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1. Observation of a single protein by ultrafast X-ray diffraction

Author

Ekeberg, Tomas, Assalauova, Dameli, Bielecki, Johan, Boll, Rebecca, Daurer, Benedikt J., Eichacker, Lutz A., Franken, Linda E., Galli, Davide E., Gelisio, Luca, Gumprecht, Lars, Gunn, Laura H., Hajdu, Janos, Hartmann, Robert, Hasse, Dirk, Ignatenko, Alexandr, Koliyadu, Jayanath, Kulyk, Olena, Kurta, Ruslan, Kuster, Markus, Lugmayr, Wolfgang, Lübke, Jannik, Mancuso, Adrian P., Mazza, Tommaso, Nettelblad, Carl, Ovcharenko, Yevheniy, Rivas, Daniel E., Rose, Max, Samanta, Amit K., Schmidt, Philipp, Sobolev, Egor, Timneanu, Nicusor, Usenko, Sergey, Westphal, Daniel, Wollweber, Tamme, Worbs, Lena, Xavier, Paul Lourdu, Yousef, Hazem, Ayyer, Kartik, Chapman, Henry N., Sellberg, Jonas A., Seuring, Carolin, Vartanyants, Ivan A., Küpper, Jochen, Meyer, Michael, and Maia, Filipe R. N. C.

Published
2024
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2. In-Situ Observation of the Formation of Laser-Induced Periodic Surface Structures with Extreme Spatial and Temporal Resolution

Author

Sokolowski-Tinten, Klaus, Bonse, Jörn, Barty, Anton, Chapman, Henry N., Bajt, Saša, Bogan, Mike J., Boutet, Sebastien, Cavalleri, Andrea, Düsterer, Stefan, Frank, Matthias, Hajdu, Janos, Hau-Riege, Stefan, Marchesini, Stefano, Stojanovic, Nikola, Treusch, Rolf, Lotsch, H.K.V., Founding Editor, Rhodes, William T., Editor-in-Chief, Adibi, Ali, Series Editor, Asakura, Toshimitsu, Series Editor, Hänsch, Theodor W., Series Editor, Krausz, Ferenc, Series Editor, Masters, Barry R., Series Editor, Midorikawa, Katsumi, Series Editor, Venghaus, Herbert, Series Editor, Weber, Horst, Series Editor, Weinfurter, Harald, Series Editor, Kobayashi, Kazuya, Series Editor, Markel, Vadim, Series Editor, Stoian, Razvan, editor, and Bonse, Jörn, editor

Published
2023
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3. An advanced workflow for single particle imaging with the limited data at an X-ray free-electron laser

Author

Assalauova, Dameli, Kim, Young Yong, Bobkov, Sergey, Khubbutdinov, Ruslan, Rose, Max, Alvarez, Roberto, Andreasson, Jakob, Balaur, Eugeniu, Contreras, Alice, DeMirci, Hasan, Gelisio, Luca, Hajdu, Janos, Hunter, Mark S., Kurta, Ruslan P., Li, Haoyuan, McFadden, Matthew, Nazari, Reza, Schwander, Peter, Teslyuk, Anton, Walter, Peter, Xavier, P. Lourdu, Yoon, Chun Hong, Zaared, Sahba, Ilyin, Viacheslav A., Kirian, Richard A., Hogue, Brenda G., Aquila, Andrew, and Vartanyants, Ivan A.

Subjects
Physics - Biological Physics, Physics - Data Analysis, Statistics and Probability
Abstract

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 AMO instrument at the Linac Coherent Light Source (LCLS) as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from the half of the detector and small fraction of single hits. 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 three-dimensional structure of the 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., Comment: 40 pages, 7 figures (main text), 2 tables (main text), 14 figures (supplementary information), 1 table (supplementary information)

Published
2020

4. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

Author

Li, Haoyuan, Nazari, Reza, Abbey, Brian, Alvarez, Roberto, Aquila, Andrew, Ayyer, Kartik, Barty, Anton, Berntsen, Peter, Bielecki, Johan, Pietrini, Alberto, Bucher, Maximilian, Carini, Gabriella, Chapman, Henry N, Contreras, Alice, Daurer, Benedikt J, DeMirci, Hasan, Flűckiger, Leonie, Frank, Matthias, Hajdu, Janos, Hantke, Max F, Hogue, Brenda G, Hosseinizadeh, Ahmad, Hunter, Mark S, Jönsson, H Olof, Kirian, Richard A, Kurta, Ruslan P, Loh, Duane, Maia, Filipe RNC, Mancuso, Adrian P, Morgan, Andrew J, McFadden, Matthew, Muehlig, Kerstin, Munke, Anna, Reddy, Hemanth Kumar Narayana, Nettelblad, Carl, Ourmazd, Abbas, Rose, Max, Schwander, Peter, Marvin Seibert, M, Sellberg, Jonas A, Sierra, Raymond G, Sun, Zhibin, Svenda, Martin, Vartanyants, Ivan A, Walter, Peter, Westphal, Daniel, Williams, Garth, Xavier, P Lourdu, Yoon, Chun Hong, and Zaare, Sahba

Subjects
Chemical Sciences, Synchrotrons and Accelerators, Physical Sciences, Coliphages, Lasers, Particle Accelerators, Virion, X-Ray Diffraction
Abstract

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

Published
2020

5. Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

Author

Gorkhover, Tais, Ulmer, Anatoli, Ferguson, Ken, Bucher, Max, Maia, Filipe, Bielecki, Johan, Ekeberg, Tomas, Hantke, Max F., Daurer, Benedikt J., Nettelblad, Carl, Andreasson, Jakob, Barty, Anton, Bruza, Petr, Carron, Sebastian, Hasse, Dirk, Krzywinski, Jacek, Larsson, Daniel S. D., Morgan, Andrew, Muehlig, Kerstin, Mueller, Maria, Okamoto, Kenta, Pietrini, Alberto, Rupp, Daniela, Sauppe, Mario, van der Schot, Gijs, Seibert, Marvin, Sellberg, Jonas A., Svenda, Martin, Swiggers, Michelle, Timneanu, Nicusor, Westphal, Daniel, Williams, Garth, Zani, Alessandro, Chapman, Henry N., Faigel, Gyula, Moeller, Thomas, Hajdu, Janos, and Bostedt, Christoph

Subjects
Physics - Atomic and Molecular Clusters, Physics - Optics
Abstract

Ultrafast X-ray imaging provides high resolution information on individual fragile specimens such as aerosols, metastable particles, superfluid quantum systems and live biospecimen, which is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely-defined. Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers in order to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lat- eral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond time scale.

Published
2017
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6. Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging

Author

Lundholm, Ida V, Sellberg, Jonas A, Ekeberg, Tomas, Hantke, Max F, Okamoto, Kenta, van der Schot, Gijs, Andreasson, Jakob, Barty, Anton, Bielecki, Johan, Bruza, Petr, Bucher, Max, Carron, Sebastian, Daurer, Benedikt J, Ferguson, Ken, Hasse, Dirk, Krzywinski, Jacek, Larsson, Daniel SD, Morgan, Andrew, Mühlig, Kerstin, Müller, Maria, Nettelblad, Carl, Pietrini, Alberto, Reddy, Hemanth KN, Rupp, Daniela, Sauppe, Mario, Seibert, Marvin, Svenda, Martin, Swiggers, Michelle, Timneanu, Nicusor, Ulmer, Anatoli, Westphal, Daniel, Williams, Garth, Zani, Alessandro, Faigel, Gyula, Chapman, Henry N, Möller, Thomas, Bostedt, Christoph, Hajdu, Janos, Gorkhover, Tais, and Maia, Filipe RNC

Subjects
Physical Sciences, Condensed Matter Physics, Biomedical Imaging, LCLS, Melbournevirus, XFELs, coherent diffractive imaging, image reconstruction, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.

Published
2018

7. Megahertz serial crystallography

Author

Wiedorn, Max O, Oberthür, Dominik, Bean, Richard, Schubert, Robin, Werner, Nadine, Abbey, Brian, Aepfelbacher, Martin, Adriano, Luigi, Allahgholi, Aschkan, Al-Qudami, Nasser, Andreasson, Jakob, Aplin, Steve, Awel, Salah, Ayyer, Kartik, Bajt, Saša, Barák, Imrich, Bari, Sadia, Bielecki, Johan, Botha, Sabine, Boukhelef, Djelloul, Brehm, Wolfgang, Brockhauser, Sandor, Cheviakov, Igor, Coleman, Matthew A, Cruz-Mazo, Francisco, Danilevski, Cyril, Darmanin, Connie, Doak, R Bruce, Domaracky, Martin, Dörner, Katerina, Du, Yang, Fangohr, Hans, Fleckenstein, Holger, Frank, Matthias, Fromme, Petra, Gañán-Calvo, Alfonso M, Gevorkov, Yaroslav, Giewekemeyer, Klaus, Ginn, Helen Mary, Graafsma, Heinz, Graceffa, Rita, Greiffenberg, Dominic, Gumprecht, Lars, Göttlicher, Peter, Hajdu, Janos, Hauf, Steffen, Heymann, Michael, Holmes, Susannah, Horke, Daniel A, Hunter, Mark S, Imlau, Siegfried, Kaukher, Alexander, Kim, Yoonhee, Klyuev, Alexander, Knoška, Juraj, Kobe, Bostjan, Kuhn, Manuela, Kupitz, Christopher, Küpper, Jochen, Lahey-Rudolph, Janine Mia, Laurus, Torsten, Le Cong, Karoline, Letrun, Romain, Xavier, P Lourdu, Maia, Luis, Maia, Filipe RNC, Mariani, Valerio, Messerschmidt, Marc, Metz, Markus, Mezza, Davide, Michelat, Thomas, Mills, Grant, Monteiro, Diana CF, Morgan, Andrew, Mühlig, Kerstin, Munke, Anna, Münnich, Astrid, Nette, Julia, Nugent, Keith A, Nuguid, Theresa, Orville, Allen M, Pandey, Suraj, Pena, Gisel, Villanueva-Perez, Pablo, Poehlsen, Jennifer, Previtali, Gianpietro, Redecke, Lars, Riekehr, Winnie Maria, Rohde, Holger, Round, Adam, Safenreiter, Tatiana, Sarrou, Iosifina, Sato, Tokushi, Schmidt, Marius, Schmitt, Bernd, Schönherr, Robert, Schulz, Joachim, Sellberg, Jonas A, Seibert, M Marvin, and Seuring, Carolin

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences
Abstract

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

Published
2018

8. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses

Author

Daurer, Benedikt J, Okamoto, Kenta, Bielecki, Johan, Maia, Filipe RNC, Mühlig, Kerstin, Seibert, M Marvin, Hantke, Max F, Nettelblad, Carl, Benner, W Henry, Svenda, Martin, Tîmneanu, Nicuşor, Ekeberg, Tomas, Loh, N Duane, Pietrini, Alberto, Zani, Alessandro, Rath, Asawari D, Westphal, Daniel, Kirian, Richard A, Awel, Salah, Wiedorn, Max O, van der Schot, Gijs, Carlsson, Gunilla H, Hasse, Dirk, Sellberg, Jonas A, Barty, Anton, Andreasson, Jakob, Boutet, Sébastien, Williams, Garth, Koglin, Jason, Andersson, Inger, Hajdu, Janos, and Larsson, Daniel SD

Subjects
Analytical Chemistry, Chemical Sciences, Physical Sciences, OmRV, Omono River virus, X-ray diffraction, diffraction before destruction, flash X-ray imaging, free-electron laser, virus, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from ∼35 to ∼300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 × 1012 photons per µm2 per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.

Published
2017

9. Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser

Author

Ekeberg, Tomas, Svenda, Martin, Seibert, M Marvin, Abergel, Chantal, Maia, Filipe RNC, Seltzer, Virginie, DePonte, Daniel P, Aquila, Andrew, Andreasson, Jakob, Iwan, Bianca, Jönsson, Olof, Westphal, Daniel, Odić, Duško, Andersson, Inger, Barty, Anton, Liang, Meng, Martin, Andrew V, Gumprecht, Lars, Fleckenstein, Holger, Bajt, Saša, Barthelmess, Miriam, Coppola, Nicola, Claverie, Jean-Michel, Loh, N Duane, Bostedt, Christoph, Bozek, John D, Krzywinski, Jacek, Messerschmidt, Marc, Bogan, Michael J, Hampton, Christina Y, Sierra, Raymond G, Frank, Matthias, Shoeman, Robert L, Lomb, Lukas, Foucar, Lutz, Epp, Sascha W, Rolles, Daniel, Rudenko, Artem, Hartmann, Robert, Hartmann, Andreas, Kimmel, Nils, Holl, Peter, Weidenspointner, Georg, Rudek, Benedikt, Erk, Benjamin, Kassemeyer, Stephan, Schlichting, Ilme, Strüder, Lothar, Ullrich, Joachim, Schmidt, Carlo, Krasniqi, Faton, Hauser, Günter, Reich, Christian, Soltau, Heike, Schorb, Sebastian, Hirsemann, Helmut, Wunderer, Cornelia, Graafsma, Heinz, Chapman, Henry, and Hajdu, Janos

Subjects
Biochemistry and Cell Biology, Physical Sciences, Biological Sciences, Biomedical Imaging, Algorithms, Computer Simulation, Crystallography, X-Ray, Data Collection, Electrons, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Lasers, Mimiviridae, Models, Theoretical, Particle Size, Scattering, Radiation, X-Ray Diffraction, X-Rays
Abstract

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

Published
2016

10. Glycogen Phosphorylase b

Author

Johnson, Louise N., primary, Hajdu, Janos, additional, Acharya, K. Ravindra, additional, Stuart, David I., additional, McLaughlin, Paul J., additional, Oikonomakos, Nikos G., additional, and Barford, David, additional

Published
2020
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11. Femtosecond Diffractive Imaging with a Soft-X-ray Free-Electron Laser

Author

Chapman, Henry N., Barty, Anton, Bogan, Michael J., Boutet, Sebastien, Frank, Matthias, Hau-Riege, Stefan P., Marchesini, Stefano, Woods, Bruce W., Bajt, Sasa, Benner, W. Henry, London, Richard A., Plonjes, Elke, Kuhlmann, Marion, Treusch, Rolf, Dusterer, Stefan, Tschentscher, Thomas, Schneider, Jochen R., Spiller, Eberhard, Moller, Thomas, Bostedt, Christoph, Hoener, Matthias, Shapiro, David A., Hodgson, Keith O., van der Spoel, David, Burmeister, Florian, Bergh, Magnus, Caleman, Carl, Huldt, Gosta, Seibert, M. Marvin, Maia, Filipe R. N. C., Lee, Richard W., Szoke, Abraham, Timneanu, Nicusor, and Hajdu, Janos

Subjects
Physics - Optics
Abstract

Theory predicts that with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus, or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft X-ray free-electron laser. An intense 25 fs, 4 10^13 W/cm^2 pulse, containing 10^12 photons at 32 nm wavelength, produced a coherent diffraction pattern from a nano-structured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling, shows no measurable damage, and extends to diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one., Comment: revtex, 6 pages, 4 figures

Published
2006
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12. Auger Electron Cascades in Water and Ice

Author

Timneanu, Nicusor, Caleman, Carl, Hajdu, Janos, and van der Spoel, David

Subjects
Condensed Matter, Physics - Chemical Physics
Abstract

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., Comment: 19 pages, 8 figures. Includes slight corrections to the version submitted for publication

Published
2003
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13. Electron Cascades Produced by Photoelectrons in Diamond

Author

Ziaja, Beata, Szoeke, Abraham, and Hajdu, Janos

Subjects
Condensed Matter, High Energy Physics - Phenomenology
Abstract

Secondary electron cascades are responsible for significant ionizations in macroscopic samples during irradiation with X-rays. A quantitative analysis of these cascades is needed, e.g. for assessing damage in optical components at X-ray free-electron lasers, and for understanding damage in samples exposed to the beam. Here we present results from Monte Carlo simulations, showing the space-time evolution of secondary electron cascades in diamond. These cascades follow the impact of a single primary electron at energies between 0.5-12 keV, representing the usual range for photoelectrons. The calculations describe the secondary ionizations caused by these electrons, the three-dimensional evolution of the electron cloud, and monitor the equivalent instantaneous temperature of the free-electron gas as the system cools during expansion. The dissipation of the impact energy proceeds predominantly through the production of secondary electrons whose energies are comparable to the binding energies of the valence (40-50 eV) and the core electrons (300 eV) in accordance with experiments and the models of interactions. The electron cloud generated by a 12 keV electron is strongly anisotropic in the early phases of the cascade (t <= 1 fs). At later times, the sample is dominated by low energy electrons, and these are scattered more isotropically by atoms in the sample. The results show that the emission of secondary electrons approaches saturation within about 100 fs, following the primary impact. At an impact energy of 12 keV, the total number of electrons liberated in the sample is <= 400 at 1000 fs. The results provide an understanding of ionizations by photoelectrons, and extend earlier models on low-energy electron cascades (E=0.25 keV, [ziaja,ziaja2]) to the higher energy regime of the photoelectrons., Comment: 17 pages, latex, 10 figures

Published
2002
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14. Space-time evolution of electron cascades in diamond

Author

Ziaja, Beata, Szoeke, Abraham, van der Spoel, David, and Hajdu, Janos

Subjects
Condensed Matter, High Energy Physics - Phenomenology
Abstract

Here we describe model calculations to follow the spatio-temporal evolution of secondary electron cascades in diamond. The band structure of the insulator has been explicitly incorporated into the calculations as it affects ionizations from the valence band. A Monte-Carlo model was constructed to describe the path of electrons following the impact of a single electron of energy E 250 eV. The results show the evolution of the secondary electron cascades in terms of the number of electrons liberated, the spatial distribution of these electrons, and the energy distribution among the electrons as a function of time. The predicted ionization rates (5-13 electrons in 100 fs) lie within the limits given by experiments and phenomenological models. Calculation of the local electron density and the corresponding Debye length shows that the latter is systematically larger than the radius of the electron cloud. This means that the electron gas generated does not represent a plasma in a single impact cascade triggered by an electron of E 250 eV energy. This is important as it justifies the independent-electron approximation used in the model. At 1 fs, the (average) spatial distribution of secondary electrons is anisotropic with the electron cloud elongated in the direction of the primary impact. The maximal radius of the cascade is about 50 A at this time. As the system cools, energy is distributed more equally, and the spatial distribution of the electron cloud becomes isotropic. At 90 fs maximal radius is about 150 A. The Monte-Carlo model described here could be adopted for the investigation of radiation damage in other insulators and has implications for planned experiments with intense femtosecond X-ray sources., Comment: 26 pages, latex, 13 figures

Published
2002
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15. Shake-up and shake-off excitations with associated electron losses in X-ray studies of proteins

Author

Persson, Petter, Lunell, Sten, Szoeke, Abraham, Ziaja, Beata, and Hajdu, Janos

Subjects
Condensed Matter, High Energy Physics - Phenomenology, Quantitative Biology
Abstract

Photoionisation of an atom by X-rays usually removes an inner-shell electron from the atom, leaving behind a perturbed "hollow ion" whose relaxation may take different routes. In light elements, emission of an Auger electron is common. However, the energy and the total number of electrons released from the atom may be modulated by shake-up and shake-off effects. When the inner-shell electron leaves, the outer-shell electrons may find themselves in a state that is not an eigen-state of the atom in its surroundings. The resulting collective excitation is called shake-up. If this process also involves the release of low energy electrons from the outer shell, then the process is called shake-off. It is not clear how significant shake-up and shake-off contributions are to the overall ionisation of biological materials like proteins. In particular, the interaction between the out-going electron and the remaining system depends on the chemical environment of the atom, which can be studied by quantum chemical methods. Here we present calculations on model compounds to represent the most common chemical environments in proteins. The results show that the shake-up and shake-off processes affect about 20% of all emissions from nitrogen, 30% from carbon, 40% from oxygen, and 23% from sulphur. Triple and higher ionisations are rare for carbon, nitrogen and oxygen, but are frequent for sulphur. The findings are relevant to the design of biological experiments at emerging X-ray free-electron lasers., Comment: 14 pages, latex, 1 figure

Published
2001

16. Auger-electron cascades in diamond and amorphous carbon

Author

Ziaja, Beata, van der Spoel, David, Szoeke, Abraham, and Hajdu, Janos

Subjects
Condensed Matter, High Energy Physics - Phenomenology
Abstract

We have analyzed the cascade of secondary electrons in diamond and amorphous carbon generated by the thermalisation of a single Auger electron. The elastic electron mean free path was calculated as a function of impact energy in the muffin-tin potential approximation. The inelastic scattering cross section and the energy loss of the electron (expressed in terms of differential inverse mean free path) were estimated from two "optical" models, that utilise the measured dielectric constants of the materials. Using these data, a Monte-Carlo model describing the time evolution of the cascade was constructed. The results show that at most around 20-40 secondary cascade electrons are released by a single Auger electron in a macroscopic sample of diamond or amorphous carbon. Consideration of the real band structure of diamond reduces this number further. The release of the cascade electrons happens within the first 100 femtoseconds after the emission of the primary Auger electron. The results have implications to planned experiments with femtosecond X-ray sources., Comment: 18 pages, latex, 9 figures

Published
2001
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17. Time-resolved protein nanocrystallography using an X-ray free-electron laser

Author

Aquila, Andrew, Hunter, Mark S, Doak, R Bruce, Kirian, Richard A, Fromme, Petra, White, Thomas A, Andreasson, Jakob, Arnlund, David, Bajt, Saša, Barends, Thomas RM, Barthelmess, Miriam, Bogan, Michael J, Bostedt, Christoph, Bottin, Hervé, Bozek, John D, Caleman, Carl, Coppola, Nicola, Davidsson, Jan, 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, 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 RNC, 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, Shoeman, Robert L, Sierra, Raymond, Soltau, Heike, Starodub, Dmitri, Stellato, Francesco, Stern, Stephan, Strüder, Lothar, Timneanu, Nicusor, Ullrich, Joachim, Wang, Xiaoyu, Williams, Garth J, Weidenspointner, Georg, Weierstall, Uwe, Wunderer, Cornelia, Barty, Anton, Spence, John CH, and Chapman, Henry N

Subjects
Crystallography, X-Ray, Electrons, Ferredoxins, Lasers, Nanostructures, Protein Conformation, X-Ray Diffraction, X-Rays, Optical Physics, Electrical and Electronic Engineering, Communications Technologies, Optics
Abstract

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.

Published
2012

18. The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters

Author

Ho, Phay J., Daurer, Benedikt J., Hantke, Max F., Bielecki, Johan, Al Haddad, Andre, Bucher, Maximilian, Doumy, Gilles, Ferguson, Ken R., Flückiger, Leonie, Gorkhover, Tais, Iwan, Bianca, Knight, Christopher, Moeller, Stefan, Osipov, Timur, Ray, Dipanwita, Southworth, Stephen H., Svenda, Martin, Timneanu, Nicusor, Ulmer, Anatoli, Walter, Peter, Hajdu, Janos, Young, Linda, Maia, Filipe R. N. C., and Bostedt, Christoph

Published
2020
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19. Lattice Electrons on a Cylinder Surface in the Presence of Rational Magnetic Flux and Disorder

Author

Schulze, Christian, Hajdu, János, Huckestein, Bodo, and Janssen, Martin

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We consider a disordered two-dimensional system of independent lattice electrons in a perpendicular magnetic field with rigid confinement in one direction and generalized periodic boundary conditions (GPBC) in the other direction. The objects investigated numerically are the orbits in the plane spanned by the energy eigenvalues and the corresponding center of mass coordinate in the confined direction, parameterized by the phase characterizing the GPBC. The Kubo Hall conductivity is expressed in terms of the winding numbers of these orbits. For vanishing disorder the spectrum of the system consists of Harper bands with energy levels corresponding to the edge states within the band gaps. Disorder leads to broadening of the bands. For sufficiently large systems localized states occur in the band tails. We find that within the mobility gaps of bulk states the Diophantine equation determines the value of the Hall conductivity as known for systems with torus geometry (PBCs in both directions). Within the spectral bands of extended states the Hall conductivity fluctuates strongly. For sufficiently large systems the generic behavior of localization-delocalization transitions characteristic for the quantum Hall effect are recovered., Comment: RevTeX, 10 pages, 14 PostScript figures

Published
1997
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20. Femtosecond diffractive imaging with a soft-X-ray free-electron laser

Author

Chapman, Henry N, Barty, Anton, Bogan, Michael J, Boutet, Sébastien, Frank, Matthias, Hau-Riege, Stefan P, Marchesini, Stefano, Woods, Bruce W, Bajt, Saša, Benner, W Henry, London, Richard A, Plönjes, Elke, Kuhlmann, Marion, Treusch, Rolf, Düsterer, Stefan, Tschentscher, Thomas, Schneider, Jochen R, Spiller, Eberhard, Möller, Thomas, Bostedt, Christoph, Hoener, Matthias, Shapiro, David A, Hodgson, Keith O, van der Spoel, David, Burmeister, Florian, Bergh, Magnus, Caleman, Carl, Huldt, Gösta, Seibert, M Marvin, Maia, Filipe RNC, Lee, Richard W, Szöke, Abraham, Timneanu, Nicusor, and Hajdu, Janos

Subjects
Biomedical Imaging, physics.optics, Mathematical Sciences, Physical Sciences, Fluids & Plasmas
Abstract

Theory predicts that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4×10 13 W cm -2 pulse, containing 10 12 photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling, shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one. © 2006 Nature Publishing Group.

Published
2006

21. Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

Author

Gorkhover, Tais, Ulmer, Anatoli, Ferguson, Ken, Bucher, Max, Maia, Filipe R. N. C., Bielecki, Johan, Ekeberg, Tomas, Hantke, Max F., Daurer, Benedikt J., Nettelblad, Carl, Andreasson, Jakob, Barty, Anton, Bruza, Petr, Carron, Sebastian, Hasse, Dirk, Krzywinski, Jacek, Larsson, Daniel S. D., Morgan, Andrew, Mühlig, Kerstin, Müller, Maria, Okamoto, Kenta, Pietrini, Alberto, Rupp, Daniela, Sauppe, Mario, van der Schot, Gijs, Seibert, Marvin, Sellberg, Jonas A., Svenda, Martin, Swiggers, Michelle, Timneanu, Nicusor, Westphal, Daniel, Williams, Garth, Zani, Alessandro, Chapman, Henry N., Faigel, Gyula, Möller, Thomas, Hajdu, Janos, and Bostedt, Christoph

Published
2018
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22. Negligible risk of surface transmission of SARS-CoV-2 in public transportation

Author

Pilipenco, Alina, primary, Forinová, Michala, additional, Mašková, Hana, additional, Hönig, Václav, additional, Palus, Martin, additional, Lynn Jr., Nicholas Scott, additional, Víšová, Ivana, additional, Vrabcová, Markéta, additional, Houska, Milan, additional, Anthi, Judita, additional, Spasovová, Monika, additional, Mustacová, Johana, additional, Štěrba, Ján, additional, Dostálek, Jakub, additional, Tung, Chao-Ping, additional, Yang, An-Suei, additional, Jack, Rachael, additional, Dejneka, Alexandr, additional, Hajdu, Janos, additional, and Vaisocherová-Lísalová, Hana, additional

Published
2023
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24. Negligible risk of surface transmission of SARS-CoV-2 in public transportation

Author

Pilipenco, Alina, Forinova, Michala, Maskova, Hana, Hönig, Vaclav, Palus, Martin, Lynn Jr, Nicholas Scott, Visova, Ivana, Vrabcova, Marketa, Houska, Milan, Anthi, Judita, Spasovova, Monika, Mustacova, Johana, Sterba, Jan, Dostalek, Jakub, Tung, Chao-Ping, Yang, An-Suei, Jack, Rachael, Dejneka, Alexandr, Hajdu, Janos, Vaisocherova-Lisalova, Hana, Pilipenco, Alina, Forinova, Michala, Maskova, Hana, Hönig, Vaclav, Palus, Martin, Lynn Jr, Nicholas Scott, Visova, Ivana, Vrabcova, Marketa, Houska, Milan, Anthi, Judita, Spasovova, Monika, Mustacova, Johana, Sterba, Jan, Dostalek, Jakub, Tung, Chao-Ping, Yang, An-Suei, Jack, Rachael, Dejneka, Alexandr, Hajdu, Janos, and Vaisocherova-Lisalova, Hana

Abstract

Background: Exposure to pathogens in public transport systems is a common means of spreading infection, mainly by inhaling aerosol or droplets from infected individuals. Such particles also contaminate surfaces, creating a potential surface-transmission pathway. Methods: A fast acoustic biosensor with an antifouling nano-coating was introduced to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on exposed surfaces in the Prague Public Transport System. Samples were measured directly without pre-treatment. Results with the sensor gave excellent agreement with parallel quantitative reverse-transcription polymerase chain reaction (qRT-PCR) measurements on 482 surface samples taken from actively used trams, buses, metro trains and platforms between 7 and 9 April 2021, in the middle of the lineage Alpha SARS-CoV-2 epidemic wave when 1 in 240 people were COVID-19 positive in Prague. Results: Only ten of the 482 surface swabs produced positive results and none of them contained virus particles capable of replication, indicating that positive samples contained inactive virus particles and/or fragments. Measurements of the rate of decay of SARS-CoV-2 on frequently touched surface materials showed that the virus did not remain viable longer than 1-4 h. The rate of inactivation was the fastest on rubber handrails in metro escalators and the slowest on hard-plastic seats, window glasses and stainless-steel grab rails. As a result of this study, Prague Public Transport Systems revised their cleaning protocols and the lengths of parking times during the pandemic. Conclusions: Our findings suggest that surface transmission played no or negligible role in spreading SARS-CoV-2 in Prague. The results also demonstrate the potential of the new biosensor to serve as a complementary screening tool in epidemic monitoring and prognosis.

Published
2023
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26. Observation of a single protein by ultrafast X-ray diffraction

Author

Ekeberg, Tomas, Assalauova, Dameli, Bielecki, Johan, Boll, Rebecca, Daurer, Benedikt J., Eichacker, Lutz A., Franken, Linda E., Galli, Davide E., Gelisio, Luca, Gumprecht, Lars, Gunn, Laura H., Hajdu, Janos, Hartmann, Robert, Hasse, Dirk, Ignatenko, Alexandr, Koliyadu, Jayanath, Kulyk, Olena, Kurta, Ruslan, Kuster, Markus, Lugmayr, Wolfgang, Lübke, Jannik, Mancuso, Adrian P., Mazza, Tommaso, Nettelblad, Carl, Ovcharenko, Yevheniy, Rivas, Daniel E., Rose, Max, Samanta, Amit K., Schmidt, Philipp, Sobolev, Egor, Timneanu, Nicusor, Usenko, Sergey, Westphal, Daniel, Wollweber, Tamme, Worbs, Lena, Lourdu Xavier, P., Yousef, Hazem, Ayyer, Kartik, Chapman, Henry N., Sellberg, Jonas A., Seuring, Carolin, Vartanyants, Ivan A., Küpper, Jochen, Meyer, Michael, and Maia, Filipe R.N.C.

Subjects
Biophysics
Abstract

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory1, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes2. This was first demonstrated on biological samples a decade ago on the giant mimivirus3. Since then a large collaboration4 has been pushing the limit of the smallest sample that can be imaged5,6. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter7 is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

Published
2022

27. Teaching and Education highlighted

Author

Dawe, Louise N., primary, García-Ruiz, Juan Manuel, additional, Hajdu, Janos, additional, McIntyre, Garry J., additional, Meilleur, Flora, additional, and Stephenson, Lisa, additional

Published
2022
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28. Observation of a single protein by ultrafast X-ray diffraction

Author

Ekeberg, Tomas, primary, Assalauova, Dameli, additional, Bielecki, Johan, additional, Boll, Rebecca, additional, Daurer, Benedikt J., additional, Eichacker, Lutz A., additional, Franken, Linda E., additional, Galli, Davide E., additional, Gelisio, Luca, additional, Gumprecht, Lars, additional, Gunn, Laura H., additional, Hajdu, Janos, additional, Hartmann, Robert, additional, Hasse, Dirk, additional, Ignatenko, Alexandr, additional, Koliyadu, Jayanath, additional, Kulyk, Olena, additional, Kurta, Ruslan, additional, Kuster, Markus, additional, Lugmayr, Wolfgang, additional, Lübke, Jannik, additional, Mancuso, Adrian P., additional, Mazza, Tommaso, additional, Nettelblad, Carl, additional, Ovcharenko, Yevheniy, additional, Rivas, Daniel E., additional, Samanta, Amit K., additional, Schmidt, Philipp, additional, Sobolev, Egor, additional, Timneanu, Nicusor, additional, Usenko, Sergej, additional, Westphal, Daniel, additional, Wollweber, Tamme, additional, Worbs, Lena, additional, Xavier, P. Lourdu, additional, Yousef, Hazem, additional, Ayyer, Kartik, additional, Chapman, Henry N., additional, Sellberg, Jonas A., additional, Seuring, Carolin, additional, Vartanyants, Ivan A., additional, Küpper, Jochen, additional, Meyer, Michael, additional, and Maia, Filipe R.N.C., additional

Published
2022
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29. Corrigendum: An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

Author

Assalauova, Dameli, Kim, Young Yong, Bobkov, Sergey, Khubbutdinov, Ruslan, Rose, Max, Alvarez, Roberto, Andreasson, Jakob, Balaur, Eugeniu, Contreras, Alice, DeMirci, Hasan, Gelisio, Luca, Hajdu, Janos, Hunter, Mark S., Kurta, Ruslan P., Li, Haoyuan, McFadden, Matthew, Nazari, Reza, Schwander, Peter, Teslyuk, Anton, Walter, Peter, Xavier, P. Lourdu, Yoon, Chun Hong, Zaare, Sahba, Ilyin, Viacheslav A., Kirian, Richard A., Hogue, Brenda G., Aquila, Andrew, and Vartanyants, Ivan A.

Subjects
ddc:530
Abstract

IUCrJ 9(2), 328 (2022). doi:10.1107/S2052252522000501, An error in Fig. 3(c) of the article by Assalauova et al. [IUCrJ (2020), 7, 1102–1113] is corrected., Published by Chester

Published
2022

30. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum

Author

Assalauova, Dameli, primary, Kim, Young Yong, additional, Bobkov, Sergey, additional, Khubbutdinov, Ruslan, additional, Rose, Max, additional, Alvarez, Roberto, additional, Andreasson, Jakob, additional, Balaur, Eugeniu, additional, Contreras, Alice, additional, DeMirci, Hasan, additional, Gelisio, Luca, additional, Hajdu, Janos, additional, Hunter, Mark S., additional, Kurta, Ruslan P., additional, Li, Haoyuan, additional, McFadden, Matthew, additional, Nazari, Reza, additional, Schwander, Peter, additional, Teslyuk, Anton, additional, Walter, Peter, additional, Xavier, P. Lourdu, additional, Yoon, Chun Hong, additional, Zaare, Sahba, additional, Ilyin, Viacheslav A., additional, Kirian, Richard A., additional, Hogue, Brenda G., additional, Aquila, Andrew, additional, and Vartanyants, Ivan A., additional

Published
2022
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34. The XBI BioLab for life science experiments at the European XFEL

Author

Han, Huijong, Round, Ekaterina, Schubert, Robin, Gül, Yasmin, Makroczyová, Jana, Meza, Domingo, Heuser, Philipp, Aepfelbacher, Martin, Barák, Imrich, Betzel, Christian, Fromme, Petra, Kursula, Inari, Nissen, Poul, Tereschenko, Elena, Schulz, Joachim, Uetrecht, Charlotte, Ulicný, Jozef, Wilmanns, Matthias, Hajdu, Janos, Lamzin, Victor S., Lorenzen, Kristina, Han, Huijong, Round, Ekaterina, Schubert, Robin, Gül, Yasmin, Makroczyová, Jana, Meza, Domingo, Heuser, Philipp, Aepfelbacher, Martin, Barák, Imrich, Betzel, Christian, Fromme, Petra, Kursula, Inari, Nissen, Poul, Tereschenko, Elena, Schulz, Joachim, Uetrecht, Charlotte, Ulicný, Jozef, Wilmanns, Matthias, Hajdu, Janos, Lamzin, Victor S., and Lorenzen, Kristina

Abstract

The science of X-ray free-electron lasers (XFELs) critically depends on the performance of the X-ray laser and on the quality of the samples placed into the X-ray beam. The stability of biological samples is limited and key biomolecular transformations occur on short timescales. Experiments in biology require a support laboratory in the immediate vicinity of the beamlines. The XBI BioLab of the European XFEL (XBI denotes XFEL Biology Infrastructure) is an integrated user facility connected to the beamlines for supporting a wide range of biological experiments. The laboratory was financed and built by a collaboration between the European XFEL and the XBI User Consortium, whose members come from Finland, Germany, the Slovak Republic, Sweden and the USA, with observers from Denmark and the Russian Federation. Arranged around a central wet laboratory, the XBI BioLab provides facilities for sample preparation and scoring, laboratories for growing prokaryotic and eukaryotic cells, a Bio Safety Level 2 laboratory, sample purification and characterization facilities, a crystallization laboratory, an anaerobic laboratory, an aerosol laboratory, a vacuum laboratory for injector tests, and laboratories for optical microscopy, atomic force microscopy and electron microscopy. Here, an overview of the XBI facility is given and some of the results of the first user experiments are highlighted.

Published
2021
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36. Camera for coherent diffractive imaging and holography with a soft-x-ray free-electron laser

Author

Bajt, Sasa, 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, and Shapiro, David

Subjects
Cameras -- Innovations, Diffraction patterns -- Research, Holography -- Research, Imaging systems -- Methods, Free electron lasers -- Usage, X-ray lasers -- Usage, Astronomy, Physics
Abstract

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.sup.14] W/[cm.sup.2]. 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 ftmdamental wavelength of the free electron laser in Hamburg (FLASH) FEL (i.e., between 6 and 60rim) 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. OCIS codes: 040.1490, 030.1670, 050.1940, 140.2600, 340.7470, 310.1210.

Published
2008

37. Femtosecond time-delay X-ray holography

Author

Chapman, Henry N., Hau-Riege, Stefan P., Bogan, Michael J., Bajt, Saša, Barty, Anton, Boutet, Sebastien, Marchesini, Stefano, Frank, Matthias, Woods, Bruce W., Benner, W. Henry, London, Richard A., Rohner, Urs, Szoke, Abraham, Spiller, Eberhard, Moller, Thomas, Bostedt, Christoph, Shapiro, David A., Kuhlmann, Marion, Treusch, Rolf, Plonjes, Elke, Burmeister, Florian, Bergh, Magnus, Caleman, Carl, Huldt, Gosta, Seibert, M. Marvin, and Hajdu, Janos

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Henry N. Chapman (corresponding author) [1, 2]; Stefan P. Hau-Riege [1]; Michael J. Bogan [1]; Saša Bajt [1]; Anton Barty [1]; Sébastien Boutet [1, 3, 4]; Stefano Marchesini [1, [...]

Published
2007
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38. Kilohertz Macromolecular Crystallography Using an EIGER Detector at Low X-ray Fluxes

Author

Khakurel, Krishna P., Espinoza, Shiny, Savko, Martin, Polovinkin, Vitaly, Dohnalek, Jan, Shepard, William, Angelova, Angelina, Hajdu, Janos, Andreasson, Jakob, Angelov, Borislay, Khakurel, Krishna P., Espinoza, Shiny, Savko, Martin, Polovinkin, Vitaly, Dohnalek, Jan, Shepard, William, Angelova, Angelina, Hajdu, Janos, Andreasson, Jakob, and Angelov, Borislay

Abstract

Time-resolved in-house macromolecular crystallography is primarily limited by the capabilities of the in-house X-ray sources. These sources can only provide a time-averaged structure of the macromolecules. A significant effort has been made in the development of in-house laser-driven ultrafast X-ray sources, with one of the goals as realizing the visualization of the structural dynamics of macromolecules at a very short timescale within the laboratory-scale infrastructure. Most of such in-house ultrafast X-ray sources are operated at high repetition rates and usually deliver very low flux. Therefore, the necessity of a detector that can operate at the repetition rate of the laser and perform extremely well under low flux conditions is essential. Here, we present experimental results demonstrating the usability of the hybrid-pixel detectors, such as Eiger X 1M, and provide experimental proof that they can be successfully operated to collect macromolecular crystallographic data up to a detector frame rate of 3 kHz from synchrotron sources. Our results also show that the data reduction and structural analysis are successful at such high frame rates and fluxes as low as 10(8) photons/s, which is comparable to the values expected from a typical laser-driven X-ray source.

Published
2020
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39. Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures

Author

Polovinkin, Vitaly, Khakurel, Krishna, Babiak, Michal, Angelov, Borislav, Schneider, Bohdan, Dohnalek, Jan, Andreasson, Jakob, Hajdu, Janos, Polovinkin, Vitaly, Khakurel, Krishna, Babiak, Michal, Angelov, Borislav, Schneider, Bohdan, Dohnalek, Jan, Andreasson, Jakob, and Hajdu, Janos

Abstract

Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitro­gen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å−2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous

Published
2020
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40. Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus

Author

Okamoto, Kenta, Ferreira, Ricardo J., Larsson, Daniel S D, Maia, Filipe R.N.C., Isawa, Haruhiko, Sawabe, Kyoko, Murata, Kazuyoshi, Hajdu, Janos, Iwasaki, Kenji, Kasson, Peter M., Miyazaki, Naoyuki, Okamoto, Kenta, Ferreira, Ricardo J., Larsson, Daniel S D, Maia, Filipe R.N.C., Isawa, Haruhiko, Sawabe, Kyoko, Murata, Kazuyoshi, Hajdu, Janos, Iwasaki, Kenji, Kasson, Peter M., and Miyazaki, Naoyuki

Abstract

Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).

Published
2020
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41. Time-Resolved XUV Opacity Measurements of Warm Dense Aluminum

Author

Vinko, S. M., Vozda, V., Andreasson, J., Bajt, S., Bielecki, J., Burian, T., Chalupsky, J., Ciricosta, O., Desjarlais, M. P., Fleckenstein, H., Hajdu, Janos, Hajkova, V, Hollebon, P., Juha, L., Kasim, M. F., McBride, E. E., Muehlig, Kerstin, Preston, T. R., Rackstraw, D. S., Roling, S., Toleikis, S., Wark, J. S., Zacharias, H., Vinko, S. M., Vozda, V., Andreasson, J., Bajt, S., Bielecki, J., Burian, T., Chalupsky, J., Ciricosta, O., Desjarlais, M. P., Fleckenstein, H., Hajdu, Janos, Hajkova, V, Hollebon, P., Juha, L., Kasim, M. F., McBride, E. E., Muehlig, Kerstin, Preston, T. R., Rackstraw, D. S., Roling, S., Toleikis, S., Wark, J. S., and Zacharias, H.

Abstract

The free-free opacity in plasmas is fundamental to our understanding of energy transport in stellar interiors and for inertial confinement fusion research. However, theoretical predictions in the challenging dense plasma regime are conflicting and there is a dearth of accurate experimental data to allow for direct model validation. Here we present time-resolved transmission measurements in solid-density Al heated by an XUV free-electron laser. We use a novel functional optimization approach to extract the temperature-dependent absorption coefficient directly from an oversampled pool of single-shot measurements, and find a pronounced enhancement of the opacity as the plasma is heated to temperatures of order of the Fermi energy. Plasma heating and opacity enhancement are observed on ultrafast timescales, within the duration of the femtosecond XUV pulse. We attribute further rises in the opacity on ps timescales to melt and the formation of warm dense matter.

Published
2020
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42. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

Author

Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A., College of Sciences, Department of Molecular Biology and Genetics, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A., College of Sciences, and Department of Molecular Biology and Genetics

Abstract

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., European Union (European Union); Horizon 2020; European Research Council (ERC); Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS); Scientific and Technological Research Council of Turkey (TÜBİTAK); Helmholtz Associations Initiative Networking Fund; Russian Science Foundation; US National Science Foundation (NSF) Science and Technology Center BioXFEL Award; European Regional Development Fund (ADONIS); Ministry of Education, Youth and Sports; National Program of Sustainability II; Human Frontier Science Program; Joachim Herz Stiftung Fellowship; Swedish Research Council; Knut and Alice Wallenberg Foundation; European Research Council (ERC); Röntgen–Ångström Cluster; Structural Dynamics of Biomolecular Systems; European Regional Development Fund; Australian Research Council Centre of Excellence in Advanced Molecular Imaging

Published
2020

43. The XBI BioLab for life science experiments at the European XFEL

Author

Han, Huijong, primary, Round, Ekaterina, additional, Schubert, Robin, additional, Gül, Yasmin, additional, Makroczyová, Jana, additional, Meza, Domingo, additional, Heuser, Philipp, additional, Aepfelbacher, Martin, additional, Barák, Imrich, additional, Betzel, Christian, additional, Fromme, Petra, additional, Kursula, Inari, additional, Nissen, Poul, additional, Tereschenko, Elena, additional, Schulz, Joachim, additional, Uetrecht, Charlotte, additional, Ulicný, Jozef, additional, Wilmanns, Matthias, additional, Hajdu, Janos, additional, Lamzin, Victor S., additional, and Lorenzen, Kristina, additional

Published
2021
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45. Unified model of secondary electron cascades in diamond

Author

Ziaja, Beata, London, Richard A., and Hajdu, Janos

Subjects
Monte Carlo method -- Usage, Electrons -- Atomic properties, Diamond crystals -- Atomic properties, Diamonds -- Atomic properties, Physics
Abstract

A study presents a detailed and unified theoretical treatment of secondary electron cascades that follow the absorption of x-ray photons. The results show that the emission of secondary electrons approaches saturation within about 100 fs following the primary impact.

Published
2005

46. Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide

Author

Carlsson, Gunilla H., Nicholls, Peter, Svistunenko, Dimitri, Berglund, Gunnar I., and Hajdu, Janos

Subjects
Horse-radish -- Research, Acetates -- Research, Acetates -- Chemical properties, Carbon monoxide -- Research, Carbon monoxide -- Chemical properties, Biological sciences, Chemistry
Abstract

Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. A description of high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate is given.

Published
2005

48. The catalytic pathway of horseradish peroxidase at high resolution

Author

Berglund, Gunnar I., Carlsson, Gunilla H., Smith, Andrew T., Szoke, Hanna, Henriksen, Anette, and Hajdu, Janos

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Gunnar I. Berglund [1, 2]; Gunilla H. Carlsson [1, 2]; Andrew T. Smith [3]; Hanna Szöke [1, 4]; Anette Henriksen [4, 5]; Janos Hajdu (corresponding author) [1] A molecular [...]

Published
2002
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49. Femtosecond X-ray protein nanocrystallography

Author

Chapman, Henry N., Fromme, Petra, Barty, Anton, White, Thomas A., Kirian, Richard A., Aquila, Andrew, Hunter, Mark S., Schulz, Joachim, DePonte, Daniel P., Weierstall, Uwe, Doak, Bruce R., Maia, Filipe R. N. C., Martin, Andrew V., Schlichting, Ilme, Lomb, Lukas, Coppola, Nicola, Shoeman, Robert L., Epp, Sascha W., Hartmann, Robert, Rolles, Daniel, Rudenko, Artem, Foucar, Lutz, Kimmel, Nils, Weidenspointner, Georg, Holl, Peter, Liang, Mengning, Barthelmess, Miriam, Caleman, Carl, Boutet, Sébastien, Bogan, Michael J., Krzywinski, Jacek, Bostedt, Christoph, Bajt, Saša, Gumprecht, Lars, Rudek, Benedikt, Erk, Benjamin, Schmidt, Carlo, Hömke, André, Reich, Christian, Pietschner, Daniel, Strüder, Lothar, Hauser, Günter, Gorke, Hubert, Ullrich, Joachim, Herrmann, Sven, Schaller, Gerhard, Schopper, Florian, Soltau, Heike, Kühnel, Kai-Uwe, Messerschmidt, Marc, Bozek, John D., Hau-Riege, Stefan P., Frank, Matthias, Hampton, Christina Y., Sierra, Raymond G., Starodub, Dmitri, Williams, Garth J., Hajdu, Janos, Timneanu, Nicusor, Seibert, Marvin M., Andreasson, Jakob, Rocker, Andrea, Jönsson, Olof, Svenda, Martin, Stern, Stephan, Nass, Karol, Andritschke, Robert, Schröter, Claus-Dieter, Krasniqi, Faton, Bott, Mario, Schmidt, Kevin E., Wang, Xiaoyu, Grotjohann, Ingo, Holton, James M., Barends, Thomas R. M., Neutze, Richard, Marchesini, Stefano, Fromme, Raimund, Schorb, Sebastian, Rupp, Daniela, Adolph, Marcus, Gorkhover, Tais, Andersson, Inger, Hirsemann, Helmut, Potdevin, Guillaume, Graafsma, Heinz, Nilsson, Björn, and Spence, John C. H.

Published
2011
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50. Single mimivirus particles intercepted and imaged with an X-ray laser

Author

Seibert, Marvin M., Ekeberg, Tomas, Maia, Filipe R. N. C., Svenda, Martin, Andreasson, Jakob, Jönsson, Olof, Odić, Duško, Iwan, Bianca, Rocker, Andrea, Westphal, Daniel, Hantke, Max, DePonte, Daniel P., Barty, Anton, Schulz, Joachim, Gumprecht, Lars, Coppola, Nicola, Aquila, Andrew, Liang, Mengning, White, Thomas A., Martin, Andrew, Caleman, Carl, Stern, Stephan, Abergel, Chantal C, Seltzer, Virginie, Claverie, Jean-Michel, Bostedt, Christoph, Bozek, John D., Boutet, Sébastien, Miahnahri, Alan A., Messerschmidt, Marc, Krzywinski, Jacek, Williams, Garth, Hodgson, Keith O., Bogan, Michael J., Hampton, Christina Y., Sierra, Raymond G., Starodub, Dmitri, Andersson, Inger, Bajt, Saša, Barthelmess, Miriam, Spence, John C. H., Fromme, Petra, Weierstall, Uwe, Kirian, Richard, Hunter, Mark, Doak, Bruce R., Marchesini, Stefano, Hau-Riege, Stefan P., Frank, Matthias, Shoeman, Robert L., Lomb, Lukas, Epp, Sascha W., Hartmann, Robert, Rolles, Daniel, Rudenko, Artem, Schmidt, Carlo, Foucar, Lutz, Kimmel, Nils, Holl, Peter, Rudek, Benedikt, Erk, Benjamin, Hömke, André, Reich, Christian, Pietschner, Daniel, Weidenspointner, Georg, Strüder, Lothar, Hauser, Günter, Gorke, Hubert, Ullrich, Joachim, Schlichting, Ilme, Herrmann, Sven, Schaller, Gerhard, Schopper, Florian, Soltau, Heike, Kühnel, Kai-Uwe, Andritschke, Robert, Schröter, Claus-Dieter, Krasniqi, Faton, Bott, Mario, Schorb, Sebastian, Rupp, Daniela, Adolph, Marcus, Gorkhover, Tais, Hirsemann, Helmut, Potdevin, Guillaume, Graafsma, Heinz, Nilsson, Björn, Chapman, Henry N., and Hajdu, Janos J

Published
2011
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