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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
Open Access
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.
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Nov 2024
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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
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.
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Nov 2024
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B21-High Throughput SAXS
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Patrick E.
Konold
,
Leonardo
Monrroy
,
Alfredo
Bellisario
,
Diogo
Filipe
,
Patrick
Adams
,
Roberto
Alvarez
,
Richard
Bean
,
Johan
Bielecki
,
Szabolcs
Bódizs
,
Gabriel
Ducrocq
,
Helmut
Grubmueller
,
Richard A.
Kirian
,
Marco
Kloos
,
Jayanath C. P.
Koliyadu
,
Faisal H. M.
Koua
,
Taru
Larkiala
,
Romain
Letrun
,
Fredrik
Lindsten
,
Michael
Maihöfer
,
Andrew
Martin
,
Petra
Mészáros
,
Jennifer
Mutisya
,
Amke
Nimmrich
,
Kenta
Okamoto
,
Adam
Round
,
Tokushi
Sato
,
Joana
Valerio
,
Daniel
Westphal
,
August
Wollter
,
Tej Varma
Yenupuri
,
Tong
You
,
Filipe
Maia
,
Sebastian
Westenhoff
Open Access
Abstract: Detecting microsecond structural perturbations in biomolecules has wide relevance in biology, chemistry and medicine. Here we show how MHz repetition rates at X-ray free-electron lasers can be used to produce microsecond time-series of protein scattering with exceptionally low noise levels of 0.001%. We demonstrate the approach by examining Jɑ helix unfolding of a light-oxygen-voltage photosensory domain. This time-resolved acquisition strategy is easy to implement and widely applicable for direct observation of structural dynamics of many biochemical processes.
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Jul 2024
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Open Access
Abstract: Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX, available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation.
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May 2024
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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
Open Access
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.
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May 2024
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Hitoshi
Soyama
,
Xiaoyu
Liang
,
Wataru
Yashiro
,
Kentaro
Kajiwara
,
Eleni Myrto
Asimakopoulou
,
Valerio
Bellucci
,
Sarlota
Birnsteinova
,
Gabriele
Giovanetti
,
Chan
Kim
,
Henry J.
Kirkwood
,
Jayanath C. P.
Koliyadu
,
Romain
Letrun
,
Yuhe
Zhang
,
Jozef
Ulicny
,
Richard
Bean
,
Adrian P.
Mancuso
,
Pablo
Villanueva-Perez
,
Tokushi
Sato
,
Patrik
Vagovic
,
Daniel
Eakins
,
Alexander M.
Korsunsky
Open Access
Abstract: Hydrodynamic cavitation is useful in many processing applications, for example, in chemical reactors, water treatment and biochemical engineering. An important type of hydrodynamic cavitation that occurs in a Venturi tube is vortex cavitation known to cause luminescence whose intensity is closely related to the size and number of cavitation events. However, the mechanistic origins of bubbles constituting vortex cavitation remains unclear, although it has been concluded that the pressure fields generated by the cavitation collapse strongly depends on the bubble geometry. The common view is that vortex cavitation consists of numerous small spherical bubbles. In the present paper, aspects of vortex cavitation arising in a Venturi tube were visualized using high-speed X-ray imaging at SPring-8 and European XFEL. It was discovered that vortex cavitation in a Venturi tube consisted of angulated rather than spherical bubbles. The tangential velocity of the surface of vortex cavitation was assessed considering the Rankine vortex model.
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Dec 2023
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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
Open Access
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.
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Nov 2023
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Fabian
Reuter
,
Tokushi
Sato
,
Valerio
Bellucci
,
Sarlota
Birnsteinova
,
Carsten
Deiter
,
Jayanath C. P.
Koliyadu
,
Romain
Letrun
,
Pablo
Villanueva-Perez
,
Richard
Bean
,
Adrian P.
Mancuso
,
Alke
Meents
,
Patrik
Vagovic
,
Claus-Dieter
Ohl
Open Access
Abstract: The fragmentation dynamics of single water droplets from laser irradiation is studied with megahertz frame rate x-ray microscopy. Owed to the nearly refraction-free and penetrating imaging technique, we could look into the interior of the droplet and reveal that two mechanisms are responsible for the initial explosive fragmentation of the droplet. First, reflection and diffraction of the laser beam at the droplet interface result in the formation of laser ray caustics that lead to non-homogeneous heating of the droplet, locally above the critical temperature. Second, homogeneous cavitation in the droplet that is likely caused from shockwaves reflected as tension waves at the acoustic soft boundaries of the droplet. Further atomization occurs in three stages, first a fine sub-micrometer sized mist forms on the side of the droplet posterior to laser incidence, then micrometer sized droplets are expelled from the rim of an expanding liquid sheet, and finally into droplets of larger size through hole and ligament formation in the thinning liquid sheet where ligaments pinch off.
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Nov 2023
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Open Access
Abstract: Many coherent imaging applications that utilize ultrafast X-ray free-electron laser (XFEL) radiation pulses are highly sensitive to fluctuations in the shot-to-shot statistical properties of the source. Understanding and modelling these fluctuations are key to successful experiment planning and necessary to maximize the potential of XFEL facilities. Current models of XFEL radiation and their shot-to-shot statistics are based on theoretical descriptions of the source and are limited in their ability to capture the shot-to-shot intensity fluctuations observed experimentally. The lack of accurate temporal statistics in simulations that utilize these models is a significant barrier to optimizing and interpreting data from XFEL coherent diffraction experiments. Presented here is a phenomenological model of XFEL radiation that is capable of capturing the shot-to-shot statistics observed experimentally using a simple time-dependent approximation of the pulse wavefront. The model is applied to reproduce non-stationary shot-to-shot intensity fluctuations observed at the European XFEL, whilst accurately representing the single-shot properties predicted by FEL theory. Compared with previous models, this approach provides a simple, robust and computationally inexpensive method of generating statistical representations of XFEL radiation.
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Nov 2023
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Open Access
Abstract: The noise caused by sample heterogeneity (including sample solvent) has been identified as one of the determinant factors for a successful X-ray single-particle imaging experiment. It influences both the radiation damage process that occurs during illumination as well as the scattering patterns captured by the detector. Here, we investigate the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. Orientation recovery is a critical step for single-particle imaging. It enables to sort a set of diffraction patterns scattered by identical particles placed at unknown orientations and assemble them into a 3D reciprocal space volume. The recovery quality is characterized by a “disconcurrence” metric. Our results show that while a water layer mitigates protein damage, the noise generated by the scattering from it can introduce challenges for orientation recovery and is anticipated to cause problems in the phase retrieval process to extract the desired protein structure. Compared to these disadvantageous effects due to the thick water layer, the effects of radiation damage on the orientation recovery are relatively small. Therefore, minimizing the amount of residual sample solvent should be considered a crucial step in improving the fidelity and resolution of X-ray single-particle imaging experiments.
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Sep 2023
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