Simulation of X-ray Hartmann wavefront sensing with the Synchrotron Radiation Workshop.

X-ray wavefront measurement is an important beam diagnostic tool, especially for the diffraction-limited X-ray beam. These in situ diagnostics give a better understanding of beam imperfections, and they enable feedback for possible corrections and/or optical alignment improvements. Hartmann wavefront sensing is one of the promising techniques to perform in situ X-ray wavefront measurements. In this work, a simulation tool of the X-ray Hartmann Wavefront Sensor (HWS) is developed under the Synchrotron Radiation Workshop (SRW) framework. Using this new simulation capability, one can take advantage of the full SRW package to simulate Hartmann wavefront sensing with the beam traveling from the X-ray source to the sample through different X-ray optical components. This SRW HWS simulation tool can help to optimize the wavefront sensor parameters for a specific X-ray energy range. It can also simulate an in situ wavefront measurement experiment with a particular beamline optical layout and predict the expected results of the wavefront measurement under different beamline configurations.

The Inner Shell Spectroscopy beamline at NSLS-II: a facility for in situ and operando X-ray absorption spectroscopy for materials research.

The Inner Shell Spectroscopy (ISS) beamline on the 8-ID station at the National Synchrotron Light Source II (NSLS-II), Upton, NY, USA, is a high-throughput X-ray absorption spectroscopy beamline designed for in situ, operando, and time-resolved material characterization using high monochromatic flux and scanning speed. This contribution discusses the technical specifications of the beamline in terms of optics, heat load management, monochromator motion control, and data acquisition and processing. Results of the beamline tests demonstrating the quality of the data obtainable on the instrument, possible energy scanning speeds, as well as long-term beamline stability are shown. The ability to directly control the monochromator trajectory to define the acquisition time for each spectral region is highlighted. Examples of studies performed on the beamline are presented. The paper is concluded with a brief outlook for future developments.

New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting.

Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. The design and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.

Noise reduction in X-ray photon correlation spectroscopy with convolutional neural networks encoder-decoder models.

Like other experimental techniques, X-ray photon correlation spectroscopy is subject to various kinds of noise. Random and correlated fluctuations and heterogeneities can be present in a two-time correlation function and obscure the information about the intrinsic dynamics of a sample. Simultaneously addressing the disparate origins of noise in the experimental data is challenging. We propose a computational approach for improving the signal-to-noise ratio in two-time correlation functions that is based on convolutional neural network encoder-decoder (CNN-ED) models. Such models extract features from an image via convolutional layers, project them to a low dimensional space and then reconstruct a clean image from this reduced representation via transposed convolutional layers. Not only are ED models a general tool for random noise removal, but their application to low signal-to-noise data can enhance the data's quantitative usage since they are able to learn the functional form of the signal. We demonstrate that the CNN-ED models trained on real-world experimental data help to effectively extract equilibrium dynamics' parameters from two-time correlation functions, containing statistical noise and dynamic heterogeneities. Strategies for optimizing the models' performance and their applicability limits are discussed.

Tools for supporting solution scattering during the COVID-19 pandemic.

During the COVID-19 pandemic, synchrotron beamlines were forced to limit user access. Performing routine measurements became a challenge. At the Life Science X-ray Scattering (LiX) beamline, new instrumentation and mail-in protocols have been developed to remove the access barrier to solution scattering measurements. Our efforts took advantage of existing instrumentation and coincided with the larger effort at NSLS-II to support remote measurements. Given the limited staff-user interaction for mail-in measurements, additional software tools have been developed to ensure data quality, to automate the adjustments in data processing, as users would otherwise rely on the experience of the beamline staff, and produce a summary of the initial assessments of the data. This report describes the details of these developments.

Sirepo: an open-source cloud-based software interface for X-ray source and optics simulations.

Sirepo, a browser-based GUI for X-ray source and optics simulations, is presented. Such calculations can be performed using SRW (Synchrotron Radiation Workshop), which is a physical optics computer code, allowing simulation of entire experimental beamlines using the concept of a `virtual beamline' with accurate treatment of synchrotron radiation generation and propagation through the X-ray optical system. SRW is interfaced with Sirepo by means of a Python application programming interface. Sirepo supports most of the optical elements currently used at beamlines, including recent developments in SRW. In particular, support is provided for the simulation of state-of-the-art X-ray beamlines, exploiting the high coherence and brightness of modern light source facilities. New scientific visualization and reporting capabilities have been recently implemented within Sirepo, as well as automatic determination of electron beam and undulator parameters. Publicly available community databases can be dynamically queried for error-free access to material characteristics. These computational tools can be used for the development and commissioning of new X-ray beamlines and for testing feasibility and optimization of experiments. The same interface can guide simulation on a local computer, a remote server or a high-performance cluster. Sirepo is available online and also within the NSLS-II firewall, with a growing number of users at other light source facilities. Our open source code is available on GitHub.

Novel magnesium borides and their superconductivity.

With the motivation of searching for new superconductors in the Mg-B system, we performed ab initio evolutionary searches for all the stable compounds in this binary system in the pressure range of 0-200 GPa. We found previously unknown, yet thermodynamically stable, compositions MgB3 and Mg3B10. Experimentally known MgB2 is stable in the entire pressure range 0-200 GPa, while MgB7 and MgB12 are stable at pressures below 90 GPa and 35 GPa, respectively. We predict a reentrant behavior for MgB4, which becomes unstable against decomposition into MgB2 and MgB7 at 4 GPa and then becomes stable above 61 GPa. We find ubiquity of phases with boron sandwich structures analogous to the AlB2-type structure. However, with the exception of MgB2, all other magnesium borides have low electron-phonon coupling constants λ of 0.32-0.39 and are predicted to have Tc below 3 K.

Superconductivity of novel tin hydrides (Sn(n)H(m)) under pressure.

With the motivation of discovering high-temperature superconductors, evolutionary algorithm USPEX is employed to search for all stable compounds in the Sn-H system. In addition to the traditional SnH4, new hydrides SnH8, SnH12 and SnH14 are found to be thermodynamically stable at high pressure. Dynamical stability and superconductivity of tin hydrides are systematically investigated. I4m2-SnH8, C2/m-SnH12 and C2/m-SnH14 exhibit higher superconducting transition temperatures of 81, 93 and 97 K compared to the traditional compound SnH4 with Tc of 52 K at 200 GPa. An interesting bent H3-group in I4m2-SnH8 and novel linear H in C2/m-SnH12 are observed. All the new tin hydrides remain metallic over their predicted range of stability. The intermediate-frequency wagging and bending vibrations have more contribution to electron-phonon coupling parameter than high-frequency stretching vibrations of H2 and H3.

A novel phase of beryllium fluoride at high pressure.

A previously unknown thermodynamically stable high-pressure phase of BeF2 has been predicted using the evolutionary algorithm USPEX. This phase occurs in the pressure range 18-27 GPa. Its structure has C2/c space group symmetry and contains 18 atoms in the primitive unit cell. Given the analogy between BeF2 and SiO2, silica phases have been investigated as well, but the new phase has not been observed to be thermodynamically stable for this system. However, it is found to be metastable and to have comparable energy to the known metastable phases of SiO2, suggesting a possibility of its synthesis.