Publications by authors named "Jayanath Koliyadu"

We report on recent developments that enable megahertz hard X-ray phase contrast imaging (MHz XPCI) experiments at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL facility (EuXFEL). We describe the technical implementation of the key components, including an MHz fast camera and a modular indirect X-ray microscope system based on fast scintillators coupled through a high-resolution optical microscope, which enable full-field X-ray microscopy with phase contrast of fast and irreversible phenomena. The image quality for MHz XPCI data showed significant improvement compared with a pilot demonstration of the technique using parallel beam illumination, which also allows access to up to 24 keV photon energies at the SPB/SFX instrument of the EuXFEL.

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X-ray multi-projection imaging (XMPI) is an emerging experimental technique for the acquisition of rotation-free, time-resolved, volumetric information on stochastic processes. The technique is developed for high-brilliance light-source facilities, aiming to address known limitations of state-of-the-art imaging methods in the acquisition of 4D sample information, linked to their need for sample rotation. XMPI relies on a beam-splitting scheme, that illuminates a sample from multiple, angularly spaced viewpoints, and employs fast, indirect, X-ray imaging detectors for the collection of the data.

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  • Scientists have found a new way to see tiny changes in proteins very quickly, which is important for biology and medicine.
  • They used special X-ray lasers that can take pictures millions of times a second without much background noise.
  • This new method helps them study how proteins unfold and change shape, making it useful for understanding many different biological processes.
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  • Nanoparticles with varied structures are a major focus in research, and new techniques like high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) are now enabling the analysis of millions of these particles.
  • To effectively utilize this technology, researchers faced three key challenges: understanding structural variability, extracting relevant parameters from measurements, and comparing multiple structural models to the data collected.
  • By addressing these challenges, scientists mapped the diverse shapes of gold nanoparticles, revealing important insights into their asymmetry, stable shape patterns, and how external factors like surfactants influence their structure, making nanoparticle characterization more reliable.
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  • The main protease (M) of SARS-CoV-2 is crucial for the virus's functionality and is considered a potential target for drug development, as it is only active in its reduced form.
  • When oxidized, M's activity halts but can be restored, indicating an evolutionary adaptation to oxidative environments, although the protective mechanisms haven't been fully elucidated.
  • Researchers determined the crystal structure of oxidized M, revealing a disulfide bond that affects its dimer stability and crystallization, providing insights into the protein's response to oxidative stress and its structural study conditions.*
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X-ray Free Electron Lasers (XFEL) are cutting-edge pulsed x-ray sources, whose extraordinary pulse parameters promise to unlock unique applications. Several new methods have been developed at XFELs; however, no methods are known, which allow ab initio atomic level structure determination using only a single XFEL pulse. Here, we present experimental results, demonstrating the determination of the 3D atomic structure from data obtained during a single 25 fs XFEL pulse.

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The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.

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  • Understanding signal transduction in photoreceptor proteins is crucial for how organisms respond to light, and this study focuses on the photoactivatable adenylate cyclase from Oscillatoria acuminata under blue light.
  • The research reveals that ATP binds in an energetically unfavorable conformation at room temperature, which only transitions to a favorable state after light activation.
  • Time-resolved crystallography and cryo-trapping experiments show significant structural changes in the BLUF domain, especially the pivotal rotation of a specific amino acid, Gln48, that stabilizes the light-sensitive FAD chromophore for effective signal transmission.
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  • Hydrodynamic cavitation is a process that helps with things like cleaning water and making chemicals in special reactors.
  • In a specific tube called a Venturi tube, there are many fast-spinning bubbles called vortex cavitation that can glow in the dark, and how bright they are depends on how big and how many there are.
  • Researchers found out that these bubbles are actually shaped differently than what people thought; instead of being round, they're angulated, and they studied how fast the surface of these bubbles moves.
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Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment.

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The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition.

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X-ray free-electron lasers (XFELs) can probe chemical and biological reactions as they unfold with unprecedented spatial and temporal resolution. A principal challenge in this pursuit involves the delivery of samples to the X-ray interaction point in such a way that produces data of the highest possible quality and with maximal efficiency. This is hampered by intrinsic constraints posed by the light source and operation within a beamline environment.

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Pump-probe experiments at X-ray free-electron laser (XFEL) facilities are a powerful tool for studying dynamics at ultrafast and longer timescales. Observing the dynamics in diverse scientific cases requires optical laser systems with a wide range of wavelength, flexible pulse sequences and different pulse durations, especially in the pump source. Here, the pump-probe instrumentation available for measurements at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL is reported.

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Serial femtosecond crystallography is a rapidly developing method for determining the structure of biomolecules for samples which have proven challenging with conventional X-ray crystallography, such as for membrane proteins and microcrystals, or for time-resolved studies. The European XFEL, the first high repetition rate hard X-ray free electron laser, provides the ability to record diffraction data at more than an order of magnitude faster than previously achievable, putting increased demand on sample delivery and data processing. This work describes a publicly available serial femtosecond crystallography dataset collected at the SPB/SFX instrument at the European XFEL.

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Article Synopsis
  • * Two innovative methods are proposed: common-line principal component analysis (PCA) for rough, automated classification, and variation auto-encoders (VAEs) for generating detailed 3D structures of objects.
  • * Implemented with a noise-tolerant algorithm, these methods show effectiveness on experimental datasets from gold nanoparticles, paving the way for new research on diverse topics like nanocrystal growth and phase transitions.
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The structural changes of water upon deep supercooling were studied through wide-angle x-ray scattering at SwissFEL. The experimental setup had a momentum transfer range of 4.5 Å, which covered the principal doublet of the x-ray structure factor of water.

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  • The study focuses on how enzymes interact with substrates or ligands in real time, specifically observing the first phase of the reaction using advanced imaging techniques.* -
  • Researchers utilized the European XFEL (EuXFEL) to achieve near-atomic resolution and track ceftriaxone binding to β-lactamase, combining high repetition rates and mix-and-inject technology for time-resolved measurements.* -
  • The findings included calculating a diffusion coefficient to understand concentrations in enzyme crystals over time and describing the binding of the inhibitor sulbactam, showcasing the potential of EuXFEL for biomedical research.*
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Knowledge of the temperature dependence of the isobaric specific heat (C) upon deep supercooling can give insights regarding the anomalous properties of water. If a maximum in C exists at a specific temperature, as in the isothermal compressibility, it would further validate the liquid-liquid critical point model that can explain the anomalous increase in thermodynamic response functions. The challenge is that the relevant temperature range falls in the region where ice crystallization becomes rapid, which has previously excluded experiments.

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We present a novel, to the best of our knowledge, Hartmann wave front sensor for extreme ultraviolet (EUV) spectral range with a numerical aperture (NA) of 0.15. The sensor has been calibrated using an EUV radiation source based on gas high harmonic generation.

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With high-harmonic generation (HHG), spatially and temporally coherent XUV to soft x-ray (100 nm to 10 nm) table-top sources can be realized by focusing a driving infrared (IR) laser on a gas target. For applications such as coherent diffraction imaging, holography, plasma diagnostics, or pump-probe experiments, it is desirable to have control over the wave front (WF) of the HHs to maximize the number of XUV photons on target or to tailor the WF. Here, we demonstrate control of the XUV WF by tailoring the driving IR WF with a deformable mirror.

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