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NASA NTRS1990

A study of the topology of dissipating motions in direct numerical simulations of time-developing compressible and incompressible mixing layers

A preliminary investigation of the geometry of flow patterns in numerically simulated compressible and incompressible mixing layers was carried out using 3-D critical point methodology. Motions characterized by high rates of kinetic energy dissipation and/or high enstrophy were of particular interest. In the approach the partial derivatives of the velocity field are determined at every point in the flow. These are used to construct the invariants of the velocity gradient tensor and the rate-of-strain tensor (P, Q, R, and P(sub s), Q(sub s), R(sub s) respectively). For incompressible flow the first invariant is zero. For the conditions of the compressible simulation, the first invariant is found to be everywhere small, relative to the second and third invariants, and so in both cases the local topology at a point is mainly determined by the second and third invariants. The data at every grid point is used to construct scatter plots of Q versus R and Q(sub s) versus R(sub s). Most points map to a cluster near the origin in Q-R space. However, fine scale motions, that is motions which are characterized by velocity derivatives which scale with the square root of R(sub delta), tend to map to regions which lie far from the origin. Definite trends are observed for motions characterized by high enstrophy and/or high dissipation. The observed trends suggest that, for these motions, the second and third invariants of the velocity gradient and rate-of-strain tensors are strongly correlated. The second and third invariants of the rate-of-strain tensor are related by K(-Q(sub s))(exp 3/2), which is consistent with the above scaling of velocity derivatives. The quantity K appears to depend on Reynolds number with an upper limit K = 2(the square root of 3)/9 corresponding to locally axisymmetric flow. For both the compressible and incompressible mixing layer, regions corresponding to high rates of dissipation are found to be characterized by comparable magnitudes of R(sub ij)R(sub ij) and S(sub ij)S(sub ij). For the incompressible mixing layer, regions characterized by the highest values of enstrophy are found to have relatively low strain rates.

Chen, J. H.↗

DOE OSTI2023

Simultaneous bright- and dark-field X-ray microscopy at X-ray free electron lasers

Abstract The structures, strain fields, and defect distributions in solid materials underlie the mechanical and physical properties across numerous applications. Many modern microstructural microscopy tools characterize crystal grains, domains and defects required to map lattice distortions or deformation, but are limited to studies of the (near) surface. Generally speaking, such tools cannot probe the structural dynamics in a way that is representative of bulk behavior. Synchrotron X-ray diffraction based imaging has long mapped the deeply embedded structural elements, and with enhanced resolution, dark field X-ray microscopy (DFXM) can now map those features with the requisite nm-resolution. However, these techniques still suffer from the required integration times due to limitations from the source and optics. This work extends DFXM to X-ray free electron lasers, showing how the $$10^{12}$$ 10 12 photons per pulse available at these sources offer structural characterization down to 100 fs resolution (orders of magnitude faster than current synchrotron images). We introduce the XFEL DFXM setup with simultaneous bright field microscopy to probe density changes within the same volume. This work presents a comprehensive guide to the multi-modal ultrafast high-resolution X-ray microscope that we constructed and tested at two XFELs, and shows initial data demonstrating two timing strategies to study associated reversible or irreversible lattice dynamics.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Complex genetics cause and constrain fungal persistence in different parts of the mammalian body

Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae. Employing chromosomally encoded DNA barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain vs the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in nonbrain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1996

Interferometric Radar Observations of Glaciar San Rafael, Chile

Interferometric radar observations of Glaciar San Rafael, Chile, were collected in October 1994 by NASA's Spaceborne Imaging Radar C (SIR-C) at both L- (24cm) and C-band frequency (5.6cm), with vertical transmit and receive polarization. The C-band data did not yield good geophysical products, because the temporal coherence of the signal was significantly reduced after 24h. The L-band data were, however, successfully employed to map the surface topography of the icefield with a 10m uncertainty in height, and measure ice velocity with a precision of 4 mm/d or 1.4 m/a. The corresponding error in strain rates is 0.05/a at a 30 m horizontal spacing. The one-dimensional interferometric velocities were subsequently converted to horizontal displacements by assuming a flow direction and complemented by feature-tracking results near the calving front. The results provide a comprehensive view of the ice-flow dynamics of Glaciar San Rafael. The glacier has a core of rapid flow, 4.5 km in width and 3.5 degrees in average slope,surrounded by slower moving ice, not by rock. Ice velocity is 2.6 m/d or 0.95 km/a near the equilibrium line altitude (1200m), increasing rapidly before the glacier enters the narrower terminal valley, to reach 17.5 m/d or 6.4 km/a at the calving front. Strain rates are dominated by lateral shearing at the glacier margins (0.4-0.7/a), except for the terminal-valley section, where longitudinal strain rates average close to 1/a. This spectacular longitudinal increase in ice velocity in the last few kilometers may be a fundamental feature of tidewater glaciers.

Rignot, Eric↗

DOE OSTI2024

Oil-Pressure Based Apparatus for In-Situ High-Energy Synchrotron X-Ray Diffraction Studies During Biaxial Deformation

Background: Understanding biaxial loading response at the microstructural level is crucial in helping better design sheet manufacturing processes and calibrate/validate material deformation models. Objective: The objective of this work was to develop a low-cost testing apparatus to probe, with sufficient spatial resolution, the micro-mechanical response of a sheet material in-situ under biaxial loading conditions. Methods: The testing apparatus fabricated as a part of this study operates in a similar fashion to a standard bulge test and uses oil pressure to generate biaxial loading conditions. This biaxial testing apparatus was operated within a synchrotron beamline to characterize the mechanical response of a flash-processed steel sheet using in-situ high-energy X-ray diffraction (XRD) measurements. Further, the GSAS-II package was utilized to develop a workflow for the analysis of the large volume of diffraction data acquired. The workflow was then used to extract the peak position, width, and integrated intensity of the XRD peaks corresponding to the major body-centered cubic phase. Results: The equi-biaxial nature of the loading in the measured area was independently corroborated using experimental (XRD) and simulation (finite element analysis) methods. Furthermore, we discuss the evolution of elastic strain in the major body-centered cubic phase as a function of applied oil pressure and location on the steel sheet. Conclusions: A key advantage of the biaxial apparatus fabricated in this synchrotron study is demonstrated using the results obtained for the flash-processed steel sheet – i.e., mapping the lattice plane-dependent response to biaxial loading for a relatively large sample area in a spatially resolved manner.

36 MATERIALS SCIENCE↗

NASA NTRS2016

Probabilistic Modeling Of Ocular Biomechanics In VIIP: Risk Stratification

Visual Impairment and Intracranial Pressure (VIIP) syndrome is a major health concern for long-duration space missions. Currently, it is thought that a cephalad fluid shift in microgravity causes elevated intracranial pressure (ICP) that is transmitted along the optic nerve sheath (ONS). We hypothesize that this in turn leads to alteration and remodeling of connective tissue in the posterior eye which impacts vision. Finite element (FE) analysis is a powerful tool for examining the effects of mechanical loads in complex geometries. Our goal is to build a FE analysis framework to understand the response of the lamina cribrosa and optic nerve head to elevations in ICP in VIIP. To simulate the effects of different pressures on tissues in the posterior eye, we developed a geometric model of the posterior eye and optic nerve sheath and used a Latin hypercubepartial rank correlation coef-ficient (LHSPRCC) approach to assess the influence of uncertainty in our input parameters (i.e. pressures and material properties) on the peak strains within the retina, lamina cribrosa and optic nerve. The LHSPRCC approach was repeated for three relevant ICP ranges, corresponding to upright and supine posture on earth, and microgravity [1]. At each ICP condition we used intraocular pressure (IOP) and mean arterial pressure (MAP) measurements of in-flight astronauts provided by Lifetime Surveillance of Astronaut Health Program, NASA Johnson Space Center. The lamina cribrosa, optic nerve, retinal vessel and retina were modeled as linear-elastic materials, while other tissues were modeled as a Mooney-Rivlin solid (representing ground substance, stiffness parameter c1) with embedded collagen fibers (stiffness parameters c3, c4 and c5). Geometry creationmesh generation was done in Gmsh [2], while FEBio was used for all FE simulations [3]. The LHSPRCC approach resulted in correlation coefficients in the range of 1. To assess the relative influence of the uncertainty in an input parameter on the peak strains, we ranked and then normalized these coefficients, considering that normalized values 0.5 implied a substantial influence on the range of the peak strains in the optic nerve head (ONH). IOP and ICP were found to have a major influence on the peak strains in the ONH, as did optic nerve and LC stiffness. Interestingly, the stiffness of the sclera far from the scleral canal did not have a large influence on peak strains in ONH tissues; however, the collagen fiber stiffness in the peripapillary sclera and annular ring both influenced the peak strains within the ONH. We have created a physiologically relevant model that incorporated collagen fibers to study the effects of elevated ICP. Elevated ICP resulted in strains in the optic nerve that are not predicted to occur on earth: the upright or supine conditions. We found that IOP, ICP, lamina cribrosa stiffness and optic nerve stiffness had the highest association with these extreme strains in the ONH. These extreme strains may activate mechanosensitive cells that induce tissue remodeling and are a risk factor for the development of VIIP.

biomechanics↗

DOE OSTI2022

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Experimental and theoretical investigation of the crystalline surface, film, and interface properties of antiperovskite Mn 3 GaN grown by molecular beam epitaxy on MgO(001)

Here, we present a study of the epitaxial growth, characterization, and theoretical modeling of thin film antiperovskite Mn 3 GaN, an antiferromagnetic material with kagome structure which is grown on MgO (001) substrates using N-plasma-assisted molecular beam epitaxy. Reflection high energy electron diffraction is used to assess the in-plane evolution of the film structure during growth, and the surface is investigated in-situ using scanning tunneling microscopy and Auger electron spectroscopy. These results are combined with precision measurements done ex-situ determining the film lattice constants using a combination of x-ray diffraction with reciprocal space mapping and scanning transmission electron microscopy. Overall, a uniform, homogeneous film with an atomically smooth vacuum surface and atomically sharp substrate interface is found having very small in-plane tensile strain and mild out-of-plane compressive strain. First-principles theoretical calculations are applied in order to ascertain the lowest energy models for both the Mn 3 GaN surface and the Mn 3 GaN/MgO film/substrate interface. Models including MnGa versus MnN surface layers and MnGa versus MnN interfacial layers are considered as functions of both the Mn and Ga chemical potentials. The predictions are discussed in comparison to the experimental results. The overall findings suggest that Mn 3 GaN on MgO(001) is a viable epitaxial film which can be further explored in connection with antiferromagnetic spintronics.

Density functional theory↗

DOE OSTI2023

Neural networks for large eddy simulations of wall-bounded turbulence: numerical experiments and challenges

Here, we examine the application of neural network-based methods to improve the accuracy of large eddy simulations of incompressible turbulent flows. The networks are trained to learn a mapping between flow features and the subgrid scales, and applied locally and instantaneously—in the same way as traditional physics-based subgrid closures. Models that use only the local resolved strain rate are poorly correlated with the actual subgrid forces obtained from filtering direct numerical simulation data. We see that highly accurate models in a priori testing are inaccurate in forward calculations, owing to the preponderance of numerical errors in implicitly filtered large eddy simulations. A network that accounts for the discretization errors is trained and found to be unstable in a posteriori testing. We identify a number of challenges that the approach faces, including a distribution shift that affects networks that fail to account for numerical errors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Mapping nanocrystal orientations via scanning Laue diffraction microscopy for multi-peak Bragg coherent diffraction imaging

The recent commissioning of a movable monochromator at the 34-ID-C endstation of the Advanced Photon Source has vastly simplified the collection of Bragg coherent diffraction imaging (BCDI) data from multiple Bragg peaks of sub-micrometre scale samples. Laue patterns arising from the scattering of a polychromatic beam by arbitrarily oriented nanocrystals permit their crystal orientations to be computed, which are then used for locating and collecting several non-co-linear Bragg reflections. The volumetric six-component strain tensor is then constructed by combining the projected displacement fields that are imaged using each of the measured reflections via iterative phase retrieval algorithms. Complications arise when the sample is heterogeneous in composition and/or when multiple grains of a given lattice structure are simultaneously illuminated by the polychromatic beam. Here, a workflow is established for orienting and mapping nanocrystals on a substrate of a different material using scanning Laue diffraction microscopy. The capabilities of the developed algorithms and procedures with both synthetic and experimental data are demonstrated. The robustness is verified by comparing experimental texture maps obtained with Laue diffraction microscopy at the beamline with maps obtained from electron back-scattering diffraction measurements on the same patch of gold nanocrystals. Such tools provide reliable indexing for both isolated and densely distributed nanocrystals, which are challenging to image in three dimensions with other techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Role of ferroelectric polarization during growth of highly strained ferroelectric materials

In ferroelectric thin films and superlattices, the polarization is intricately linked to crystal structure. Here we show that it can also play an important role in the growth process, influencing growth rates, relaxation mechanisms, electrical properties and domain structures. This is studied by focusing on the properties of BaTiO 3 thin films grown on very thin layers of PbTiO 3 using x-ray diffraction, piezoforce microscopy, electrical characterization and rapid in-situ x-ray diffraction reciprocal space maps during the growth using synchrotron radiation. Using a simple model we show that the changes in growth are driven by the energy cost for the top material to sustain the polarization imposed upon it by the underlying layer, and these effects may be expected to occur in other multilayer systems where polarization is present during growth. This motivates the concept of polarization engineering as a complementary approach to strain engineering.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Atomic-Scale Scanning of Domain Network in the Ferroelectric HfO 2 Thin Film

Ferroelectric HfO 2 -based thin films have attracted much interest in the utilization of ferroelectricity at the nanoscale for next-generation electronic devices. However, the structural origin and stabilization mechanism of the ferroelectric phase are not understood because the film is typically nanocrystalline with active yet stochastic ferroelectric domains. Here, in this study, electron microscopy is used to map the in-plane domain network structures of epitaxially grown ferroelectric Y:HfO 2 films in atomic resolution. The ferroelectricity is confirmed in free-standing Y:HfO 2 films, allowing for investigating the structural origin for their ferroelectricity by 4D-STEM, high-resolution STEM, and iDPC-STEM. At the grain boundaries of <111>-oriented Pca2 1 orthorhombic grains, a high-symmetry mixed-(R3m, Pnm2 1 ) phase is induced, exhibiting enhanced polarization due to in-plane compressive strain. Nanoscale Pca2 1 orthorhombic grains and their grain boundaries with mixed-(R3m, Pnm2 1 ) phases of higher symmetry cooperatively determine the ferroelectricity of the Y:HfO 2 film. It is also found that such ferroelectric domain networks emerge when the film thickness is beyond a finite value. Furthermore, in-plane mapping of oxygen positions overlaid on ferroelectric domains discloses that polarization is suppressed at vertical domain walls, while it is active when domains are aligned horizontally with subangstrom domain walls. In addition, randomly distributed 180° charged domain walls are confined by spacer layers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A taxogenomic view of the genus Torulaspora : an expansion from ten to twenty-two species

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species, T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains 10 species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how the complex relationship between key genes and the physiological traits they control both between and within species. This remarkable increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomic approaches can foster the assessment of species circumscriptions in fungi.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Nanoscale Superconducting States in the Fe-Based Filamentary Superconductor of Pr-Doped CaFe 2 As 2

The low-temperature scanning tunneling microscope and spectroscopy (STM/STS) are used to visualize superconducting states in the cleaved single crystal of 9% praseodymium-doped CaFe 2 As 2 (Pr-Ca122) with Tc ≈ 30 K. The spectroscopy shows strong spatial variations in the density of states (DOS), and the superconducting map constructed from spectroscopy discloses a localized superconducting phase, as small as a single unit cell. The comparison of the spectra taken at 4.2 K and 22 K (below vs. close to the bulk superconducting transition temperature) from the exact same area confirms the superconducting behavior. Nanoscale superconducting states have been found near Pr dopants, which can be identified using dI/dV conductance maps at +300 mV. There is no correlation of the local superconductivity to the surface reconstruction domain and surface defects, which reflects its intrinsic bulk behavior. We, therefore, suggest that the local strain of Pr dopants is competing with defects induced local magnetic moments; this competition is responsible for the local superconducting states observed in this Fe-based filamentary superconductor.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Genome assembly UWOPS 85-398.1-1

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.

Sampaio, Jose P. [UCIBIO, Departamento de Ciências↗

DOE OSTI2025

Genome assembly UFMG-CM Y6992

Sampaio, Jose P. [UCIBIO, Departamento de Ciências↗

NASA NTRS2020

Spatial U-Pb Age Distribution in Shock-Recrystallized Zircon – A Case Study from the Rochechouart Impact Structure, France

Age determination of impact structures via the zircon U–Pb system remains challenging and often ambiguous due to highly variable effects of shock metamorphism on U-Pb geochronology. It is, therefore, crucial to link the observed zircon microtextures, including their temperature and pressure conditions associated with their formation, directly to the U–Pb ages preserved. Here, we analyzed three recrystallized zircon grains and one plastically deformed zircon crystal from the medium-sized Rochechouart impact structure in the northwestern Massif Central of France. For the Rochechouart impact structure the impact age (206.92 ± 0.32 Ma [40Ar/39Ar]) as well as the 2 tectono-themal history is well established making this study site ideal to test concepts about U-Pb systematics in shocked zircon and to differentiate between shock-driven age resetting and preimpact crystallization and metamorphic overprinting. Zircon microstructures were studied using scanning electron imaging, cathodoluminescence imaging, and electron backscatter diffraction (EBSD) mapping. Further, we conducted U–Pb Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) depth-profiling analysis, allowing us to interpret the resultant age data in discrete steps with increasing ablation time/depth. The U–Pb depth profiling data demonstrate that plastically strained grains are incompletely reset and preserve rim and interior age domains reflecting typical pre-impact (pre-Variscan and Variscan) regional tectonic ages. Our results also reveal that the granular crystals encountered contain microstructural evidence for “former reidite in granular neoblastic” (FRIGN) zircon, reflecting both high-pressure (⩾30GPa) and high temperature (⩾1200℃) conditions. This signifies that FRIGN zircon is now known from an additional, medium sized, impact structure further supporting the hypothesis that this impact induced microstructure is commonly preserved. In addition, FRIGN zircon has a high potential to preserve completely impact-reset crystal domains (~204 to 207 Ma) that can be identified by our combined analytical approach of U–Pb depth profiling and EBSD mapping, and thus are suitable for determining reliable impact ages

U-Pb depth profiling↗

DOE OSTI2024

Revealing the hidden structure of disordered materials by parameterizing their local structural manifold

Abstract Durable interest in developing a framework for the detailed structure of glassy materials has produced numerous structural descriptors that trade off between general applicability and interpretability. However, none approach the combination of simplicity and wide-ranging predictive power of the lattice-grain-defect framework for crystalline materials. Working from the hypothesis that the local atomic environments of a glassy material are constrained by enthalpy minimization to a low-dimensional manifold in atomic coordinate space, we develop a generalized distance function, the Gaussian Integral Inner Product (GIIP) distance, in connection with agglomerative clustering and diffusion maps, to parameterize that manifold. Applying this approach to a two-dimensional model crystal and a three-dimensional binary model metallic glass results in parameters interpretable as coordination number, composition, volumetric strain, and local symmetry. In particular, we show that a more slowly quenched glass has a higher degree of local tetrahedral symmetry at the expense of cyclic symmetry. While these descriptors require post-hoc interpretation, they minimize bias rooted in crystalline materials science and illuminate a range of structural trends that might otherwise be missed.

36 MATERIALS SCIENCE↗