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  • 1.
    Adams, Christopher
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Kjeldsen, Frank
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Ion Physics.
    Patriksson, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gräslund, Astrid
    Papadopolous, Evangelos
    Zubarev, Roman
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques2006In: International Journal of Mass Spectrometry, ISSN 1387-3806, E-ISSN 1873-2798, Vol. 253, no 3, p. 263-273Article in journal (Refereed)
    Abstract [en]

    The relevance of gas-phase protein structure to its solution structure is of the utmost importance in studying biomolecules by mass spectrometry. D-Amino acid substitutions within a minimal protein. Trp-cage. were used to correlate solution-phase properties as measured by circular dichroism with solution/gas-phase conformational features of protein cations probed via charge state distribution (CSD) in electrospray ionization. and gas-phase features revealed by tandem mass spectrometry (MS/MS). The gas-phase features were additionally supported by force-field molecular dynamics simulations. CD data showed that almost any single-residue D-substitution destroys the most prominent CD feature of the "native" all-L isomer, alpha-helicity. CSD was able to qualitatively assess the degree of compactness of solution-phase molecular structures. CSD results were consistent with the all-L form being the most compact in solution among all studied stereoisomers except for the D-Asn(1) isomer. D-substitutions of the aromatic Y(3), W(6) and Q(5) residues generated the largest deviations in CSD data among single amino acid substitutions. consistent with the critical role of these residues in Trp-cage stability. Electron capture dissociation of the stereoisomer dications gave an indication that some gas-phase structural features of Trp-cage are similar to those in solution. This result is supported by MDS data oil five of the studied stereoisomer dications in the gas-phase. The MDS-derived minimum-energy structures possessed more extensive hydrogen bonding than the solution-phase structure of the native form, deviating from the latter by 3-4 angstrom and were not 'inside-out' compared to native structures. MDS data could be correlated with CD data and even with ECD results. which aided in providing a long-range structural constraint for MDS. The overall conclusion is the general resemblance, despite the difference on the detailed level, of the preferred structures in both phases for the mini protein Trp-cage.

  • 2. 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)
  • 3.
    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.

  • 4.
    Ancker Persson, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structural and biophysical studies on infection phenotypes in totivirus-like viruses2023Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Viruses pose significant threats to human health, making it crucial to understand their structure and behavior to develop effective treatments. This study focuses on two strains of Giardia Lamblia virus (GLV) (a cat strain and human strain) a virus that infects the parasite Giardia Lamblia which in turn can infect humans or animals. Understanding viruses helps immensely with treating people who are infected as well as our ability to utilize the virus for good. The Omono River virus (OmRV) and saccharomyces cerevisae virus (ScV-L-A) is used for comparison. OmRV belongs to a group called totivirus-like viruses and ScV-L-A and GLV belong to the Totiviridae group. They have some common characteristics such as isometric virions, double-stranded RNA genomes, and 120 chemically identical subunits. What sets them apart is their hosts, viruses in the Totiviridae group only infect protozoan hosts intracellularly while OmRV only infects metazoan hosts extracellularly. GLV is interesting because it has displayed both an intra- and extracellular mode of infection. Finding out more about GLV could give us insight into viral evolution. Cryo-electron microscopy (cryoEM) is used to investigate the structure of GLV. From the cryoEM data models were created using Coot and Chimera with resolutions of 4.0 Å for the human strain and 4.2 Å for the cat strain. Found in these models were an open pore compared to the closed one of OmRV as well as lack of a C-terminal, which is used to increase stability. Signs of conserved 𝛼-helices are also found indicating their evolutionary relationship. 

    The full text will be freely available from 2026-07-04 18:21
  • 5.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca Stella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andrejczuk, A.
    Abreu, E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bergh, M.
    Caleman, Carl
    Nelson, A. J.
    Bajt, S.
    Chalupsky, J.
    Chapman, H. N.
    Faeustlin, R. R.
    Hajkova, V.
    Heimann, P. A.
    Hjörvarsson, Björgvin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Juha, L.
    Klinger, D.
    Krzywinski, J.
    Nagler, B.
    Pålsson, Gunnar Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Singer, W.
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sobicrajski, R.
    Tolcikis, S.
    Tschentscher, T.
    Vinko, S. M.
    Lee, R. W.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser2011In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 83, no 1, p. 016403-Article in journal (Refereed)
    Abstract [en]

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

  • 6.
    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, 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

    Download full text (pdf)
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  • 7.
    Andreasson, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Chapman, Henry N.
    Bielecki, Johan
    Abergel, C.
    Seltzer, V.
    Claverie, J.-M.
    Svenda, M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Time of Flight Mass Spectrometry to Monitor Sample Expansion in Flash Diffraction Studies on Single Virus ParticlesManuscript (preprint) (Other academic)
  • 8.
    Andrikopoulos, Prokopis C.
    et al.
    Czech Acad Sci, BIOCEV, Inst Biotechnol, Prumyslova 595, CZ-25250 Vestec, Czech Republic..
    Liu, Yingliang
    Czech Acad Sci, BIOCEV, Inst Biotechnol, Prumyslova 595, CZ-25250 Vestec, Czech Republic..
    Picchiotti, Alessandra
    Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic..
    Lenngren, Nils
    Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic..
    Kloz, Miroslav
    Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic..
    Chaudhari, Aditya S.
    Czech Acad Sci, BIOCEV, Inst Biotechnol, Prumyslova 595, CZ-25250 Vestec, Czech Republic..
    Precek, Martin
    Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic..
    Rebarz, Mateusz
    Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic..
    Andreasson, Jakob
    Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic.;Chalmers Univ Technol, Dept Phys, Condensed Matter Phys, S-41296 Gothenburg, Sweden..
    Hajdu, J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Czech Acad Sci, ELI Beamlines, Inst Phys, Za Radnici 835, CZ-25241 Dolni Brezany, Czech Republic.
    Schneider, Bohdan
    Czech Acad Sci, BIOCEV, Inst Biotechnol, Prumyslova 595, CZ-25250 Vestec, Czech Republic..
    Fuertes, Gustavo
    Czech Acad Sci, BIOCEV, Inst Biotechnol, Prumyslova 595, CZ-25250 Vestec, Czech Republic..
    Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations2020In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 22, no 12, p. 6538-6552Article in journal (Refereed)
    Abstract [en]

    Flavin mononucleotide (FMN) belongs to the large family of flavins, ubiquitous yellow-coloured biological chromophores that contain an isoalloxazine ring system. As a cofactor in flavoproteins, it is found in various enzymes and photosensory receptors, like those featuring the light-oxygen-voltage (LOV) domain. The photocycle of FMN is triggered by blue light and proceeds via a cascade of intermediate states. In this work, we have studied isolated FMN in an aqueous solution in order to elucidate the intrinsic electronic and vibrational changes of the chromophore upon excitation. The ultrafast transitions of excited FMN were monitored through the joint use of femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy encompassing a time window between 0 ps and 6 ns with 50 fs time resolution. Global analysis of the obtained transient visible absorption and transient Raman spectra in combination with extensive quantum chemistry calculations identified unambiguously the singlet and triplet FMN populations and addressed solvent dynamics effects. The good agreement between the experimental and theoretical spectra facilitated the assignment of electronic transitions and vibrations. Our results represent the first steps towards more complex experiments aimed at tracking structural changes of FMN embedded in light-inducible proteins upon photoexcitation.

  • 9. 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, E-ISSN 2329-7778, 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.

  • 10. 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, 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.

  • 11.
    Assalauova, Dameli
    et al.
    DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Kim, Young Yong
    DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Bobkov, Sergey
    Natl Res Ctr, Kurchatov Inst, Akad Kurchatova Pl 1, Moscow 123182, Russia.
    Khubbutdinov, Ruslan
    DESY, Notkestr 85, D-22607 Hamburg, Germany; Natl Res Nucl Univ MEPhI, Moscow Engn Phys Inst, Kashirskoe Sh 31, Moscow 115409, Russia.
    Rose, Max
    DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Alvarez, Roberto
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA; Arizona State Univ, Sch Math & Stat Sci, Tempe, AZ 85287 USA.
    Andreasson, Jakob
    Acad Sci Czech Republ, ELI Beamlines, Inst Phys, CZ-18221 Prague, Czech Republic.
    Balaur, Eugeniu
    La Trobe Univ, Australian Res Council, La Trobe Inst Mol Sci LIMS, Dept Chem & Phys,Ctr Excellence Adv Mol Imaging, Melbourne, Vic 3086, Australia.
    Contreras, Alice
    Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA; Arizona State Univ, Biodesign Inst Ctr Immunotherapy Vaccines & Virot, Tempe, AZ 85287 USA.
    DeMirci, Hasan
    SLAC Natl Accelerator Lab, Stanford Pulse Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA; Koc Univ, Dept Mol Biol & Genet, TR-34450 Istanbul, Turkey.
    Gelisio, Luca
    DESY, Ctr Free Electron Laser Sci CFEL, 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. Acad Sci Czech Republ, ELI Beamlines, Inst Phys, CZ-18221 Prague, Czech Republic.
    Hunter, Mark S.
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
    Kurta, Ruslan P.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.
    Li, Haoyuan
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA; Stanford Univ, Phys Dept, 450 Jane Stanford Way, Stanford, CA 94305 USA.
    McFadden, Matthew
    Arizona State Univ, Biodesign Inst Ctr Immunotherapy Vaccines & Virot, Tempe, AZ 85287 USA.
    Nazari, Reza
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA; Arizona State Univ, Sch Engn Matter Transport & Energy, Tempe, AZ 85287 USA.
    Schwander, Peter
    Univ Wisconsin, Milwaukee, WI 53211 USA.
    Teslyuk, Anton
    Natl Res Ctr, Kurchatov Inst, Akad Kurchatova Pl 1, Moscow 123182, Russia; Moscow Inst Phys & Technol, Moscow 141700, Russia.
    Walter, Peter
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
    Xavier, P. Lourdu
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany; SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA; Max Planck Inst Struct & Dynam Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany.
    Yoon, Chun Hong
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
    Zaare, Sahba
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA; SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
    Ilyin, Viacheslav A.
    Natl Res Ctr, Kurchatov Inst, Akad Kurchatova Pl 1, Moscow 123182, Russia; Moscow Inst Phys & Technol, Moscow 141700, Russia.
    Kirian, Richard A.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA.
    Hogue, Brenda G.
    Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA; Arizona State Univ, Biodesign Inst Ctr Immunotherapy Vaccines & Virot, Tempe, AZ 85287 USA; Arizona State Univ, Ctr Appl Struct Discovery, Biodesign Inst, Tempe, AZ 85287 USA.
    Aquila, Andrew
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.
    Vartanyants, Ivan A.
    DESY, Notkestr 85, D-22607 Hamburg, Germany; Natl Res Nucl Univ MEPhI, Moscow Engn Phys Inst, Kashirskoe Sh 31, Moscow 115409, Russia.
    An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser2020In: IUCrJ, E-ISSN 2052-2525, Vol. 7, p. 1102-1113Article in journal (Refereed)
    Abstract [en]

    An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.

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  • 12.
    Ayyer, Kartik
    et al.
    Max Planck Inst Struct & Dynam Matter, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci, D-22761 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany..
    Xavier, P. Lourdu
    Max Planck Inst Struct & Dynam Matter, D-22761 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany.;Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany..
    Bielecki, Johan
    European XFEL, D-22869 Schenefeld, Germany..
    Shen, Zhou
    Natl Univ Singapore, Ctr Biolmaging Sci, Singapore 117557, Singapore..
    Daurer, Benedikt J.
    Natl Univ Singapore, Ctr Biolmaging Sci, Singapore 117557, Singapore..
    Samanta, Amit K.
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany..
    Awel, Salah
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany..
    Bean, Richard
    European XFEL, D-22869 Schenefeld, Germany..
    Barty, Anton
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany..
    Bergemann, Martin
    European XFEL, D-22869 Schenefeld, Germany..
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Estillore, Armando D.
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany..
    Fangohr, Hans
    European XFEL, D-22869 Schenefeld, Germany..
    Giewekemeyer, Klaus
    European XFEL, D-22869 Schenefeld, Germany..
    Hunter, Mark S.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA..
    Karnevskiy, Mikhail
    European XFEL, D-22869 Schenefeld, Germany..
    Kirian, Richard A.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Kirkwood, Henry
    European XFEL, D-22869 Schenefeld, Germany..
    Kim, Yoonhee
    European XFEL, D-22869 Schenefeld, Germany..
    Koliyadu, Jayanath
    European XFEL, D-22869 Schenefeld, Germany..
    Lange, Holger
    Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany.;Univ Hamburg, Inst Phys Chem, D-20146 Hamburg, Germany..
    Letrun, Romain
    European XFEL, D-22869 Schenefeld, Germany..
    Lübke, Jannik
    Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany.;Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-22761 Hamburg, Germany..
    Michelat, Thomas
    European XFEL, D-22869 Schenefeld, Germany..
    Morgan, Andrew J.
    Univ Melbourne, Phys, Melbourne, Vic, Australia..
    Roth, Nils
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-22761 Hamburg, Germany..
    Sato, Tokushi
    European XFEL, D-22869 Schenefeld, Germany..
    Sikorski, Margin
    European XFEL, D-22869 Schenefeld, Germany..
    Schulz, Florian
    Univ Hamburg, Inst Phys Chem, D-20146 Hamburg, Germany..
    Spence, John C. H.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Vagovic, Patrik
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;European XFEL, D-22869 Schenefeld, Germany..
    Wollweber, Tamme
    Max Planck Inst Struct & Dynam Matter, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci, D-22761 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany..
    Worbs, Lena
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-22761 Hamburg, Germany..
    Yefanov, Oleksandr
    Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany..
    Zhuang, Yulong
    Max Planck Inst Struct & Dynam Matter, D-22761 Hamburg, Germany.;Ctr Free Electron Laser Sci, D-22761 Hamburg, Germany..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. NERSC, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Horke, Daniel A.
    Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany.;Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;Radboud Univ Nijmegen, Inst Mol & Mat, NL-6525 AJ Nijmegen, Netherlands..
    Küpper, Jochen
    Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany.;Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-22761 Hamburg, Germany.;Univ Hamburg, Dept Chem, D-20146 Hamburg, Germany..
    Loh, N. Duane
    Natl Univ Singapore, Ctr Biolmaging Sci, Singapore 117557, Singapore.;Natl Univ Singapore, Dept Phys, Singapore 117551, Singapore..
    Mancuso, Adrian P.
    European XFEL, D-22869 Schenefeld, Germany.;La Trobe Univ, La Trobe Inst Mol Sci, Dept Chem & Phys, Melbourne, Vic 3086, Australia..
    Chapman, Henry N.
    Univ Hamburg, Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany.;Ctr Free Electron LaserSci, DESY, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, D-22761 Hamburg, Germany..
    3D diffractive imaging of nanoparticle ensembles using an x-ray laser2021In: Optica, E-ISSN 2334-2536, Vol. 8, no 1, p. 15-23Article in journal (Refereed)
    Abstract [en]

    Single particle imaging at x-ray free electron lasers (XFELs) has the potential to determine the structure and dynamics of single biomolecules at room temperature. Two major hurdles have prevented this potential from being reached, namely, the collection of sufficient high-quality diffraction patterns and robust computational purification to overcome structural heterogeneity. We report the breaking of both of these barriers using gold nanoparticle test samples, recording around 10 million diffraction patterns at the European XFEL and structurally and orientationally sorting the patterns to obtain better than 3-nm-resolution 3D reconstructions for each of four samples. With these new developments, integrating advancements in x-ray sources, fast-framing detectors, efficient sample delivery, and data analysis algorithms, we illuminate the path towards sub-nano meter biomolecular imaging. The methods developed here can also be extended to characterize ensembles that are inherently diverse to obtain their full structural landscape. Published by The Optical Society under the terms of the Creative Commons Attribution 4.0 License.

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  • 13.
    Bacic, Luka
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gaullier, Guillaume
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mohapatra, Jugal
    Mao, Guanzhong
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Brackmann, Klaus
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Panfilov, Mikhail
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Liszczak, Glen
    Sabantsev, Anton
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Deindl, Sebastian
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC12024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1000Article in journal (Refereed)
    Abstract [en]

    The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.

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  • 14.
    Baier, Florian
    et al.
    Univ British Columbia, Michael Smith Lab, Vancouver, BC, Canada.
    Hong, Nansook
    Australian Natl Univ, Res Sch Chem, Canberra, ACT, Australia.
    Yang, Gloria
    Univ British Columbia, Michael Smith Lab, Vancouver, BC, Canada.
    Pabis, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Miton, Charlotte M.
    Univ British Columbia, Michael Smith Lab, Vancouver, BC, Canada.
    Barrozo, Alexandre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Carr, Paul D.
    Australian Natl Univ, Res Sch Chem, Canberra, ACT, Australia.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Jackson, Colin J.
    Australian Natl Univ, Res Sch Chem, Canberra, ACT, Australia.
    Tokuriki, Nobuhiko
    Univ British Columbia, Michael Smith Lab, Vancouver, BC, Canada.
    Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes2019In: eLIFE, E-ISSN 2050-084X, Vol. 8, article id e40789Article in journal (Refereed)
    Abstract [en]

    Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may impact the evolvability of proteins, but the underlying molecular basis remains unclear. Here, we performed comparative directed evolution of four orthologous metallo-beta-lactamases toward a new function and found that different starting genotypes evolved to distinct evolutionary outcomes. Despite a low initial fitness, one ortholog reached a significantly higher fitness plateau than its counterparts, via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show how cryptic molecular properties and conformational variation of active site residues in the initial genotypes cause epistasis, that could lead to distinct evolutionary outcomes. Our work highlights the importance of understanding the molecular details that connect genetic variation to protein function to improve the prediction of protein evolution.

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  • 15. 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.

  • 16. 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.

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

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

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  • 18.
    Behzadi, Hadi
    et al.
    Teheran.
    Esrafili, Mehdi D
    Teheran.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hadipour, Nasser L
    Teheran.
    Parsafar, Gholamabbas
    Teheran.
    A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors2008In: Biophysical Chemistry, ISSN 0301-4622, E-ISSN 1873-4200, Vol. 137, no 2-3, p. 76-80Article in journal (Refereed)
    Abstract [en]

    Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and (17)O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with alpha-helix initial structure. It was found that peptide loses its initial alpha-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate (17)O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31+G basis set. Calculated (17)O EFG tensors were used to evaluate quadrupole coupling constants, QCC, and asymmetry parameters, eta(Q). Difference between the calculated QCC and eta(Q) values revealed how hydrogen-bonding interactions affect EFG tensors at the sites of each oxygen nucleus.

  • 19.
    Bellisario, Alfredo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Noise reduction and mask removal neural network for X-ray single-particle imaging2022In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 55, p. 122-132Article in journal (Refereed)
    Abstract [en]

    Free-electron lasers could enable X-ray imaging of single biological macro-molecules and the study of protein dynamics, paving the way for a powerful new imaging tool in structural biology, but a low signal-to-noise ratio and missing regions in the detectors, colloquially termed 'masks', affect data collection and hamper real-time evaluation of experimental data. In this article, the challenges posed by noise and masks are tackled by introducing a neural network pipeline that aims to restore diffraction intensities. For training and testing of the model, a data set of diffraction patterns was simulated from 10 900 different proteins with molecular weights within the range of 10-100 kDa and collected at a photon energy of 8 keV. The method is compared with a simple low-pass filtering algorithm based on autocorrelation constraints. The results show an improvement in the mean-squared error of roughly two orders of magnitude in the presence of masks compared with the noisy data. The algorithm was also tested at increasing mask width, leading to the conclusion that demasking can achieve good results when the mask is smaller than half of the central speckle of the pattern. The results highlight the competitiveness of this model for data processing and the feasibility of restoring diffraction intensities from unknown structures in real time using deep learning methods. Finally, an example is shown of this preprocessing making orientation recovery more reliable, especially for data sets containing very few patterns, using the expansion-maximization-compression algorithm.

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  • 20.
    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.

  • 21.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S. P.
    Scott, H. A.
    Interaction of Ultrashort X-ray Pulses with B4C, SiC and Si2008In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 77, no 2, p. 026404-1-026404-8Article in journal (Refereed)
    Abstract [en]

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

  • 22.
    Bergh, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Model for the Dynamics of a Water Cluster in an X-ray Free Electron Laser Beam2004In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 70, no 5:1, p. 051904-Article in journal (Refereed)
    Abstract [en]

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

  • 23.
    Beyerlein, Kenneth
    et al.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Alonso-Mori, Roberto
    SLAC National Accelerator Laboratory, USA.
    Aquila, Andrew
    SLAC National Accelerator Laboratory, USA.
    Bajt, Sasa
    Photon Science, DESY, Hamburg, Germany.
    Barty, Anton
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Bean, Richard
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Koglin, Jason E.
    SLAC National Accelerator Laboratory, USA.
    Messerschmidt, Marc
    SLAC National Accelerator Laboratory, USA.
    Ragazzon, Davide
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Soklaras, Dimosthenis
    SLAC National Accelerator Laboratory, USA.
    Williams, Garth J.
    SLAC National Accelerator Laboratory, USA.
    Hau-Riege, Stefan
    Lawrence Livermore National Laboratory, USA.
    Boutet, Sebastien
    SLAC National Accelerator Laboratory, USA.
    Chapman, Henry N.
    Center for Free-Electron Laser Science,Deutsches Elektronen-Synchrotron, Hamburg, Germany; Department of Physics, University of Hamburg, Hamburg, Germany; Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany .
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science,Deutsches Elektronen-Synchrotron, Hamburg, Germany.
    Ultrafast non-thermal heating of water initiated by an X-ray laser2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 22, p. 5652-5657Article in journal (Refereed)
    Abstract [en]

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

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  • 24.
    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)
  • 25.
    Bielecki, Johan
    et al.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany..
    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.
    European XFEL, Holzkoppel 4, D-22869 Schenefeld, Germany.;La Trobe Univ, La Trobe Inst Mol Sci, Dept Chem & Phys, Melbourne, Vic 3086, Australia..
    Perspectives on single particle imaging with x rays at the advent of high repetition rate x-ray free electron laser sources2020In: Structural Dynamics, E-ISSN 2329-7778, Vol. 7, no 4, article id 040901Article in journal (Refereed)
    Abstract [en]

    X-ray free electron lasers (XFELs) now routinely produce millijoule level pulses of x-ray photons with tens of femtoseconds duration. Such x-ray intensities gave rise to the idea that weakly scattering particles-perhaps single biomolecules or viruses-could be investigated free of radiation damage. Here, we examine elements from the past decade of so-called single particle imaging with hard XFELs. We look at the progress made to date and identify some future possible directions for the field. In particular, we summarize the presently achieved resolutions as well as identifying the bottlenecks and enabling technologies to future resolution improvement, which in turn enables application to samples of scientific interest.

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  • 26.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Parker, Stewart F.
    Ekanayake, Dharshani
    Rahman, Seikh M. H.
    Borjesson, Lars
    Karlsson, Maths
    Short-range structure of the brownmillerite-type oxide Ba2In2O5 and its hydrated proton-conducting form BaInO3H2014In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 2, no 40, p. 16915-16924Article in journal (Refereed)
    Abstract [en]

    The vibrational spectra and short-range structure of the brownmillerite-type oxide Ba2In2O6 and its hydrated form BaInO3H, are investigated by means of Raman, infrared, and inelastic neutron scattering spectroscopies together with density functional theory calculations. For Ba2In2O6, which may be described as an oxygen deficient perovskite structure with alternating layers of InO6 octahedra and InO4 tetrahedra, the results affirm a short-range structure of Icmm symmetry, which is characterized by random orientation of successive layers of InO4 tetrahedra. For the hydrated, proton conducting, form, BaInO3H, the results suggest that the short-range structure is more complicated than the P4/mbm symmetry that has been proposed previously on the basis of neutron diffraction, but rather suggest a proton configuration close to the lowest energy structure predicted by Martinez et al. [J.-R. Martinez, C. E. Moen, S. Stoelen, N. L. Allan, J. Solid State Chem., 180, 3388, (2007)]. An intense Raman active vibration at 150 cm(-1) is identified as a unique fingerprint of this proton configuration.

  • 27.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Chalmers, Dept Appl Phys, SE-41296 Gothenburg, Sweden..
    Parker, Stewart F.
    Rutherford Appleton Lab, STFC, ISIS Facil, Didcot OX11 0QX, Oxon, England..
    Mazzei, Laura
    Chalmers, Dept Appl Phys, SE-41296 Gothenburg, Sweden..
    Börjesson, Lars
    Chalmers, Dept Appl Phys, SE-41296 Gothenburg, Sweden..
    Karlsson, Maths
    Chalmers, Dept Appl Phys, SE-41296 Gothenburg, Sweden..
    Structure and dehydration mechanism of the proton conducting oxide Ba2In2O5(H2O)(x)2016In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 4, no 4, p. 1224-1232Article in journal (Refereed)
    Abstract [en]

    The structure and dehydration mechanism of the proton conducting oxide Ba2In2O5(H2O)(x) are investigated by means of variable temperature (20-600 degrees C) Raman spectroscopy together with thermal gravimetric analysis and inelastic neutron scattering. At room temperature, Ba2In2O5(H2O)(x) is found to be fully hydrated (x = 1) and to have a perovskite-like structure, which dehydrates gradually with increasing temperature and at around 600 degrees C the material is essentially dehydrated (x approximate to 0.2). The dehydrated material exhibits a brownmillerite structure, which is featured by alternating layers of InO6 octahedra and InO4 tetrahedra. The transition from a perovskite-like to a brownmillerite-like structure upon increasing temperature occurs through the formation of an intermediate phase at ca. 370 degrees C, corresponding to a hydration degree of approximately 50%. The structure of the intermediate phase is similar to the structure of the dehydrated material, but with the difference that it exhibits a non-centrosymmetric distortion of the InO6 octahedra that is not present in the dehydrated material. The dehydration process upon heating is a two-stage mechanism; for temperatures below the hydrated-to-intermediate phase transition, dehydration is characterized by a homogenous release of protons over the entire oxide lattice, whereas above the transition a preferential desorption of protons originating in the nominally tetrahedral layers is observed. Furthermore, our spectroscopic results point towards the co-existence of two structural phases, which relate to the two lowest-energy proton configurations in the material. The relative contributions of the two proton configurations depend on how the sample is hydrated.

  • 28.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rata, A. D.
    Borjesson, L.
    Femtosecond optical reflectivity measurements of lattice-mediated spin repulsions in photoexcited LaCoO3 thin films2014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, no 3, p. 035129-Article in journal (Refereed)
    Abstract [en]

    We present results on the temperature dependence of ultrafast electron and lattice dynamics, measured with pump-probe transient reflectivity experiments, of an epitaxially grown LaCoO3 thin film under tensile strain. Probing spin-polarized transitions into the antibonding e(g) band provides a measure of the low-spin fraction, both as a function of temperature and time after photoexcitation. It is observed that femtosecond laser pulses destabilize the constant low-spin fraction (similar to 63%-64%) in equilibrium into a thermally activated state, driven by a subpicosecond change in spin gap Delta. From the time evolution of the low-spin fraction, it is possible to disentangle the thermal and lattice contributions to the spin state. A lattice mediated spin repulsion, identified as the governing factor determining the equilibrium spin state in thin-film LaCoO3, is observed. These results suggests that time-resolved spectroscopy is a sensitive probe of the spin state in LaCoO3 thin films, with the potential to bring forward quantitative insight into the complicated interplay between structure and spin state in LaCoO3.

  • 29.
    Björling, Alexander
    et al.
    Lund Univ, Max Lab 4, S-22100 Lund, Sweden..
    Marcal, Lucas A. B.
    Lund Univ, Synchrotron Radiat Res & NanoLund, S-22100 Lund, Sweden..
    Solla-Gullon, Jose
    Univ Alicante, Inst Electrochem, Alicante 03080, Spain..
    Wallentin, Jesper
    Lund Univ, Synchrotron Radiat Res & NanoLund, S-22100 Lund, Sweden..
    Carbone, Dina
    Lund Univ, Max Lab 4, S-22100 Lund, Sweden..
    Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-Dimensional Coherent Bragg Imaging of Rotating Nanoparticles2020In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 125, no 24, article id 246101Article in journal (Refereed)
    Abstract [en]

    Bragg coherent diffraction imaging is a powerful strain imaging tool, often limited by beam-induced sample instability for small particles and high power densities. Here, we devise and validate an adapted diffraction volume assembly algorithm, capable of recovering three-dimensional datasets from particles undergoing uncontrolled and unknown rotations. We apply the method to gold nanoparticles which rotate under the influence of a focused coherent x-ray beam, retrieving their three-dimensional shapes and strain fields. The results show that the sample instability problem can be overcome, enabling the use of fourth generation synchrotron sources for Bragg coherent diffraction imaging to their full potential.

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  • 30. Bogan, M. J.
    et al.
    Boutet, S.
    Barty, A.
    Benner, W. H.
    Frank, M.
    Lomb, L.
    Shoeman, R.
    Starodub, D.
    Seibert, Marvin M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hau-Riege, S. P.
    Woods, B.
    Decorwin-Martin, P.
    Bajt, S.
    Schulz, J.
    Rohner, U.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, S.
    Schlichting, I.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, H. N.
    Single-shot femtosecond x-ray diffraction from randomly oriented ellipsoidal nanoparticles2010In: Physical Review Special Topics - Accelerators and Beams, E-ISSN 1098-4402, Vol. 13, no 9, p. 094701-Article in journal (Refereed)
    Abstract [en]

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

  • 31. 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.

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

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

  • 33.
    Bonito, Catia A.
    et al.
    Univ Porto, Fac Sci, Dept Chem & Biochem, LAQV REQUIMTE, Rua Campo Alegre, P-4169007 Porto, Portugal..
    Ferreira, Ricardo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ferreira, Maria-Jose. U.
    Univ Lisbon, Fac Pharm, Res Inst Med iMed ULisboa, Ave Prof Gama Pinto, P-1649003 Lisbon, Portugal..
    Gillet, Jean-Pierre
    Univ Namur, Lab Mol Canc Biol, Mol Physiol Res Unit URPhyM, Namur Res Inst Life Sci NARILIS,Fac Med, B-5000 Namur, Belgium..
    Cordeiro, M. Natalia D. S.
    Univ Porto, Fac Sci, Dept Chem & Biochem, LAQV REQUIMTE, Rua Campo Alegre, P-4169007 Porto, Portugal..
    dos Santos, Daniel J. V. A.
    Univ Porto, Fac Sci, Dept Chem & Biochem, LAQV REQUIMTE, Rua Campo Alegre, P-4169007 Porto, Portugal.;Univ Lisbon, Fac Pharm, Res Inst Med iMed ULisboa, Ave Prof Gama Pinto, P-1649003 Lisbon, Portugal..
    Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 9823Article in journal (Refereed)
    Abstract [en]

    P-glycoprotein (P-gp, ABCB1) overexpression is, currently, one of the most important multidrug resistance (MDR) mechanisms in tumor cells. Thus, modulating drug efflux by P-gp has become one of the most promising approaches to overcome MDR in cancer. Yet, more insights on the molecular basis of drug specificity and efflux-related signal transmission mechanism between the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) are needed to develop molecules with higher selectivity and efficacy. Starting from a murine P-gp crystallographic structure at the inward-facing conformation (PDB ID: 4Q9H), we evaluated the structural quality of the herein generated human P-gp homology model. This initial human P-gp model, in the presence of the "linker" and inserted in a suitable lipid bilayer, was refined through molecular dynamics simulations and thoroughly validated. The best human P-gp model was further used to study the effect of four single-point mutations located at the TMDs, experimentally related with changes in substrate specificity and drug-stimulated ATPase activity. Remarkably, each P-gp mutation is able to induce transmembrane alpha-helices (TMHs) repacking, affecting the drug-binding pocket volume and the drug-binding sites properties (e.g. volume, shape and polarity) finally compromising drug binding at the substrate binding sites. Furthermore, intracellular coupling helices (ICH) also play an important role since changes in the TMHs rearrangement are shown to have an impact in residue interactions at the ICH-NBD interfaces, suggesting that identified TMHs repacking affect TMD-NBD contacts and interfere with signal transmission from the TMDs to the NBDs.

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

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

  • 35. Braun, Tatjana
    et al.
    Orlova, Albina
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lindas, Ann-Christin
    Schroeder, Gunnar F.
    Egelman, Edward H.
    Archaeal actin from a hyperthermophile forms a single-stranded filament2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 30, p. 9340-9345Article in journal (Refereed)
    Abstract [en]

    The prokaryotic origins of the actin cytoskeleton have been firmly established, but it has become clear that the bacterial actins form a wide variety of different filaments, different both from each other and from eukaryotic F-actin. We have used electron cryomicroscopy (cryo-EM) to examine the filaments formed by the protein crenactin (a crenarchaeal actin) from Pyrobaculum calidifontis, an organism that grows optimally at 90 degrees C. Although this protein only has similar to 20% sequence identity with eukaryotic actin, phylogenetic analyses have placed it much closer to eukaryotic actin than any of the bacterial homologs. It has been assumed that the crenactin filament is double-stranded, like F-actin, in part because it would be hard to imagine how a single-stranded filament would be stable at such high temperatures. We show that not only is the crenactin filament single-stranded, but that it is remarkably similar to each of the two strands in F-actin. A large insertion in the crenactin sequence would prevent the formation of an F-actin-like double-stranded filament. Further, analysis of two existing crystal structures reveals six different subunit-subunit interfaces that are filament-like, but each is different from the others in terms of significant rotations. This variability in the subunit-subunit interface, seen at atomic resolution in crystals, can explain the large variability in the crenactin filaments observed by cryo-EM and helps to explain the variability in twist that has been observed for eukaryotic actin filaments.

  • 36. Broeker, N. K.
    et al.
    Gohlke, U.
    Müller, J. J.
    Uetrecht, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Heinemann, U.
    Seckler, R.
    Barbirz, S.
    Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity2013In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 23, no 1, p. 59-68Article in journal (Refereed)
    Abstract [en]

    Bacteriophage HK620 recognizes and cleaves the O-antigen polysaccharide of Escherichia coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent-mediated hydrogen bonds between carbohydrate and protein. At room temperature, association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case, a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: first, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Second, a region where the specific exchange of glutamate for glutamine created a site for an additional water molecule. Side-chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high-affinity scaffold.

  • 37.
    Burke, Jason R.
    et al.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA;Calif State Univ San Bernardino, San Bernardino, CA 92407 USA.
    La Clair, James J.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Philippe, Ryan N.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA;Manus Biosynth, Cambridge, MA USA.
    Pabis, Anna
    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, Biology, Department of Cell and Molecular Biology, Structural Biology.
    Corbella, Marina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Jez, Joseph M.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA;Washington Univ, Dept Biol, Howard Hughes Med Inst, Campus Box 1137, St Louis, MO 63130 USA.
    Cortina, George A.
    Univ Virginia, Dept Mol Physiol & Biomed Engn, Charlottesville, VA 22903 USA.
    Kaltenbach, Miriam
    Weizmann Inst Sci, Dept Biomol Sci, IL-76100 Rehovot, Israel.
    Bowman, Marianne E.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Louie, Gordon V.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Woods, Katherine B.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Nelson, Andrew T.
    Univ Texas Austin, Dept Chem, Austin, TX 78712 USA.
    Tawfik, Dan S.
    Weizmann Inst Sci, Dept Biomol Sci, IL-76100 Rehovot, Israel.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Noel, Joseph P.
    Salk Inst Biol Studies, Jack H Skirball Ctr Chem Biol & Prote, Howard Hughes Med Inst, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases2019In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 9, no 9, p. 8388-8396Article in journal (Refereed)
    Abstract [en]

    Chalcone isomerases are plant enzymes that perform enantioselective oxa-Michael cyclizations of 2'-hydroxychalcones into flavanones. An X-ray crystal structure of an enzyme-product complex combined with molecular dynamics simulations reveal an enzyme mechanism wherein the guanidinium ion of a conserved arginine positions the nucleophilic phenoxide and activates the electrophilic enone for cyclization through Bronsted and Lewis acid interactions. The reaction terminates by asymmetric protonation of the carbanion intermediate syn to the guanidinium. Interestingly, bifunctional guanidine- and urea-based chemical reagents, increasingly used for asymmetric organocatalytic applications, share mechanistic similarities with this natural system. Comparative protein crystal structures and molecular dynamics simulations further demonstrate how two active site water molecules coordinate a hydrogen bond network that enables expanded substrate reactivity for 6'-deoxychalcones in more recently evolved type-2 chalcone isomerases.

  • 38.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Towards Single Molecule Imaging - Understanding Structural Transitions Using Ultrafast X-ray Sources and Computer Simulations2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    X-ray lasers bring us into a new world in photon science by delivering extraordinarily intense beams of x-rays in very short bursts that can be more than ten billion times brighter than pulses from other x-ray sources. These lasers find applications in sciences ranging from astrophysics to structural biology, and could allow us to obtain images of single macromolecules when these are injected into the x-ray beam.

    A macromolecule injected into vacuum in a microdroplet will be affected by evaporation and by the dynamics of the carrier liquid before being hit by the x-ray pulse. Simulations of neutral and charged water droplets were performed to predict structural changes and changes of temperature due to evaporation. The results are discussed in the aspect of single molecule imaging.

    Further studies show ionization caused by the intense x-ray radiation. These simulations reveal the development of secondary electron cascades in water. Other studies show the development of these cascades in KI and CsI where experimental data exist. The results are in agreement with observation, and show the temporal, spatial and energetic evolution of secondary electron cascades in the sample.

    X-ray diffraction is sensitive to structural changes on the length scale of chemical bonds. Using a short infrared pump pulse to trigger structural changes, and a short x-ray pulse for probing it, these changes can be studied with a temporal resolution similar to the pulse lengths. Time resolved diffraction experiments were performed on a phase transition during resolidification of a non-thermally molten InSb crystal. The experiment reveals the dynamics of crystal regrowth.

    Computer simulations were performed on the infrared laser-induced melting of bulk ice, giving a comprehension of the dynamics and the wavelength dependence of melting. These studies form a basis for planning experiments with x-ray lasers.

    List of papers
    1. Auger electron cascades in water and ice
    Open this publication in new window or tab >>Auger electron cascades in water and ice
    2004 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 299, p. 277-283Article in journal (Refereed) Published
    Abstract [en]

    Secondary electron cascades can induce significant ionisation in condensed matter due to electron–atom collisions. This is of interest in the context of diffraction and imaging using X-rays, where radiation damage is the main limiting factor for achieving high resolution data. Here we present new results on electron-induced damage on liquid water and ice, from the simulation of Auger electron cascades. We have compared our theoretical estimations to the available experimental data on elastic and inelastic electron–molecule interactions for water and found the theoretical results for elastic cross-sections to be in very good agreement with experiment. As a result of the cascade we find that the average number of secondary electrons after 100 fs in ice is about 25, slightly higher than in water, where it is about 20. The difference in damage between ice and water is discussed in the context of sample handling for biomolecular systems.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-95959 (URN)10.1016/j.chemphys.2003.10.011 (DOI)2004 (PubMedID)
    Available from: 2007-05-16 Created: 2007-05-16 Last updated: 2017-12-14Bibliographically approved
    2. Studies if resolidification of non-thermally molten InSb using time-resolved X-ray diffraction
    Open this publication in new window or tab >>Studies if resolidification of non-thermally molten InSb using time-resolved X-ray diffraction
    Show others...
    2005 In: Applied Physics A, Vol. 81, p. 893-900Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95960 (URN)
    Available from: 2007-05-16 Created: 2007-05-16 Last updated: 2016-04-12Bibliographically approved
    3. Temperature and structural changes of water in vacuum due to evaporation
    Open this publication in new window or tab >>Temperature and structural changes of water in vacuum due to evaporation
    2006 In: Journal of Chemical Physics, Vol. 125, p. 154508-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95961 (URN)
    Available from: 2007-05-16 Created: 2007-05-16Bibliographically approved
    4. Picosecond Melting of Ice by an Infrared Laser Pulse
    Open this publication in new window or tab >>Picosecond Melting of Ice by an Infrared Laser Pulse
    2008 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 8, p. 1417-1420Article in journal (Refereed) Published
    Abstract [en]

    Cold as ice: Molecular dynamics simulation provides snapshots of a melting ice crystal (see picture). The laser pulse heats up the system, and the energy is absorbed in the OH bonds. After a few picoseconds, the energy is transferred to rotational and translational energy, causing the crystal to melt. The melting starts as a nucleation process, and even long after the first melting is initialized, pockets of crystalline structures can be found.

    Keywords
    Computer Simulation, Crystallization, Ice, Infrared Rays, Kinetics, Lasers, Models; Molecular, Molecular Conformation, Phase Transition/*radiation effects, Temperature, Time Factors
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95962 (URN)10.1002/anie.200703987 (DOI)000253345700010 ()18176920 (PubMedID)
    Available from: 2007-05-16 Created: 2007-05-16 Last updated: 2022-01-28Bibliographically approved
    5. Secondary Electron Cascade Dynamics in KI and CsI
    Open this publication in new window or tab >>Secondary Electron Cascade Dynamics in KI and CsI
    2007 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 111, no 46, p. 17442-17447Article in journal (Refereed) Published
    Abstract [en]

    We present a study of the characteristics of secondary electron cascades in two photocathode materials, KI and CsI. To do so, we have employed a model that enables us to explicitly follow the electron trajectories once the dielectric properties have been derived semiempirically from the energy loss function. Furthermore, we introduce a modification to the model by which the energy loss function is calculated in a first-principle manner using the GW approximation for the self-energy of the electrons. We find good agreement between the two approaches. Our results show comparable saturation times and secondary electron yields for the cascades in the two materials, and a narrower electron energy distribution (51%) for KI compared to that for CsI.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-102110 (URN)10.1021/jp0736692 (DOI)000251024500041 ()
    Available from: 2009-05-06 Created: 2009-05-05 Last updated: 2022-01-28Bibliographically approved
    6. Evaporation from water clusters containing singly charged ions
    Open this publication in new window or tab >>Evaporation from water clusters containing singly charged ions
    2007 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 9, no 37, p. 5105-5111Article in journal (Refereed) Published
    Abstract [en]

    Molecular dynamics simulations were used to study the evaporation from water clusterscontaining either ClÀ, H2PO4À, Na+ or NH4+ ions. The simulations ranged between 10 and500 ns, and were performed in vacuum starting at 275 K. A number of different models were usedincluding polarizable models. The clusters contain 216 or 512 molecules, 0, 4 or 8 of which wereions. The ions with hydrogen bonding properties do not affect evaporation, even though thephosphate ions have a pronounced ion–ion structure and tend to be inside the cluster whereasammonium shows little ion–ion structure and has a distribution within the cluster similar to thatof the water molecules. Since the individual ion–water interactions are much stronger in the caseof Na+–water and ClÀ–water clusters, evaporation is somewhat slower for clusters containingthese ions. It seems therefore that the main determinant of the evaporation rate in ion–waterclusters is the strength of the interaction. Fission of droplets that contain more ions than allowedaccording to the Rayleigh limit seems to occur more rapidly in clusters containing ammoniumand sodium ions.

    Keywords
    Sodium ion, Droplet, Aqueous solution, Distribution, Ammonium ion, Structure, Phosphates, Hydrogen bond, Models, Simulation, Molecular dynamics method, Ions, Water, Evaporation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95964 (URN)10.1039/b706243e (DOI)000249564300005 ()17878986 [ (PubMedID)
    Available from: 2007-05-16 Created: 2007-05-16 Last updated: 2022-01-28Bibliographically approved
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  • 39. Caleman, Carl
    et al.
    Bergh, Magnus
    Scott, Howard A.
    Spence, John C. H.
    Chapman, Henry N.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses2011In: Journal of Modern Optics, ISSN 0950-0340, E-ISSN 1362-3044, Vol. 58, no 16, p. 1486-1497Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 41.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Huldt, Gösta
    Ortiz, Carlos
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Parak, Fritz G.
    van der Spool, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nanocrystal imaging using intense and ultrashort X-ray pulsesManuscript (preprint) (Other (popular science, discussion, etc.))
    Abstract [en]

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

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  • 42.
    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.

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  • 43.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Aquila, Andrew
    Barty, Anton
    Scott, Howard A.
    White, Thomas A.
    Chapman, Henry N.
    Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser2015In: Optics Express, E-ISSN 1094-4087, Vol. 23, no 2, p. 1213-1231Article in journal (Refereed)
    Abstract [en]

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

  • 44.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Tîmneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, A. V.
    White, T. A.
    Scott, H. A.
    Barty, A.
    Aquila, A.
    Chapman, H. N.
    Modeling of XFEL induced ionization and atomic displacement in protein nanocrystals2012In: Proceedings of SPIE: The International Society for Optical Engineering, 2012, p. 85040H-Conference paper (Refereed)
    Abstract [en]

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

  • 45.
    Caleman, Carl
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Temperature and structural changes of water in vacuum due to evaporation2006In: Journal of Chemical Physics, Vol. 125, p. 154508-Article in journal (Refereed)
  • 46.
    Calixto, Ana R.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Moreira, Catia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Pabis, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kötting, Carsten
    Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany.
    Gerwert, Klaus
    Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany.
    Rudack, Till
    Ruhr Univ Bochum, Dept Biophys, D-44801 Bochum, Germany.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 27, p. 10684-10701Article in journal (Refereed)
    Abstract [en]

    GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the G(alpha i), subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.

  • 47.
    Carlsson, Gunilla H.
    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.
    Cardinale, Francesca
    Univ Turin, Dept Agr Forestry & Food Sci, Largo Paolo Braccini 2, I-10095 Grugliasco 2, Italy.
    Prandi, Cristina
    Univ Turin, Dept Chem, Via P Giuria 7, I-10125 Turin, Italy.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    The elusive ligand complexes of the DWARF14 strigolactone receptor2018In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 69, no 9, p. 2345-2354Article in journal (Refereed)
    Abstract [en]

    Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.

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  • 48.
    Cervantes, Marcos
    et al.
    Univ Virginia, Dept Mol Physiol & Biomed Engn, Charlottesville, VA 22908 USA.
    Hess, Tobin
    Univ Virginia, Dept Mol Physiol & Biomed Engn, Charlottesville, VA 22908 USA.
    Morbioli, Giorgio G. G.
    Univ Virginia, Dept Mol Physiol & Biomed Engn, Charlottesville, VA 22908 USA.;Tufts Univ, Dept Chem, Lab Living Devices, Medford, MA 02155 USA.
    Sengar, Anjali
    Univ Virginia, Dept Mol Physiol & Biomed Engn, Charlottesville, VA 22908 USA.
    Kasson, Peter M.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Virginia, Dept Mol Physiol & Biomed Engn, Charlottesville, VA 22908 USA.
    The ACE2 receptor accelerates but is not biochemically required for SARS-CoV-2 membrane fusion2023In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 14, no 25, p. 6997-7004Article in journal (Refereed)
    Abstract [en]

    The SARS-CoV-2 coronavirus infects human cells via the ACE2 receptor. Structural evidence suggests that ACE2 may not just serve as an attachment factor but also conformationally activate the SARS-CoV-2 spike protein for membrane fusion. Here, we test that hypothesis directly, using DNA-lipid tethering as a synthetic attachment factor in place of ACE2. We find that SARS-CoV-2 pseudovirus and virus-like particles are capable of membrane fusion without ACE2 if activated with an appropriate protease. Thus, ACE2 is not biochemically required for SARS-CoV-2 membrane fusion. However, addition of soluble ACE2 speeds up the fusion reaction. On a per-spike level, ACE2 appears to promote activation for fusion and then subsequent inactivation if an appropriate protease is not present. Kinetic analysis suggests at least two rate-limiting steps for SARS-CoV-2 membrane fusion, one of which is ACE2 dependent and one of which is not. Since ACE2 serves as a high-affinity attachment factor on human cells, the possibility to replace it with other factors implies a flatter fitness landscape for host adaptation by SARS-CoV-2 and future related coronaviruses.

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  • 49. Chalupsky, J.
    et al.
    Juha, L.
    Kuba, J.
    Cihelka, J.
    Hajkova, V.
    Koptyaev, S.
    Krasa, J.
    Velyhan, A.
    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.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bionta, R. M.
    Chapman, H.
    Hau-Riege, S. P.
    London, R. A.
    Jurek, M.
    Krzywinski, J.
    Nietubyc, R.
    Pelka, J. B.
    Sobierajski, R.
    Meyer-ter-Vehn, J.
    Tronnier, A.
    Sokolowski-Tinten, K.
    Stojanovic, N.
    Tiedtke, K.
    Toleikis, S.
    Tschentscher, T.
    Wabnitz, H.
    Zastrau, U.
    Characteristics of focused soft X-ray free-electron laser beam determined by ablation of organic molecular solids2007In: Optics Express, E-ISSN 1094-4087, Vol. 15, no 10, p. 6036-6043Article in journal (Refereed)
    Abstract [en]

    A linear accelerator based source of coherent radiation, FLASH (Free-electron LASer in Hamburg) provides ultra-intense femtosecond radiation pulses at wavelengths from the extreme ultraviolet (XUV; lambda< 100nm) to the soft X-ray (SXR; lambda<30nm) spectral regions. 25-fs pulses of 32-nm FLASH radiation were used to determine the ablation parameters of PMMA - poly ( methyl methacrylate). Under these irradiation conditions the attenuation length and ablation threshold were found to be (56.9 +/- 7.5) nm and similar to 2 mJ center dot cm(-2), respectively. For a second wavelength of 21.7 nm, the PMMA ablation was utilized to image the transverse intensity distribution within the focused beam at mu m resolution by a method developed here.

  • 50. 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.

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