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Software Platform for European XFEL: Towards Online Experimental Data Analysis
摘要： Large amount of data being generated at large scale facilities like European X-ray Free-Electron Laser (XFEL) requires new approaches for data processing and analysis. One of the most computationally challenging experiments at an XFEL is single-particle structure determination. In this paper we propose a new design for an integrated software platform which combines well-established techniques for XFEL data analysis with High Performance Data Analysis (HPDA) methods. In our software platform we use streaming data analysis algorithms with high performance computing solutions. This approach should allow analysis of the experimental dataflow in quasi-online regime.
关键词： single particle imaging,X-ray Free-Electron Laser,High Performance Data Analysis,X-ray Cross-Correlation Analysis,Expectation-Maximization
更新于2025-09-23 15:22:29
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Possibilities for serial femtosecond crystallography sample delivery at future light sourcesa)
摘要： Serial femtosecond crystallography (SFX) uses X-ray pulses from free-electron laser (FEL) sources that can outrun radiation damage and thereby overcome long-standing limits in the structure determination of macromolecular crystals. Intense X-ray FEL pulses of sufficiently short duration allow the collection of damage-free data at room temperature and give the opportunity to study irreversible time-resolved events. SFX may open the way to determine the structure of biological molecules that fail to crystallize readily into large well-diffracting crystals. Taking advantage of FELs with high pulse repetition rates could lead to short measurement times of just minutes. Automated delivery of sample suspensions for SFX experiments could potentially give rise to a much higher rate of obtaining complete measurements than at today’s third generation synchrotron radiation facilities, as no crystal alignment or complex robotic motions are required. This capability will also open up extensive time-resolved structural studies. New challenges arise from the resulting high rate of data collection, and in providing reliable sample delivery. Various developments for fully automated high-throughput SFX experiments are being considered for evaluation, including new implementations for a reliable yet flexible sample environment setup. Here, we review the different methods developed so far that best achieve sample delivery for X-ray FEL experiments and present some considerations towards the goal of high-throughput structure determination with X-ray FELs.
关键词： automation,serial femtosecond crystallography,X-ray free-electron laser,sample delivery,high-throughput
更新于2025-09-23 15:22:29
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Maximizing magnetic field generation in high power laser–solid interactions
摘要： In order to understand the transport of fast electrons within solid density targets driven by an optical high power laser, we have numerically investigated the dynamics and structure of strong self-generated magnetic fields in such experiments. Here we present a systematic study of the bulk magnetic field generation due to the ponderomotive current, Weibel-like instability and resistivity gradient between two solid layers. Using particle-in-cell simulations, we observe the effect of varying the laser and target parameters, including laser intensity, focal size, incident angle, preplasma scale length, target thickness and material and experimental geometry. The simulation results suggest that the strongest magnetic field is generated with laser incident angles and preplasma scale lengths that maximize laser absorption efficiency. The recent commissioning of experimental platforms equipped with both optical high power laser and X-ray free electron laser (XFEL), such as European XFEL-HED, LCLS-MEC and SACLA beamlines, provides unprecedented opportunities to probe the self-generated bulk magnetic field by X-ray polarimetry via Faraday rotation with simultaneous high spatial and temporal resolution. We expect that this systematic numerical investigation will pave the way to design and optimize near future experimental setups to probe the magnetic fields in such experimental platforms.
关键词： laser–plasmas interaction,X-ray free electron laser probing,high energy density physics
更新于2025-09-19 17:13:59
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An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser
摘要： Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.
关键词： oxygen-oxygen coupling,photosystem II,x-ray free-electron laser,water oxidation,oxyl/oxo mechanism
更新于2025-09-19 17:13:59
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Reconstruction of 3D structure for nanoscale biological objects from experiments data on super-bright X-ray free electron lasers (XFELs): dependence of the 3D resolution on the experiment parameters
摘要： The ability to investigate 3D structure of biomolecules, such as proteins and viruses, is essential in biology and medicine. With the invention of super-bright X-ray free electron lasers (e.g. European XFEL and Linac Coherent Light Source (LCLS)) the Single Particle Imaging (SPI) approach allows to reconstruct 3D structures from many 2D diffraction images produced in the experiment by X-rays scattered on the biomolecule exposed in different orientations. In the same time, there are still many challenging problems in experiment setup, sample preparation and injection, which limit number and quality of obtained diffraction patterns and, consequently, limit achievable resolution of recovered 3D structure. However even with the current experimental limitations it is possible to reconstruct 3D structures of some large biomolecules. An important question arises: what range of 3D resolution is possible to achieve under experimental conditions available now. We investigated how the number and quality of diffraction images affect the 3D resolution. First the SPI experiment was simulated and reconstructed with the Dragonfly software. Then we analyzed how the number of diffraction images and the beam intensity affect the final 3D resolution. We come to the following conclusions: 1) starting from the beam intensity value (fluence) equal to 3×1012 photons/μm2 the resolution becomes to be almost constant; 2) the resolution strongly depends on the number of diffraction patterns. More than 10 000 diffraction images are required to get 4 nm resolution.
关键词： Single Particle Imaging,Three-dimensional Reconstruction,X-ray Free Electron Laser,space resolution
更新于2025-09-19 17:13:59
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Virus Structures by X-Ray Free-Electron Lasers
摘要： Until recently X-ray crystallography has been the standard technique for virus structure determinations. Available X-ray sources have continuously improved over the decades, leading to the realization of X-ray free-electron lasers (XFELs). They provide high-intensity femtosecond X-ray pulses, which allow for new kinds of experiments by making use of the diffraction-before-destruction principle. By overcoming classical dose constraints, they at least in principle allow researchers to perform X-ray virus structure determination for single particles at room temperature. Simultaneously, the availability of XFELs led to the development of the method of serial femtosecond crystallography, where a crystal structure is determined from the measurement of hundreds to thousands of microcrystals. In the case of virus crystallography this method does not require freezing of the crystals and allows researchers to perform experiments under non-equilibrium conditions (e.g., by laser-induced temperature jumps or rapid chemical mixing), which is currently not possible with electron microscopy.
关键词： structure determination,serial crystallography,XFEL,single particle imaging,virus crystallography,X-ray free-electron laser
更新于2025-09-16 10:30:52
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A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser
摘要： The hydroxymethylation of cytosine bases plays a vital role in the phage DNA protection system inside the host Escherichia coli. This modification is known to be catalyzed by the dCMP hydroxymethylase from bacteriophage T4 (T4dCH); structural information on the complexes with the substrate, dCMP and the co-factor, tetrahydrofolate is currently available. However, the detailed mechanism has not been understood clearly owing to a lack of structure in the complex with a reaction intermediate. We have applied the X-ray free electron laser (XFEL) technique to determine a high-resolution structure of a T4dCH D179N active site mutant. The XFEL structure was determined at room temperature and exhibited several unique features in comparison with previously determined structures. Unexpectedly, we observed a bulky electron density at the active site of the mutant that originated from the physiological host (i.e., E. coli). Mass-spectrometric analysis and a cautious interpretation of an electron density map indicated that it was a dTMP molecule. The bound dTMP mimicked the methylene intermediate from dCMP to 5′-hydroxymethy-dCMP, and a critical water molecule for the final hydroxylation was convincingly identified. Therefore, this study provides information that contributes to the understanding of hydroxymethylation.
关键词： hydroxymethylation,XFEL,dCMP hydroxymethylase,X-ray free electron laser,T4dCH,hydroxylation,cytosine bases,phage DNA protection,dTMP,Escherichia coli,bacteriophage T4,methylene intermediate
更新于2025-09-12 10:27:22
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Stripline beam position monitor for X-ray free electron laser of Pohang Accelerator Laboratory
摘要： Beam position monitors (BPMs) are important instruments even in the case of an X-ray free-electron laser (XFEL). Pohang Accelerator Laboratory (PAL) finished the construction of an XFEL (PAL-XFEL) in 2015, and new stripline BPMs were installed in PAL-XFEL. New BPMs were designed to have a strong signal and a high resolution. In addition, the impedance matching was considered to reduce a signal reflection. These features of the BPM design were confirmed with a simulation study as well. Fabricated BPMs were tested by using a wire test stand. Two-dimensional position errors and offsets were measured to select best BPMs for PAL-XFEL. Finally, a real beam test was tried to check the BPM performance and a better resolution than the requirement was obtained.
关键词： stripline BPM,X-ray free-electron laser,Beam position monitors,impedance matching,PAL-XFEL
更新于2025-09-11 14:15:04