European XFEL Research Articles

Abstract P-1: Analysis of Tick-borne Encephalitis Virus Single-particle Imaging on X-ray Free-electron Laser

Background: Tick-borne encephalitis virus (TBEV) is a dangerous human pathogen which envelope structure is already known from cryoEM study. TBEV mature viral particle size (~50 nm in diameter) makes it suitable for single-particle imaging (SPI) on X-ray free-electron laser (XFEL). XFEL SPI studies are at the early stages of development; thus, a well-described and conformationally homogeneous sample is required to develop approaches for experimental setup and data analysis. Here we present the image analysis results of data collected in October 2019 during the European XFEL experiment #2316. Methods: The detector was placed at 1.62 m from the injector; photon energy was around 6 keV, pulse energy 4 mJ, beam diameter ~ 500 nm. All runs were processed to detect hits with threshold filter (5th percentile of lit pixels) and further filtered to omit low-intensity images and images that lack detector modules. Filtered hits were background and geometry corrected with SPImage library and custom python scripts. Then hits were azimuthally integrated using PyFAI library. Scattering profiles were further clustered using the affinity propagation algorithm with cosine similarity metric in log space. Extracted classes were used to build averaged images. All hit profiles were fitted with model scattering to estimate the diameter of the particle. Simulated diffraction patterns were prepared using Condor from the cryoEM electron density map (EMDB ID 3752). Results: During the analysis after the filtering, only 276 clean and bright hits were collected per 135 min of injection (from 27287 hits detected via lit pixels threshold). Thus the hit rate was around ~ 2 hits/min, which is expected to rise in the future. The majority of hits correspond to the 40-50 nm particles (Fig. 1a), which is expected for TBEV. However, the exact size may vary due to solvent evaporation, ion condensation, and possible variability in the sample. Conclusion: The averaged images and their scattering profiles correlate with the simulated scattering patterns, though not ideally (Fig. 1 bc). Such discrepancy is expected due to the absence of electron density in the center of modeled viral structures.

New frontiers in extreme conditions science at synchrotrons and free electron lasers

Synchrotrons and free electron lasers are unique facilities to probe the atomic structure and electronic properties of matter at extreme thermodynamical conditions. In this context, ‘matter at extreme pressures and temperatures’ was one of the science drivers for the construction of low emittance 4th generation synchrotron sources such as the Extremely Brilliant Source of the European Synchrotron Radiation Facility and hard x-ray free electron lasers, such as the European x-ray free electron laser. These new user facilities combine static high pressure and dynamic shock compression experiments to outstanding high brilliance and submicron beams. This combination not only increases the data-quality but also enlarges tremendously the accessible pressure, temperature and density space. At the same time, the large spectrum of available complementary x-ray diagnostics for static and shock compression studies opens unprecedented insights into the state of matter at extremes. The article aims at highlighting a new horizon of scientific opportunities based on the synergy between extremely brilliant synchrotrons and hard x-ray free electron lasers.

Probabilistic model-based fault diagnosis for the cavities of the European XFEL

Abstract The European X-ray Free Electron Laser (EuXFEL) is a complex system with many interconnected components and sensor measurements. We use factor graphs to systematically design a probabilistic fault diagnosis method for its cavity system. This approach is expandable to further subsystems and considers uncertainties from measurements and modeling. After representing a model of the cavity system in the factor graph framework, we infer marginal distributions, e. g., of the fault classes using tabulated message-passing definitions. The emerging fault diagnosis method consists of an unscented Kalman filter-based residual generator and an evaluation of the residuals using a Gaussian mixture model. We include message-passing definitions for the training of the Gaussian Mixture Model from noisy data using the expectation-maximization algorithm.

Immunity of States and International Organizations in the Court of Justice of the European Union Practice and its Significance in the Implementation of Megascience Projects

In recent years, Russia has invested significant assets in unique scientific facility of the “Megascience” class that are being built or are already operating on the territory of foreign countries, mainly member states of the European Union: the International Thermonuclear Research Reactor-ITER (France), the European X-ray Free Electron Laser-European XFEL, the Large Hadron Collider (Switzerland and France), etc.How reliable and safe are such investments in the context of the sanctions policy of the West, including the EU, against our country? To what extent are they protected by the principle of immunity of states and international organizations, which is generally recognized, but is not interpreted and applied in different legal systems? The paper considers these issues in the context of the development of the judicial practice of the supranational institution of the judicial power of the EU, namely the Court of Justice of the European Union and the concept of relative immunity (immunité relative) formulated herein.Having conducted a comparative legal review of the current state of the sources of law and doctrine on the issues of immunity of states and international organizations, the author analyses and evaluates the decisions of the EU Court of Justice and the legal positions of its attorneys General: — Mahamdia v. Algeria, 2012: for the first time ECJ formulates the concept of relative immunity in relation to states;— "Rina" and "Suprim" cases, 2020: EU Court clarifies the interpretation of the concept of acta iure imperii (acts of public authority), in respect of which states retain immunity in the EU, and extends its concept of relative immunity to international intergovernmental organizations.The final section deals with legal issues that yet to get a clear answer in the practice of the EU Court of Justice. In this regard, the author highlights possible directions of its evolution, and studies other recent decisions of the EU Court of Justice that may affect Russia’s national interests in the context of cooperation with EU member states in the scientific and technical sphere, including megascience, and in other areas.

Theory of polarization-averaged core-level molecular-frame photoelectron angular distributions: II. Extracting the x-ray-induced fragmentation dynamics of carbon monoxide dication from forward and backward intensities

Recent developments in high-repetition-rate x-ray free electron lasers (XFELs) such as the European XFEL and the LSCS-II, combined with coincidence measurements using the COLTRIMS-reaction microscope, are now opening a door to realize the long-standing dream of creating molecular movies of photo-induced chemical reactions in gas-phase molecules. In this paper, we propose a new theoretical method to experimentally visualize the dissociation of diatomic molecules via time-resolved polarization-averaged molecular-frame photoelectron angular distribution (PA-MFPAD) measurements using the COLTRIMS-reaction microscope and the two-color XFEL pump–probe set-up. We used first- and second-order scattering theory within the muffin-tin approximation, which is valid for a sufficiently high kinetic energy of photoelectrons, typically above 100 eV, and for long bond lengths. This leads to a simple extended x-ray absorption fine structure (EXAFS)-type formula for the forward and backward scattering peaks in the PA-MFPAD structure. This formula relies only on three semi-empirical parameters obtainable from the time-resolved measurements. It can be used as a ‘bond length ruler’ on experimental results. The accuracy and applicability of the new ruler equation are numerically examined against the PA-MFPADs of CO2+ calculated with full-potential multiple scattering theory as a function of the C–O bond length reported in the preceding work (Ota et al J. Phys. B: At. Mol. Opt.). The bond lengths retrieved from the PA-MFPADs via our EXAFS-like formula coincide within an accuracy of 0.1 Å with the original C–O bond lengths used in the reference ab initio PA-MFPADs. We expect time-resolved PA-MFPADs to become a new attractive tool to make molecular movies visualizing intramolecular reactions.

Nanosecond timing and synchronization scheme for holographic pump-probe studies at the MID instrument at European XFEL.

Single-pulse holographic imaging at XFEL sources with 1012 photons delivered in pulses shorter than 100 fs reveal new quantitative insights into fast phenomena. Here, a timing and synchronization scheme for stroboscopic imaging and quantitative analysis of fast phenomena on time scales (sub-ns) andlength-scales (≲100 nm) inaccessible by visible light is reported. A fully electronic delay-and-trigger system has been implemented at the MID station at the European XFEL, and applied to the study of emerging laser-driven cavitation bubbles in water. Synchronization and timing precision have been characterized to be better than 1 ns.

Novel experimental setup for megahertz X-ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X-ray Free-Electron Laser (EuXFEL).

The high-precision X-ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X-ray Free-Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump-probe X-ray diffraction experiments in the DAC are described and their implementation demonstrated during the FirstUser Community Assisted Commissioning experiment. X-ray heating and diffraction of Bi under pressure, obtained using 20 fs X-ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in theDAC.

Design and first tests of the Gotthard-II readout ASIC for the European X-ray Free-Electron Laser

Gotthard-II is a charge-integrating microstrip detector developed for experiments and diagnostics at free-electron lasers using hard X-rays of 5 keV–20 keV. Thanks to its excellent single photon sensitivity, large dynamic range as well as high frame rate of 4.5 MHz in burst mode, its potential scientific applications include X-ray absorption/emission spectroscopy, hard X-ray high resolution single-shot spectrometry (HiREX), beam diagnostics, as well as veto signal generation for pixel detectors. The Gotthard-II ASIC has been designed and fabricated using UMC-110 nm technology. The final ASIC design and performance in terms of noise, linearity, dynamic range, coupling between channels and speed will be discussed in the paper. In addition, a first measurement of an X-ray absorption spectrum of a standard copper sample has been done. The performance of the Gotthard-II in an experiment using energy dispersive X-rays has been demonstrated.

Alternative Geometric Arrangements of the Nozzle Outlet Orifice for Liquid Micro-Jet Focusing in Gas Dynamic Virtual Nozzles.

Liquid micro-jets are crucial for sample delivery of protein crystals and other macromolecular samples in serial femtosecond crystallography. When combined with MHz repetition rate sources, such as the European X-ray free-electron laser (EuXFEL) facility, it is important that the diffraction patterns are collected before the samples are damaged. This requires extremely thin and very fast jets. In this paper we first explore numerically the influence of different nozzle orifice designs on jet parameters and finally compare our simulations with the experimental data obtained for one particular design. A gas dynamic virtual nozzle (GDVN) model, based on a mixture formulation of Newtonian, compressible, two-phase flow, is numerically solved with the finite volume method and volume of fluid approach to deal with the moving boundary between the gas and liquid phases. The goal is to maximize the jet velocity and its length while minimizing the jet thickness. The design studies incorporate differently shaped nozzle orifices, including an elongated orifice with a constant diameter and an orifice with a diverging angle. These are extensions of the nozzle geometry we investigated in our previous studies. Based on these simulations it is concluded that the extension of the constant diameter channel makes a negligible contribution to the jet’s length and its velocity. A change in the angle of the nozzle outlet orifice, however, has a significant effect on jet parameters. We find these kinds of simulation extremely useful for testing and optimizing novel nozzle designs.

Observation of harmonic lasing in the Angstrom regime at European X-ray Free Electron Laser

Harmonic lasing provides an opportunity to extend the photon energy range of existing and planned x-ray free electron laser (FEL) user facilities. Contrary to nonlinear harmonic generation, harmonic lasing can generate a much more intense, stable, and narrow-band FEL beam. Another interesting application is harmonic lasing self-seeding that allows to improve the longitudinal coherence and spectral power of a self-amplified spontaneous emission FEL. This concept was tested at the soft x-ray FEL user facility FLASH in the range of 4.5--15 nm and at Pohang accelerator laboratory X-ray Free Electron Laser (XFEL) at 1 nm. In this paper we present recent results from the European XFEL where we successfully demonstrated harmonic lasing at 5.9 Angstrom and 2.8 Angstrom. In the latter case we obtained both third and fifth harmonic lasing and, for the first time, operated a harmonic lasing cascade (fifth-third-first harmonics of the undulator). These results pave the way for reaching very high photon energies, up to 100 keV.

Online Detuning Computation and Quench Detection for Superconducting Resonators

Superconducting cavities are responsible for beam acceleration in superconducting linear accelerators. Challenging cavity control specifications are necessary to reduce radio frequency (RF) costs and to maximize the availability of the accelerator. Cavity detuning and bandwidth are two critical parameters to monitor when operating particle accelerators. Cavity detuning is strongly related to the power required to generate the desired accelerating gradient. Cavity bandwidth is related to the cavity RF losses. A sudden increase in bandwidth can indicate the presence of a quench or multipacting event. Therefore, calculating these parameters in real time in the low-level RF (LLRF) system is highly desirable. A real-time estimation of the bandwidth allows for a faster response of the machine protection system in the case of quench events, whereas the estimation of cavity detuning can be used to drive piezoelectric tuner-based resonance control algorithms. In this article, a new field programmable gate array (FPGA)-based estimation component is presented. Such a component is designed to be used either in continuous wave (CW) or pulsed operation mode with loaded quality factors between $10^{6}$ and $10^{8}$ . Results of this component with free-electron LASer in Hamburg (FLASH), European X-ray free electron laser (EuXFEL), cryo module test bench (CMTB), and electron linac for beams with high brilliance and low emittance (ELBE) are presented.

Publisher's Note: "High-resolution inelastic x-ray scattering at the high energy density scientific instrument at the European X-Ray Free-Electron Laser" [Rev. Sci. Instrum. 92, 013101 (2021)

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Materials Imaging and Dynamics (MID) instrument at the European X-ray Free-Electron Laser Facility.

The Materials Imaging and Dynamics (MID) instrument at the European X-ray Free-Electron Laser (EuXFEL) facility is described. EuXFEL is the first hard X-ray free-electron laser operating in the MHz repetition range which provides novel science opportunities. The aim of MID is to enable studies of nano-structured materials, liquids, and soft- and hard-condensed matter using the bright X-ray beams generated by EuXFEL. Particular emphasis is on studies of structure and dynamics in materials by coherent scattering and imaging using hard X-rays. Commission of MID started at the end of 2018 and first experiments were performed in 2019.

Experimental validation of collective effects modeling at injector section of X-ray free-electron laser

We consider the collective beam dynamics at the injector section of the European XFEL. The results of the measurements for the longitudinal phase space (LPS) of the electron beam are compared with those obtained from numerical modeling. A new approach is proposed for the analysis of the self-field effects in the LPS measurements. It allows to determine accurately the synchronous RF phase in an accelerating module and to subtract properly the RF curvature imprinted in the LPS. A further incorporation with the simulation made it possible to separate the collective effects originating from different sources and thus to quantify, individually, the impact of these effects on the beam dynamics. This includes the space-charge dominated beam dynamics in the RF gun as well as the collective effects dominated by the wake fields after the gun up to the end of the injector section. A new analytical model is also proposed for the short-range wake function of a finite chain of RF cavities and verified by both numerical analysis and experimental results. It is shown that the physical models used in the simulation of the beam dynamics after the gun allow to reduce the absolute error in the modeling of the correlated energy chirp by order of magnitude in comparison with the case when the collective effects after the gun are neglected.

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

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.

The 1-Megapixel pnCCD detector for the Small Quantum Systems Instrument at the European XFEL: system and operation aspects.

The X-ray free-electron lasers that became available during the last decade, like the European XFEL (EuXFEL), place high demands on their instrumentation. Especially at low photon energies below 1 keV, detectors with high sensitivity, and consequently low noise and high quantum efficiency, are required to enable facility users to fully exploit the scientific potential of the photon source. A 1-Megapixel pnCCD detector with a 1024 × 1024 pixel format has been installed and commissioned for imaging applications at the Nano-Sized Quantum System (NQS) station of the Small Quantum System (SQS) instrument at EuXFEL. The instrument is currently operating in the energy range between 0.5 and 3 keV and the NQS station is designed for investigations of the interaction of intense FEL pulses with clusters, nano-particles and small bio-molecules, by combining photo-ion and photo-electron spectroscopy with coherent diffraction imaging techniques. The core of the imaging detector is a pn-type charge coupled device (pnCCD) with a pixel pitch of 75 µm × 75 µm. Depending on the experimental scenario, the pnCCD enables imaging of single photons thanks to its very low electronic noise of 3 e- and high quantum efficiency. Here an overview on the EuXFEL pnCCD detector and the results from the commissioning and first user operation at the SQS experiment in June 2019 are presented. The detailed descriptions of the detector design and capabilities, its implementation at EuXFEL both mechanically and from the controls side as well as important data correction steps aim to provide useful background for users planning and analyzing experiments at EuXFEL and may serve as a benchmark for comparing and planning future endstations at other FELs.

Advances in Nb3Sn superconducting radiofrequency cavities towards first practical accelerator applications

Nb3Sn is a promising next-generation material for superconducting radiofrequency cavities, with significant potential for both large scale and compact accelerator applications. However, so far, Nb3Sn cavities have been limited to continuous wave accelerating fields <18 MV m−1. In this paper, new results are presented with significantly higher fields, as high as 24 MV m−1 in single cell cavities. Results are also presented from the first ever Nb3Sn-coated 1.3 GHz 9-cell cavity, a full-scale demonstration on the cavity type used in production for the European XFEL and LCLS-II. Results are presented together with heat dissipation curves to emphasize the potential for industrial accelerator applications using cryocooler-based cooling systems. The cavities studied have an atypical shiny visual appearance, and microscopy studies of witness samples reveal significantly reduced surface roughness and smaller film thickness compared to typical Nb3Sn films for superconducting cavities. Possible mechanisms for increased maximum field are discussed as well as implications for physics of RF superconductivity in the low coherence length regime. Outlook for continued development is presented.

ReLaX: the Helmholtz International Beamline for Extreme Fields high-intensity short-pulse laser driver for relativistic laser–matter interaction and strong-field science using the high energy density instrument at the European X-ray free electron laser facility

AbstractHigh-energy and high-intensity lasers are essential for pushing the boundaries of science. Their development has allowed leaps forward in basic research areas, including laser–plasma interaction, high-energy density science, metrology, biology and medical technology. The Helmholtz International Beamline for Extreme Fields user consortium contributes and operates two high-peak-power optical lasers using the high energy density instrument at the European X-ray free electron laser (EuXFEL) facility. These lasers will be used to generate transient extreme states of density and temperature to be probed by the X-ray beam. This paper introduces the ReLaX laser, a short-pulse high-intensity Ti:Sa laser system, and discusses its characteristics as available for user experiments. It will also present the first experimental commissioning results validating its successful integration into the EuXFEL infrastructure and viability as a relativistic-intensity laser driver.

High-resolution inelastic x-ray scattering at the high energy density scientific instrument at the European X-Ray Free-Electron Laser.

We introduce a setup to measure high-resolution inelastic x-ray scattering at the High Energy Density scientific instrument at the European X-Ray Free-Electron Laser (XFEL). The setup uses the Si (533) reflection in a channel-cut monochromator and three spherical diced analyzer crystals in near-backscattering geometry to reach a high spectral resolution. An energy resolution of 44 meV is demonstrated for the experimental setup, close to the theoretically achievable minimum resolution. The analyzer crystals and detector are mounted on a curved-rail system, allowing quick and reliable changes in scattering angle without breaking vacuum. The entire setup is designed for operation at 10 Hz, the same repetition rate as the high-power lasers available at the instrument and the fundamental repetition rate of the European XFEL. Among other measurements, it is envisioned that this setup will allow studies of the dynamics of highly transient laser generated states of matter.

Impact of real mirror profiles inside a split-and-delay unit on the spatial intensity profile in pump/probe experiments at the European XFEL.

For the High-Energy-Density (HED) beamline at the SASE2 undulator of theEuropean XFEL, a hard X-ray split-and-delay unit (SDU) has been built enabling time-resolved pump/probe experiments with photon energies between 5 keV and 24 keV. The optical layout of the SDU is based on geometrical wavefront splitting and multilayer Bragg mirrors. Maximum delays between Δτ= ±1 ps at 24 keV and Δτ = ±23 ps at 5 keV will be possible. Time-dependent wavefront propagation simulations were performed by means of theSynchrotron Radiation Workshop (SRW) software in order to investigate theimpact of the optical layout, including diffraction on the beam splitter and recombiner edges and the three-dimensional topography of all eight mirrors, on the spatio-temporal properties of the XFEL pulses. The radiation is generated from noise by the code FAST which simulates the self-amplified spontaneous emission (SASE) process. A fast Fourier transformation evaluation of the disturbed interference pattern yields for ideal mirror surfaces a coherence time of τc = 0.23 fs and deduces one of τc = 0.21 fs for the real mirrors, thus with an error of Δτ = 0.02 fs which is smaller than the deviation resulting from shot-to-shot fluctuations of SASE2 pulses. The wavefronts are focused by means of compound refractive lenses in order to achieve fluences of a few hundred mJ mm-2 within a spot width of 20 µm (FWHM) diameter. Coherence effects and optics imperfections increase the peak intensity between 200 and 400% for pulse delays within the coherence time. Additionally, the influence of two off-set mirrors in the HED beamline are discussed. Further, we show the fluence distribution for Δz = ±3 mm around the focal spot along the optical axis. The simulations show that the topographies of the mirrors of the SDU are good enough to support X-ray pump/X-ray probe experiments.