Publications for FEL

The collapse of a sonoluminescent cavitation bubble imaged with X-ray free-electron laser pulses

Single bubble sonoluminescence (SBSL) is the phenomenon of synchronous light emission due to the violent collapse of a single spherical bubble in a liquid, driven by an ultrasonic field. During the bubble collapse, matter inside the bubble reaches extreme conditions of several gigapascals and temperatures on the order of 10000 K, leading to picosecond flashes of visible light. To this day, details regarding the energy focusing mechanism rely on simulations due to the fast dynamics of the bubble collapse and spatial scales below the optical resolution limit. In this work we present phase-contrast holographic imaging with single x-ray free-electron laser (XFEL) pulses of a SBSL cavitation bubble in water. X-rays probe the electron density structure and by that provide a uniquely new view on the bubble interior and its collapse dynamics. The involved fast time-scales are accessed by sub-100 fs XFEL pulses and a custom synchronization scheme for the bubble oscillator. We find that during the whole oscillation cycle the bubble’s density profile can be well described by a simple step-like structure, with the radius R following the dynamics of the Gilmore model. The quantitatively measured internal density and width of the boundary layer exhibit a large variance. Smallest reconstructed bubble sizes reach down to R ≃ 0.8 μ, and are consistent with spherical symmetry. While we here achieved a spatial resolution of a few 100 nm, the visibility of the bubble and its internal structure is limited by the total x-ray phase shift which can be scaled with experimental parameters.

Keywords: FEL Photon science Imaging

The low-barrier methyl internal rotation in the rotational spectrum of 3-methylphenylacetylene

The rotational spectrum of 3-methylphenylacetylene has been recorded in the 2–8 GHz region using a chirped-pulse broadband microwave spectrometer. Torsion-rotation transition splittings are observed from a tunneling motion along the methyl internal rotation axis. The XIAM program was used to characterize the splitting, yielding an internal rotation barrier, , of cm−1. While this barrier is considered low, fits of A-state only transitions yield a quality, rigid-rotor fit, and are compared to the combined A/E fits. Computationally predicted barriers are estimated between 14.4 and 28.9 cm−1.

Keywords: Photon science

Exploring key ionic interactions for magnesium degradation in simulated body fluid

We have studied the degradation of pure magnesium wire in simulated body fluid and its subsets under physiological conditions to enable the prediction of the degradation rate based on the medium's ionic composition. To this end, micro-computed tomography and scanning electron microscopy with energy-dispersive X-ray spectroscopy were used, followed by a tree regression analysis. A non-linear relationship was found between degradation rate and the precipitation of calcium salts. The mean absolute error for predicting the degradation rate was 1.35 mm/yr. This comparatively high value indicates that ionic interactions were exceedingly complex or that an unknown parameter determining the degradation may exist.

Keywords: Photon Science Materials

The New SARS-CoV-2 Strain Shows a Stronger Binding Affinity to ACE2 Due to N501Y Mutation

SARS-CoV-2 is a global challenge due to its ability to spread much faster than SARS-CoV, which was attributed to the mutations in the receptor binding domain (RBD). These mutations enhanced the electrostatic interactions. Recently, a new strain was reported in the UK that includes a mutation (N501Y) in the RBD, that possibly increases the infection rate. Using Molecular Dynamics simulations (MD) and Monte Carlo (MC) sampling, we showed that the N501 mutation enhances the electrostatic interactions due to the formation of a strong hydrogen bond between SARS-CoV-2-T500 and ACE2-D355 near the mutation site. In addition, we observed that the electrostatic interactions between the SARS-CoV-2 and ACE2 in the wild type and the mutant are dominated by salt-bridges formed between SARS-CoV-2-K417 and ACE2-D30, SARS-CoV-2-K458, ACE2-E23, and SARS-CoV-2-R403 and ACE2-E37. These interactions contributed more than 40 % of the total binding energies.

Keywords: Photon Science Structural Biology

Inhibition of SARS-CoV-2 main protease by allosteric drug-binding

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous health problems and economical challenges for mankind. To date, no effective drug is available to directly treat the disease and prevent virus spreading. In a search for a drug against COVID-19, we have performed a massive X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for the virus replication and, thus, a potent drug target. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds binding to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and five non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.

Keywords: Photon Science Structural Biology

Detailed imaging of the three-dimensionally complex architecture of xylary plants is important for studying biological and mechanical functions of woody plants. Apart from common two-dimensional microscopy, X-ray micro-computed tomography has been established as a three-dimensional (3D) imaging method for studying the hydraulic function of wooden plants. However, this X-ray imaging method can barely reach the resolution needed to see the minute structures (e.g. pit membrane). To complement the xylem structure with 3D views at the nanoscale level, X-ray near-field nano-holotomography (NFH) was applied to analyze the wood species Pinus sylvestris and Fagus sylvatica. The demanded small specimens required focused ion beam (FIB) application. The FIB milling, however, influenced the image quality through gallium implantation on the cell-wall surfaces. The measurements indicated that NFH is appropriate for imaging wood at nanometric resolution. With a 26 nm voxel pitch, the structure of the cell-wall surface in Pinus sylvestris could be visualized in genuine detail. In wood of Fagus sylvatica, the structure of a pit pair, including the pit membrane, between two neighboring fibrous cells could be traced tomographically.

Keywords: Photon Science Imaging Tomography

Scalable spectral solver in Galilean coordinates for eliminating the numerical Cherenkov instability in particle-in-cell simulations of streaming plasmas

Discretizing Maxwell's equations in Galilean (comoving) coordinates allows the derivation of a pseudospectral solver that eliminates the numerical Cherenkov instability for electromagnetic particle-in-cell simulations of relativistic plasmas flowing at a uniform velocity. Here we generalize this solver by incorporating spatial derivatives of arbitrary order, thereby enabling efficient parallelization by domain decomposition. This allows scaling of the algorithm to many distributed compute units. We derive the numerical dispersion relation of the algorithm and present a comprehensive theoretical stability analysis. The method is applied to simulations of plasma acceleration in a Lorentz-boosted frame of reference.

Keywords: Plasma Physics Simulations

Optimization and stability of a high-gain harmonic generation seeded oscillator amplifier

The free-electron laser (FEL) community is interested in taking full advantage of the high-repetition-rates of FELs run by superconducting machines while maintaining the spectral properties achieved with external seeding techniques. Since the feasibility of seed lasers operating at a repetition-rate of MHz and with sufficient energy in a useful wavelength range, such as the ultraviolet (UV) range is challenging, a seeded oscillator-amplifier scheme is proposed instead for generation of fully coherent and high-repetition-rate radiation. The process is triggered by an external seed laser while an optical feedback system feeds the radiation back to the entrance of the modulator where it overlaps with the next electron bunch. Downstream from the feedback system, the electron bunches are then used for harmonic generation. We discuss the optimization of dedicated simulations and we investigate the stability of this scheme with numerical simulations. As a result, we address the control of the reflectivity of the resonator as a key parameter to achieve a stable HGHG seeded radiation. Finally, we show the impact of the power fluctuations in the oscillator on the bunching amplitude with analytical and simulated results. The output FEL radiation wavelengths considered are 4.167 nm and 60 nm.

Keywords: FEL

Reinforcement learning-trained optimisers and Bayesian optimisation for online particle accelerator tuning

Online tuning of particle accelerators is a complex optimisation problem that continues to require manual intervention by experienced human operators. Autonomous tuning is a rapidly expanding field of research, where learning-based methods like Bayesian optimisation (BO) hold great promise in improving plant performance and reducing tuning times. At the same time, reinforcement learning (RL) is a capable method of learning intelligent controllers, and recent work shows that RL can also be used to train domain-specialised optimisers in so-called reinforcement learning-trained optimisation (RLO). In parallel efforts, both algorithms have found successful adoption in particle accelerator tuning. Here we present a comparative case study, assessing the performance of both algorithms while providing a nuanced analysis of the merits and the practical challenges involved in deploying them to real-world facilities. Our results will help practitioners choose a suitable learning-based tuning algorithm for their tuning tasks, accelerating the adoption of autonomous tuning algorithms, ultimately improving the availability of particle accelerators and pushing their operational limits.

Keywords: Ai Accelerator Bayesian optimisation Reinforcement learning

Active learning of potential-energy surfaces of weakly-bound complexes with regression-tree ensembles

Several pool-based active learning algorithms were employed to model potential energy surfaces (PESs) with a minimum number of electronic structure calculations. Among these algorithms, the class of uncertainty-based algorithms are popular. Their key principle is to query molecular structures corresponding to high uncertainties in their predictions. We empirically show that this strategy is not optimal for nonuniform data distributions as it collects many structures from sparsely sampled regions, which are less important to applications of the PES. We exploit a simple stochastic algorithm to correct for this behavior and implement it using regression trees, which have relatively small computational costs. We show that this algorithm requires around half the data to converge to the same accuracy than the uncertainty-based algorithm query-by-committee. Simulations on a 6D PES of pyrrole(H2O) show that <15000 configurations are enough to build a PES with a generalization error of 16 cm−1, whereas the final model with around 50000 configurations has a generalization error of 11 cm−1.

Keywords: Artificial Intelligence

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

Keywords: Photon Science Structural Biology

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

he coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.

Keywords: Photon Science Structural Biology

Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation

Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.

Keywords: Structural Biology Electron Microscopy

Upscaling of multi-beam x-ray ptychography for efficient x-ray microscopy with high resolution and large field of view

Nondestructive imaging with both a large field of view and a high spatial resolution is crucial to understand complex materials and processes in science and technology. X-ray ptychography can provide highest spatial resolution but is limited in the field of view by the acquisition time and coherent flux at modern x-ray sources. By multi-beam ptychography, the sample can be imaged in parallel by several spatially separated and mutually incoherent beams. We have implemented this method using 3D nanoprinted x-ray optics to create tailor-made x-ray multi-beam arrays. The use of 3D printing allows us to create focusing optics with a minimum of nonfunctional support structures. In this way, large sample areas can be efficiently scanned in parallel with up to six illuminating beams.

Keywords: Photon Science Ptychography

Structure and dynamics of a mycobacterial type VII secretion system

Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year(1). Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope(2,3). Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP(5) protease. A trimer of MycP(5) caps a central periplasmic dome-like chamber that is formed by three EccB(5) dimers, with the proteolytic sites of MycP(5) facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP(5) show disruption of the EccB(5) periplasmic assembly and increased flexibility, which highlights the importance of MycP(5) for complex integrity. Beneath the EccB(5)-MycP(5) chamber, dimers of the EccC(5) ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC(5) domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen.

Keywords: Structural Biology Electron Microscopy

Interactive analysis notebooks on DESY batch resources

Batch scheduling systems are usually designed to maximise fair resource utilisation and efficiency, but are less well designed for demanding interactive processing, which requires fast access to resources while low upstart latency is only of secondary significance for high throughput of high performance computing scheduling systems. The computing clusters at DESY are intended as batch systems for end users to run massive analysis and simulation jobs enabling fast turnaround systems, in particular when processing is expected to feed back to operation of instruments in near real-time. The continuously increasing popularity of Jupyter Notebooks for interactive and online processing made an integration of this technology into the DESY batch systems indispensable. We present here our approach to utilise the HTCondor and SLURM backends to integrate Jupyter Notebook servers and the techniques involved to provide fast access. The chosen approach offers a smooth user experience allowing users to customize resource allocation tailored to their computational requirements. In addition, we outline the differences between the HPC and the HTC implementations and give an overview of the experience of running Jupyter Notebook services.

Keywords: Information Technology

Pump-probe X-ray holographic imaging of laser-induced cavitation bubbles with femtosecond FEL pulses

Cavitation bubbles can be seeded from a plasma following optical breakdown, by focusing an intense laser in water. The fast dynamics are associated with extreme states of gas and liquid, especially in the nascent state. This offers a unique setting to probe water and water vapor far-from equilibrium. However, current optical techniques cannot quantify these early states due to contrast and resolution limitations. X-ray holography with single X-ray free-electron laser pulses has now enabled a quasi-instantaneous high resolution structural probe with contrast proportional to the electron density of the object. In this work, we demonstrate cone-beam holographic flash imaging of laser-induced cavitation bubbles in water with nanofocused X-ray free-electron laser pulses. We quantify the spatial and temporal pressure distribution of the shockwave surrounding the expanding cavitation bubble at time delays shortly after seeding and compare the results to numerical simulations.

Keywords: FEL Imaging

3-D X-ray Nanotomography Reveals Different Carbon Deposition Mechanisms in a Single Catalyst Particle

Catalyst deactivation involves a complex interplay of processes taking place at different length and time scales. Understanding this phenomenon is one of the grand challenges in solid catalyst characterization. A process contributing to deactivation is carbon deposition (i. e., coking), which reduces catalyst activity by limiting diffusion and blocking active sites. However, characterizing coke formation and its effects remains challenging as it involves both the organic and inorganic phase of the catalytic process and length scales from the atomic scale to the scale of the catalyst body. Here we present a combination of hard X-ray imaging techniques able to visualize in 3-D the distribution, effect and nature of carbon deposits in the macro-pore space of an entire industrially used catalyst particle. Our findings provide direct evidence for coke promoting effects of metal poisons, pore clogging by coke, and a correlation between carbon nature and its location. These results provide a better understanding of the coking process, its relation to catalyst deactivation and new insights into the efficiency of the industrial scale process of fluid catalytic cracking.

Keywords: Photon Science Tomography Materials

Heterogeneity in the Fragmentation of Ziegler Catalyst Particles during Ethylene Polymerization Quantified by X-ray Nanotomography

Ziegler-type catalysts are the grand old workhorse of the polyolefin industry, yet their hierarchically complex nature complicates polymerization activity–catalyst structure relationships. In this work, the degree of catalyst framework fragmentation of a high-density polyethylene (HDPE) Ziegler-type catalyst was studied using ptychography X-ray-computed nanotomography (PXCT) in the early stages of ethylene polymerization under mild reaction conditions. An ensemble consisting of 434 fully reconstructed ethylene prepolymerized Ziegler catalyst particles prepared at a polymer yield of 3.4 g HDPE/g catalyst was imaged. This enabled a statistical route to study the heterogeneity in the degree of particle fragmentation and therefore local polymerization activity at an achieved 3-D spatial resolution of 74 nm without requiring invasive imaging tools. To study the degree of catalyst fragmentation within the ensemble, a fragmentation parameter was constructed based on a k-means clustering algorithm that relates the quantity of polyethylene formed to the average size of the spatially resolved catalyst fragments. With this classification method, we have identified particles that exhibit weak, moderate, and strong degrees of catalyst fragmentation, showing that there is a strong heterogeneity in the overall catalyst particle fragmentation and thus polymerization activity within the entire ensemble. This hints toward local mass transfer limitations or other deactivation phenomena. The methodology used here can be applied to all polyolefin catalysts, including metallocene and the Phillips catalysts to gain statistically relevant fundamental insights in the fragmentation behavior of an ensemble of catalyst particles.

Keywords: Photon Science Tomography Materials

Helical reconstruction of Salmonella and Shigella needle filaments attached to type 3 basal bodies

Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development.

Keywords: Structural Biology Electron Microscopy

Scaling the U-net: segmentation of biodegradable bone implants in high-resolution synchrotron radiation microtomograms

Highly accurate segmentation of large 3D volumes is a demanding task. Challenging applications like the segmentation of synchrotron radiation microtomograms (SRμCT) at high-resolution, which suffer from low contrast, high spatial variability and measurement artifacts, readily exceed the capacities of conventional segmentation methods, including the manual segmentation by human experts. The quantitative characterization of the osseointegration and spatio-temporal biodegradation process of bone implants requires reliable, and very precise segmentation. We investigated the scaling of 2D U-net for high resolution grayscale volumes by three crucial model hyper-parameters (i.e., the model width, depth, and input size). To leverage the 3D information of high-resolution SRμCT, common three axes prediction fusing is extended, investigating the effect of adding more than three axes prediction. In a systematic evaluation we compare the performance of scaling the U-net by intersection over union (IoU) and quantitative measurements of osseointegration and degradation parameters. Overall, we observe that a compound scaling of the U-net and multi-axes prediction fusing with soft voting yields the highest IoU for the class “degradation layer”. Finally, the quantitative analysis showed that the parameters calculated with model segmentation deviated less from the high quality results than those obtained by a semi-automatic segmentation method.

Keywords: Photon Science Tomography Materials Artificial Intelligence

Recovery time of a plasma-wakefield accelerator

The interaction of intense particle bunches with plasma can give rise to plasma wakes1,2 capable of sustaining gigavolt-per-metre electric fields3,4, which are orders of magnitude higher than provided by state-of-the-art radio-frequency technology5. Plasma wakefields can, therefore, strongly accelerate charged particles and offer the opportunity to reach higher particle energies with smaller and hence more widely available accelerator facilities. However, the luminosity and brilliance demands of high-energy physics and photon science require particle bunches to be accelerated at repetition rates of thousands or even millions per second, which are orders of magnitude higher than demonstrated with plasma-wakefield technology6,7. Here we investigate the upper limit on repetition rates of beam-driven plasma accelerators by measuring the time it takes for the plasma to recover to its initial state after perturbation by a wakefield. The many-nanosecond-level recovery time measured establishes the in-principle attainability of megahertz rates of acceleration in plasmas. The experimental signatures of the perturbation are well described by simulations of a temporally evolving parabolic ion channel, transferring energy from the collapsing wake to the surrounding media. This result establishes that plasma-wakefield modules could be developed as feasible high-repetition-rate energy boosters at current and future particle-physics and photon-science facilities.

Keywords: Accelerator Plasma Physics

Optical Funnel to Guide and Focus Virus Particles for X-Ray Diffractive Imaging

Photophoretic forces are induced when light causes a net momentum exchange between a particle and a surrounding gas. Such forces have been shown to be a robust means for trapping and guiding particles in air over long distances. Here, we apply the concept of an optical funnel for the delivery of bioparticles to the focus of an x-ray free-electron laser (XFEL) for femtosecond x-ray diffractive imaging. We provide the experimental demonstration of transversely compressing a high-speed beam of aerosolized viruses via photophoretic forces in a low-pressure gas environment. Relative temperature gradients induced on the viruses by the laser are estimated via particle-velocimetry measurements. The results demonstrate the potential for an optical funnel to improve particle-delivery efficiency in XFEL imaging and spectroscopy.

Keywords: Photon Science Imaging FEL Structural Biology

Illuminating Rembrandts Chiaroscuro in The Night Watch: the painting process of Van Ruytenburchs costume

This study examines Rembrandt’s use of chiaroscuro to depict the costume of Lieutenant Willem Van Ruytenburch, a prominently lit figure in The Night Watch (1642). As part of Operation Night Watch, the painting was analyzed using noninvasive imaging techniques, including reflectance imaging spectroscopy (RIS), macroscopic X-ray powder diffraction (MA-XRPD), and macroscopic X-ray fluorescence (MA-XRF). These methods enabled the mapping of the artist’s pigment palette, which includes lead white, lead-tin yellow, ochres, vermilion, arsenic sulfide pigments, red lakes, smalt, and azurite. Rembrandt applied these pigments in a consistent, systematic way, combining them in groups to achieve pictorial unity. Notably, arsenic-based pigments were used to capture the warm reflections of gold threads, unique to Van Ruytenburch’s costume. MA-XRPD also identified degradation products—mimetite, weddellite, and palmierite—associated with the original pigments. These results provide new insights into Rembrandt’s modus operandi and inform understanding of the current condition and implications for its conservation.

Keywords: Humanities Photon Science

Real-time swelling-collapse kinetics of nanogels driven by XFEL pulses

Stimuli-responsive polymers are an important class of materials with many applications in nanotechnology and drug delivery. The most prominent one is poly- N -isopropylacrylamide (PNIPAm). The characterization of the kinetics of its change after a temperature jump is still a lively research topic, especially at nanometer-length scales where it is not possible to rely on conventional microscopic techniques. Here, we measured in real time the collapse of a PNIPAm shell on silica nanoparticles with megahertz x-ray photon correlation spectroscopy at the European XFEL. We characterize the changes of the particles diffusion constant as a function of time and consequently local temperature on sub-microsecond timescales. We developed a phenomenological model to describe the observed data and extract the characteristic times associated to the swelling and collapse processes. Different from previous studies tracking the turbidity of PNIPAm dispersions and using laser heating, we find collapse times below microsecond timescales and two to three orders of magnitude slower swelling times.

Keywords: FEL Materials

Rapid aberration correction for diffractive X-ray optics by additive manufacturing

Photophoretic forces are induced when light causes a net momentum exchange between a particle and a surrounding gas. Such forces have been shown to be a robust means for trapping and guiding particles in air over long distances. Here, we apply the concept of an optical funnel for the delivery of bioparticles to the focus of an x-ray free-electron laser (XFEL) for femtosecond x-ray diffractive imaging. We provide the experimental demonstration of transversely compressing a high-speed beam of aerosolized viruses via photophoretic forces in a low-pressure gas environment. Relative temperature gradients induced on the viruses by the laser are estimated via particle-velocimetry measurements. The results demonstrate the potential for an optical funnel to improve particle-delivery efficiency in XFEL imaging and spectroscopy.

Keywords: Photon Science FEL

Genomic-Phenomic Reciprocal Illumination: Desyopone hereon gen. et sp. nov., an Exceptional Aneuretine-like Fossil Ant from Ethiopian Amber

Fossils are critical for understanding the evolutionary diversification, turnover, and morphological disparification of extant lineages. While fossils cannot be sequenced, phenome-scale data may be generated using micro-computed tomography (μ-CT), thus revealing hidden structures andinternal anatomy, when preserved. Here, we adduce the male caste of a new fossil ant species from Miocene Ethiopian amber that resembles members of the Aneuretinae, matching the operational definition of the subfamily. Through the use of synchrotron radiation for μ-CT, we critically test the aneuretine-identity hypothesis. Our results indicate that the new fossils do not belong to the Aneuretinae, but rather the Ponerini (Ponerinae). Informed by recent phylogenomic studies, we were able to place the fossils close to the extant genus Cryptopone based on logical character analysis, with the two uniquely sharing absence of the subpetiolar process among all ponerine genera. Consequently, we: (1) revise the male-based key to the global ant subfamilies; (2) revise the definitions of Aneuretinae, Ponerinae, Platythyreini, and Ponerini; (3) discuss the evolution of ant mandibles; and (4) describe the fossils as †Desyopone hereon gen. et sp. nov. Our study highlights the value of malesfor ant systematics and the tremendous potential of phenomic imaging technologies for the study of ant evolution

Keywords: Photon Science Tomography Imaging

Speckle contrast of interfering fluorescence X-rays

With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity–intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to measure the size of a focusedX-ray beam, for example. Here it is shown that it is also possible to observe the interference of fluorescence photons through the measurement of the speckle contrast of angle-resolved fluorescence patterns. Speckle contrast is often used as a measure of the degree of coherence of the incident beam or the fluctuations of the illuminated sample as determined from X-ray diffraction patterns formed by elastic scattering, rather than from fluorescence patterns as addressed here. Commonly used approaches to estimate speckle contrast were found to suffer when applied to XFEL-generated fluorescence patterns due to low photon counts and a significant variation of the excitation pulse energy from shot to shot. A new method to reliably estimate speckle contrast under such conditions, using a weighting scheme, is introduced. The method is demonstrated by comparing the speckle contrast of fluorescence observed with pulses of 3 fs to 15 fs duration.

Keywords: Photon Science

Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water

Interactions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the chromophores, potential radiation damage, and their dependence on solvation are important open questions. The microsolvation effect is challenging to study due to the inherent mix of the produced gas-phase aggregates. We use the electrostatic deflector to spatially separate different molecular species in combination with pump-probe velocity-map-imaging experiments. We demonstrate that this powerful experimental approach reveals intimate details of the UV-induced dynamics in the near-UV-absorbing prototypical biomolecular indole-water system. We determine the time-dependent appearance of the different reaction products and disentangle the occurring ultrafast processes. This approach ensures that the reactants are well-known and that detailed characteristics of the specific reaction products are accessible – paving the way for the complete chemical-reactivity experiment.

Keywords: Photon Science Materials

Using SXRF and LA-ICP-TOFMS to Explore Evidence of Treatment and Physiological Responses to Leprosy in Medieval Denmark

Leprosy, a chronic infectious disease, leads to blood mineral imbalances: low levels of zinc, calcium, magnesium, and iron and high levels of copper. Interestingly, in late medieval Europe, minerals were used to treat leprosy. We investigated physiological responses to leprosy and possible evidence of treatment in dental tissues of leprosy sufferers from medieval Denmark and early 20th century Romania when multidrug therapy was not then yet invented. Using Synchrotron Fluorescence (SXRF) and laser ablation (LA-ICP-TOFMS), we show marked covariations in the zinc, calcium, and magnesium distributions, which are compatible with clinical studies but cannot be directly attributed to leprosy. Minerals used historically as a treatment for leprosy show no detectable intake (arsenic, mercury) or a diffuse distribution (lead) related to the daily consumption of contaminated water and food. Intense lead enrichments indicate acute incorporations, potentially through the administration of lead-enriched medication or the mobilization of lead from bone stores to the bloodstream during intense physiological stress related to leprosy. However, comparisons with a healthy control group are needed to ascertain these interpretations. The positive correlations and the patterns observed between lead and essential elements may indicate underlying pathophysiological conditions, demonstrating the potential of the two techniques for investigating diseases in past populations.

Keywords: Photon Science Materials

A tunable despeckling neural network stabilized via diffusion equation

The removal of multiplicative Gamma noise is a critical research area in the application of synthetic aperture radar (SAR) imaging, where neural networks serve as a potent tool. However, real-world data often diverges from theoretical models, exhibiting various disturbances, which makes the neural network less effective. Adversarial attacks can be used as a criterion for judging the adaptability of neural networks to real data, since they can find the most extreme perturbations that make neural networks ineffective. In this work, we propose a tunable, regularized neural network framework that unrolls a shallow neural denoising block and a diffusion regularization block into a single network for end-to-end training. The linear heat equation, known for its inherent smoothness and low-pass filtering properties, is adopted as the diffusion regularization block. The smoothness of our outputs is controlled by a single time step hyperparameter that can be adjusted dynamically. The stability and convergence of our model are theoretically proven. Experimental results demonstrate that the proposed model effectively eliminates high-frequency oscillations induced by adversarial attacks. Finally, the proposed model is benchmarked against several state-of-the-art denoising methods on simulated images, adversarial samples, and real SAR images, achieving superior performance in both quantitative and visual evaluations.

Keywords: Artificial Intelligence Convolutional neural network Adversarial attack Image despeckling

Active energy compression of a laser-plasma electron beam

Radio-frequency (RF) accelerators providing high-quality relativistic electron beams are an important resource enabling many areas of science, as well as industrial and medical applications. Two decades ago, laser-plasma accelerators that support orders of magnitude higher electric fields than those provided by modern RF cavities produced quasi-monoenergetic electron beams for the first time. Since then, high-brightness electron beams at gigaelectronvolt (GeV) beam energy and competitive beam properties have been demonstrated from only centimetre-long plasmas, a substantial advantage over the hundreds of metres required by RF-cavity-based accelerators. However, despite the considerable progress, the comparably large energy spread and the fluctuation (jitter) in beam energy still effectively prevent laser-plasma accelerators from driving real-world applications. Here we report the generation of a laser-plasma electron beam using active energy compression, resulting in a performance so far only associated with modern RF-based accelerators. Using a magnetic chicane, the electron bunch is first stretched longitudinally to imprint an energy correlation, which is then removed with an active RF cavity. The resulting energy spread and energy jitter are reduced by more than an order of magnitude to below the permille level, meeting the acceptance criteria of a modern synchrotron, thereby opening the path to a compact storage ring injector and other applications

Keywords: Plasma Physics Accelerator

A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses

Structure predictions have become invaluable tools, but viral proteins are absent from the EMBL/DeepMind AlphaFold database. Here, we provide proteome-wide structure predictions for all nine human herpesviruses and analyze them in depth with explicit scoring thresholds. By clustering these predictions into structural similarity groups, we identified new families, such as the HCMV UL112-113 cluster, which is conserved in alpha- and betaherpesviruses. A domain-level search found protein families consisting of subgroups with varying numbers of duplicated folds. Using large-scale structural similarity searches, we identified viral proteins with cellular folds, such as the HSV-1 US2 cluster possessing dihydrofolate reductase folds and the EBV BMRF2 cluster that might have emerged from cellular equilibrative nucleoside transporters. Our HerpesFolds database is available at https://www.herpesfolds.org/herpesfolds and displays all models and clusters through an interactive web interface. Here, we show that system-wide structure predictions can reveal homology between viral species and identify potential protein functions.

Keywords: Artificial Intelligence Photon Science Structural Biology