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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1979

Technique to determine location of radio sources from measurements taken on spinning spacecraft

The procedure developed to extract average source direction and average source size from spin-modulated radio astronomy data measured on the IMP-6 spacecraft is described. Because all measurements are used, rather than just finding maxima or minima in the data, the method is very sensitive, even in the presence of large amounts of noise. The technique is applicable to all experiments with directivity characteristics. It is suitable for onboard processing on satellites to reduce the data flow to Earth. The application to spin-modulated nonpolarized radio astronomy data is made and includes the effects of noise, background, and second source interference. The analysis was tested with computer simulated data and the results agree with analytic predictions. Applications of this method with IMP-6 radio data have led to: (1) determination of source positions of traveling solar radio bursts at large distances from the Sun; (2) mapping of magnetospheric radio emissions by radio triangulation; and (3) detection of low frequency radio emissions from Jupiter and Saturn.

Fainberg, J.↗
NASA NTRS2015

A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery Using a Probabilistic Learning Framework

Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets, which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

Segments↗
NASA NTRS2019

Forecasting the Ambient Solar Wind with Numerical Models. I. On the Implementation of an Operational Framework

The ambient solar wind conditions in interplanetary space and in the near-Earth environment are determined by activity on the Sun. Steady solar wind streams modulate the propagation behavior of interplanetary coronal mass ejections and are themselves an important driver of recurrent geomagnetic storm activity. The knowledge of the ambient solar wind flows and fields is thus an essential component of successful space weather forecasting. Here, we present an implementation of an operational framework for operating, validating, and optimizing models of the ambient solar wind flow on the example of Carrington Rotation 2077. We reconstruct the global topology of the coronal magnetic field using the potential field source surface model (PFSS) and the Schatten current sheet model (SCS) and discuss three empirical relationships for specifying the solar wind conditions near the Sun, namely the Wang–Sheeley (WS) model, the distance from the coronal hole boundary model (DCHB), and the Wang-Sheeley–Arge (WSA) model. By adding uncertainty in the latitude about the sub-Earth point, we select an ensemble of initial conditions and map the solutions to Earth by the Heliospheric Upwind eXtrapolation (HUX) model. We assess the forecasting performance from a continuous variable validation and find that the WSA model most accurately predicts the solar wind speed time series (RMSE≈83 km/s). We note that the process of ensemble forecasting slightly improves the forecasting performance of all solar wind models investigated. We conclude that the implemented framework is well suited for studying the relationship between coronal magnetic fields and the properties of the ambient solar wind flow in the near-Earth environment.

Reiss, Martin A.↗
NASA NTRSDate not supplied

Exploring the Capabilities of a Machine Learning Algorithm to Detect Space Weather-Significant Emerging Active Regions

Active regions are a source of various phenomena responsible for Space Weather disturbances; therefore, developing a technology for early warning about upcoming magnetic activity is crucial to mitigate its impact. However, observational limitations and the high nonlinearity of processes associated with the accumulation of magnetic flux and its interaction with the surrounding plasma during the emergence through the convection zone make early activity detection a challenging problem. To address these challenges, we developed a physics-driven machine learning model that allows us to detect active regions (ARs) before they become visible on the solar surface by analyzing the power spectra of acoustic oscillations observed by the SDO/HMI instrument. This study is based on a time series of Doppler shift maps of 31x31-degree areas tracked with the Carrington rotation rate for four days before and after the emergence. The Doppler shift time series are processed into the oscillation power maps for four frequency ranges and accompanied by line-of-sight magnetograms and the continuum intensity maps from SDO/HMI. The resulting data are converted into a 1D time series representing the mean temporal variations of these quantities. The redacted time series are used as input to predict AR emergence using the Long Short Term Memory (LSTM) method. The training of the LSTM model is based on 40 ARs, which includes an independent analysis for each sub region that exhibits AR emergence or remains quiet. The emergence of magnetic flux (defined as a decrease of the continuum intensity) was detected with the developed LSTM algorithm from 5 to 48 hours before the reported time by NOAA. The developed model is capable of pointing to the time and location of active region formation. In this presentation, we discuss reasons that impact how early in advance the model can identify the upcoming activity and the possibility of improving the current predictive skills and steps to transition to the operational forecast.

Heliophysics↗
DOE OSTI2022

NEAR CRITICAL POINT TESTING AND PERFORMANCE RESULTS OF A SCO2 COMPRESSOR FOR A 10MWE BRAYTON CYCLE

Development and commercial acceptance of sCO2 Brayton cycles for power generation applications are growing rapidly as they offer performance advantages over other cycles. To maximize the cycle performance, the compressors are designed to operate near the critical point of the working fluid. At the critical point the fluid properties change rapidly with variations in inlet conditions. This makes it challenging to both accurately predict the performance and guarantee the operability of the compressor, as the behavior is affected by these slight variations in inlet conditions. A full scale 1st stage main compressor for a 10MWe-Class recompression Brayton cycle was built and tested to validate performance and operability in this unique operating range. The compressor was tested in a laboratory environment with additional instrumentation, beyond what is required by PTC-10, to minimize the uncertainty in the measured performance. Complete constant speed characteristics were collected at multiple supercritical points, operating at constant inlet conditions for each speed line covering a range of compressor inlet densities from 400 to 600 kg/m3. Variations in the compressor stage efficiency and choke margin were observed, and the overall operability and stability of the compressor in response to changes in operating condition were also monitored. The compressor was shown to have excellent performance that closely matched the original design prediction. The performance at various inlet conditions showed minimal change in isentropic head coefficient at the design flow, but did show some variation in efficiency and choke margin across the map. These changes in performance were observed to be minimal, and did not affect the stable operation of the compressor. The results demonstrate that a commercial scale sCO2 compressor can operate near the critical point and achieve the high levels of performance and stability required for power generation applications.

pelton, rob↗
NASA NTRS1990

Finite element analysis of thermal distortion effects on optical performance of solar dynamic concentrator for Space Station Freedom

An analysis was performed to predict the thermal distortion of the solar dynamic concentrator for Space Station Freedom in low earth orbit and to evaluate the effects of that thermal distortion on concentrator on-orbit performance. The analysis required substructural finite element modeling of critical concentrator structural subsystems, structural finite element modeling of the concentrator, mapping of thermal loading onto the structural finite element model, and the creation of specialized postprocessors to assist in interpreting results. Concentrator temperature distributions and thermally induced displacements and slope errors and the resulting receiver flux distribution profiles are discussed. Results determined for a typical orbit indicate that concentrator facet rotations are less than 0.2 mrad and that the change in facet radius due to thermal flattening is less than 5 percent. The predicted power loss due to thermal distortion effects is less than 0.3 percent. As a consequence the thermal distortions of the solar dynamic concentrator in low earth orbit will have a negligible effect on the flux distribution profiles within the receiver.

Doherty, Michael P.↗
DOE OSTI2021

Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions

Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSFs) or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from golden eagles Aquila chrysaetos from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During the summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2017

Curved Displacement Transfer Functions for Geometric Nonlinear Large Deformation Structure Shape Predictions

For shape predictions of structures under large geometrically nonlinear deformations, Curved Displacement Transfer Functions were formulated based on a curved displacement, traced by a material point from the undeformed position to deformed position. The embedded beam (depth-wise cross section of a structure along a surface strain-sensing line) was discretized into multiple small domains, with domain junctures matching the strain-sensing stations. Thus, the surface strain distribution could be described with a piecewise linear or a piecewise nonlinear function. The discretization approach enabled piecewise integrations of the embedded-beam curvature equations to yield the Curved Displacement Transfer Functions, expressed in terms of embedded beam geometrical parameters and surface strains. By entering the surface strain data into the Displacement Transfer Functions, deflections along each embedded beam can be calculated at multiple points for mapping the overall structural deformed shapes. Finite-element linear and nonlinear analyses of a tapered cantilever tubular beam were performed to generate linear and nonlinear surface strains and the associated deflections to be used for validation. The shape prediction accuracies were then determined by comparing the theoretical deflections with the finiteelement- generated deflections. The results show that the newly developed Curved Displacement Transfer Functions are very accurate for shape predictions of structures under large geometrically nonlinear deformations.

displacement theory↗
DOE OSTI2023

Machine learning predictions of near-surface permafrost extent at Teller 27, Teller 47, and the Kougarok 64 Hillslope sites on the Seward Peninsula, Alaska: Supporting Data

Geophysical surveys were conducted at the NGEE Arctic Teller mile marker 27 site, Teller mile marker 47 site, and Kougarok mile marker 64 site during the summers of 2018, 2019, and 2021. Additional data was collected at Teller mile marker 47 during September 2021 and August 2022. These surveys were used to identify locations of near-surface permafrost during the period of maximum seasonal thaw depth for ground truth data used in machine learning predictions of near-surface permafrost extent at each site. This dataset contains CSV files of ground truth observations of near-permafrost presence or absence for each site, where PF = 1 indicates permafrost presence and PF = 0 indicates permafrost absence. The dataset also includes 2 sets of binary rasters (WGS84 UTM zone 3) of permafrost extent for each site using 1) all of the training data and 2) the transferred model. For both sets of rasters, 0 = non-permafrost and 1 = permafrost. Included are 6 *.tif files and 5 *.csv files that include a data dictionary (dd.csv) and file-level metadata (flmd.csv). This dataset is in support of the paper "Machine learning-derived high-resolution maps of near-surface permafrost for three watersheds on the Seward Peninsula, Alaska" that is in review (May 2023). The Next-Generation Experiments: Arctic (NGEE Arctic), a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Atomic-Scale Structure of Chemically Distinct Surface Oxygens in Redox Reactions

During redox reactions, oxide-supported catalytic systems undergo structural and chemical changes. Improving subsequent catalytic properties requires an understanding of the atomic-scale structure with chemical state specificity under reaction conditions. For the case of 1/2 monolayer vanadia on α-TiO 2 (110), we use X-ray standing wave (XSW) excited X-ray photoelectron spectroscopy to follow the redox induced atomic positional and chemical state changes of this interface. Furthermore, while the resulting XSW 3D composite atomic maps include the Ti and O substrate atoms and V surface atoms, our focus in this report is on the previously unseen surface oxygen species with comparison to density functional theory predictions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Observation of the molecular response to light upon photoexcitation

Abstract When a molecule interacts with light, its electrons can absorb energy from the electromagnetic field by rapidly rearranging their positions. This constitutes the first step of photochemical and photophysical processes that include primary events in human vision and photosynthesis. Here, we report the direct measurement of the initial redistribution of electron density when the molecule 1,3-cyclohexadiene (CHD) is optically excited. Our experiments exploit the intense, ultrashort hard x-ray pulses of the Linac Coherent Light Source (LCLS) to map the change in electron density using ultrafast x-ray scattering. The nature of the excited electronic state is identified with excellent spatial resolution and in good agreement with theoretical predictions. The excited state electron density distributions are thus amenable to direct experimental observation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism

Critical to a sustainable energy future are microbial platforms that can process aromatic carbons from the largely untapped reservoir of lignin and plastic feedstocks. Comamonas species present promising bacterial candidates for such platforms because they can use a range of natural and xenobiotic aromatic compounds and often possess innate genetic constraints that avoid competition with sugars. However, the metabolic reactions of these species are underexplored, and the regulatory mechanisms are unknown. Here we identify multilevel regulation in the conversion of lignin-related natural aromatic compounds, 4-hydroxybenzoate and vanillate, and the plastics-related xenobiotic aromatic compound, terephthalate, in Comamonas testosteroni KF-1. Transcription-level regulation controls initial catabolism and cleavage, but metabolite-level thermodynamic regulation governs fluxes in central carbon metabolism. Quantitative 13 C mapping of tricarboxylic acid cycle and cataplerotic reactions elucidates key carbon routing not evident from enzyme abundance changes. This scheme of transcriptional activation coupled with metabolic fine-tuning challenges outcome predictions during metabolic manipulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Direct Measurement of ICRF-Enhanced Plasma Potentials on WEST Using Reciprocating Emissive Probes

An extensive documentation of ICRF-enhanced plasma potentials has been conducted over two experimental campaigns on the WEST tokamak using reciprocating emissive probes magnetically connected to two ICRF antennas. The collected data spans a wide range of antenna electrical settings (coupled power, toroidal phasing, left–right power balance) and plasma parameters (density at the antenna limiter above and below the lower hybrid resonance, plasma current, minority fraction). By scanning the edge safety factor across multiple probe plunges, the magnetic connection between the probe and the antenna varied, enabling the construction of a 2D map of the plasma and floating potentials around an active ICRF antenna. This dataset will be used to validate RF simulation tools equipped with the sheath boundary condition and used to predict RF rectified potentials and ICRF-induced impurity sputtering in future machines. This paper presents the diagnostic and some initial measurements, while the rest will be reported elsewhere.

Diab, Raymond [Massachusetts Inst. of Technology (↗
DOE OSTI2021

Dark matter microhalos from simplified models

Here, we introduce simplified models for enhancements in the matter power spectrum at small scales and study their implications for dark matter substructure and gravitational observables. These models capture the salient aspects of a variety of early Universe scenarios that predict enhanced small-scale structure, such as axionlike particle dark matter, light vector dark matter, and epochs of early matter domination. We use a model-independent, semianalytic treatment to map bumps in the matter power spectrum to early forming subsolar mass dark matter halos and estimate their evolution, disruption, and contribution to the substructure of clusters and galaxies at late times. We discuss the sensitivity of gravitational observables, including pulsar timing arrays and caustic microlensing, to both the presence of bumps in the power spectrum and variations in their basic properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Measurement of Triple-Differential Inclusive Muon Neutrino Charged-Current Cross Sections on Argon with the MicroBooNE Detector

We report the first measurement of the differential cross section $d^2σ(E_ν)/dcos(θ_µ)dP_µ$for inclusive muon neutrino charged-current scattering on argon. This measurement utilizes data from6.5×10 20 protons on target of exposure collected using the MicroBooNE liquid argon time projection chamber located on-axis in the Fermilab Booster Neutrino Beam with a mean neutrino energy of approximately 0.8 GeV. In this note, the mapping from reconstructed kinematics to truth quantities, particularly from reconstructed to true neutrino energy, is validated by comparing the distribution of reconstructed hadronic energy in data to that of the model prediction in different muon scattering angle bins after conditional constraint from the muon momentum distribution in data. The success of this validation gives confidence that the missing energy in the MicroBooNE detector is well-modeled within its uncertainties in simulation, enabling the unfolding to an energy-dependent triple-differential measurement over muon momentum, muon scattering angle, and neutrino energy. The unfolded measurement covers an extensive phase space, providing a wealth of information useful for future LArTPC experiments measuring neutrino oscillations. Comparisons with model predictions show the best agreement with Neut 5.4.0.1 at low energy, and with NuWro 19.02.01 at higher energies, particularly at forward muon scattering angles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Importance of Multiplicity Fluctuations in Entropy Scaling

One of the greatest uncertainties in heavy-ion collisions is the description of the initial state. Different models predict a wide range of initial energy density distributions based on their underlying assumptions. Final flow harmonics are sensitive to these differences in the initial state due to the nearly linear mapping between eccentricities and anisotropic flow harmonics. The Trento code uses a model-agnostic approach by phenomenologically parameterizing the initial state and constraining those parameters from a Bayesian analysis. There the multiplicity fluctuations were determined by a one parameter Γ distribution. However, initial-state models arising from the Color-Glass Condensate (CGC) framework lead to an initial energy density which is outside the functional form considered in Trento and its later Bayesian analyses because they rely on log-normal multiplicity fluctuations. We compare T A T B scaling (CGC-like) to √T A T B scaling (preferred from a Trento Bayesian analysis) and find that the T A T B form together with log-normal fluctuations is a reasonable candidate to describe the multiplicity fluctuations but leads to larger eccentricities, which would affect the extraction of viscosity in small systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Soil Temperature and Moisture, Teller Road Mile Marker 27, Seward Peninsula, Alaska, 2016-2023

Daily averages of soil temperature and moisture measured once every hour at different heights located at Intensive Monitoring Stations at Teller Road Mile Marker 27 site. Data are retrieved annually from 2016-2023. This is the final update to this dataset: no changes to previous data files with the addition of 2022-2023 data files. Data files have header rows, NaN fields indicate invalid or missing data, and negative vertical offsets are above ground. UPDATED 2025-07: Seven new data files collected in 2022-2023 were added and no previously archived data were changed. This represents the final collection of data and text in the title was changed to reflect the defined timespan. Other files that were added: file-level metadata, a data dictionary, a site location map, and a data file inventory by year. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗