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14 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2 [Next/Last]

Instruments / Technical Area	Publication Details	Published
	Development of crystal optics for X-ray multi-projection imaging for synchrotron and XFEL sources Valerio Bellucci , Sarlota Birnsteinova , Tokushi Sato , Romain Letrun , Jayanath C. P. Koliyadu , Chan Kim , Gabriele Giovanetti , Carsten Deiter , Liubov Samoylova , Ilia Petrov , Luis Lopez Morillo , Rita Graceffa , Luigi Adriano , Helge Huelsen , Heiko Kollmann , Thu Nhi Tran Calliste , Dusan Korytar , Zdenko Zaprazny , Andrea Mazzolari , Marco Romagnoni , Eleni Myrto Asimakopoulou , Zisheng Yao , Yuhe Zhang , Jozef Ulicny , Alke Meents , Henry N. Chapman , Richard Bean , Adrian Mancuso , Pablo Villanueva-Perez , Patrik Vagovic Journal Of Synchrotron Radiation 31 DOI: 10.1107/S1600577524008488 Open Access Show Abstract ▼ Abstract: X-ray multi-projection imaging (XMPI) is an emerging experimental technique for the acquisition of rotation-free, time-resolved, volumetric information on stochastic processes. The technique is developed for high-brilliance light-source facilities, aiming to address known limitations of state-of-the-art imaging methods in the acquisition of 4D sample information, linked to their need for sample rotation. XMPI relies on a beam-splitting scheme, that illuminates a sample from multiple, angularly spaced viewpoints, and employs fast, indirect, X-ray imaging detectors for the collection of the data. This approach enables studies of previously inaccessible phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. In this work, we discuss in detail the beam-splitting scheme of XMPI. More specifically, we explore the relevant properties of X-ray splitter optics for their use in XMPI schemes, both at synchrotron insertion devices and XFEL facilities. Furthermore, we describe two distinct XMPI schemes, designed to faciliate large samples and complex sample environments. Finally, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL. This detailed overview aims to state the challenges and the potential of XMPI and act as a stepping stone for future development of the technique.	Nov 2024
	Development of MHz X-ray phase contrast imaging at the European XFEL Jayanath C. P. Koliyadu , Daniel Moško , Eleni Myrto Asimakopoulou , Valerio Bellucci , Šarlota Birnšteinová , Richard Bean , Romain Letrun , Chan Kim , Henry Kirkwood , Gabriele Giovanetti , Nerea Jardon , Janusz Szuba , Trey Guest , Andreas Koch , Jan Grünert , Peter Szeles , Pablo Villanueva-Perez , Fabian Reuter , Claus-Dieter Ohl , Mike Andreas Noack , Francisco Garcia-Moreno , Zuzana Kuglerová-Valdová , Libor Juha , Martin Nikl , Wataru Yashiro , Hitoshi Soyama , Daniel Eakins , Alexander M. Korsunsky , Jozef Ulicny , Alke Meents , Henry N. Chapman , Adrian P. Mancuso , Tokushi Sato , Patrik Vagovic Journal Of Synchrotron Radiation 32 DOI: 10.1107/S160057752400986X Show Abstract ▼ Abstract: We report on recent developments that enable megahertz hard X-ray phase contrast imaging (MHz XPCI) experiments at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL facility (EuXFEL). We describe the technical implementation of the key components, including an MHz fast camera and a modular indirect X-ray microscope system based on fast scintillators coupled through a high-resolution optical microscope, which enable full-field X-ray microscopy with phase contrast of fast and irreversible phenomena. The image quality for MHz XPCI data showed significant improvement compared with a pilot demonstration of the technique using parallel beam illumination, which also allows access to up to 24 keV photon energies at the SPB/SFX instrument of the EuXFEL. With these developments, MHz XPCI was implemented as a new method offered for a broad user community (academic and industrial) and is accessible via standard user proposals. Furthermore, intra-train pulse diagnostics with a high few-micrometre spatial resolution and recording up to 128 images of consecutive pulses in a train at up to 1.1 MHz repetition rate is available upstream of the instrument. Together with the diagnostic camera upstream of the instrument and the MHz XPCI setup at the SPB/SFX instrument, simultaneous two-plane measurements for future beam studies and feedback for machine parameter tuning are now possible.	Nov 2024
	Resolving nonequilibrium shape variations among millions of gold nanoparticles Zhou Shen , Paul Lourdu Xavier , Richard Bean , Johan Bielecki , Martin Bergemann , Benedikt Daurer , Tomas Ekeberg , Armando D. Estillore , Hans Fangohr , Klaus Giewekemeyer , Mikhail Karnevskiy , Richard A. Kirian , Henry Kirkwood , Yoonhee Kim , Jayanath C. P. Koliyadu , Holger Lange , Romain Letrun , Jannik Lübke , Abhishek Mall , Thomas Michelat , Andrew J. Morgan , Nils Roth , Amit K. Samanta , Tokushi Sato , Marcin Sikorski , Florian Schulz , Patrik Vagovic , Tamme Wollweber , Lena Worbs , Filipe Maia , Daniel A. Horke , Jochen Küpper , Adrian P. Mancuso , Henry Chapman , Kartik Ayyer , N. Duane Loh Acs Nano DOI: 10.1021/acsnano.4c00378 Open Access Show Abstract ▼ Abstract: Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) creates opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between 105 structural models and 106 XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the nonequilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable “shape envelope” among nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles’ shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.	May 2024
	Observation of a single protein by ultrafast X-ray diffraction Tomas Ekeberg , Dameli Assalauova , Johan Bielecki , Rebecca Boll , Benedikt J. Daurer , Lutz A. Eichacker , Linda E. Franken , Davide E. Galli , Luca Gelisio , Lars Gumprecht , Laura H. Gunn , Janos Hajdu , Robert Hartmann , Dirk Hasse , Alexandr Ignatenko , Jayanath Koliyadu , Olena Kulyk , Ruslan Kurta , Markus Kuster , Wolfgang Lugmayr , Jannik Lübke , Adrian P. Mancuso , Tommaso Mazza , Carl Nettelblad , Yevheniy Ovcharenko , Daniel E. Rivas , Max Rose , Amit K. Samanta , Philipp Schmidt , Egor Sobolev , Nicusor Timneanu , Sergey Usenko , Daniel Westphal , Tamme Wollweber , Lena Worbs , Paul Lourdu Xavier , Hazem Yousef , Kartik Ayyer , Henry N. Chapman , Jonas A. Sellberg , Carolin Seuring , Ivan A. Vartanyants , Jochen Küpper , Michael Meyer , Filipe R. N. C. Maia Light: Science & Applications 13 DOI: 10.1038/s41377-023-01352-7 Open Access Show Abstract ▼ 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 theory, 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 explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. 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 diameter 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.	Jan 2024
	Online dynamic flat-field correction for MHz microscopy data at European XFEL Sarlota Birnsteinova , Danilo E. Ferreira De Lima , Egor Sobolev , Henry J. Kirkwood , Valerio Bellucci , Richard J. Bean , Chan Kim , Jayanath C. P. Koliyadu , Tokushi Sato , Fabio Dall'Antonia , Eleni Myrto Asimakopoulou , Zisheng Yao , Khachiwan Buakor , Yuhe Zhang , Alke Meents , Henry N. Chapman , Adrian P. Mancuso , Pablo Villanueva-Perez , Patrik Vagovic Journal Of Synchrotron Radiation 30 DOI: 10.1107/S1600577523007336 Open Access Show Abstract ▼ Abstract: The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.	Nov 2023
I13-1-Coherence	Hard X-ray stereographic microscopy for single-shot differential phase imaging Valerio Bellucci , Marie-Christine Zdora , Ladislav Mikes , Šarlota Birnšteinová , Peter Oberta , Marco Romagnoni , Andrea Mazzolari , Pablo Villanueva-Perez , Rajmund Mokso , Christian David , Mikako Makita , Silvia Cipiccia , Jozef Ulicny , Alke Meents , Adrian P. Mancuso , Henry N. Chapman , Patrik Vagovic Optics Express 31 DOI: 10.1364/OE.492137 Diamond Proposal Number(s): [17739] Open Access Show Abstract ▼ Abstract: The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.	May 2023
	Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease Vasundara Srinivasan , Hévila Brognaro , Prince R. Prabhu , Edmarcia Elisa De Souza , Sebastian Günther , Patrick Y. A. Reinke , Thomas J. Lane , Helen Ginn , Huijong Han , Wiebke Ewert , Janina Sprenger , Faisal H. M. Koua , Sven Falke , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Bruno Alves Franca , Mengying Wang , Angélica Luana C. Barra , Markus Perbandt , Martin Schwinzer , Christina Schmidt , Lea Brings , Kristina Lorenzen , Robin Schubert , Rafael Rahal Guaragna Machado , Erika Donizette Candido , Danielle Bruna Leal Oliveira , Edison Luiz Durigon , Stephan Niebling , Angelica Struve Garcia , Oleksandr Yefanov , Julia Lieske , Luca Gelisio , Martin Domaracky , Philipp Middendorf , Michael Groessler , Fabian Trost , Marina Galchenkova , Aida Rahmani Mashhour , Sofiane Saouane , Johanna Hakanpää , Markus Wolf , Maria Garcia Alai , Dusan Turk , Arwen R. Pearson , Henry N. Chapman , Winfried Hinrichs , Carsten Wrenger , Alke Meents , Christian Betzel Communications Biology 5 DOI: 10.1038/s42003-022-03737-7 Open Access Show Abstract ▼ Abstract: SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.	Aug 2022
	X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease Sebastian Gunther , Patrick Y. A. Reinke , Yaiza Fernández-García , Julia Lieske , Thomas J. Lane , Helen M. Ginn , Faisal H. M. Koua , Christiane Ehrt , Wiebke Ewert , Dominik Oberthuer , Oleksandr Yefanov , Susanne Meier , Kristina Lorenzen , Boris Krichel , Janine-Denise Kopicki , Luca Gelisio , Wolfgang Brehm , Ilona Dunkel , Brandon Seychell , Henry Gieseler , Brenna Norton-Baker , Beatriz Escudero-Pérez , Martin Domaracky , Sofiane Saouane , Alexandra Tolstikova , Thomas A. White , Anna Hänle , Michael Groessler , Holger Fleckenstein , Fabian Trost , Marina Galchenkova , Yaroslav Gevorkov , Chufeng Li , Salah Awel , Ariana Peck , Miriam Barthelmess , Frank Schluenzen , Paulraj Lourdu Xavier , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Sven Falke , Vasundara Srinivasan , Bruno Alves França , Martin Schwinzer , Hévila Brognaro , Cromarte Rogers , Diogo Melo , Joanna J. Zaitseva-Doyle , Juraj Knoska , Gisel E. Peña-Murillo , Aida Rahmani Mashhour , Vincent Hennicke , Pontus Fischer , Johanna Hakanpää , Jan Meyer , Philip Gribbon , Bernhard Ellinger , Maria Kuzikov , Markus Wolf , Andrea R. Beccari , Gleb Bourenkov , David Von Stetten , Guillaume Pompidor , Isabel Bento , Saravanan Panneerselvam , Ivars Karpics , Thomas R. Schneider , Maria Marta Garcia-Alai , Stephan Niebling , Christian Günther , Christina Schmidt , Robin Schubert , Huijong Han , Juliane Boger , Diana C. F. Monteiro , Linlin Zhang , Xinyuanyuan Sun , Jonathan Pletzer-Zelgert , Jan Wollenhaupt , Christian G. Feiler , Manfred S. Weiss , Eike-Christian Schulz , Pedram Mehrabi , Katarina Karničar , Aleksandra Usenik , Jure Loboda , Henning Tidow , Ashwin Chari , Rolf Hilgenfeld , Charlotte Uetrecht , Russell Cox , Andrea Zaliani , Tobias Beck , Matthias Rarey , Stephan Günther , Dusan Turk , Winfried Hinrichs , Henry N. Chapman , Arwen R. Pearson , Christian Betzel , Alke Meents Science DOI: 10.1126/science.abf7945 Open Access Show Abstract ▼ Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.	Apr 2021
	Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source Haoyuan Li , Reza Nazari , Brian Abbey , Roberto Alvarez , Andrew Aquila , Kartik Ayyer , Anton Barty , Peter Berntsen , Johan Bielecki , Alberto Pietrini , Maximilian Bucher , Gabriella Carini , Henry N. Chapman , Alice Contreras , Benedikt J. Daurer , Hasan Demirci , Leonie Flűckiger , Matthias Frank , Janos Hajdu , Max F. Hantke , Brenda G. Hogue , Ahmad Hosseinizadeh , Mark S. Hunter , H. Olof Jönsson , Richard A. Kirian , Ruslan P. Kurta , Duane Loh , Filipe R. N. C. Maia , Adrian P. Mancuso , Andrew J. Morgan , Matthew Mcfadden , Kerstin Muehlig , Anna Munke , Hemanth Kumar Narayana Reddy , Carl Nettelblad , Abbas Ourmazd , Max Rose , Peter Schwander , M. Marvin Seibert , Jonas A. Sellberg , Raymond G. Sierra , Zhibin Sun , Martin Svenda , Ivan A. Vartanyants , Peter Walter , Daniel Westphal , Garth Williams , P. Lourdu Xavier , Chun Hong Yoon , Sahba Zaare Scientific Data 7 DOI: 10.1038/s41597-020-00745-2 Open Access Show Abstract ▼ 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.	Nov 2020
	Segmented flow generator for serial crystallography at the European X-ray free electron laser Austin Echelmeier , Jorvani Cruz Villarreal , Marc Messerschmidt , Daihyun Kim , Jesse D. Coe , Darren Thifault , Sabine Botha , Ana Egatz-Gomez , Sahir Gandhi , Gerrit Brehm , Chelsie E. Conrad , Debra T. Hansen , Caleb Madsen , Saša Bajt , J. Domingo Meza-Aguilar , Dominik Oberthuer , Max O. Wiedorn , Holger Fleckenstein , Derek Mendez , Juraj Knoška , Jose M. Martin-Garcia , Hao Hu , Stella Lisova , Aschkai Allahgoli , Yaroslav Gevorkov , Kartik Ayyer , Steve Aplin , Helen M. Ginn , Heinz Graafsma , Andrew J. Morgan , Dominic Greiffenberg , Alexander Klujev , Torsten Laurus , Jennifer Poehlsen , Ulrich Trunk , Davide Mezza , Bernd Schmitt , Manuela Kuhn , Raimund Fromme , Jolanta Sztuk-Dambietz , Natascha Raab , Steffen Hauf , Alessandro Silenzi , Thomas Michelat , Chen Xu , Cyril Danilevski , Andrea Parenti , Leonce Mekinda , Britta Weinhausen , Grant Mills , Patrik Vagovic , Yoonhee Kim , Henry Kirkwood , Richard Bean , Johan Bielecki , Stephan Stern , Klaus Giewekemeyer , Adam Round , Joachim Schulz , Katerina Dörner , Thomas D. Grant , Valerio Mariani , Anton Barty , Adrian P. Mancuso , Uwe Weierstall , John C. H. Spence , Henry N. Chapman , Nadia Zatsepin , Petra Fromme , Richard A. Kirian , Alexandra Ros Nature Communications 11 DOI: 10.1038/s41467-020-18156-7 Open Access Show Abstract ▼ Abstract: Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.	Sep 2020

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