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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 361 records · Page 20

ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.

54 ENVIRONMENTAL SCIENCES↗

Association between the findings of metachronous secondary primary malignancies and the number of Lugol-voiding lesions

Summary This study was designed to evaluate the relation between dysplastic squamous epithelium in the esophageal mucosa and the development of metachronous secondary primary malignancies (mSPM) other than esophagus after endoscopic resection (ER) in patients with early esophageal squamous cell carcinoma (SCC). We studied 330 patients with early esophageal SCC who underwent ER as a post hoc analysis of a prospective multicenter cohort study (UMIN Clinical Trials Registry ID UMIN000001676). Lugol-voiding lesions (LVL) were graded into 3 categories (A = no lesion; B = 1 to 9 lesions; C ≥ 10 lesions). The following variables were studied: (i) the incidences of mSPM other than esophagus; (ii) the standardized incidence ratios (SIRs) of mSPM; (iii) the cumulative incidence and total number of mSPM other than esophagus; and (iv) predictors of mSPM other than esophagus on analysis with a multivariate Cox proportional-hazards model. After a median follow-up of 46.6 months, mSPM other than esophagus was diagnosed in a total of 73 patients (90 lesions). Among the 106 patients in group C, 37 patients had mSPM (51 lesions), including head and neck cancer in 14 patients (24 lesions) and gastric cancer in 12 patients (16 lesions). The SIR of mSPM was 3.61 in this study subjects. An increase in the LVL grade (A to B to C) was associated with a progressive increase in the cumulative incidence rate of mSPM other than esophagus (P = 0.017 for A vs. C, P = 0.023 for B vs. C). An increase in the LVL grade (A to B to C) was also associated with a progressive increase in the total number of mSPM other than esophagus per 100 person-years (primary events, relative risk [RR] = 1.66 and 3.24 for grades B and C, respectively, vs. A, P = 0.002 for trend; all events, RR = 1.81 and 4.66 for grades B and C, respectively, vs. A, P < 0.0001 for trend). LVL grade C was a strong predictor of mSPM other than esophagus (RR = 3.41 for A vs. C). LVL grade may be a useful predictor of the risk of mSPM other than esophagus after ER in patients with early esophageal SCC.

Katada, Chikatoshi↗

Low Mutation Rate and Atypical Mutation Spectrum in Prasinoderma coloniale : Insights From an Early Diverging Green Lineage

Mutations are the ultimate source of genetic diversity on which natural selection and genetic drift act, playing a crucial role in evolution and long-term adaptation. At the molecular level, the spontaneous mutation rate (µ), defined as the number of mutations per base per generation, thus determines the adaptive potential of a species. Through a mutation accumulation experiment, we estimate the mutation rate and spectrum in Prasinoderma coloniale, a phytoplankton species from an early-branching lineage within the Archaeplastida, characterized by an unusually high genomic guanine-cytosine (GC) content (69.8%). We find that P. coloniale has a very low total mutation rate of µ = 2.00 × 10 -10 . The insertion–deletion mutation rate is almost 5 times lesser than the single nucleotide mutation rate with µ ID = 3.40 × 10 -11 and µ SNM = 1.62 × 10 -10 . Prasinoderma coloniale also exhibits an atypical mutational spectrum: While essentially all other eukaryotes show a bias toward GC to AT mutations, no evidence of this AT-bias is observed in P. coloniale. Since cytosine methylation is known to be mutagenic, we hypothesized that this may result from an absence of C-methylation. Surprisingly, we found high levels of C-methylation (14% in 5mC, 25% in 5mCG contexts). Methylated cytosines did not show increased mutation rates compared with unmethylated ones, not supporting the prevailing notion that C-methylation universally leads to higher mutation rates. Overall, P. coloniale combines a GC-rich genome with a low mutation rate and original mutation spectrum, suggesting the almost universal AT-bias may not have been present in the ancestor of the green lineage.

59 BASIC BIOLOGICAL SCIENCES↗

DNA Sequence-Based Identification of Fusarium : A Work in Progress

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue ( Torres-Cruz et al. 2022 ), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

Plant Sciences↗

Bioapatite in shark centra studied by wide-angle and by small-angle X-ray scattering

Members of subclass Elasmobranchii possess cartilage skeletons; the centra of many species are mineralized with a bioapatite, but virtually nothing is known about the mineral's organization. This study employed high-energy, small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS, i.e. X-ray diffraction) to investigate the bioapatite crystallography within blocks cut from centra of four species (two carcharhiniform families, one lamniform family and 1-ID of the Advanced Photon Source). All species' crystallographic quantities closely matched and indicated a bioapatite closely related to that in bone. The centra's lattice parameters a and c were somewhat smaller and somewhat larger, respectively, than in bone. Nanocrystallite sizes (WAXS peak widths) in shark centra were larger than typical of bone, and little microstrain was observed. Compared with bone, shark centra exhibited SAXS D-period peaks with larger D magnitudes, and D-period arcs with narrower azimuthal widths. The shark mineral phase, therefore, is closely related to that in bone but does possess real differences which probably affect mechanical property and which are worth further study.

59 BASIC BIOLOGICAL SCIENCES↗

Assessment of diagenesis in archaeological human second metacarpal bones using the intensity of the small angle X-ray scattering D -period peak

Bone consists mainly of carbonated apatite (cAp) nanoplatelets embedded in a matrix of collagen fibrils. Earlier, high-energy small angle X-ray scattering (SAXS) studies of archaeological adult human second metacarpal bones (mc2) found collagen D-period peaks with high-intensity I D in specimens in which microcomputed tomography (microCT) showed little diagenesis and I D ~ 0 for specimens where microCT revealed severe diagenesis (Park et al. 2022 Int. J. Osteoarchaeol. 32, 170–181 (doi:10.1002/oa.3053); Stock et al. 2022 Int. J. Osteoarchaeol. 32, 120–131 (doi:10.1002/oa.3049)). Here, the present paper uses SAXS at beamline 1-ID, Advanced Photon Source, Argonne National Laboratory and other techniques to study a set of 10 mc2 from an early Medieval cemetery at Greding, Germany. We hypothesized that non-invasive measurement of I D would provide an accurate and rapid (approx. 6 min/specimen) assessment of diagenesis in archaeological mc2. Results of Raman spectroscopy, laboratory microCT and backscattered electron, reflected light and polarized transmitted light microscopies confirmed the SAXS determinations, but lattice parameter values from X-ray diffraction were uncorrelated with I D value. Age-at-death estimates placed the 10 mc2 in three age categories (young adult, middle adult, old adult): lattice parameters from X-ray diffraction were uncorrelated with age at death. Cross-sectional bone area fraction from microCT dropped noticeably for the older age cohort.

Raman spectroscopy↗

Temperature Mapping of Stacked Silicon Dies from X-Ray-Diffraction Intensities

Increasing power densities in integrated circuits have led to an increased prevalence of thermal hotspots in integrated circuits. Tracking these thermal hotspots is imperative to prevent circuit failures. In three- dimensional (3D) integrated circuits, conventional surface techniques like infrared thermometry are unable to measure the 3D temperature distribution, and optical and magnetic resonance techniques are difficult to apply due to the presence of metals and large current densities. X-rays offer a high penetration depth and can be used to probe 3D structures. We report a method utilizing the temperature dependence of x-ray-diffraction intensity via the Debye-Waller factor to simultaneously map the temperature of individual silicon dies in a stack. Here, utilizing beamline 1-ID-E at the Advanced Photon Source (Argonne), we demonstrate, for each individual silicon die, a temperature resolution of 3 K, a spatial resolution of 100 × 400 μm 2 , and a temporal resolution of 20 s. Utilizing a sufficiently high-intensity laboratory source, e.g., from a liquid-anode source, this method can be scaled down to laboratories for noninvasive temperature mapping of 3D integrated circuits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Nematic superconductivity in twisted bilayer graphene

Twisted bilayer graphene displays insulating and superconducting phases caused by exceptional flattening of its lowest energy bands. Superconductivity with highest T c appears near half filling of the valence band (n ≈ –2). The data show that in the large part of the superconducting dome near n = –2, threefold lattice rotation symmetry is broken in the superconducting phase, i.e., a superconductor is also a nematic. We perform a comprehensive analysis of superconductivity in twisted-bilayer graphene within an itinerant approach and present a mechanism for nematic superconductivity. We take as an input the fact that at dopings, where superconductivity has been observed, the Fermi energy lies in the vicinity of twist-induced Van Hove singularities in the density of states. We argue that the low-energy physics can be properly described by patch models with either six or twelve Van Hove points. We obtain pairing interactions for the patch models in terms of parameters of the microscopic model for the flat bands, which contains both local and twist-induced nonlocal interactions. Here, we show that the latter give rise to attraction in different superconducting channels. For six Van Hove points, there is just one attractive d-wave channel, and we find chiral d ± id superconducting order, which breaks time-reversal symmetry but leaves the lattice rotation symmetry intact. For twelve Van Hove points, we find two attractive channels, g and i waves, with almost equal coupling constants. We show that both order parameters are nonzero in the ground state and explicitly demonstrate that in this co-existence state the threefold lattice rotation symmetry is broken, i.e., the superconducting state is also a nematic. We find two possible nematic states, one is time-reversal symmetric, the other additionally breaks time-reversal symmetry. We apply our scenario to twisted bilayer graphene near n = –2 and argue that it is applicable also to other systems with two (or more) attractive channels with similar couplings as our reasoning for a nematic superconductivity is based on generic symmetry considerations.

36 MATERIALS SCIENCE↗

Topological and nematic superconductivity mediated by ferro-SU(4) fluctuations in twisted bilayer graphene

We propose an SU(4) spin-valley-fermion model to investigate the superconducting instabilities of twisted bilayer graphene (TBG). In this approach, bosonic fluctuations associated with an emergent SU(4) symmetry, corresponding to combined rotations in valley and spin spaces, couple to the low-energy fermions that comprise the flat bands. These fluctuations are peaked at zero wave vector, reflecting the “ferromagnetic-like” SU(4) ground state recently found in strong-coupling solutions of microscopic models for TBG. Focusing on electronic states related to symmetry-imposed points of the Fermi surface, dubbed here “valley hot-spots” and “van Hove hot-spots,” we find that the coupling to the itinerant electrons partially lifts the huge degeneracy of the ferro-SU(4) ground state manifold, favoring intervalley order, spin-valley coupled order, ferromagnetic order, spin-current order, and valley-polarized order, depending on details of the band structure. Here, these fluctuations, in turn, promote attractive pairing interactions in a variety of closely competing channels, including a nodeless f-wave state, a nodal i-wave state, and topological d+id and p+ip states with unusual Chern numbers 2 and 4, respectively. Nematic superconductivity, although not realized as a primary instability of the system, appears as a consequence of the near-degeneracy of superconducting order parameters that transform as one-dimensional and two-dimensional irreducible representations of the point group D 6 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Role of electromagnetic gauge-field fluctuations in the selection between chiral and nematic superconductivity

Motivated by the observation of nematic superconductivity in several systems, we revisit the problem of the leading pairing instability of two-component unconventional superconductors on the triangular lattice—such as (p x , p y )-wave and (d x 2 –y 2 , d xy )-wave superconductors. Such a system has two possible superconducting states: the chiral state (e.g., p + ip or d + id), which breaks time-reversal symmetry, and the nematic state (e.g., p + p or d + d), which breaks the threefold rotational symmetry of the lattice. Weak-coupling calculations generally favor the chiral over the nematic superconducting state, raising the question of what mechanism can stabilize the latter. Here, we show that the electromagnetic field fluctuations can play a crucial role in selecting between these two states. Specifically, we derive and analyze the effective free energy for the two-component superconducting order parameter after integrating out the gauge-field fluctuations, which is formally justified if the spatial order parameter fluctuations can be neglected. A nonanalytic cubic term arises, as in the case of a conventional s -wave superconductor. However, unlike the latter, the cubic term depends on the relative phase and on the relative amplitudes between the two order parameter components, in such a way that it generally favors the nematic state. This result is a direct consequence of the fact that the stiffness of the superconducting order parameter is not isotropic. Competition with the quartic term, which favors the chiral state, leads to a renormalized phase diagram in which the nematic state displaces the chiral state over a wide region in the parameter space. Here, we analyze the stability of the fluctuation-induced nematic phase, generalize our results to tetragonal lattices, and discuss their applicability to candidate nematic superconductors, including twisted bilayer graphene.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Superconducting gap symmetry from Bogoliubov quasiparticle interference analysis on Sr 2 RuO 4

Here, the nature of the superconducting order parameter in Sr 2 RuO 4 has generated intense interest in recent years. Since the superconducting gap is very small, high-resolution methods such as scanning tunneling spectroscopy might be the best chance to directly resolve the gap symmetry. Recently, a Bogoliubov quasiparticle interference imaging (BQPI) experiment has suggested that the d x 2 –y 2 gap symmetry is appropriate for Sr 2 RuO 4 . In this work, we use a material-specific theoretical approach based onWannier functions of the surface of Sr 2 RuO 4 to calculate the continuum density of states as detected in scanning tunneling microscopy experiments. We examine several different proposed gap order parameters and calculate the expected BQPI pattern for each case. Comparing to the available experimental data, our results suggest that a s' + id xy gap order parameter is the most probable state, but the measured BQPI patterns still display features unaccounted for by the theory for any of the states currently under discussion.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Persistent Josephson tunneling between Bi 2 Sr 2 CaCu 2 O 8 + x flakes twisted by 45 ° across the superconducting dome

There is a heated debate on the Josephson effect in twisted Bi 2 Sr 2 CaCu 2 O 8+x flakes. Recent experimental results suggest the presence of either anomalously isotropic pairing or exotic d+id-wave pairing, in addition to the commonly believed d-wave one. Here, we address this controversy by fabricating ultraclean junctions with uncompromised crystalline quality and stoichiometry at the junction interfaces. In the optimally doped regime, we obtain prominent Josephson coupling (2-4 mV) in multiple junctions with the twist angle of 45°, in sharp contrast to a recent report that shows two orders of magnitude suppression around 45° from the value at 0°. We further extend this study to the previously unexplored overdoped regime and observe pronounced Josephson tunneling at 45° together with Josephson diode effect up to 50 K. In conclusion, our work helps establish the persistent presence of an isotropic pairing component across the entire superconducting phase diagram.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Flow matching beyond kinematics: Generating jets with particle identification and trajectory displacement information

We introduce the first generative model trained on the etlass dataset. Our model generates jets at the constituent level, and it is a permutation-equivariant continuous normalizing flow (CNF) trained with the flow matching technique. It is conditioned on the jet type, so that a single model can be used to generate the ten different jet types of etlass. For the first time, we also introduce a generative model that goes beyond the kinematic features of jet constituents. The etlass dataset includes more features, such as particle-ID and track impact parameter, and we demonstrate that our CNF can accurately model all of these additional features as well. Our generative model for etlass expands on the versatility of existing jet generation techniques, enhancing their potential utility in high-energy physics research, and offering a more comprehensive understanding of the generated jets. Published by the American Physical Society 2025

Birk, Joschka (ORCID:0000000219310127)↗

Quantum Phase Diagram and Spontaneously Emergent Topological Chiral Superconductivity in Doped Triangular-Lattice Mott Insulators

The topological superconducting state is a highly sought-after quantum state hosting topological order and Majorana excitations. Here, in this Letter, we explore the mechanism to realize the topological superconductivity (TSC) in the doped Mott insulators with time-reversal symmetry (TRS). Through large-scale density matrix renormalization group study of an extended triangular-lattice t–J model on the six- and eight-leg cylinders, we identify a d + id-wave chiral TSC with spontaneous TRS breaking, which is characterized by a Chern number C=2 and quasi-long-range superconducting order. We map out the quantum phase diagram with by tuning the next-nearest-neighbor (NNN) electron hopping and spin interaction. In the weaker NNN-coupling regime, we identify a pseudogaplike phase with a charge stripe order coexisting with fluctuating superconductivity, which can be tuned into d -wave superconductivity by increasing the doping level and system width. The TSC emerges in the intermediate-coupling regime, which has a transition to a d-wave superconducting phase with larger NNN couplings. The emergence of the TSC is driven by geometrical frustrations and hole dynamics which suppress spin correlation and charge order, leading to a topological quantum phase transition.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Identifying topological superconductivity in two-dimensional transition-metal dichalcogenides

Here we study the superconducting pairing instabilities and gap functions for prototypical two-dimensional (2D) transition-metal dichalcogenides (TMDCs) WS 2 , MoTe 2 , and MoS 2 in the 2H phase under both hole and electron doping at 10 K. Our first-principles quantum many-body Green's function approach allows us to treat the full d and p manifold of orbitals with strong spin-orbit coupling, yielding pairing predictions with material-specific detail. The resulting gap functions exhibit a variety of mixed-parity superconducting states, including s, p, d, f, d ± id, and p ± ip pairing modes. In particular, we predict 3% and 4% hole-doped WS 2 to be a chiral p ± ip topological superconductor. For 1% hole-doped MoS 2 , we find a competition between three doubly degenerate chiral and nonchiral instabilities. Overall, the relative pairing strengths are found to follow the Fermi-surface topology, due to nesting between the Fermi-surface sheets. Finally, we discuss our predictions in relation to available experimental data and classify the topology of the predicted superconducting pairing symmetries.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Focusing with saw-tooth refractive lenses at a high-energy X-ray beamline

The Advanced Photon Source 1-ID beamline, operating in the 40–140 keV X-ray energy range, has successfully employed continuously tunable saw-tooth refractive lenses to routinely deliver beams focused in both one and two dimensions to experiments for over 15 years. The practical experience of implementing such lenses, made of silicon and aluminium, is presented, including their properties, control, alignment, and diagnostic methods, achieving ∼1 µm focusing (vertically). Ongoing development and prospects towards submicrometre focusing at these high energies are also mentioned.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Repeatability and sensitivity characterization of the far-field high-energy diffraction microscopy instrument at the Advanced Photon Source

In the last two decades, far-field high-energy diffraction microscopy (FF-HEDM) and similar non-destructive techniques have been actively developed at synchrotron light sources around the world. As these techniques (and associated analysis tools) are becoming more available for the general users of these light sources, it is important and timely to characterize their performance and capabilities. In this work, the FF-HEDM instrument implemented at the 1-ID-E endstation of the Advanced Photon Source (APS) is summarized. The set of measurements conducted to characterize the instrument's repeatability and sensitivity to changes in grain orientation and position are also described. When an appropriate grain matching method is used, the FF-HEDM instrument's repeatability is approximately 5 µm in translation, 0.02° in rotation, and 2 × 10 −4 in strain; the instrument sensitivity is approximately 5 µm in translation and 0.05° in rotation.

3DXRD↗