 Siegen, Germany..
    Ullrich, Joachim
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Phys Tech Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany..
    Schmidt, Carlo
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Krasniqi, Faton
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Hauser, Guenter
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Reich, Christian
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Soltau, Heike
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Schorb, Sebastian
    Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany..
    Hirsemann, Helmut
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Wunderer, Cornelia
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Graafsma, Heinz
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Notkestr 85, D-22607 Hamburg, Germany..
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed)
    Abstract [en]

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

  • 23. Gaffney, K J
    et al.
    Lindenberg, A M
    Larsson, J
    Sokolowski-Tinten, K
    Blome, C
    Synnergren, O
    Sheppard, J
    Caleman, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    MacPhee, A G
    Weinstein, D
    Lowney, D P
    Allison, T
    Matthews, T
    Falcone, R W
    Cavalieri, A L
    Fritz, D M
    Lee, S H
    Bucksbaum, P H
    Reis, D A
    Rudati, J
    Macrander, A T
    Fuoss, P H
    Kao, C C
    Siddons, D P
    Pahl, R
    Moffat, K
    Als-Nielsen, J
    Duesterer, S
    Ischebeck, R
    Schlarb, H
    Schulte-Schrepping, H
    Schneider, J
    von der Linde, D
    Hignette, O
    Sette, F
    Chapman, H N
    Lee, R W
    Hansen, T N
    Wark, J S
    Bergh, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Huldt, G
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Timneanu, N
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molecular Biophysics.
    Akre, R A
    Bong, E
    Krejcik, P
    Arthur, J
    Brennan, S
    Luening, K
    Hastings, J B
    Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb.2005In: Phys Rev Lett, ISSN 0031-9007, Vol. 95, no 12, p. 125701-Article in journal (Other scientific)
  • 24. 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. 

  • 25. Glownia, James M.
    et al.
    Cryan, J.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Belkacem, A.
    Berrah, N.
    Blaga, C. I.
    Bostedt, C.
    Bozek, J.
    DiMauro, L. F.
    Fang, L.
    Frisch, J.
    Gessner, O.
    Guehr, M.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hertlein, M. P.
    Hoener, M.
    Huang, G.
    Kornilov, O.
    Marangos, J. P.
    March, A. M.
    McFarland, B. K.
    Merdji, H.
    Petrovic, V. S.
    Raman, C.
    Ray, D.
    Reis, D. A.
    Trigo, M.
    White, J. L.
    White, W.
    Wilcox, R.
    Young, L.
    Coffee, R. N.
    Bucksbaum, P. H.
    Time-resolved pump-probe experiments at the LCLS2010In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 18, no 17, p. 17620-17630Article in journal (Refereed)
    Abstract [en]

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

  • 26. Gorkhover, Tais
    et al.
    Ulmer, Anatoli
    Ferguson, Ken
    Bucher, Max
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bruza, Petr
    Carron, Sebastian
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rupp, Daniela
    Sauppe, Mario
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N.
    Faigel, Gyula
    Möller, Thomas
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bostedt, Christoph
    Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles2018In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal (Refereed)
  • 27.
    Hajdu, J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Biochemistry.
    Hodgson, K
    Miao, J
    van der Spoel, D
    Neutze, R
    Robinson, C. V
    Faigel, G
    Jacobsen, C
    Kirz, J
    Sayre, D
    Weckert, E
    Materlik, G
    Szöke, A
    Structural studies on single particles and biomolecules. LCLS: The First Experiments.2000Other (Other scientific)
  • 28.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. AS CR, Inst Phys, European Extreme Light Infrastruct, Slovance 2, Prague 18221 8, Czech Republic..
    Structures from poorly diffracting crystals: a new start for macromolecular crystallography?2017In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 50, p. 982-984Article in journal (Other academic)
  • 29.
    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.

  • 30.
    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.

  • 31.
    Hantke, Max Felix
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Oxford, Dept Chem, Chem Res Lab, 12 Mansfield Rd, Oxford OX1 3TA, England.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Kulyk, Olena
    Acad Sci Czech Republ, Inst Phys, ELI Beamlines, Na Slovance 2, CZ-18221 Prague, Czech Republic.
    Westphal, Daniel
    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.
    Svenda, Martin
    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.
    Kirian, Richard A.
    Arizona State Univ, Dept Phys, 550 E Tyler Dr, Tempe, AZ 85287 USA.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Acad Sci Czech Republ, Inst Phys, ELI Beamlines, Na Slovance 2, CZ-18221 Prague, Czech Republic;Chalmers Univ Technol, Dept Phys, Condensed Matter Phys, Gothenburg, Sweden.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Acad Sci Czech Republ, Inst Phys, ELI Beamlines, Na Slovance 2, CZ-18221 Prague, Czech Republic.
    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 USA.
    Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams2018In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 673-680Article in journal (Refereed)
    Abstract [en]

    Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70-2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the 'Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100-500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.

  • 32.
    Helliwell, John R.
    et al.
    Univ Manchester, Sch Chem, Brunswick St, Manchester M13 9PL, Lancs, England.
    Minor, Wladek
    Univ Virginia, Dept Mol Physiol & Biol Phys, 1340 Jefferson Pk Ave Pinn Hall, Charlottesville, VA 22908 USA.
    Weiss, Manfred S.
    Helmholtz Zentrum Berlin, Macromol Crystallog HZB MX, Albert Einstein Str 15, D-12489 Berlin, Germany.
    Garman, Elspeth F.
    Univ Oxford, Dept Biochem, South Parks Rd, Oxford OX1 3QU, England.
    Read, Randy J.
    Univ Cambridge, Dept Haematol, Cambridge Inst Med Res, Keith Peters Bldg,Hills Rd, Cambridge CB2 0XY, England.
    Newman, Janet
    CSIRO, C3, 343 Royal Parade, Parkville, Vic 3052, Australia.
    van Raaij, Mark J.
    CSIC, Ctr Nacl Biotecnol, C Darwin 3, Madrid 28049, Spain.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. AS CR, Inst Phys, European Extreme Light Infrastruct, Slovance 2, Prague 18221 8, Czech Republic.
    Baker, Edward N.
    Univ Auckland, Sch Biol Sci, Private Bag 92-019, Auckland, New Zealand.
    Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography2019In: ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, ISSN 2059-7983, Vol. 75, p. 455-457Article in journal (Other academic)
  • 33.
    Iwan, Bianca
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Thomas, Heiko
    Rupp, Daniela
    Gorkhover, Tais
    Adolph, Markus
    Bostedt, Christoph
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Explosion, ion acceleration and molecular fragmentation of methane clusters in the pulsed beam of a free-electron laser2012In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 86, no 3, p. 033201-Article in journal (Refereed)
    Abstract [en]

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

  • 34.
    Iwan, Bianca S
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobierajski, R.
    Toleikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    TOF-OFF: A method for determining focal positions in tightly focused free-electron laser experiments by measurement of ejected ions2011In: High Energy Density Physics, ISSN 1574-1818, Vol. 7, no 4, p. 336-342Article in journal (Refereed)
    Abstract [en]

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

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

  • 35. 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.

  • 36.
    Klimesova, Eva
    et al.
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Kulyk, Olena
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Gu, Yanjun
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Dittrich, Laura
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic;Tech Univ Berlin, Inst Opt & Atomare Phys, ER 1-1,Str 17 Juni 135, D-10623 Berlin, Germany.
    Korn, Georg
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Krikunova, Maria
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic;Tech Univ Berlin, Inst Opt & Atomare Phys, ER 1-1,Str 17 Juni 135, D-10623 Berlin, Germany.
    Andreasson, Jakob
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic;Chalmers Univ Technol, Dept Phys, Gothenburg, Sweden.
    Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 8851Article in journal (Refereed)
    Abstract [en]

    Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 10(16) Wcm(-2). We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.

  • 37. Lindenberg, A M
    et al.
    Larsson, J
    Sokolowski-Tinten, K
    Gaffney, K J
    Blome, C
    Synnergren, O
    Sheppard, J
    Caleman, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Macphee, A G
    Weinstein, D
    Lowney, D P
    Allison, T K
    Matthews, T
    Falcone, R W
    Cavalieri, A L
    Fritz, D M
    Lee, S H
    Bucksbaum, P H
    Reis, D A
    Rudati, J
    Fuoss, P H
    Kao, C C
    Siddons, D P
    Pahl, R
    Als-Nielsen, J
    Duesterer, S
    Ischebeck, R
    Schlarb, H
    Schulte-Schrepping, H
    Tschentscher, Th
    Schneider, J
    von der Linde, D
    Hignette, O
    Sette, F
    Chapman, H N
    Lee, R W
    Hansen, T N
    Techert, S
    Wark, J S
    Bergh, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Huldt, G
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Timneanu, N
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology. Molekylär biofysik.
    Akre, R A
    Bong, E
    Krejcik, P
    Arthur, J
    Brennan, S
    Luening, K
    Hastings, J B
    Atomic-scale visualization of inertial dynamics.2005In: Science, ISSN 1095-9203, Vol. 308, no 5720, p. 392-5Article in journal (Refereed)
    Abstract [en]

    The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of liquids and solids. An accelerator-based source of femtosecond x-ray pulses allowed us to follow directly atomic displacements on an optically modified energy landscape, leading eventually to the transition from crystalline solid to disordered liquid. We show that, to first order in time, the dynamics are inertial, and we place constraints on the shape and curvature of the transition-state potential energy surface. Our measurements point toward analogies between this nonequilibrium phase transition and the short-time dynamics intrinsic to equilibrium liquids.

  • 38. 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.

  • 39.
    Lundholm, Ida V.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Okamoto, Kenta
    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.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bruza, Petr
    Bucher, Max
    Carron, Sebastian
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ferguson, Ken
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Krzywinski, Jacek
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Morgan, Andrew
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Müller, Maria
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pietrini, Alberto
    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.
    Rupp, Daniela
    Sauppe, Mario
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Swiggers, Michelle
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ulmer, Anatoli
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Williams, Garth
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Faigel, Gyula
    Chapman, Henry N.
    Möller, Thomas
    Bostedt, Christoph
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gorkhover, Tais
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging2018In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed)
  • 40.
    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.

  • 41.
    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.

  • 42.
    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, Biology, Department of Cell and Molecular Biology, Molecular biophysics. 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)
  • 43.
    Mühlig, Kerstin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ganan-Calvo, Alfonso M.
    Univ Seville, ETSI, Dept Ingn Aerospacial & Mecan Fluidos, ES-41092 Seville, Spain.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Acad Sci Czech Republ, Inst Phys, ELI Beamlines, CZ-18221 Prague, Czech Republic;Chalmers Univ Technol, Dept Phys, Condensed Matter Phys, SE-41258 Gothenburg, Sweden.
    Larsson, Daniel S D
    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. Acad Sci Czech Republ, Inst Phys, ELI Beamlines, CZ-18221 Prague, Czech Republic.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. KTH AlbaNova, KTH Royal Inst Technol, Dept Appl Phys, Biomed & Xray Phys, SE-10691 Stockholm, Sweden.
    Nanometre-sized droplets from a gas dynamic virtual nozzle2019In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 52, p. 800-808Article in journal (Refereed)
    Abstract [en]

    This paper reports on improved techniques to create and characterize nanometre-sized droplets from dilute aqueous solutions by using a gas dynamic virtual nozzle (GDVN). It describes a method to measure the size distribution of uncharged droplets, using an environmental scanning electron microscope, and provides theoretical models for the droplet sizes created. The results show that droplet sizes can be tuned by adjusting the gas and liquid flow rates in the GDVN, and at the lowest liquid flow rates, the size of the water droplets peaks at about 120nm. This droplet size is similar to droplet sizes produced by electrospray ionization but requires neither electrolytes nor charging of the solution. The results presented here identify a new operational regime for GDVNs and show that predictable droplet sizes, comparable to those obtained by electrospray ionization, can be produced by purely mechanical means in GDVNs.

  • 44. Nelson, A. J.
    et al.
    Toleikis, S.
    Chapman, H.
    Bajt, S.
    Krzywinski, J.
    Chalupsky, J.
    Juha, L.
    Cihelka, J.
    Hajkova, V.
    Vysin, L.
    Burian, T.
    Kozlova, M.
    Fäustlin, R. R.
    Nagler, B.
    Vinko, S. M.
    Whitcher, T.
    Dzelzainis, T.
    Renner, O.
    Saksl, K.
    Khorsand, A. R.
    Heimann, P. A.
    Sobierajski, R.
    Klinger, D.
    Jurek, M.
    Pelka, J.
    Iwan, Bianca
    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.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fajardo, M.
    Wark, J. S.
    Riley, D.
    Tschentscher, T.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lee, R. W.
    Soft x-ray free electron laser microfocus for exploring matter under extreme conditions2009In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 17, no 20, p. 18271-18278Article in journal (Refereed)
    Abstract [en]

    We have focused a beam (BL3) of FLASH (Free-electron LASer in Hamburg: lambda = 13.5 nm, pulse length 15 fs, pulse energy 10-40 mu J, 5Hz) using a fine polished off-axis parabola having a focal length of 270 mm and coated with a Mo/Si multilayer with an initial reflectivity of 67% at 13.5 nm. The OAP was mounted and aligned with a picomotor controlled six-axis gimbal. Beam imprints on poly(methyl methacrylate) -PMMA were used to measure focus and the focused beam was used to create isochoric heating of various slab targets. Results show the focal spot has a diameter of <= 1 mu m. Observations were correlated with simulations of best focus to provide further relevant information.

  • 45. Neutze, R
    et al.
    Wouts, R
    van der Spoel, D
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Weckert, E
    Hajdu, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Potential for biomolecular imaging with femtosecond X-ray pulses2000In: NATURE, ISSN 0028-0836, Vol. 406, no 6797, p. 752-757Article in journal (Refereed)
    Abstract [en]

    Sample damage by X-rays and other radiation limits the resolution of structural studies on non-repetitive and non-reproducible structures such as individual biomolecules or cells(1). Cooling can slow sample deterioration, but cannot eliminate damage-induc

  • 46.
    Okamoto, Kenta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Miyazaki, Naoyuki
    National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585 Japan.
    Reddy, Hemanth K.N.
    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.
    Maia, Filipe R.N.C.
    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.
    Abergel, Chantal
    Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille 13288, France.
    Claverie, Jean-Michel
    Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille 13288, France; Assistance Publique des Hôpitaux de Marseille, La Timone, 13005 Marseille, France.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Institute of Physics AS CR, v.v.i., Na Slovance 2, 18221 Prague 8, Czech Republic.
    Murata, Kazuyoshi
    National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585 Japan.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly2018In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 516, p. 239-245, article id S0042-6822(18)30028-XArticle in journal (Refereed)
    Abstract [en]

    Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.

  • 47.
    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.

  • 48.
    Pietrini, Alberto
    et al.
    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.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hantke, Max F.
    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.
    Loh, N. Duane
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    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.
    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.
    A statistical approach to detect protein complexes at X-ray free electron laser facilities2018In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed)
  • 49.
    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.

  • 50.
    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, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    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.
    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)
12 1 - 50 of 62
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