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DOE OSTI2026

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗

DOE OSTI2025

Geometric Interpretation of the Cluster Location Problem Part I: Theory

We present a new framing of the seismic location problem using principles drawn from differential geometry. Our interpretation relies upon the common assumption that travel times observed across a network are continuous, differentiable functions of source location. In consequence, travel‐time functions constitute a differentiable map between the source region and a Riemannian manifold. The manifold is said to be the image of the source region embedded in a generally high‐dimension travel‐time vector space. A cluster of events in the source region has an image of discrete points on the manifold, that, except in the simplest cases, cannot be viewed directly. However, it is possible to project the image of a cluster into a tangent space of the manifold for direct visualization. The projection operator can be computed directly from the data without a velocity model, but produces a distorted rendering of the cluster geometry. With a model we can predict the distortions and correct them to estimate cluster geometry. We develop these points with the simplest possible example, one for which direct visualization of the manifold is possible, using the example as an introduction to the relevant concepts from differential geometry in a familiar setting. The tangent space, a local linearization of the manifold, plays a key role. We develop a metric to estimate the limits of linearization, that is, to determine when the curvature of the manifold invalidates the linear assumption. We also examine the interplay of model error, inadequate network geometry, and pick error. We then generalize our results from the simple case to the general case of 3D source regions observed by general networks. Although we do suggest a new “project and correct” method for location, we do not develop it into a practical algorithm. In conclusion, our intention rather is to highlight new analytical methods grounded in differential geometry.

East Pacific Ocean Islands↗

DOE OSTI2024

Inferring the scrape-off layer heat flux width in a divertor with a low degree of axisymmetry

Plasma facing components (PFCs) in the next generation of tokamak devices will operate in challenging environments, with heat loads predicted to exceed 10 MWm -2 . The magnitude of these heat loads is set by the width of the channel, the ‘scrape-off layer’ (SOL), into which heat is exhausted, and can be characterised by an e-folding length scale for the decay of heat flux across the channel. It is expected this channel will narrow as tokamaks move towards reactor relevant conditions. Understanding the processes involved in setting the SOL heat flux width is imperative to be able to predict the heat loads PFCs must handle in future devices. Measurements of the SOL width are performed on the high-field spherical tokamak, ST40, using a newly commissioned infrared thermography system. With its high on-axis toroidal magnetic field (≥1.5 T) ST40 is uniquely positioned to investigate the influence of toroidal field on the heat flux width in spherical tokamaks, whilst also extending measurements of the SOL width in spherical tokamaks to increased poloidal field (≥0.3 T). Due to the divertor on ST40 having a low degree of axisymmetry, it is necessary for a set of radial measurements of the heat flux to be taken across the divertor, made possible using an automated toolchain that fully incorporates its 3D geometry. These radial profiles are combined with the magnetic geometry of the plasma to infer the width of the SOL, with both Eich and double exponential profiles of heat flux observed. A reduction in the heat flux is observed toroidally across part of the divertor, along with increased heat loads observed locally around the edges of the tiles. Future work in characterising the impact of tile misalignment and uncertainties in the reconstructed divertor magnetic geometry is required in order to further understand the observed heat flux patterns, as are additional investigations into the role potentially being played by an inhomogeneous sheath electric field.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1973

Geometric interpretation of the ratio of overall diameter to rim crest diameter for lunar and terrestrial craters.

An empirical linear relationship has been established by Pike (1967) between the overall diameter and the rim crest diameter for rimmed, flat-floored as well as bowl-shaped, lunar and terrestrial craters formed by impact and explosion. A similar relationship for experimentally formed fluidization craters has been established by Siegal (1971). This relationship is examined in terms of the geometry of the crater and the slope angles of loose materials. The parameter varies from 1.40 to 1.65 and is found to be dependent on mean interior flat floor radius, exterior and interior rim slope angles, angle of aperture of the crater cone, and the volume fraction of crater void accounted for in the rim. The range of the observed parameter can be understood in terms of simple crater geometry by realistic values of the five parameters.

Siegal, B. S.↗

NASA NTRS1985

Quantitative non-destructive testing

The work undertaken during this period included two primary efforts. The first is a continuation of theoretical development from the previous year of models and data analyses for NDE using the Optical Thermal Infra-Red Measurement System (OPTITHIRMS) system, which involves heat injection with a laser and observation of the resulting thermal pattern with an infrared imaging system. The second is an investigation into the use of the thermoelastic effect as an effective tool for NDE. As in the past, the effort is aimed towards NDE techniques applicable to composite materials in structural applications. The theoretical development described produced several models of temperature patterns over several geometries and material types. Agreement between model data and temperature observations was obtained. A model study with one of these models investigated some fundamental difficulties with the proposed method (the primitive equation method) for obtaining diffusivity values in plates of thickness and supplied guidelines for avoiding these difficulties. A wide range of computing speeds was found among the various models, with a one-dimensional model based on Laplace's integral solution being both very fast and very accurate.

Welch, C. S.↗

NASA NTRSDate not supplied

Development of a Global Reference Surface Reflectance and BRDF Datasets from Geostationary Satellite Observations and AERONET Measurements

Surface reflectances and their dependency on illumination-view geometries (i.e., BRDF) are the foundation of many high-level satellite products for land and water monitoring. Yet it is difficult to evaluate the quality of satellite-based surface reflectances with ground-based measurements due to the spatial scale differences. In order to fill the gap, here we develop a reference dataset of surface reflectance and BRDF at the global AERONET sites with data streams from operational geostationary sensors including Himawari 8/9 AHI, GK-2A AMI, and GOES 16/17 ABI. Taking the top-of-atmosphere (TOA) reflectance and the site measured atmospheric aerosol optical depth (AOD) as the main inputs, we apply the GeoNEX-AC algorithm to performance accurate atmospheric correction and derive 10-minute surface reflectance and daily Ross-Thick-Li-Sparse (RTLS) BRDF parameters at AERONET sites where coincident AOD measurements and TOA observations are available from 2016 (for Himawari) or 2018 (for GOES) onwards. The algorithm ensures that the retrieved surface BRDF parameters, along with the site-measured AOD, allow the atmospheric radiative transfer model, SHARM, accurately simulate the observed TOA reflectance at diurnal and longer time scales. They are our best estimates of the surface optical properties and thus can serve as the “reference” to evaluate the performance of operational atmospheric correction algorithms (where AOD is assumed unknown and needs to be retrieved). The reference BRDF also allow us to evaluate the spectral band ratios between the SWIR (e.g., 2200 nm) and the visible (e.g., 650 nm) regions, which are commonly used in operational atmospheric correction algorithms. Finally, we demonstrate that the reference dataset can be used to develop potential data synergies between different GEO satellites as well as GEO-LEO sensors.

Weile Wang↗

NASA NTRS1987

The EOS SAR program

The goal of the Spaceborne Imaging Radar (SIR) program is to develop a multipolarization, multifrequency synthetic aperture radar (SAR) with variable imaging geometry which will be ready for flight on the Earth Observing System (EOS) in the mid 1990's. Nominally, this SAR will be a three frequency (L-, C- and X-band) system with quad-polarization available for the L- and C-bands and dual polarization for the X-band system. It will be capable of acquiring multiincidence angle data using electronic beam steering and other imaging geometries by mechanically pitching, yawing and rolling the antenna. The EOS SAR will play a key role along with the other EOS instruments in understanding the earth as a system.

Cimino, Jobea↗

NASA NTRS1996

Imaging Polarized Dust Emission in Star Formation Regions with the OVRO MM Array

We present OVRO interferometric observations of linearly polarized emission from magnetically aligned dust grains which allow the magnetic field geometry in nearby star formation regions to be probed on scales ranging from 100 to 3000 AU. Current results include observations of the young stellar objects NGC1333/IRAS 4A, IRAS 16293-2422 and Orion IRc2-KL.

Akeson, Rachel↗

DOE OSTI2022

Comparison of Irradiated and Unirradiated Graphite Oxidation Performance

This work examines the oxidation behavior of NBG-25 graphite using irradiated specimens and (not irradiated) companion specimens from the Advanced Graphite Creep (AGC) Experiment. Irradiated and companion specimens were quartered, split into four small samples, to enable four oxidation test runs for each (0.5 inch diameter by 0.25 inch tall) piggyback button obtained from the AGC Experiment inventory. These split samples were oxidized in air in a thermogravimetric analyzer (TGA) and benchmarked against observations with separately sourced same-grade specimens of three geometries oxidized either in the TGA or in a vertical furnace built and operated to satisfy the specifications of ASTM D7542. The study considers both irradiation damage and relief of damage by thermal annealing. A range of isothermal oxidation temperatures were tested for specimens exposed to a similar irradiation environment, nominally 6.5 dpa at 650°C. To assess the dose dependency of observed oxidation behavior, specimens with a range of irradiation exposures (up to 6.8 dpa) were tested at the single oxidation temperature of 650°C. In the conventional analysis (rate determined over the 5-10% mass loss range) any annealing effects appear to be negligible, while irradiation to ~6.5 dpa may double or triple the subsequent oxidation rate. However, examination of rate with extent of reaction (over incremental ranges from initial onset up to 5% mass loss) illustrates that (at least for ~6.5 dpa) irradiation initially inhibits oxidation. Slower rates of oxidation than companion split samples are clearly indicated across all oxidation temperatures tested up to ~0.5% mass loss. Over the range of 0.5-1% mass loss, regardless of normalization strategy, there is no statistically meaningful difference in oxidation rate. However, beyond 0.5% mass loss oxidation of the irradiated sample becomes progressively faster than the companion sample (up to the 10% mass loss level observed).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS1999

Some Peculiar Properties of Magnetic Clouds as Observed by the WIND Spacecraft

We aimed at understanding the common characteristics of magnetic clouds, relevant to solar-interplanetary connections, but exceptional ones were noted and are stressed here through a short compendium. The study is based on analyses of 28 good or better events (Out of 33 candidates) as identified in WIND magnetic field and plasma data. These cloud intervals are provided by WIND-MFI's Website under the URL (http://lepmfi.gsfc.nasa.gov/mfi/mag_cloud_publ.html#table). The period covered is from early 1995 to November 1998. A force free, cylindrically symmetric, magnetic field model has been applied to the field data in usually 1-hour averaged form for the cloud analyses. Some of the findings are: (1) one small duration event turned out to have an approximately normal size which was due to a distant almost "skimming" passage by the spacecraft; (2) One truly small event was observed, where 10 min averages had to be used in the model fitting; it had an excellent model fit and the usual properties of a magnetic cloud, except it possessed a small axial magnetic flux; (3) One cloud ha a dual axial-field-polarity, in the sense that the "core" had one polarity and the annular region around it had an opposite polarity. This event also satisfied the model and with a ve3ry good chi-squared value. Some others show a hint of this dual polarity; (4) The temporal distribution of occurrence clouds over the 4 years show a dip in 1996; (5) About 50 % of the clouds had upstream shocks; any others had upstream pressure pulses; (6) The overall average speed (390 km/s) of the best 28 events is less than the normally quoted for the average solar wind speed (420 km/s) The average of central cloud speed to the upstream solar wind speed was not much greater than one (1.08), even though many of these clouds were drivers of interplanetary shocks. Cloud expansion is partly the reason for the existence of upstream shocks; (7) The cloud axes often (about 50 % of the time) revealed reasonable attitudes with respect to the interpreted solar source, from simple geometry, but many bore no relationship, suggesting that their observations at 1 AU were probably those of the legs of the global cloud often having near-radial axes; (8) many clouds appear to have magnetic holes at or their their boundaries.

Berdichevsky, D.↗

NASA NTRS2020

Continuity of MODIS and VIIRS Snow Cover Extent Data Products for Development of an Earth Science Data Record

An Earth Observing System global snow cover extent data products record at moderate spatial resolution (375–500 m) began in February 2000 with the Moderate-resolution Imaging Spectroradiometer (MODIS) instrument onboard the Terra satellite. The record continued with the Aqua MODIS in July 2002, the Suomi-National Polar Platform (S-NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) in January 2012 and continues with the Joint Polar Satellite System-1 (JPSS-1) VIIRS, launched in November of 2017. The objective of this work is to develop a snow cover extent Earth Science Data Record (ESDR) using different satellites, sensors and algorithms. There are many issues to understand when data from different algorithms and sensors are used over a decade-scale time period to create a continuous dataset. Issues may also arise with sensor degradation and even differences in sensor band locations. In this paper we describe development of an ESDR derived from existing MODIS and VIIRS data products and demonstrate continuity among the products. The MODIS and VIIRS snow cover detection algorithms produce very similar daily snow cover maps, with 90–97% agreement in snow cover extent (SCE) in different landscapes. Differences in SCE between products ranged from 2–15% and are attributable to convolved factors of viewing geometry, pixel spread across a scan and time of observation. Compared at a common grid size of 1 km, there is a mean of 95% agreement in SCE and a difference range of 1–10% between the MODIS and VIIRS SCE maps. Mapping sensor observations to a coarser resolution grid reduces the effect of the factors convolved in the 500 m tile to tile comparisons. We conclude that the MODIS and VIIRS SCE data products are reliable constituents of a moderate-resolution ESDR.

snow cover extent↗

NASA NTRS1993

Low cloud investigations for project FIRE: Island studies of cloud properties, surface radiation, and boundary layer dynamics. A simulation of the reflectivity over a stratocumulus cloud deck by the Monte Carlo method

The radiation field over a broken stratocumulus cloud deck is simulated by the Monte Carlo method. We conducted four experiments to investigate the main factor for the observed shortwave reflectively over the FIRE flight 2 leg 5, in which reflectivity decreases almost linearly from the cloud center to cloud edge while the cloud top height and the brightness temperature remain almost constant through out the clouds. From our results, the geometry effect, however, did not contribute significantly to what has been observed. We found that the variation of the volume extinction coefficient as a function of its relative position in the cloud affects the reflectivity efficiently. Additional check of the brightness temperature of each experiment also confirms this conclusion. The cloud microphysical data showed some interesting features. We found that the cloud droplet spectrum is nearly log-normal distributed when the clouds were solid. However, whether the shift of cloud droplet spectrum toward the larger end is not certain. The decrease of number density from cloud center to cloud edges seems to have more significant effects on the optical properties.

Ackerman, Thomas P.↗

NASA NTRS2024

NASA HECC Geometry and Performance Review Part 2: Geometric Differences Between the As-Manufactured and Design-Intent Impeller Geometry and their Effects on the Vaneless Diffuser Configuration Performance

An investigation of the NASA High Efficiency Centrifugal Compressor (HECC) vaneless diffuser configuration was performed. This multipart investigation focused on validating the computational model against experimental data. The validated model was then used to explore the effects of observed geometric differences between the As-Manufactured and Design-Intent impellers. Lastly, the validated model was used for comparison against an experimental tip clearance study. Part II of the investigation of the NASA HECC vaneless diffuser configuration focused on understanding the differences in geometry and performance between the As-Manufactured impeller and the Design-Intent impeller. This was achieved through comparison of the As-Manufactured HECC vaneless computational model, developed from the solid model of the impeller and validated in Part I, against a new model developed from the Design-Intent blade sections published in NASA/CR-2014-218114/Rev1. The 1D performance values showed that the As-Manufactured impeller underperformed compared to the Design-Intent for all four speedlines that were simulated. Further investigation of profiles, loading and contours showed consistent underperformance of the As-Manufactured relative to the Design-Intent. An investigation into the source of the performance differences led to the discovery of several significant variations in the impeller geometries. The differences that were observed can be summarized into four categories: fillets, trailing-edge exit radii variation, dissimilarity in the splitter leading-edge geometry and main blade thickness differences. The investigation then shifted its effort to quantify the performance effects caused by geometric differences. The investigation showed that out of the four geometric differences that were explored, the differences in the splitter blade had the largest impact. These differences most notably changed flow physics near the splitter leading edge, especially near the tip of the impeller.

centrifugal compressor↗

DOE OSTI2023

Noise Optimization for MKIDs with Different Design Geometries and Material Selections

The separation and optimization of noise components is critical to microwave-kinetic inductance detector (MKID) development. We analyze the effect of several changes to the lumped-element inductor and interdigitated capacitor geometry on the noise performance of a series of MKIDs intended for millimeter-wavelength experiments. We extract the contributions from two-level system noise in the dielectric layer, the generation-recombination noise intrinsic to the superconducting thin-film, and system white noise from each detector noise power spectrum and characterize how these noise components depend on detector geometry, material, and measurement conditions such as driving power and temperature. We observe a reduction in the amplitude of two-level system noise with both an elevated sample temperature and an increased gap between the fingers within the interdigitated capacitors for both aluminum and niobium detectors. We also verify the expected reduction of the generation-recombination noise and associated quasiparticle lifetime with reduced inductor volume. This study also iterates over different materials, including aluminum, niobium, and aluminum manganese, and compares the results with an underlying physical model.

generation-recombination noise↗

NASA NTRS2011

Using the Moon to Track MODIS Reflective Solar Bands Calibration Stability

MODIS has 20 reflective solar bands (RSB) in the visible (VIS), near infrared (NIR), and short-wave infrared (SWIR) spectral regions. In addition to instrument on-board calibrators (OBC), lunar observations have been used by both Terra and Aqua MODIS to track their reflective solar bands (RSB) on-orbit calibration stability. On a near monthly basis, lunar observations are scheduled and implemented for each instrument at nearly the same lunar phase angles. A time series of normalized detector responses to the Moon is used to monitor its on-orbit calibration stability. The normalization is applied to correct the differences of lunar viewing geometries and the Sun-Moon-Sensor distances among different lunar observations. Initially, the lunar calibration stability monitoring was only applied to MODIS bands (1-4 and 8-12) that do not saturate while viewing the Moon. As the mission continued, we extended the lunar calibration stability monitoring to other RSB bands (bands 13-16) that contain saturated pixels. For these bands, the calibration stability is monitored by referencing their non-saturated pixels to the matched pixels in a non-saturation band. In this paper, we describe this relative approach and apply it to MODIS regularly scheduled lunar observations. We present lunar trending results for both Terra and Aqua MODIS over their entire missions. Also discussed in the paper are the advantages and limitations of this approach and its potential applications to other earth-observing sensors. Keywords: Terra, Aqua, MODIS, sensor, Moon, calibration, stability

Xiong, Xiaoxiong↗

NASA NTRS1979

Localized deposition and sputtering of Jovian ionospheric sodium on Io

Because of relative motion between the innermost Galilean satellite Io and Jupiter's ionosphere, a current is drawn from the ionosphere that can be a source of both deposition on, and sputtering from, the surface of Io. It is shown that the ions in this current strike Io in a localized region in the quadrant bounded by a line connecting Io and Jupiter and a tangent line extended in the direction of Io's orbital motion. If these ions are the principal source of sodium that is sputtered from Io, then this current provides a simple explanation of the observation of a localized area from which sodium ions escape from Io. The geometry of this current may also affect the optical surface of Io. Several experimental tests are suggested that can determine the compatibility of this hypothesis with the directly observable properties of Io's surface.

Hill, T. W.↗

NASA NTRS2008

Comparative In Situ Measurements of Plasma Instabilities in the Equatorial and Auroral Electrojets

This presentation provides a comparison of in situ measurements of plasma instabilities gathered by rocket-borne probes in the equatorial and auroral electrojets. Specifically, using detailed measurements of the DC electric fields, current density, and plasma number density within the unstable daytime equatorial electrojet from Brazil (Guara Campaign) and in the auroral electrojet from Sweden (ERRIS Campaign), we present comparative observations and general conclusions regarding the observed physical properties of Farley-Buneman two-stream waves and large scale, gradient drift waves. The two stream observations reveal coherent-like waves propagating near the E x B direction but at reduced speeds (nearer to the presumed acoustic velocity) with wavelengths of approximately 5-10m in both the equatorial and auroral electrojet, as measured using the spaced-receiver technique. The auroral electrojet data generally shows extensions to shorter wavelengths, in concert with the fact that these waves are driven harder. With respect to gradient-drift driven waves, observations of this instability are much more pronounced in the equatorial electrojet, given the more favorable geometry for growth provided by the vertical gradient and horizontal magnetic field lines. We present new analysis of Guara rocket observations of electric field and plasma density data that reveal considerable structuring in the middle and lower portion of the electrojet (90-105 km) where the ambient plasma density gradient is unstable. Although the electric field amplitudes are largest (approximately 10-15 mV/m) in the zonal direction, considerable structure (approximately 5-10 mV/m) is also observed in the vertical electric field component as well, implying that the dominant large scale waves involve significant vertical interaction and coupling within the narrow altitude range where they are observed. Furthermore, a detailed examination of the phase of the waveforms show that on some, but not all occasions, locally enhanced eastward fields are associated with locally enhanced upwards (polarization) electric fields. The measurements are discussed in terms of theories involving the non-linear evolution and structuring of plasma waves.

Pfaff, Robert F.↗

NASA NTRS1987

Observations of the Jovian UV aurora by Voyager

The observations of the Jovian aurora made by the Voyager UV spectrometer (UVS) during 1979 are analyzed, with special consideration given to the model fitting process. Several different estimates of the function specifying auroral arc geometry were tried, with the Broadfoot et al. (1981) estimate, found by probing with the tip of the UVS slit, giving the best agreement; this agreement is slightly better than the agreement with the Io torus footprint computed by Roederer et al. (1977). The results suggest that the UVS observations are more sensitive to the surface field geometry than are the Voyager flyby in situ observations. The results of a study of intensity maximum positions indicate that the particles exciting the spatially variable portion of the aurora are drifting west, implying either that these particles are electrons or that they are positive ions drifting east more slowly than the corotation lag of the Io torus region carries them to the west. The latter case is most consistent with the high-energy charged particle measurements.

Herbert, Floyd↗