58 research outputs found
Classification of diffraction patterns in single particle imaging experiments performed at X-ray free-electron lasers using a convolutional neural network
Single particle imaging (SPI) is a promising method for native structure
determination which has undergone a fast progress with the development of X-ray
Free-Electron Lasers. Large amounts of data are collected during SPI
experiments, driving the need for automated data analysis. The necessary data
analysis pipeline has a number of steps including binary object classification
(single versus multiple hits). Classification and object detection are areas
where deep neural networks currently outperform other approaches. In this work,
we use the fast object detector networks YOLOv2 and YOLOv3. By exploiting
transfer learning, a moderate amount of data is sufficient for training of the
neural network. We demonstrate here that a convolutional neural network (CNN)
can be successfully used to classify data from SPI experiments. We compare the
results of classification for the two different networks, with different depth
and architecture, by applying them to the same SPI data with different data
representation. The best results are obtained for YOLOv2 color images linear
scale classification, which shows an accuracy of about 97% with the precision
and recall of about 52% and 61%, respectively, which is in comparison to manual
data classification.Comment: 23 pages, 6 figures, 3 table
Anisotropic atom displacement in Pd nanocubes resolved by molecular dynamics simulations supported by x-ray diffraction imaging
Nearly identical Pd nanocubes yield an x-ray powder diffraction pattern with interference fringes affording access to unprecedented structural details of nanocrystal size, shape, and complex atomic displacement for a billion-sized population. The excellent agreement between diffraction data and molecular dynamics (MD) provides strong experimental validation of MD simulations and the proposed data-interpretation paradigm. These results show that individual atomic displacements within the nanocubes are not only a function of disrupted bonds and the crystallographic plane of the adjacent surface, but are complex strain gradients extending across all surfaces of the particle strongly influenced by atomic displacements. This observation of nonuniform surface strain and the manner in which it is affected by different sizes, shapes, and locations within each facet could be the key to understanding many surface related properties of shaped nanocrystals including those associated with important catalysis applications
Gas-induced segregation in Pt-Rh alloy nanoparticles observed by in-situ Bragg coherent diffraction imaging
Bimetallic catalysts can undergo segregation or redistribution of the metals
driven by oxidizing and reducing environments. Bragg coherent diffraction
imaging (BCDI) was used to relate displacement fields to compositional
distributions in crystalline Pt-Rh alloy nanoparticles. 3D images of internal
composition showed that the radial distribution of compositions reverses
partially between the surface shell and the core when gas flow changes between
O2 and H2. Our observation suggests that the elemental segregation of
nanoparticle catalysts should be highly active during heterogeneous catalysis
and can be a controlling factor in synthesis of electrocatalysts. In addition,
our study exemplifies applications of BCDI for in situ 3D imaging of internal
equilibrium compositions in other bimetallic alloy nanoparticles
Single Alloy Nanoparticle X-Ray Imaging during a Catalytic Reaction
The imaging of active nanoparticles represents a milestone in decoding
heterogeneous catalysts dynamics. We report the facet resolved, surface strain
state of a single PtRh alloy nanoparticle on SrTiO3 determined by coherent
x-ray diffraction imaging under catalytic reaction conditions. Density
functional theory calculations allow us to correlate the facet surface strain
state to its reaction environment dependent chemical composition. We find that
the initially Pt terminated nanoparticle surface gets Rh enriched under CO
oxidation reaction conditions. The local composition is facet orientation
dependent and the Rh enrichment is non-reversible under subsequent CO
reduction. Tracking facet resolved strain and composition under operando
conditions is crucial for a rational design of more efficient heterogeneous
catalysts with tailored activity, selectivity and lifetime.Comment: 15 pages, 4 figures, 32 reference
Photon shot-noise limited transient absorption soft X-ray spectroscopy at the European XFEL
Femtosecond transient soft X-ray Absorption Spectroscopy (XAS) is a very
promising technique that can be employed at X-ray Free Electron Lasers (FELs)
to investigate out-of-equilibrium dynamics for material and energy research.
Here we present a dedicated setup for soft X-rays available at the Spectroscopy
& Coherent Scattering (SCS) instrument at the European X-ray Free Electron
Laser (EuXFEL). It consists of a beam-splitting off-axis zone plate (BOZ) used
in transmission to create three copies of the incoming beam, which are used to
measure the transmitted intensity through the excited and unexcited sample, as
well as to monitor the incoming intensity. Since these three intensity signals
are detected shot-by-shot and simultaneously, this setup allows normalized
shot-by-shot analysis of the transmission. For photon detection, the DSSC
imaging detector, which is capable of recording up to 800 images at 4.5 MHz
frame rate during the FEL burst, is employed and allows approaching the photon
shot-noise limit. We review the setup and its capabilities, as well as the
online and offline analysis tools provided to users.Comment: 11 figure
Massive X-ray screening reveals two allosteric drug binding sites of SARS-CoV-2 main protease
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 repurposing drug libraries containing 5953 individual compounds against the SARS-CoV-2 main protease (Mpro), which is a potent drug target as it is essential for the virus 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 binding to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and five non-peptidic compounds showed antiviral activity at non-toxic concentrations. Interestingly, two compounds bind outside the active site to the native dimer interface in close proximity to the S1 binding pocket. Another compound binds in a cleft between the catalytic and dimerization domain of Mpro. Neither binding site is related to the enzymatic active site and both represent attractive targets for drug development against SARS-CoV-2. This X-ray screening approach thus has the potential to help deliver an approved drug on an accelerated time-scale for this and future pandemics
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