Optimizing pink-beam fast X-ray microtomography for multiphaseflow in 3D porous media
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The powder diffraction profile obtained with a pink-beam synchrotron X-ray source is described as the convolution of a back-to-back pair of exponentials convoluted with the Gaussian and Lorentzian components of a pseudo-Voigt. We report this new function is employed for the first time in a Rietveld refinement using data collected from a single 100 ps synchrotron X-ray micropulse.
Time-resolved x-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is often difficult. Extracting small, time-dependent changes in signal is frequently a bottleneck for practitioners. Recent work demonstrated this challenge can be addressed when merging redundant observations by a statistical technique known as variational inference (VI). However, the variational approach to time-resolved data analysis requires identification of successful hyperparameters in order to optimally extract signal. In this case study, we present a successful application of VI to time-resolved changes in an enzyme, DJ-1, upon mixing with a substrate molecule, methylglyoxal. We present a strategy to extract high signal-to-noise changes in electron density from these data. Furthermore, we conduct an ablation study, in which we systematically remove one hyperparameter at a time to demonstrate the impact of each hyperparameter choice on the success of our model. We expect this case study will serve as a practical example for how others may deploy VI in order to analyze their time-resolved diffraction data.
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Diffraction images with crystal hits from the large bandwidth (2.2 % BW) data set (thaumatin 6), and nominal SASE (0.17 % BW) data set (thaumatin 8 + thaumatin 10) with bad pixel masks, online indexing results and CrystFEL stream files from final processing.
The Hayabusa2 space mission recently retrieved 5.4 g of material from asteroid Ryugu, providing the first direct access to pristine material from a carbonaceous asteroid. This study employs a novel combination of non-invasive synchrotron X-ray techniques to examine microscale chemistry (elemental distributions and element-specific chemical speciation and local structure) inside Ryugu grains without physically cutting the samples. Manganese primarily occurs in carbonate: Mn-bearing dolomite with minor earlier ankerite. Iron sulfides present as large single grains and as smaller particles in the finer-grained matrix are both predominantly pyrrhotite. At the 5 μm scale, Fe sulfides do not show the mineralogical heterogeneity seen in many carbonaceous meteorites but exhibit some heterogeneous localized oxidation. Iron is present often as intergrowths of oxide and sulfide, indicating incomplete replacement. Trace selenium substitutes for S in pyrrhotite. Copper is present as Fe-poor Cu sulfide. These results demonstrate multiple episodes of fluid alteration on the parent body, including partial oxidation, and help constrain the sequence or evolution of fluids and processes that resulted in the current grain-scale mineralogical composition of Ryugu materials.
The radiation shielding analysis of the external concrete enclosure of a feature long beamline of the Advanced Photon Source Upgrade project is described in this work. The beamline has 2 undulators that can operate in two different configurations and the source terms are estimated for the worst configuration using the SRW code in the OASYS package as well as the STAC8 code. The shielding analysis is carried out using the STAC8 code, and for the case of pink beam, with the FLUKA code also. Effective dose rates on contact with the outside surface of the concrete walls for pink, reflected full spectrum and monochromatic beams are calculated. For the monochromatic beams, 2 sets of discrete bandwidths (BW) from the Double Crystal Monochromator (DCM) and the full reflectance of the Double Multilayer Monochromator (DMM) are used. Further, due to the size of the direct beam and the energy domain of interest in the direct and scattered fields, the importance of the equivalent dose to the lens of the eye is discussed with respect to the shielding calculations of such facilities. The dose rates outside the concrete hutch in the lateral directions calculated using STAC8 is about 50% higher than the FLUKA results for the case of pink beam but may be considered as a reasonable agreement due to the differences in the calculational methodologies. Those dose rates in the lateral and forward directions are higher for the pink beam to allow full occupancy from the radiation protection point of view. For the full spectrum after 3 reflections, the effective dose rates are less than 0.5 Sv/h in the lateral direction but is higher in the forward region below about 22° with respect to the beam direction. For the DCM beams, except for the scenario with one mirror and 0.1%BW, all dose rates are less than 0.5 Sv/h outside the concrete hutch in the lateral directions. Here, the higher harmonics are what contributes to the dose outside the shield and the bandwidths assumed to derive the photon flux thus becomes important. The dose rates with the DMM are generally lower compared to the 0.1% BW DCM beam but are higher than the results obtained with XOP calculated bandwidths.
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The Dual Imaging and Diffraction (DIAD) beamline at Diamond Light Source is a new dual-beam instrument for full-field imaging/tomography and powder diffraction. This instrument provides the user community with the capability to dynamically image 2D and 3D complex structures and perform phase identification and/or strain mapping using micro-diffraction. The aim is to enable in situ and in operando experiments that require spatially correlated results from both techniques, by providing measurements from the same specimen location quasi-simultaneously. Using an unusual optical layout, DIAD has two independent beams originating from one source that operate in the medium energy range (7–38 keV) and are combined at one sample position. Here, either radiography or tomography can be performed using monochromatic or pink beam, with a 1.4 mm × 1.2 mm field of view and a feature resolution of 1.2 µm. Micro-diffraction is possible with a variable beam size between 13 µm × 4 µm and 50 µm × 50 µm. One key functionality of the beamline is image-guided diffraction, a setup in which the micro-diffraction beam can be scanned over the complete area of the imaging field-of-view. This moving beam setup enables the collection of location-specific information about the phase composition and/or strains at any given position within the image/tomography field of view. The dual beam design allows fast switching between imaging and diffraction mode without the need of complicated and time-consuming mode switches. Real-time selection of areas of interest for diffraction measurements as well as the simultaneous collection of both imaging and diffraction data of (irreversible) in situ and in operando experiments are possible.
The CSSI beamline of the APSU will have a 20.5 m long, 2.75 m diameter SS end station designed to accept pink beam. In this work, the radiation shielding analysis of this end station is analyzed using STAC8 and FLUKA codes. Effect of mirror properties such as reflectivity, coating, inclination and roughness as well as variation in the steel composition are also studied. 8 mm thick SS is found to be adequate if the source is defined by a pinhole and the white beam is reflected with two mirrors inclined at 3.0 mradian or more. The dose rates from monochromatic beams are found to be below the desired levels when the XOP calculated bandwidth (BW) are used while the use of a flat 0.1% BW requires the mirror inclinations to be above 2.5 mradian or more. STAC8 results are consistently higher than the FLUKA results by about 1.5–2.0 times.
Measurement modalities in Bragg coherent diffraction imaging (BCDI) rely on finding a signal from a single nanoscale crystal object which satisfies the Bragg condition among a large number of arbitrarily oriented nanocrystals. However, even when the signal from a single Bragg reflection with ( hkl ) Miller indices is found, the crystallographic axes on the retrieved three-dimensional (3D) image of the crystal remain unknown, and thus localizing in reciprocal space other Bragg reflections becomes time-consuming or requires good knowledge of the orientation of the crystal. Here, the commissioning of a movable double-bounce Si (111) monochromator at the 34-ID-C endstation of the Advanced Photon Source is reported, which aims at delivering multi-reflection BCDI as a standard tool in a single beamline instrument. The new instrument enables, through rapid switching from monochromatic to broadband (pink) beam, the use of Laue diffraction to determine crystal orientation. With a proper orientation matrix determined for the lattice, one can measure coherent diffraction patterns near multiple Bragg peaks, thus providing sufficient information to image the full strain tensor in 3D. The design, concept of operation, the developed procedures for indexing Laue patterns, and automated measuring of Bragg coherent diffraction data from multiple reflections of the same nanocrystal are discussed.
GSAS-II is a comprehensive data analysis and simulation software package for determining atomistic structures from single-crystal and powder diffraction data. X-ray, neutron and electron data may be used. Constant-wavelength, time-of-flight and pink-beam sources may be employed and analyses may combine different types of data. The package is oriented towards materials characterization problems, but protein crystallography, pair-distribution function analysis, small-angle scattering and reflectometry analysis are all included. GSAS-II provides tools for indexing and solving structures from powder diffraction data, in addition to structure, data and results visualization tools
Two conformational polymorphs of a donor–bridge–acceptor (D-B-A) dyad, p-(CH 3 ) 2 N-C 6 H 4 -(CH 2 ) 2 -(1-pyrenyl)/PyCHDMA, were studied, where the electron donor (D) moiety p-(CH 3 ) 2 N-C 6 H 4 /DMA is connected through a bridging group (B), –CH 2 –CH 2 –, to the electron acceptor (A) moiety pyrene. Though molecular dyads like PyCHDMA have the potential to change solar energy into electrical current through the process of photoinduced intramolecular charge transfer (ICT), the major challenge is the real-time investigation of the photoinduced ICT process in crystals, necessary to design solid-state optoelectronic materials. The time-correlated single photon counting (TCSPC) measurements with the single crystals showed that the ICT state lifetime of the thermodynamic form, PyCHDMA1 (pyrene and DMA: axial), is ~3 ns, whereas, for the kinetic form, PyCHDMA20 (pyrene and DMA: equatorial), it is ~7 ns, while photoexcited with 375 nm radiation. The polymorphic crystals were photo-excited and subsequently probed with a pink Laue x-ray beam in time-resolved x-ray diffraction (TRXRD) measurements. The TRXRD results suggest that in the ICT state, due to electron transfer from the tertiary N-atom in DMA moiety to the bridging group and pyrene moiety, a decreased repulsion between the lone-pair and the bond-pair at N-atom induces planarity in the C–N–(CH 3 ) 2 moiety, in both polymorphs. The Natural Bond Orbital calculations and partial atomic charge analysis by Hirshfeld partitioning also corroborated the same. Although the interfragment charge transfer (IFCT) analysis using the TDDFT results showed that for the charge transfer excitation in both conformers, the electrons were transferred from the DMA moiety to mostly the pyrene moiety, the bridging group has little role to play in that.
Introduction: Magnesian rocks from the lunar highlands are collectively termed the Mg-suite. Characterized by high (>60) Mg# (molar 100×Mg/[Mg+Fe]) in mafic phases and calcic plagioclase, these rocks are plutonic to hypabyssal in origin, and include a range of bulk mineralogies such as troctolites, dunites, norites, gabbronorites, and spinel troctolites [1]. These Mg-suite lithologies have distinct trace element concentrations and ratios that differentiate them from other lunar rock types. These rocks are ancient, generally dated to between 4.5 and 4.1 Ga, although it is unknown if this represents the full range of Mg-suite ages [1–2]. Among the Mg-suite lithologies, the spinel troctolites are relatively rare, to date only found in polymict breccias [3]. Spinel troctolites, as their name suggests, consist of calcic plagioclase and forsteritic olivine, with minor amounts of spinel (MgAl2O4), ± pyroxene and cordierite [1,4]. This form of spinel is often called ‘pink’ spinel because of its appearance in thin section under plane polarized light (PPL; Fig. 1), due to minor amounts of Cr. Spinel troctolites are generally plutonic or hypabyssal in origin (subsequently exhumed and incorporated into polymict breccias), or formed through impact processes (e.g., crystalline impact melt) [5]. A spinel-rich lithology has also been found in the Moscoviense region of the Moon via the Moon Mineralogy Mapper (M3) and lacks other mafic phases [6]. Finally, while the Mg-suite sampled thus far consists of plutonic (or hypabyssal) rocks, the question remains if such magmas could have erupted on the surface of the Moon [7]. These magmas have much lower density than mare basalts, but little sample or remote sensing evidence has been found to support the idea that extrusive Mg-suite volcanism occurred [7]. Here, we present a coordinated microanalytical study of spinel-bearing lithic and mineral clasts found in Apollo sample 68815. These data will be used to understand their petrogenesis (magmatic or impact) and modification histories, and to shed light on the existence of volcanic Mg-suite rocks. Sample Description: Apollo sample 68815 is a polymict impact melt breccia containing a variety of lithic and mineral fragments embedded in devitrified impact melt. This sample was chipped off the top of a boulder at Station 8 during the Apollo 16 mission and had an original weight of nearly 1.8 kg. In this study, we investigated two polished thin sections of 68815: 68815,17 and 68815,148, both containing spinel. Methods: The thin sections of 68815 were studied using optical light microscopy (PPL, cross-polarized light, and reflected light) with a Keyence VHX-7100 Digital Microscope. Each section was then X-ray mapped for 13–14 elements using a Cameca SX100 electron probe microanalyzer (EPMA) located in the Kuiper Materials Imaging and Characterization Facility (KMICF) at the University of Arizona. We have obtained geochemical information about the phases (olivine, plagioclase, spinel, pyroxene) in the thin sections also using the EPMA. In addition, we have used ThermoScientific Helios NanoLab 660 Focused-Ion-Beam Scanning-Electron Microscope (FIB-SEM) and a Hitachi S-4800 SEM (both in KMICF) to obtain backscattered electron (BSE) images and energy dispersive Xray spectrometry (EDS) maps of areas of interest. Using a JEOL 7900F SEM at the Astromaterials Research & Exploration Science (ARES) at NASA Johnson Space Center (JSC), we have obtained electron backscatter diffraction (EBSD) maps of the spinel-bearing portions of the thin sections. The EBSD data were collected under beam conditions of 20 kV, and ~90 μA, with step sizes varying from 0.05 to 2 μm. Following EBSD data collection, we processed the data using AZtecCrystal and MTEX, a free MATLAB toolbox. Results: We have found clasts with subophitic textures, that consist of primarily olivine and plagioclase, with minor amounts of pink Mg-Al spinel and pyroxene (Fig. 1). These clasts are up to ~1 mm in length and contain spinels up to 50 μm across. We have additionally identified pink Mg-Al spinels within the impact melt (i.e., not contained in lithic clasts) in both thin sections. In one instance, a single spinel grain is approximately 300 μm across (Fig. 1b, 2). The spinel fragments embedded in impact melt have varying compositions, typically distinct from the compositions of spinels in the lithic clasts. Spinel-Bearing Clasts: Ten lithic clasts with similar textures and mineral compositions were identified between 68815,17 (two clasts) and ,148 (eight clasts). These clasts fall into two groups. The first has skeletal olivine with intergranular plagioclase, with minor amounts of pyroxene and spinel (Fig. 1a, 2c, 2d). The spinel in these clasts are found amid the plagioclase. The second group have an intergranular texture of olivine and plagioclase, again with minor spinel and pyroxene. The second group may contain spinels surrounded by plagioclase, and spinels enclosed in olivine. Spinels located within both clast types range from no apparent Cr zoning, to reverse zoning (Cr-enrichment inward; Fig. 2d), to normal zoning (Cr-enrichment outward). In the clasts thus far investigated with EPMA, plagioclase compositions range from An# (molar 100×Ca/[Ca+Na+K]) 92–96. Olivine Mg# ranged from 77 to 94, while pyroxene had Mg# from 54–84. Spinel in the clasts have Cr# (molar 100×Cr/[Cr+Al]) 2–4 and Mg# 88–91, which is within the range of pristine and plutonic spinel troctolites [8]. Isolated Spinels: These crystals are generally euhedral to subhedral, and can exhibit reverse Cr zoning (Cr enrichment inward) or no apparent Cr zoning. The spinels thus far investigated via EPMA have Cr# 9–14 and Mg# 65–82. The Cr# for these spinels is within the range reported by [8], but have lower Mg#. Future Work: We will continue to process the EBSD data for these lithic and mineral clasts. We will also continue to characterize these clasts using EPMA and SEM. By thoroughly characterizing the various spinels and spinel-bearing clasts, we aim to constrain the petrogenesis of these minerals and rock fragments. Acknowledgments: We thank NASA for the loan of these thin sections. We thank Ken Domanik and Jerry Chang for their support with data collection. Work was supported by a University of Arizona RII Core Facilities Pilot Program grant and start-up funds to JJB. We acknowledge support from NASA’s Planetary Science Research program for analysis performed at JSC. References: [1] Shearer C. K. et al. (2015) Am. Min. 100, 294–325. [2] Borg L. E. et al. (2020) GCA 290, 312–332. [3] Warren P. H. (1993) Am. Min. 78, 360–376. [4] Dymek R. F. et al. (1976) LPS VII, 2335–2378. [5] Treiman et al. (2019) Am. Min. 104, 370–384. [6] Pieters et al. (2011) JGR: Plan. 116:E00G08. [7] Prissel et al. (2016) Icarus 277, 319–329. [8] Prissel et al. (2016) Am. Min. 101, 1624–1635.