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Instruments / Technical Area	Publication Details	Published
	The single-particle, clusters and biomolecules and serial femtosecond crystallography instrument of the European X-ray Free-Electron Laser: Interaction region downstream at atmospheric pressure (IRD) Adam Round , Pierre Aller , Richard Bean , Johan Bielecki , Agata Butryn , Nicholas E. Devenish , Raphael De Wijn , Thomas Dietze , Katerina Doerner , Fabio Dall'Antonia , Gabriele Giovanetti , Huijong Han , Vincent Hennicke , Chan Kim , Yoonhee Kim , Marco Kloos , Jayanath C. P. Koliyadu , Gabriel Leen , Romain Letrun , Luis Lopez Morillo , Allen M. Orville , Tim Pakendorf , Marco Ramilli , Nadja Reimers , Patrick Reinke , Juan Sanchez-Weatherby , Tokushi Sato , Robin Schubert , Joachim Schulz , Cedric Signe Takem , Marcin Sikorski , Prasad Thute , Fabian Trost , Oleksii Turkot , Patrik Vagovic , Mohammad Vakili , Raul Villanueva Guerrero , Henry N. Chapman , Alke Meents , Serguei Molodtsov , Sakura Pascarelli , Thomas Tschentschera , Adrian Mancuso , Pontus Fischer , Sebastian Guenther Journal Of Synchrotron Radiation 33 DOI: 10.1107/S1600577525008999 Open Access Show Abstract ▼ Abstract: The Single-Particle, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) scientific instrument at the European X-Ray Free-Electron Laser (EuXFEL) became operational with user experiments in September 2017. The unique properties and capabilities of the EuXFEL, enabling megahertz data collection rates, provide more rapid data collection with improved statistics compared with other XFEL facilities. This improves the feasibility of obtaining multiple data points in time-resolved experiments and hence enables the observation of reactions in greater detail (molecular movies). In collaboration with the SFX User Consortium (SFX UC), the SPB/SFX instrument was designed to further increase user access and research outcomes. Focusing the pulses downstream of the first interaction region [described previously (Mancuso et al., 2019)], a second experiment plane is enabled, which allows for greater optimization and more efficient usage of available beam time. Additionally, the SFX UC provided further instrumentation to provide improved capabilities on SPB/SFX. The aim for additional and extended functionality for the second interaction region was to enable sample-efficient data collection at atmospheric pressure in an environment where the sample temperature and humidity can be controlled. This paper describes the extended capabilities of the downstream interaction region of the SPB/SFX instrument and its major components, in particular its X-ray focusing optics, vacuum to atmospheric pressure out-coupling, available sample delivery methods and 2D detector, and the supporting optical laser systems for pump–probe experiments.	Nov 2025
	Ultrasonic cavitation shock wave exfoliation dynamics of 2D materials revealed in situ by MHz XFEL imaging and multiphysics modeling Kang Xiang , Ling Qin , Shi Huang , Hongyuan Song , Vasilii Bazhenov , Sarlota Birnšteinová , Raphael De Wijn , Jayanath C. P. Koliyadu , Faisal H. M. Koua , Adam Round , Ekaterina Round , Abhisakh Sarma , Tokushi Sato , Marcin Sikorski , Yuhe Zhang , Eleni Myrto Asimakopoulou , Pablo Villanueva-Perez , Kyriakos Porfyrakis , Iakovos Tzanakis , Dmitry G. Eskin , Nicole Grobert , Adrian Mancuso , Richard Bean , Patrik Vagovic , Jiawei Mi , Valerio Bellucci Science Advances 11 DOI: 10.1126/sciadv.ady9558 Open Access Show Abstract ▼ Abstract: Using megahertz x-ray free electron laser imaging with x-ray pulses of ~25 femtoseconds and a machine-learning strategy, we have conducted comprehensive in situ imaging studies on the dynamics of cavitation bubble clouds in ultrasound fields at the SPB/SFX beamline of the European XFEL. The research unambiguously revealed the quasi-simultaneous implosion of multiple bubbles and simultaneous collapse of bubble cloud in nanosecond scale and their dynamic impacts onto two-dimensional (2D) materials for layer exfoliation. We have also performed multiphysics modeling to simulate the shock wave emission, propagation, impact, and stresses produced. We elucidated the critical conditions for producing instant or fatigue exfoliation and the effects of bonding strengths and structural defects on the exfoliation rate. The discoveries have filled the long-standing missing knowledge gaps in the underlying physics of exfoliating 2D materials in ultrasound fields, providing a solid theoretical foundation for optimizing and scaling-up operation to produce 2D materials in a much more cost-effective and sustainable way.	Nov 2025
	Real-time analysis of liquid jet sample delivery stability for an X-ray free-electron laser using machine vision Jaydeep Patel , Adam Round , Raphael De Wijn , Mohammad Vakili , Gabriele Giovanetti , Diogo Filipe Monrroy Vilan E Melo , Juncheng E , Marcin Sikorski , Jayanth Koliyadu , Faisal H. M. Koua , Tokushi Sato , Adrian Mancuso , Andrew Peele , Brian Abbey Journal Of Applied Crystallography 57 DOI: 10.1107/S1600576724009853 Open Access Show Abstract ▼ Abstract: Automated evaluation of optical microscopy images of liquid jets, commonly used for sample delivery at X-ray free-electron lasers (XFELs), enables real-time tracking of the jet position and liquid jet hit rates, defined here as the proportion of XFEL pulses intersecting with the liquid jet. This method utilizes machine vision for preprocessing, feature extraction, segmentation and jet detection as well as tracking to extract key physical characteristics (such as the jet angle) from optical microscopy images captured during experiments. To determine the effectiveness of these tools in monitoring jet stability and enhancing sample delivery efficiency, we conducted XFEL experiments with various sample compositions (pure water, buffer and buffer with crystals), nozzle designs and jetting conditions. We integrated our real-time analysis algorithm into the Karabo control system at the European XFEL. The results indicate that the algorithm performs well in monitoring the jet angle and provides a quantitative characterization of liquid jet stability through optical image analysis conducted during experiments.	Dec 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
	Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography Mohammad Vakili , Huijong Han , Christina Schmidt , Agnieszka Wrona , Marco Kloos , Iñaki De Diego , Katerina Dörner , Tian Geng , Chan Kim , Faisal H. M. Koua , Diogo V. M. Melo , Mathieu Rappas , Adam Round , Ekaterina Round , Marcin Sikorski , Joana Valerio , Tiankun Zhou , Kristina Lorenzen , Joachim Schulz Journal Of Applied Crystallography 56 DOI: 10.1107/S1600576723004405 Open Access Show Abstract ▼ Abstract: Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.	Aug 2023
I03-Macromolecular Crystallography	Megahertz serial crystallography Max O. Wiedorn , Dominik Oberthuer , Richard Bean , Robin Schubert , Nadine Werner , Brian Abbey , Martin Aepfelbacher , Luigi Adriano , Aschkan Allahgholi , Nasser Al-Qudami , Jakob Andreasson , Steve Aplin , Salah Awel , Kartik Ayyer , Saša Bajt , Imrich Barák , Sadia Bari , Johan Bielecki , Sabine Botha , Djelloul Boukhelef , Wolfgang Brehm , Sandor Brockhauser , Igor Cheviakov , Matthew A. Coleman , Francisco Cruz-Mazo , Cyril Danilevski , Connie Darmanin , R. Bruce Doak , Martin Domaracky , Katerina Dörner , Yang Du , Hans Fangohr , Holger Fleckenstein , Matthias Frank , Petra Fromme , Alfonso M. Gañán-Calvo , Yaroslav Gevorkov , Klaus Giewekemeyer , Helen Mary Ginn , Heinz Graafsma , Rita Graceffa , Dominic Greiffenberg , Lars Gumprecht , Peter Göttlicher , Janos Hajdu , Steffen Hauf , Michael Heymann , Susannah Holmes , Daniel A. Horke , Mark S. Hunter , Siegfried Imlau , Alexander Kaukher , Yoonhee Kim , Alexander Klyuev , Juraj Knoška , Bostjan Kobe , Manuela Kuhn , Christopher Kupitz , Jochen Küpper , Janine Mia Lahey-Rudolph , Torsten Laurus , Karoline Le Cong , Romain Letrun , P. Lourdu Xavier , Luis Maia , Filipe R. N. C. Maia , Valerio Mariani , Marc Messerschmidt , Markus Metz , Davide Mezza , Thomas Michelat , Grant Mills , Diana C. F. Monteiro , Andrew Morgan , Kerstin Mühlig , Anna Munke , Astrid Münnich , Julia Nette , Keith A. Nugent , Theresa Nuguid , Allen M. Orville , Suraj Pandey , Gisel Pena , Pablo Villanueva-Perez , Jennifer Poehlsen , Gianpietro Previtali , Lars Redecke , Winnie Maria Riekehr , Holger Rohde , Adam Round , Tatiana Safenreiter , Iosifina Sarrou , Tokushi Sato , Marius Schmidt , Bernd Schmitt , Robert Schönherr , Joachim Schulz , Jonas A. Sellberg , M. Marvin Seibert , Carolin Seuring , Megan L. Shelby , Robert L. Shoeman , Marcin Sikorski , Alessandro Silenzi , Claudiu A. Stan , Xintian Shi , Stephan Stern , Jola Sztuk-Dambietz , Janusz Szuba , Aleksandra Tolstikova , Martin Trebbin , Ulrich Trunk , Patrik Vagovic , Thomas Ve , Britta Weinhausen , Thomas A. White , Krzysztof Wrona , Chen Xu , Oleksandr Yefanov , Nadia Zatsepin , Jiaguo Zhang , Markus Perbandt , Adrian P. Mancuso , Christian Betzel , Henry Chapman , Anton Barty Nature Communications 9 DOI: 10.1038/s41467-018-06156-7 Open Access Show Abstract ▼ 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.	Oct 2018
	Structure of photosystem II and substrate binding at room temperature Iris D. Young , Mohamed Ibrahim , Ruchira Chatterjee , Sheraz Gul , Franklin D. Fuller , Sergey Koroidov , Aaron S. Brewster , Rosalie Tran , Roberto Alonso-Mori , Thomas Kroll , Tara Michels-Clark , Hartawan Laksmono , Raymond G. Sierra , Claudiu A. Stan , Rana Hussein , Miao Zhang , Lacey Douthit , Markus Kubin , Casper De Lichtenberg , Long Vo Pham , Håkan Nilsson , Mun Hon Cheah , Dmitriy Shevela , Claudio Saracini , Mackenzie A. Bean , Ina Seuffert , Dimosthenis Sokaras , Tsu-Chien Weng , Ernest Pastor , Clemens Weninger , Thomas Fransson , Louise Lassalle , Philipp Bräuer , Pierre Aller , Peter T. Docker , Babak Andi , Allen M. Orville , James M. Glownia , Silke Nelson , Marcin Sikorski , Diling Zhu , Mark S. Hunter , Thomas J. Lane , Andy Aquila , Jason E. Koglin , Joseph Robinson , Mengning Liang , Sébastien Boutet , Artem Y. Lyubimov , Monarin Uervirojnangkoorn , Nigel W. Moriarty , Dorothee Liebschner , Pavel V. Afonine , David G. Waterman , Gwyndaf Evans , Philippe Wernet , Holger Dobbek , William I. Weis , Axel T. Brunger , Petrus H. Zwart , Paul D. Adams , Athina Zouni , Johannes Messinger , Uwe Bergmann , Nicholas K. Sauter , Jan Kern , Vittal K. Yachandra , Junko Yano Nature DOI: 10.1038/nature20161 Show Abstract ▼ Abstract: Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution2, 3. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site4, 5, 6. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL7 provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions8, 9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10, 11, 12, 13. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.	Nov 2016

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