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Ibrahim
Dawod
,
Kajwal
Patra
,
Sebastian
Cardoch
,
H. Olof
Jönsson
,
Jonas A.
Sellberg
,
Andrew V.
Martin
,
Jack
Binns
,
Oscar
Grånäs
,
Adrian P.
Mancuso
,
Carl
Caleman
,
Nicusor
Timneanu
Open Access
Abstract: Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular-dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.
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May 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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Open Access
Abstract: We describe a method to compute photon–matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump–probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump–probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds.
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May 2024
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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
Open Access
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.
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Jan 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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Open Access
Abstract: The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.
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Aug 2023
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