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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
NASA NTRS2005

Seismic Shaking Removal of Craters 0.2-0.5 km in Diameter on Asteroid 433 Eros

Impact cratering acts in a variety of ways to create a surprising range of scenery on small satellites and asteroids. The visible crater population is a self-modifying characteristic of these airless objects, and determining the various ways younger craters can add or subtract from the population is an important aspect of small body "geology." Asteroid 433 Eros, the most closely studied of any small body, has two aspects of its crater population that have attracted attention: a fall-off of crater densities below approx.100 m diameter relative to an expected equilibrium population [1] and regions of substantially lower large crater densities [2, 3, 4]. In this work we examine the global variation of the density of craters on Eros larger than 0.177 km, a size range above that involved in small crater depletion hypotheses [1, 5]. We counted all craters on Eros to a size range somewhat below 0.177 km diameter (and different from data used in [3]). The primary metric for this study is the number of craters between 0.177 and 1.0 km within a set radius of each grid point on the 2deg x 2deg shape model of Eros. This number can be expressed as an R-value [6], provided that it is remembered that the large bin size makes individual R values slightly different from those obtained in the usual root-2 bins.

Thomas, P. C.↗
DOE OSTI2021

CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin

Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Combined Cr and S poisoning behaviors of La 1-x Sr x MnO 3±δ and La 1-x Sr x Co 1-y FeyO 3-δ cathodes in solid oxide fuel cells

Although the individual effects of airborne Cr and S contaminants on SOFC cathode performance degradation have been extensively studied, the combined effects of Cr and S contaminants remain largely unexplored. Under the real SOFC operating condition where the Cr and S species coexist, their effects may compete, affecting the poisoning behavior. Here, our investigation reveals that the combined Cr and S poisoning behavior of LSCF remains different from those of individual Cr and S poisonings, while the combined poisoning mechanism of LSM is equivalent to the sum of those of individual Cr and S effects. For LSCF electrode, gaseous Cr species are deposited mainly at the LSCF/GDC interface by electrochemical reduction, rather than forming SrCrO 4 on LSCF surfaces (as in the case of Cr-only poisoning), indicating no reaction between Cr vapors and SrO on the LSCF surface. Thermodynamic analysis demonstrates that the SrO on LSCF surface absorbs SO 2 (g) and thereby loses the Cr-gettering effect, allowing Cr vapors to flow through LSCF and to reach the LSCF/GDC interface where the Cr deposition occurs. Unlike LSCF, LSM electrode shows cumulative effects of Cr and S, as Cr accumulation occurs at the triple-phase boundary and S absorption takes place at localized Sr-rich regions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Electronic energy loss and ion velocity correlation effects in track production in swift-ion-irradiated LiNbO3: A quantitative assessment between structural damage morphology and energy deposition

The primary motivation for studying how irradiation modifies the structures and properties of solid materials involves the understanding of undesirable phenomena, including irradiation-induced degradation of components in nuclear reactors and space exploration, and beneficial applications, including material performance tailoring through ion beam modification and defect engineering. In this work, the formation mechanism of latent tracks with different damage morphologies in LiNbO 3 crystals under 0.09–6.17 MeV/u ion irradiation with an electronic energy loss from 2.6–13.2 keV/nm is analyzed by experimental characterizations and numerical calculations. Irradiation-induced damage is preliminarily evaluated via the prism coupling technique to analyze the correlation between the dark-mode spectra and energy loss profiles of irradiated regions. Under the irradiation conditions of different ion velocities and electronic energy losses, different damage morphologies, from individual spherical defects to discontinuous and continuous tracks, are experimentally characterized. During ion penetration process, the ion velocity determines the spatiotemporal distribution of deposited irradiation energy induced by electronic energy loss, meaning that the two essential factors including electronic energy loss and ion velocity co-affect the track damage. The inelastic thermal spike model is used to numerically calculate the spatiotemporal evolutions of energy deposition and the corresponding atomic temperature under different irradiation conditions, and a quantitative relationship is proposed by comparison with corresponding experimentally observed track damage morphologies. Additionally, the obtained quantitative relationship between irradiation conditions and track damage provides deep insight and guidance for understanding the damage behavior of crystal materials in extreme radiation environments and selecting irradiation parameters, including ion species and energies, for ion beam technique application in atomic-level defect manipulation, material modification, and micro/nanofabrication.

36 MATERIALS SCIENCE↗
NASA NTRS2020

Comparing X-ray Color Selection in Separating X-ray Binary Classes using Color-Color-Intensity Diagrams

X-ray binaries exhibit a wide range of properties but there are few accepted methods to determine the nature of the compact object. Color-Color-Intensity diagrams have been suggested as a means of distinguishing between systems containing black holes from those containing neutron stars. However, this technique has been verified with data from only one instrument (RXTE/ASM) with a single set of X-ray colors defined using data available only in pre-determined energy bands. We test a selection of X-ray colors with a more sensitive instrument to determine the reliability of this method. We use data from the MAXI/Gas Slit Camera, which allows users to specify energy-bands. We test X-ray colors that have been previously defined in the literature as well as ones that we define specifically in this paper. A representative set of systems are used to construct Color-Color-Intensity diagrams in each set of colors to determine which are best for separating different classes. For studying individual sources certain bands are more effective than others. For a specified energy range, the separation of soft states in black hole binaries was possible only where both soft and hard colors included information from the lowest energy band. We confirm that Color-Color-Intensity diagrams can distinguish between systems containing black holes or neutron stars in all X-ray colors tested; this suggests an universality in the accretion processes governing these different classes. We suggest possible physical processes driving different classes of X-ray binaries to different locations in Color-Color-Intensity diagrams.

N Islam↗
DOE OSTI2024

Plasma performance and operational space with an RMP-ELM suppressed edge

Abstract The operational space and global performance of plasmas with edge-localized modes (ELMs) suppressed by resonant magnetic perturbations (RMPs) are surveyed by comparing AUG, DIII-D, EAST, and KSTAR stationary operating points. RMP-ELM suppression is achieved over a range of plasma currents, toroidal fields, and RMP toroidal mode numbers. Consistent operational windows in edge safety factor are found across devices, while windows in plasma shaping parameters are distinct. Accessed pedestal parameters reveal a quantitatively similar pedestal-top density limit for RMP-ELM suppression in all devices of just over 3 × 10 19 m −3 . This is surprising given the wide variance of many engineering parameters and edge collisionalities, and poses a challenge to extrapolation of the regime. Wide ranges in input power, confinement time, and stored energy are observed, with the achieved triple product found to scale like the product of current, field, and radius. Observed energy confinement scaling with engineering parameters for RMP-ELM suppressed plasmas are presented and compared with expectations from established H and L-mode scalings, including treatment of uncertainty analysis. Different scaling exponents for individual engineering parameters are found as compared to the established scalings. However, extrapolation to next-step tokamaks ITER and SPARC find overall consistency within uncertainties with the established scalings, finding no obvious performance penalty when extrapolating from the assembled multi-device RMP-ELM suppressed database. Overall this work identifies common physics for RMP-ELM suppression and highlights the need to pursue this no-ELM regime at higher magnetic field and different plasma physical size.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Direct Visualization of Defect‐Controlled Diffusion in van der Waals Gaps

Abstract Diffusion processes govern fundamental phenomena such as phase transformations, doping, and intercalation in van der Waals (vdW) bonded materials. Here, the diffusion dynamics of W atoms by visualizing the motion of individual atoms at three different vdW interfaces: hexagonal boron nitride (BN)/vacuum, BN/BN, and BN/WSe 2 , by recording scanning transmission electron microscopy movies is quantified. Supported by density functional theory (DFT) calculations, it is inferred that in all cases diffusion is governed by intermittent trapping at electron beam‐generated defect sites. This leads to diffusion properties that depend strongly on the number of defects. These results suggest that diffusion and intercalation processes in vdW materials are highly tunable and sensitive to crystal quality. The demonstration of imaging, with high spatial and temporal resolution, of layers and individual atoms inside vdW heterostructures offers possibilities for direct visualization of diffusion and atomic interactions, as well as for experiments exploring atomic structures, their in situ modification, and electrical property measurements of active devices combined with atomic resolution imaging.

Chemistry↗
NASA NTRS1994

Surface property variations in Venusian fluidized ejecta blanket craters

A comprehensive study of Magellan Cycles 1 and 2 radar data from Venus reveals surface roughness and dielectric variations associated with fluidized ejecta blanket (FEB) craters that help illuminate styles of flow ejecta emplacement. This study develops new procedures of digital unit mapping and polygon-filling algorithms using Magellan synthetic aperture radar (SAR), altimetry, and radiometry data. These techniques allow the extraction of radiophysical information for FEB crater materials, nearby plains, and lava flows. Backscatter curve slopes of the FEBs studied here are consistent with surface textures that are transitional between a'a and pahoehoe-like. Average surface property values of ejecta units are relatively similar for a given crater, but are discernibly different from other craters. Individual crater ejecta reflectivity and emissivity values are relatively similar to those for the surrounding plains, which may suggest a link between plains material and ejecta dielectric properties. Increasing FEB roughness downflow are interpreted to be associated with more lava-like flows, while decreasing roughness are more similar to trends typical of gravity (pyroclastic-like or debris-like) flows. Most commonly, FEB crater flow materials exhibit transitions from proximal, lava/melt-like flow styles to distal, gravity flow-like styles. Some FEBs show more complicated behavior, however, or appear to be more dominated by dielectric differences downflow, as inferred from correlations between the data sets. Such transitions may result from changes in local topography or from overlapping of flow lobes during FEB emplacement.

Johnson, Jeffrey R.↗
NASA NTRS2012

Thermal Behaviour of Unusual Local-Scale Surface Features on Vesta

On Vesta, the region of the infrared spectrum beyond approximately 3.5 micrometers is dominated by the thermal emission of the asteroid's surface, which can be used to determine surface temperature by means of temperature-retrieval algorithms. The thermal behavior of areas of unusual albedo seen at the local scale can be related to physical properties that can provide information about the origin of those materials. Dawn's Visible and Infrared Mapping Spectrometer (VIR) hyperspectral cubes are used to retrieve surface temperatures, with high accuracy as long as temperatures are greater than 180 K. Data acquired in the Survey phase (23 July through 29 August 2011) show several unusual surface features: 1) high-albedo (bright) and low-albedo (dark) material deposits, 2) spectrally distinct ejecta, 3) regions suggesting finer-grained materials. Some of the unusual dark and bright features were re-observed by VIR in the subsequent High-Altitude Mapping Orbit (HAMO) and Low-Altitude Mapping Orbit (LAMO) phases at increased pixel resolution. To calculate surface temperatures, we applied a Bayesian approach to nonlinear inversion based on the Kirchhoff law and the Planck function. These results were cross-checked through application of alternative methods. Here we present temperature maps of several local-scale features that were observed by Dawn under different illumination conditions and different local solar times. Some bright terrains have an overall albedo in the visible as much as 40% brighter than surrounding areas. Data from the IR channel of VIR show that bright regions generally correspond to regions with lower thermal emission, i.e. lower temperature, while dark regions correspond to areas with higher thermal emission, i.e. higher temperature. This behavior confirms that many of the dark appearances in the VIS mainly reflect albedo variations. In particular, it is shown that during maximum daily insolation, dark features in the equatorial region may rise to temperatures greater than 270 K. However, individual features may show different thermal behaviours, as a result of differences in composition and/or structure (e.g, average grain size of the surface regolith, porosity, etc.). To complement the temperature and near-infrared emissivity derived from the infrared spectra, a separate work is devoted to calculate thermal inertia and other thermal properties using theoretical models which solve the heat equation for airless bodies, and model the distribution of temperatures due to surface roughness variations.

Tosi, F.↗
DOE OSTI2026

Comparative Analysis of Report-Back of Research Results Strategies for Personal Chemical Exposure Data

Background. Report-back of research results (RBRR) is ethically supported and highly requested by participants yet lacks broadly transferable guidelines for RBRR. Effective RBRR must be responsive to target audience needs and may not be addressed by a ‘one-size-fits-all’ approach. Objective. Within a subset of our 19 studies on RBRR, we had the unique opportunity to carry out a comparative analysis of RBRR strategies across cohorts with similar development and evaluation methods, yet distinct in life stage, geography, number and type of chemicals assessed, and community contexts. Methods. We highlight key outcomes from three environmental health studies: an ongoing New York, NY cohort (Fair Start; n=486) and a Detroit, MI cohort (CLEAR; n=34) assessing exposure to ambient urban pollution during pregnancy, and a longitudinal cohort in Houston, TX (Houston-3H) following Hurricane Harvey (n=312). Focus group and survey data were analyzed to identify lessons learned and explore how RBRR supports understanding of environmental health. Results. Commonalities emerged in RBRR development, design, organization, and data visualization, as well as in how RBRR can contribute to an understanding of health-environment connections. Differences included preferences for individual versus community level findings, as well as distinguishable contextual considerations. For pregnancy cohorts, messaging was framed with cultural sensitivity, and to avoid unintended consequences of parental guilt due to prenatal exposures. In the post-disaster Houston-3H study, participants requested additional transparency regarding sampling design and study rationale. Significance. All RBRR case studies reported chemicals without known regulatory or health guidelines, so results were contextualized within the study population. Participants across cohorts requested multi-study comparisons to better understand their results beyond their communities. While foundational RBRR elements (e.g. plain language, graphic organizers) may supersede cohort-specific differences, RBRR should be personalized to encompass perceptions of health across different life-stage, cultural, and environmental contexts.

Vogel, Taylor J.↗
DOE OSTI2022

Grid-Interactive Electric Vehicle and Building Coordination Using Coupled Distributed Control: Preprint

As an increasing number of controllable devices are introduced onto the grid, they can individually provide ancillary services in support of grid stability. However, the goals of each device differ due to their type and individual objectives, causing instances where they may conflict. To reduce the chances of these devices contributing to grid instability, these devices must effectively communicate in a cooperative manner to both meet their own needs while providing services to the grid. Previous work demonstrates that the NALD (Network Lasso-ADMM - Limited Communication - DMPC) algorithm allows coordination between two subsystems that use different control algorithms (building and charging stations) to provide services to the grid and individually optimize their performance in a specific scenario. The ideal NALD algorithm should be generalized to allow plug-and-play capabilities across devices of differing characteristics. This paper takes a step toward generalizability by updating the electric vehicle charging objective and re-defining the communication scheme compared to prior work to generalize the coordination and, as a result, improve the performance of the NALD algorithm.

ADVANCED PROPULSION SYSTEMS,ENERGY CONSERVATION, C↗
NASA NTRS1997

An Accurate Potential Energy Surface for H2O

We have carried out extensive high quality ab initio electronic structure calculations of the ground state potential energy surface (PES) and dipole moment function (DMF) for H2O. A small adjustment is made to the PES to improve the agreement of line positions from theory and experiment. The theoretical line positions are obtained from variational ro-vibrational calculations using the exact kinetic energy operator. For the lines being fitted, the root-mean-square error was reduced from 6.9 to 0.08 /cm. We were then able to match 30,092 of the 30,117 lines from the HITRAN 96 data base to theoretical lines, and 80% of the line positions differed less than 0.1 /cm. About 3% of the line positions in the experimental data base appear to be incorrect. Theory predicts the existence of many additional weak lines with intensities above the cutoff used in the data base. To obtain results of similar accuracy for HDO, a mass dependent correction to the PH is introduced and is parameterized by simultaneously fitting line positions for HDO and D2O. The mass dependent PH has good predictive value for T2O and HTO. Nonadiabatic effects are not explicitly included. Line strengths for vibrational bands summed over rotational levels usually agree well between theory and experiment, but individual line strengths can differ greatly. A high temperature line list containing about 380 million lines has been generated using the present PES and DMF

Schwenke, David W.↗
NASA NTRS1987

Analysis of the breakdown of the Antarctic circumpolar vortex using TOMS ozone data

Climatological analysis of data from the Total Ozone Mapping Spectrometer (TOMS) on the Nimbus 7 satellite has shown that the annual cycles of ozone are very different in the Arctic and Antarctic. The annual cycle in the Arctic is a relatively smooth annual sine wave; but in the Antarctic the circumpolar vortex breaks down rapidly during the Southern Hemisphere spring (September through November), producing a rapid rise in total ozone and a sawtooth-shaped annual cycle. The evolution of the Antarctic total ozone field during the vortex breakdown was studied by computing areally-integrated ozone amounts from the TOMS data. This technique avoids substantial difficulties with using zonally-averaged ozone amounts to study the asymmetric breakdown phenomenon. Variability of total ozone is found to be large both within an individual year and between different years. During the last decade monthly-mean total ozone values in the Antarctic during the springtime vortex breakdown period have decreased dramatically. The ozone-area statistics indicate that the decrease has resulted in part from changes in the timing of the vortex breakdown and resultant ozone increase, which have occurred later during recent years. Analysis of the spatial scales involved in the ozone transport and mixing that occur during the vortex breakdown is now underway. Reliable calculation of diagnostic quantities like areally-integrated ozone is possible only with the high-resolution, two-dimensional, daily coverage provided by the TOMS instrument.

Bowman, Kenneth P.↗
NASA NTRS2012

The Use of Satellite-Measured Aerosol Optical Depth to Constrain Biomass Burning Emissions Source Strength in a Global Model GOCART

Small particles in the atmosphere, called "atmospheric aerosol" have a direct effect on Earth climate through scattering and absorbing sunlight, and also an indirect effect by changing the properties of clouds, as they interact with solar radiation as well. Aerosol typically stays in the atmosphere for several days, and can be transported long distances, affecting air quality, visibility, and human health not only near the source, but also far downwind. Smoke from vegetation fires is one of the main sources of atmospheric aerosol; other sources include anthropogenic pollution, dust, and sea salt. Chemistry transport models (CTMs) are among the major tools for studying the atmospheric and climate effects of aerosol. Due to the considerable variation of aerosol concentrations and properties on many temporal and spatial scales, and the complexity of the processes involved, the uncertainties in aerosol effects on climate are large, as is featured in the latest report of Intergovernmental Panel on Climate Change (IPCC) in 2007. Reducing this uncertainty in the models is very important both for predicting future climate scenarios and for regional air quality forecasting and mitigation. During vegetation fires, also called biomass burning (BB) events, complex mixture of gases and particles is emitted. The amount of BB emissions is usually estimated taking into account the intensity and size of the fire and the properties of burning vegetation. These estimates are input into CTMs to simulate BB aerosol. Unfortunately, due to large variability of fire and vegetation properties, the quantity of BB emissions is very difficult to estimate and BB emission inventories provide numbers that can differ by up to the order of magnitude in some regions. Larger uncertainties in data input make uncertainties in model output larger as well. A powerful way to narrow the range of possible model estimates is to compare model output to observations. We use satellite observations of aerosol properties, specifically aerosol optical depth, which is directly proportional to the amount of aerosol in the atmosphere, and compare it to the model output. Assuming the model represents aerosol transport and particle properties correctly, the amount of BB emissions determines the simulated aerosol optical depth. In this study, we explore the regional performance of 13 commonly used emission estimates. These are each input to global Goddard Chemistry Aerosol Radiation and Transport (GOCART) model. We then evaluate how well each emission estimate reproduces the smoke aerosol optical depth measured by the MODIS instrument. We compared GOCART-simulate aerosol optical depth with that measured from the satellite for 124 fire cases around the world during 2006 and 2007. We summarize the regional performance of each emission inventory and discuss reasons for their differences by considering the assumptions made during their development. We also show that because stronger wind disperses smoke plumes more readily, in cases with stronger wind, a larger increase in emission amount is needed to increase aerosol optical depth. In quiet, low-wind-speed environments, BB emissions produce a more significant increase in aerosol optical depth, other things being equal. Using the region-specific, quantitative relationships derived in our paper, together with the wind speed obtained from another source for a given fire case, we can constrain the amount of emission required in the model to reproduce the observations. The results of this paper are useful to the developers of BB emission inventories, as they show the strengths and weaknesses of individual emission inventories in different regions of the globe, and also for modelers who use these inventories and wish to improve their model results.

Petrenko, Mariya↗
DOE OSTI2023

Hunting for gamma-ray emission from fast radio bursts

Context. Fast radio bursts (FRBs) are a recently discovered class of GHz-band, ms-duration, Jansky-level-flux astrophysical transients. Although hundreds of models have been proposed so far for FRB progenitors (the most popular ones involve magnetars), their physical origin and emission mechanism are still a mystery, making them one of the most compelling problems in astrophysics. Aims. FRBs are caused by astrophysical processes that are not yet understood. Exploring their high-energy counterpart is crucial for constraining their origin and emission mechanism. Methods. Thanks to more than 13 years of gamma-ray data collected by the Large Area Telescope on board the Fermi Gamma-ray Space Telescope, and to more than 1000 FRB events (from 561 non-repeating and 22 repeating sources), one of the largest samples created thus far, we performed the largest and deepest search for high-energy emission from FRB sources to date (between 100 MeV and 1 TeV). In addition to the analysis involving individual FRB events on different timescales (from a few seconds up to several years), we performed, for the first time, a stacking analysis on the full sample of FRB events as well as a search for triplet photons in coincidence with the radio event. Results. We do not detect significant emission, reporting the most stringent constraints, on short timescales, for the FRB-like emission from SGR 1935+2154 with E γ <10 41 erg, corresponding to a factor η < 10 7 with respect to the emitted radio energy. Similarly, for the stacked signal of steady emission from all repeaters, the obtained upper limit (UL) on the FRBs luminosity (L γ < 1.6 × 10 43 erg s -1 is more than two orders of magnitude lower than those derived from the individual sources. Finally, no individual or triplet photons have been significantly associated with FRB events. We derived the LAT ms-sensitivity to be ~0.3 ph cm -2 s -1 and constrained the gamma-ray energy E γ,δT = 1 ms ≲ 10 47 (D L /150 Mpc) 2 erg, ruling out a gamma-ray-to-radio energy ratio greater than 10 9 on ms timescales. Conclusions. The results reported here represent the most stringent UL reported so far on the high-energy emission from FRBs on short and long time scales, as well as on cumulative emission and individual photon searches. While the origin of FRBs is still unclear, our work provides important constraints for FRB modelling, which might shed light on their emission mechanism.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Association mapping across a multitude of traits collected in diverse environments in maize

Abstract Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data—18M markers—from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

Ab Initio Calculations of Water Line Strengths

We report on the determination of a high quality ab initiu potential energy surface (PES) and dipole moment function for water. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base with J less than 6 for H2O. The changes in the PES are small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Using this adjusted PES, we can match 30,092 of the 30,117 transitions in the HITRAN 96 data base for H2O with theoretical lines. The 10,25,50,75, and 90 percentiles of the difference between the calculated and tabulated line positions are -0.11, -0.04, -0.01, 0.02, and 0.07 l/cm. Non-adiabatic effects are not explicitly included. About 3% of the tabulated line positions appear to be incorrect. Similar agreement using this adjusted PES is obtained for the oxygen 17 and oxygen 18 isotopes. For HDO, the agreement is not as good, with root-mean-square error of 0.25 l/cm for lines with J less than 6. This error is reduced to 0.02 l/cm by including a small asymmetric correction to the PES, which is parameterized by simultaneously fitting to HDO md D2O data. Scaling this correction by mass factors yields good results for T2O and HTO. The intensities summed over vibrational bands are usually in good agreement between the calculations and the tabulated results, but individual lines strengths can differ greatly. A high temperature list consisting of 307,721,352 lines is generated for H2O using our PES and dipole moment function.

Schwenke, David W.↗