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At least 343 records · Page 19

The XMM Cluster Survey: automating the estimation of hydrostatic mass for large samples of galaxy clusters – I. Methodology, validation, and application to the SDSSRM-XCS sample

ABSTRACT We describe features of the X-ray: Generate and Analyse (xga) open-source software package that have been developed to facilitate automated hydrostatic mass ($M_{\rm hydro}$) measurements from XMM X-ray observations of clusters of galaxies. This includes describing how xga measures global, and radial, X-ray properties of galaxy clusters. We then demonstrate the reliability of xga by comparing simple X-ray properties, namely the X-ray temperature and gas mass, with published values presented by the XMM Cluster Survey (XCS), the Ultimate XMM eXtragaLactic survey project (XXL), and the Local Cluster Substructure Survey (LoCuSS). xga measured values for temperature are, on average, within 1 per cent of the values reported in the literature for each sample. xga gas masses for XXL clusters are shown to be ${\sim }$10 per cent lower than previous measurements (though the difference is only significant at the $\sim 1.8\sigma$ level), LoCuSS $R_{2500}$ and $R_{500}$ gas mass re-measurements are 3 per cent and 7 per cent lower, respectively (representing 1.5$\sigma$ and 3.5$\sigma$ differences). Like-for-like comparisons of hydrostatic mass are made to LoCuSS results, which show that our measurements are $10{\pm }3~{{\rm per\ cent}}$ ($19{\pm }7~{{\rm per\ cent}}$) higher for $R_{2500}$ ($R_{500}$). The comparison between $R_{500}$ masses shows significant scatter. Finally, we present new $M_{\rm hydro}$ measurements for 104 clusters from the Sloan Digital Sky Survey (SDSS) DR8 redMaPPer XCS sample (SDSSRM-XCS). Our SDSSRM-XCS hydrostatic mass measurements are in good agreement with multiple literature estimates, and represent one of the largest samples of consistently measured hydrostatic masses. We have demonstrated that xga is a powerful tool for X-ray analysis of clusters; it will render complex-to-measure X-ray properties accessible to non-specialists.

Turner, D. J. (ORCID:0000000196581396)↗

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗

Specific Gamma-Ray Dose Constants with Current Emission Data

The specific gamma-ray dose constant represents the gamma effective dose rate due to a point source of unit activity of a given nuclide at 1 m. New tabulations of specific gamma-ray dose constants have been made using current gamma emission data from the SCALE 6.2.3 software package and International Commission on Radiological Protection Publication 107, combined with the effective dose per fluence conversion coefficients (antero-posterior orientation) of International Commission on Radiological Protection Publication 116. SCALE data cover 1,264 nuclides, and International Commission on Radiological Protection Publication 107 data include 1,192 nuclides, with only 777 nuclides in common between the two sets.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

JETSCAPE framework: p+p results

The JETSCAPE framework is a modular and versatile Monte Carlo software package for the simulation of high energy nuclear collisions. In this work we present a new tune of JETSCAPE, called PP19, and validate it by comparison to jet-based measurements in p + p collisions, including inclusive single jet cross sections, jet shape observables, fragmentation functions, charged hadron cross sections, and dijet mass cross sections. These observables in p+p collisions provide the baseline for their counterparts in nuclear collisions. Quantifying the level of agreement of JETSCAPE results with p+p data is thus necessary for meaningful applications of JETSCAPE to A+A collisions. The calculations use the JETSCAPE PP19 tune, defined in this paper, based on version 1.0 of the JETSCAPE framework. For the observables discussed in this work calculations using JETSCAPE PP19 agree with data over a wide range of collision energies at a level comparable to standard Monte Carlo codes. These results demonstrate the physics capabilities of the JETSCAPE framework and provide benchmarks for JETSCAPE users.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Abrasion-fission reactions at intermediate energies

The availability of high-intensity, heavy-ion beams coupled to sensitive, large solid-angle acceptance spectrometers has enabled a detailed examination of the fission fragments produced in induced-fission reactions. The abrasion fission process involves the formation of projectile-like prefragments in violent nuclear collisions at relative energies in excess of 100 MeV/u. At intermediate energies below this threshold, experiments suggest a change in the prefragment kinematic qualities. Information regarding the influence of this transitional phase upon the evolution of nuclei approaching the point of scission is scarce. In this article, data are presented for over 200 nuclei from nickel to palladium produced in abrasion-fission reactions of a 80 MeV/u 238 U beam. Cross sections were obtained following yield measurements performed for the principal charge states of the identified fission fragments and a detailed analysis of the ion transmission. A full kinematic analysis of the fission fragments has been performed using the LISE ++ software package, where the trajectory of an ion passing through a spectrometer can be reconstructed based upon measurements at the focal plane. Furthermore, the results obtained at the S800 spectrograph are compared with predictions obtained with a three-fission progenitor (3EER) model. Systematic studies of fission-fragment properties continue to provide a valuable experimental benchmark for theoretical efforts directed toward describing this complex decay channel, that is important in the context of planning experiments to explore the neutron-rich region of the nuclear chart at rare-isotope beam facilities.

59 ≤ A ≤ 8990 ≤ A ≤ 149↗

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part I

This two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the general real-space coordinate transformation required to correct this shear, in a compact operator formulation that easily lends itself to implementation with available software packages. Such a transformation, applied as a final post-processing step following phase retrieval, is crucial for arriving at an undistorted, correctly oriented and physically meaningful image of the 3D crystalline scatterer. As the relevance of BCDI grows in the field of materials characterization, the available sparse literature that addresses the geometric theory of BCDI and the subsequent analysis methods are generalized here. This geometrical aspect, specific to coherent Bragg diffraction and absent in 2D transmission CDI experiments, gains particular importance when it comes to spatially resolved characterization of 3D crystalline materials in a reliable nondestructive manner. This series of articles describes this theory, from the diffraction in Bragg geometry to the corrections needed to obtain a properly rendered digital image of the 3D scatterer. Part I of this series provides the experimental BCDI community with the general form of the 3D real-space distortions in the phase-retrieved object, along with the necessary post-retrieval correction method. Part II builds upon the geometric theory developed in Part I with the formalism to correct the shear distortions directly on an orthogonal grid within the phase-retrieval algorithm itself, allowing more physically realistic constraints to be applied. Taken together, Parts I and II provide the X-ray science community with a set of generalized BCDI shear-correction techniques crucial to the final rendering of a 3D crystalline scatterer and for the development of new BCDI methods and experiments.

36 MATERIALS SCIENCE↗

PtychoShelves , a versatile high-level framework for high-performance analysis of ptychographic data

Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen's transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.

97 MATHEMATICS AND COMPUTING↗

SAS PDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data

SASPDF, a method for characterizing the structure of nanoparticle assemblies (NPAs), is presented. The method is an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime. The PDFgetS3 software package for computing the PDF from SAS data is also presented. An application of the SASPDF method to characterize structures of representative NPA samples with different levels of structural order is then demonstrated. The SASPDF method quantitatively yields information such as structure, disorder and crystallite sizes of ordered NPA samples. The method was also used to successfully model the data from a disordered NPA sample. The SASPDF method offers the possibility of more quantitative characterizations of NPA structures for a wide class of samples.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages ( Dozor and DIALS ), demonstrating that this is an appropriate framework to support future extensions and improvements.

36 MATERIALS SCIENCE↗

Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

97 MATHEMATICS AND COMPUTING↗

A science-driven approach to optimize the design for a biological small-angle neutron scattering instrument

Biological small-angle neutron scattering (SANS) instruments facilitate critical analysis of the structure and dynamics of complex biological systems. However, with the growth of experimental demands and the advances in optical systems design, a new neutron optical concept is necessary to overcome the limitations of current instruments. This work presents an approach to include experimental objectives ( i.e. the science to be supported by a specific neutron scattering instrument) in the optimization of the neutron optical concept. The approach for a proposed SANS instrument at the Second Target Station of the Spallation Neutron Source at Oak Ridge National Laboratory, USA, is presented here. Further, the instrument is simulated with the McStas software package. The optimization process is driven by an evolutionary algorithm using McStas output data, which are processed to calculate an objective function designed to quantify the expected performance of the simulated neutron optical configuration for the intended purpose. Each McStas simulation covers the complete instrument, from source to detector, including realistic sample scattering functions. This approach effectively navigates a high-dimensional parameter space that is otherwise intractable; it allows the design of next-generation SANS instruments to address specific scientific cases and has the potential to increase instrument performance compared with traditional design approaches.

47 OTHER INSTRUMENTATION↗

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗

Efficient end-to-end simulation of time-dependent coherent X-ray scattering experiments

Physical optics simulations for beamlines and experiments allow users to test experiment feasibility and optimize beamline settings ahead of beam time in order to optimize valuable beam time at synchrotron light sources like NSLS-II. Further, such simulations also help to develop and test experimental data processing methods and software in advance. The Synchrotron Radiation Workshop ( SRW ) software package supports such complex simulations. We demonstrate how recent developments in SRW significantly improve the efficiency of physical optics simulations, such as end-to-end simulations of time-dependent X-ray photon correlation spectroscopy experiments with partially coherent undulator radiation (UR). The molecular dynamics simulation code LAMMPS was chosen to model the sample: a solution of silica nanoparticles in water at room temperature. Real-space distributions of nanoparticles produced by LAMMPS were imported into SRW and used to simulate scattering patterns of partially coherent hard X-ray UR from such a sample at the detector. The partially coherent UR illuminating the sample can be represented by a set of orthogonal coherent modes obtained by simulation of emission and propagation of this radiation through the coherent hard X-ray (CHX) scattering beamline followed by a coherent-mode decomposition. GPU acceleration is added for several key functions of SRW used in propagation from sample to detector, further improving the speed of the calculations. The accuracy of this simulation is benchmarked by comparison with experimental data.

36 MATERIALS SCIENCE↗

Real-space texture and pole-figure analysis using the 3D pair distribution function on a platinum thin film

An approach is described for studying texture in nanostructured materials. The approach implements the real-space texture pair distribution function (PDF), txPDF, laid out by Gong & Billinge {(2018). arXiv:1805.10342 [cond-mat]}. It is demonstrated on a fiber-textured polycrystalline Pt thin film. The approach uses 3D PDF methods to reconstruct the orientation distribution function of the powder crystallites from a set of diffraction patterns, taken at different tilt angles of the substrate with respect to the incident beam, directly from the 3D PDF of the sample. A real-space equivalent of the reciprocal-space pole figure is defined in terms of interatomic vectors in the PDF and computed for various interatomic vectors in the Pt film. Furthermore, it is shown how a valid isotropic PDF may be obtained from a weighted average over the tilt series, including the measurement conditions for the best approximant to the isotropic PDF from a single exposure, which for the case of the fiber-textured film was in a nearly grazing incidence orientation of ∼10°. Finally, an open-source Python software package, FouriGUI , is described that may be used to help in studies of texture from 3D reciprocal-space data, and indeed for Fourier transforming and visualizing 3D PDF data in general.

3D pair distribution functions↗

Universal parameters of bulk-solvent masks

The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox ( CCTBX ) and in Phenix as the default choice.

36 MATERIALS SCIENCE↗

Arginine off-kilter: guanidinium is not as planar as restraints denote

Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the N ∊ —C ζ —N η1 and N ∊ —C ζ —N η2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the C δ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the C δ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix , that take into account the asymmetry of the group and the planar deviation of the C δ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.

59 BASIC BIOLOGICAL SCIENCES↗

CERES : a cryo-EM re-refinement system for continuous improvement of deposited models

The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System ( CERES ) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.

59 BASIC BIOLOGICAL SCIENCES↗

Design and optimization of cancellation coil topologies for a ferrite-less wireless EV charging pad

Ferrite cores are widely used in conventional wireless EV charging pads to reduce stray EMF emissions, but they can be brittle, heavy, and expensive. This work furthers the development of ferrite-less wireless charging pads by comparing an active and two distinct passive cancellation coil topologies as candidates to replace the ferrite. Using the software packages FEMM and MATLAB, each topology is optimized to find the best winding positions and radii to minimize leakage at a specified position under the side of the vehicle. The optimized designs are compared for shielding effectiveness, induced current, and efficiency. All three topologies are able to sufficiently reduce the leakage field below the ICNIRP limit of 27 μTrms with just one turn. Interestingly, we find that an array of simple passive cancellation loops performs similar to the more widely studied passive cancellation coil.

Scher, Aaron D.↗