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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.

Opt. Express 30, 31519-31529 (2022) 

Frank Seiboth, Adam Kubec, Andreas Schropp, Sven Niese, Peter Gawlitza, Jan Garrevoet, Vanessa Galbierz, Silvio Achilles, Svenja Patjens, Michael E. Stuckelberger, Christian David, and Christian G. Schroer 
  • in science
  • 1 min read

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.
  • in science
  • 2 min read

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.

Nature 603, 58–62

D’Arcy, R., Chappell, J., Beinortaite, J. et al.
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  • 2 min read

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.

Sci Rep 11, 24237 (2021).

Baltruschat, I.M., Ćwieka, H., Krüger, D. et al.
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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.

Biochemistry and Biophysics Reports 27, 2021, 101039

Vadim Kotov, Michele Lunelli, Jiri Wald, Michael Kolbe, Thomas C. Marlovits,
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  • 2 min read

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.

JACS Au 2021 1 (6), 852-864

Koen W. Bossers, Roozbeh Valadian, Jan Garrevoet, Stijn van Malderen, Robert Chan, Nic Friederichs, John Severn, Arnold Wilbers, Silvia Zanoni, Maarten K. Jongkind, Bert M. Weckhuysen, and Florian Meirer
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  • 1 min read

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.

Comput Softw Big Sci 5, 16 (2021).
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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.

Vassholz, M., Hoeppe, H.P., Hagemann, J. et al.

Nat Commun 12, 3468 (2021).
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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.

Nature volume 593, pages 445–448 (2021)

Bunduc, CM, Fahrenkamp, D, Wald, J, Ummels, R, Bitter, W, Houben, ENG, Marlovits, TC