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At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Over the past several decades, electron and scanning probe microscopes have become critical components of condensed matter physics, materials science and chemistry research. At the same time, the infrastructure for establishing a connection between microscopy observations and materials behaviour over a broader parameter space is lacking. In this work, we introduce AtomAI, an open-source software package bridging instrument-specific Python libraries, deep learning and simulation tools into a single ecosystem. AtomAI allows direct applications of deep neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders for disentangling structural factors of variation and im2spec type of encoder–decoder models for mapping structure–property relationships. Finally, our framework allows seamless connection to the first principles modelling with a Python interface on the inferred atomic positions.

36 MATERIALS SCIENCE↗
NASA NTRS1973

Particle track record in Apollo 15 deep core from 54 to 80 cm depths.

Particle track measurements have been made in nearly 500 individual grains from 13 levels in the 54-80 cm depth range of the Apollo 15 deep core. They reveal a wide range of track densities at all depths and some systematic variations within layers, indicating that both predepositional mixing and subsequent layering are present and that separate sublayers exist within larger regions where no sublayers are visible. Minimum track densities are inferred to be useful measures of maximum residence times for undisturbed layers. Using the observed minimum track densities, we conclude that the average deposition rate in this section of soil column was greater than 0.4 cm/million years.

Fleischer, R. L.↗
NASA NTRS1975

Subsonic magnetosheath observations from Explorer 33

Data are presented from one orbit of Explorer 33 which entered the magnetosphere near the stagnation point. Magnetic activity as measured at the earth was relatively quiet during the orbit, although minor substorm activity began 2 hours prior to the boundary crossing. Well before entry, the magnetosheath observations show flow patterns consistent with hydrodynamic models. Near the stagnation point close to the boundary the observations show rapid variations between virtually isotropic flux (stagnated flow) and flows tangent to the boundary in alternately opposite directions. Movement of the stagnation point of the order of 1 earth radius is inferred from these observations. Multiple boundary crossings are observed in the magnetic field covering a thickness of about 500 km. Prior to the magnetic crossings, the higher-energy proton fluxes begin to disappear. The bulk of the protron flux in the lower energy ranges and also the electron flux decrease rapidly at the last magnetic crossing. No boundary is apparent in the highest energy range measured by the detector.

Crooker, N. U.↗
NASA NTRS1994

Distribution of materials excavated by the lunar crater Bullialdus and implications for the geologic history of the Nubium region

Previous spectroscopic studies of the lunar crater Bullialdus, located in the Nubium Basin, indicated an unusual stratigraphy of two gabbroic layers overlying a noritic unit. The possible existence of a layered mafic pluton at Bullialdus was suggested. To investigate the geologic context with more detailed spatial information, charge-coupled device (CCD) images of Bullialdus were obtained using eight filters. A linear mixing model was used to investigate the fractional abundances of spectral end-members chosen from within the multispectral image. Since the reflectance properties of lunar materials over this wavelength range are sensitive to variations in composition and soil maturity, fractional abundance images were used to create a new geologic map of the crater. The spatial relationships of the surface materials confirm the previously inferred stratigraphy, and further reveal the central peaks to exhibit two distinct compositional units: noritic anorthosite and anorthositic norite. Three models for the origin of the observed stratigraphy are considered: Bullialdus has excavated stratigraphic units containing (1) early mare basalt overlying anorthositic-noritic crustal material, (2) part of a layered mafic pluton, and/or (3) part of an impact melt sheet formed by the Nubium Basin impact event.

Tompkins, Stefanie↗
NASA NTRS2011

Thoughts Without Content are Empty, Intuitions Without Concepts are Blind - Determinism and Contingency Revisited

Was the emergence of life a predictable outcome of chemical evolution on earth? Could evolution produce life very different from ours? These are one of the oldest questions in the field of the origin of life that not only have broad philosophical implications but also impact how we approach the problem from the methodological standpoint. Framing the issue in terms of the dichotomy between contingency and determinism is not a fortunate because these two terms in their conventional meaning are neither mutually exclusive nor jointly exhaustive. Determinism, represented in natural sciences by Newtonian physics, relies on the assumption that every event is causally determined by a chain of previous events. In the context of the origin of life it means that once the initial conditions on the early earth have been specified further evolution follows inevitably. Considering uncertainties about conditions on the prebiotic earth, many plausible sets of initial conditions can be defined, each followed by a separate deterministic trajectory. This conventional understanding of determinism does not admit contingency. Further, it has no implications for evaluating how many sets of initial conditions lead to the emergence of life. It appears that a better framing of the problem is as follows: given plausible sets of initial conditions on the early earth how probable and broadly spread are evolutionary trajectories that lead to life? Instead of undertaking an impossible task of specifying microscopic initial conditions for all components of the system one uses a reduced representation of this system and specify only a small set of essential macroscopic parameters, values (or ranges of values) of which can be identified, inferred or estimated from experiment, theory or historical record. The following evolutionary trajectories are still governed by laws of physics and chemistry but become probabilistic and "contingency" is admitted as variations in other variables in the system. A similar reasoning is common in other fields of science, for example in statistical mechanics. Some trajectories lead to life, perhaps in different forms, whereas others do not. Of our true interest is the ratio of these two outcomes. The issue of determinism does not directly enter the picture. The debate about the likelihood of the emergence of life is quite old. One view holds that the origin of life is an event governed by chance, and the result of so many random events (contingencies) is unpredictable. This view was eloquently expressed by Monod. In his book "Chance or Necessity" he argued that life was a product of "nature's roulette." In an alternative view, expressed in particular by deDuve and Morowitz, the origin of life is considered a highly probable or even inevitable event (although its details need not be determined in every respect). Only in this sense the origin of life can be considered a "deterministic event".

Pohorille, Andrew↗
DOE OSTI2020

Amplicon Sequencing Assessment to Measure Microbial Community Response from Heavy Metal Contaminated Soils in Savannah River site, Tims Branch watershed

Long-term presence of heavy metal contamination in soils is correlated with changes in microbial community structures and can lead to the reduction of indigenous species. Tolerance to soil heavy metal toxicity varies among different microbial communities. It remains unclear whether long term effects caused by metal perturbations are associated with soil microbial community dysregulation in Tims Branch watershed. Research Questions: Does heavy metal contamination in Tims Branch soils decrease microbial species diversity significantly compared to non-contaminated soils? Does the species richness decrease in contaminated samples? between samples? Is diversity in low, mid and high contamination soils significantly different compared to control samples? Hypothesis: The relative abundance and diversity of species are significantly altered in soils which are contaminated with heavy metals in the Tims Branch watershed. Objectives: Use amplicon sequencing technology along with bioinformatics to compare bacterial communities between four sites in Tims Branch watershed. Evaluate the percent relative abundance and diversity across the site. Conclusions: All bacterial communities exposed to different heavy metal concentrations were dominated by four major groups (Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia). The dominant phyla Proteobacteria, Acidobacteria and Chloroflexi accounted for 61 % of the relative abundance. Soil bacterial α-diversity, expressed as observed species richness metric and Shannon's diversity index, was the highest in sample location four (high contamination). The lowest observed was at the control location. Species richness increased when concentrations of heavy metals were localized, inferring that the metals can alter microbial community structure. PERMANOVA analysis between contaminated groups tested significant using the Adonis (F (4,29) =1.9712; p < 0.001). There is a 20 percent variation explained between groups (R2 = 0.214). This analysis proves to be beneficial in detecting microbial communities altered by contaminated soils. Moreover, certain concentrations of heavy metals can alter microbial community structures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Inferring nuclear structure from heavy isobar collisions using Trajectum

Nuclei with equal number of baryons but varying proton number (isobars) have many commonalities, but differ in both electric charge and nuclear structure. Relativistic collisions of such isobars provide unique opportunities to study the variation of the magnetic field, provided the nuclear structure is well understood. In this work we simulate collisions using several state-of-the-art parametrizations of the ^{96}_{40} 40 96 Zr and ^{96}_{44} 44 96 Ru isobars and show that a comparison with the exciting STAR measurement [arXiv:2109.00131] of ultrarelativistic collisions can uniquely identify the structure of both isobars. This not only provides an urgently needed understanding of the structure of the Zirconium and Ruthenium isobars, but also paves the way for more detailed studies of nuclear structure using relativistic heavy ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1974

Changes in atmospheric composition inferred from ionospheric production rates

Changes in the total electron content of the ionosphere near sunrise are used to determine the integrated production rate in the ionosphere (Q) from 1965 to 1971 at latitudes of 34S, 20N, and 34N. The observed regular semiannual variation in Q through a range of 1:3:1 is interpreted as an increase in the ratio O/N2 (relative densities) near the equinoxes. It follows that there is a worldwide semiannual variation in atmospheric composition, with the above ratio maximum just after the equinoxes. There is a large seasonal variation in the Northern hemisphere with a maximum in mid-summer. This effect is absent in the Southern hemisphere. At all times except solar maximum in the Northern hemisphere there is a global asymmetry. The ratio O/N2 is about three times as large in the Northern hemisphere. The overall mechanism appears to be N2 absorption.

Titheridge, J. E.↗
NASA NTRS1986

Composition of the Cayley Formation at Apollo 16 as inferred from impact melt splashes

Abundances of major and trace elements and magnetic properties of 50 impact melt splashes (IMSs) from the Apollo 16 landing site are analzyed to determine the composition of their meteoritic component. MgO-Sc and Ca-Sc variation diagrams and least-squares mixing models are utilized to analyze the IMS, soil, and rock data. Consideration is given to progenitor lithologies of the IMS, the number of impact events represented by the IMS, and the heterogeneity of impact melts from single events. It is observed that the IMSs are composed of either a mixture of anorthosite and low-Sc impact melt rocks or anorthositic norite. It is determined that the surface Cayley layer is composed of TiO2, MgO, Sc, and La concentrations of 0.69, and 7.1 wt pct and 10.5 and 21.2 microg/g, respectively and 0.38 and 5.9 wt pct and 6.1 and 11.8 microg/g, respectively, for the subsurface Cayley layer. The Descartes Formation composition is estimated as TiO2, MgO, Sc, and La concentrations of 0.25, and 3.5 wt pct and 7.7 and 2.2 microg/g, respectively.

Morris, Richard V.↗
DOE OSTI2021

Quantifying microbial control of soil organic matter dynamics at macrosystem scales

Soil organic matter (SOM) stocks, decomposition and persistence are largely the product of controls that act locally. Yet the controls are shaped and interact at multiple spatiotemporal scales, from which macrosystem patterns in SOM emerge. Theory on SOM turnover recognizes the resulting spatial and temporal conditionality in the effect sizes of controls that play out across macrosystems, and couples them through evolutionary and community assembly processes. For example, climate history shapes plant functional traits, which in turn interact with contemporary climate to influence SOM dynamics. Selection and assembly also shape the functional traits of soil decomposer communities, but it is less clear how in turn these traits influence temporal macrosystem patterns in SOM turnover. Here, we review evidence that establishes the expectation that selection and assembly should generate decomposer communities across macrosystems that have distinct functional effects on SOM dynamics. Representation of this knowledge in soil biogeochemical models affects the magnitude and direction of projected SOM responses under global change. Yet there is high uncertainty and low confidence in these projections. To address these issues, we make the case that a coordinated set of empirical practices are required which necessitate (1) greater use of statistical approaches in biogeochemistry that are suited to causative inference; (2) long-term, macrosystem-scale, observational and experimental networks to reveal conditionality in effect sizes, and embedded correlation, in controls on SOM turnover; and (3) use of multiple measurement grains to capture local- and macroscale variation in controls and outcomes, to avoid obscuring causative understanding through data aggregation. Here, when employed together, along with process-based models to synthesize knowledge and guide further empirical work, we believe these practices will rapidly advance understanding of microbial controls on SOM and improve carbon cycle projections that guide policies on climate adaptation and mitigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Flow over an espresso cup: inferring 3-D velocity and pressure fields from tomographic background oriented Schlieren via physics-informed neural networks

Tomographic background oriented Schlieren (Tomo-BOS) imaging measures density or temperature fields in three dimensions using multiple camera BOS projections, and is particularly useful for instantaneous flow visualizations of complex fluid dynamics problems. We propose a new method based on physics-informed neural networks (PINNs) to infer the full continuous three-dimensional (3-D) velocity and pressure fields from snapshots of 3-D temperature fields obtained by Tomo-BOS imaging. The PINNs seamlessly integrate the underlying physics of the observed fluid flow and the visualization data, hence enabling the inference of latent quantities using limited experimental data. In this hidden fluid mechanics paradigm, we train the neural network by minimizing a loss function composed of a data mismatch term and residual terms associated with the coupled Navier–Stokes and heat transfer equations. We first quantify the accuracy of the proposed method based on a two-dimensional synthetic data set for buoyancy-driven flow, and subsequently apply it to the Tomo-BOS data set, where we are able to infer the instantaneous velocity and pressure fields of the flow over an espresso cup based only on the temperature field provided by the Tomo-BOS imaging. Moreover, we conduct an independent PIV experiment to validate the PINN inference for the unsteady velocity field at a centre plane. To explain the observed flow physics, we also perform systematic PINN simulations at different Reynolds and Richardson numbers and quantify the variations in velocity and pressure fields. Furthermore, the results in this paper indicate that the proposed deep learning technique can become a promising direction in experimental fluid mechanics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1976

Dynamics of the Jovian magnetosphere and energetic particle radiation

Inferences are drawn from Jovian magnetosphere data acquired in the flybys of Pioneer 10 and Pioneer 11. Data on the outer magnetosphere and the inner core, and on observed 10-hr variations in particle intensity, are summarized, with attention given to the immense size and complexity of the magnetosphere and the behavior of trapped charged particles. The data support the maintenance and acceleration of charged particles trapped in Jupiter's magnetic field by inward diffusion in violation of the third adiabatic invariant. Prodigious quantities of high-energy particles are found to escape from Jupiter into interplanetary space, and MHD waves in the circumjovian plasma are considered. Whether the 10-hr variations are spatial or temporal in origin is weighed in favor of the latter. Production and loss mechanisms for the particles, and the nature of the Jovian magnetosphere itself, are noted among questions remaining obscure.

Simpson, J. A.↗
NASA NTRS1994

The solar cycle variation of coronal temperature and density during cycle 21-22

In this paper we characterize the temperature and the density structure of the corona utilizing co-spatial spectrophotometric observations during the descending phase of cycle 21 through the ascending phase of cycle 22. The data include ground-based intensity observations of the green (5303A Fe XIV) and red (6374A Fe X) coronal forbidden lines from Sacramento Peak and synoptic maps of white-light K-coronal polarized brightness, pB from the High Altitude Observatory, and photospheric magnetographs from the National Solar Observatory, Sacramento Peak. A determination of plasma temperature T can be derived unambiguously from the intensity ratio Fe X/Fe XIV, since both emission lines come from ionized states of Fe, and the ratios are only weakly dependent on density. The latitudinal variation of the temperature and the density within the descending and the ascending phases of solar cycle 21 and 22 are presented. There is a large-scale organization of the inferred coronal temperature distribution; these structures tend to persist through most of the magnetic activity cycle. This distribution differs in spatial and temporal characterization from the traditional picture of sunspot and active region evolution over the range of sunspot cycle.

Guhathakurta, M.↗
NASA NTRS2005

Nanotube/Quantum Dot-Polymer Solar Cells

Single wall carbon nanotubes used or this study were synthesized using the pulse laser vaporization technique. The as-produced SWNTs were collected from the condensed region on the quartz tube outside the furnace and purified by modification of the previously reported procedure. Preparation of the SWNT-P3OT composite solutions was performed using a series of mixing and sonication steps as previously demonstrated for other SWNT-polymer systems. Device fabrication involved the use of commercially-obtained, high quality (i.e., less than 10 W/sq.) ITO-coated polyethylene terapthalate (PET) substrates. Initially, an intrinsic layer of pristine P3OT is spray deposited (approx. 1-2 mL of the 15 mg/mL solution) onto the masked, 1 sq in. active area of the substrate. This is followed with spray deposition of the SWNT-P3OT composite solutions at similar volumes. As seen completion of the solar cell occurs when aluminum contacts (typical thicknesses of l000A) are applied to the IT0 and SWNT-P3OT composite film layers. The homogeneous distribution of SWNTs in a polymer matrix is dependent upon the ability of the polymer chain to associate with the SWNT superstructure. Stable composite dispersions of 0.1 % and 1.0% w/w SWNTs in P3OT were produced and analyzed in this study. Optical spectroscopy was conducted to observe the SWNT doping level effects on the absorption properties and infer potential electronic interactions between dopant and polymer. Shown is an overlay of these spectra where the pristine P3OT shows strong optical absorption at energies less than 2 eV. As expected, variation in absorption properties for the SWNT-P3OT composites is observed as the doping level increases. Through modification of the SWNT doping level in the polymer, it is possible to alter the absorption pattern of these composite materials. In fact, at these relatively low doping levels, the P3OT shows a significant enhancement in absorption through the near-IR and visible regions. The gray curve for purified SWNTs is offset from the other three for clarity, but indicates the typical complex pattern observed for this spectral range.

Bailey, Sheila G.↗
NASA NTRS2006

The Interplay Between Strategic And Adaptive Control Mechanisms In Plastic Recalibration Of Locomotor Function

We have previously shown that viewing simulated rotary self-motion during treadmill locomotion causes immediate strategic modifications (Richards et al. 2004) as well as an after effect reflecting adaptive modification of the control of position and trajectory during over-ground locomotion (Mulavara et al. 2005). The process of sensorimotor adaptation is comprised of both strategic and adaptive control mechanisms. Strategic control involves cognitive, on-line corrections to limb movements once one is aware of a sensory discordance. Over an extended period of exposure to the sensory discordance, new strategic sensorimotor coordination patterns are reinforced until they become more automatic, and therefore adaptive, in nature. The objective of this study was to investigate how strategic changes in trunk control during exposure to simulated rotary self-motion during treadmill walking influences adaptive modification of locomotor heading direction during over-ground stepping. Subjects (n = 10) walked on a motorized linear treadmill while viewing a wide field-of-view virtual scene for 24 minutes. The scene was static for the first 4 minutes and then, for the last 20 minutes, depicted constant rate self-motion equivalent to walking in a counter-clockwise, circular path around the perimeter of a room. Subjects performed five stepping trials both before and after the exposure period to assess after effects. Results from our previous study showed a significant change in heading direction (HD) during post-exposure step tests that was opposite the direction in which the scene rotated during the adaptation period. For the present study, we quantified strategic modifications in trunk movement control during scene exposure using normalized root mean square (R(sub p)) variation of the subject's 3D trunk positions and normalized sum of standard deviations (R(sub o)) variation of 3D trunk orientations during scene rotation relative to that during static scene presentation. Associated 95% confidence intervals, CI(sub P) and CI(sub O), were calculated to investigate the variation of strategic modifications during scene exposure. Repeated measures ANOVA and individual subject regression analyses showed that R(sub P) and R(sub O) (i.e. strategic modifications) for trunk fore/aft (X) and yaw movements, respectively, decreased significantly over the exposure period. Furthermore, we found a significant correlation between the magnitude change in HD and the rate at which the variation of strategic modifications in trunk X decreased. We also found evidence of a correlation between HD and the rate at which strategic modifications in trunk yaw decreased (p = .06). We infer that adaptive recalibration of locomotor trajectory using optic flow stimuli depends on the rate at which strategic intervention is reduced.

Richards, J. T.↗
NASA NTRS2005

Electron Density Images of the Middle and High Latitude Magnetosphere in Response to the Solar Wind

Electron density images and plasma dynamics in the middle and high latitude dayside magnetosphere are studied with the IMAGE/RPI remote measurements of the electron densities along magnetic field lines, measured before and during a magnetic storm when the solar wind and interplanetary magnetic field (IMF) impinging on the magnetopause varied considerably. Several regions of different density distribution characteristics, including plasmasphere, plasma trough, sub-auroral/auroral density depletion, density enhancements in the aurora/cusp, and polar cap, are identified in 'two dimensional images', i.e., along the satellite orbit and field lines. The plasma dynamics, such as the plasma refilling in the outer plasmasphere and the plasma acceleration in the aurora/cusp region are inferred from density gradients along the field lines. It is shown that the densities and locations of the plasma regions vary in accordance with the solar wind, particularly with the IMF variations for the case examined. The changes in these regions reflect the way the magnetosphere reconfigures in response to changes in the solar wind.

Tu, Jiannan↗