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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Convection of tin in a Bridgman system. I - Flow characterization by effective diffusivity measurements

An electrochemical titration method was used to investigate the dynamic states in a cylindrical layer of convecting tin. The liquid tin was contained in a cell, with curved boundaries made of quartz and flat boundaries made of a solid state electrolyte - yttria-stabilized zirconia (YSZ). The electrolyte acted as a window through which a trace amount of oxygen could be pumped in or out by the application of a constant voltage. The concentration at the YSZ interface was monitored by operating the electrochemical cell in the galvanic mode. Experimentally determined effective diffusivities of oxygen were compared with the molecular diffusivity. Dynamic states in the convective flow were thus inferred. Temperature measurements were simultaneously made in order to identify the onset of oscillations from a steady convective regime. The experiments were conducted for two different aspect ratios for various imposed temperature gradients and two different orientations with respect to gravity. Transcritical states were identified and comparison to two-dimensional numerical models were made.

Sears, B.↗
NASA NTRS1994

The SeaWinds Scatterometer Instrument

The SeaWinds scatterometer instrument is currently being developed by NASA/JPL, as part of the NASA EOS Program, for flight on the Hapanese ADEOS II mission in 1999. This Ku-band radar scatterometer will infer surface wind speed and direction by measuring the radar normalized backscatter cross-section over several different azimuth angles. This paper presents the design characteristics of and operational approach to the instrument itself.

SeaWinds scatterometer EOS program ADEOS II Ku-ban↗
NASA NTRS2008

Material Units, Structures/Landforms, and Stratigraphy for the Global Geologic Map of Ganymede (1:15M)

In the coming year a global geological map of Ganymede will be completed that represents the most recent understanding of the satellite on the basis of Galileo mission results. This contribution builds on important previous accomplishments in the study of Ganymede utilizing Voyager data and incorporates the many new discoveries that were brought about by examination of Galileo data. Material units have been defined, structural landforms have been identified, and an approximate stratigraphy has been determined utilizing a global mosaic of the surface with a nominal resolution of 1 km/pixel assembled by the USGS. This mosaic incorporates the best available Voyager and Galileo regional coverage and high resolution imagery (100-200 m/pixel) of characteristic features and terrain types obtained by the Galileo spacecraft. This map has given us a more complete understanding of: 1) the major geological processes operating on Ganymede, 2) the characteristics of the geological units making up its surface, 3) the stratigraphic relationships of geological units and structures, and 4) the geological history inferred from these relationships. A summary of these efforts is provided here.

Patterson, G. Wesley↗
NASA NTRS2012

HyDE Framework for Stochastic and Hybrid Model-Based Diagnosis

Hybrid Diagnosis Engine (HyDE) is a general framework for stochastic and hybrid model-based diagnosis that offers flexibility to the diagnosis application designer. The HyDE architecture supports the use of multiple modeling paradigms at the component and system level. Several alternative algorithms are available for the various steps in diagnostic reasoning. This approach is extensible, with support for the addition of new modeling paradigms as well as diagnostic reasoning algorithms for existing or new modeling paradigms. HyDE is a general framework for stochastic hybrid model-based diagnosis of discrete faults; that is, spontaneous changes in operating modes of components. HyDE combines ideas from consistency-based and stochastic approaches to model- based diagnosis using discrete and continuous models to create a flexible and extensible architecture for stochastic and hybrid diagnosis. HyDE supports the use of multiple paradigms and is extensible to support new paradigms. HyDE generates candidate diagnoses and checks them for consistency with the observations. It uses hybrid models built by the users and sensor data from the system to deduce the state of the system over time, including changes in state indicative of faults. At each time step when observations are available, HyDE checks each existing candidate for continued consistency with the new observations. If the candidate is consistent, it continues to remain in the candidate set. If it is not consistent, then the information about the inconsistency is used to generate successor candidates while discarding the candidate that was inconsistent. The models used by HyDE are similar to simulation models. They describe the expected behavior of the system under nominal and fault conditions. The model can be constructed in modular and hierarchical fashion by building component/subsystem models (which may themselves contain component/ subsystem models) and linking them through shared variables/parameters. The component model is expressed as operating modes of the component and conditions for transitions between these various modes. Faults are modeled as transitions whose conditions for transitions are unknown (and have to be inferred through the reasoning process). Finally, the behavior of the components is expressed as a set of variables/ parameters and relations governing the interaction between the variables. The hybrid nature of the systems being modeled is captured by a combination of the above transitional model and behavioral model. Stochasticity is captured as probabilities associated with transitions (indicating the likelihood of that transition being taken), as well as noise on the sensed variables.

Narasimhan, Sriram↗
NASA NTRS2022

Vertical Structure in Phytoplankton Growth and Productivity Inferred From Biogeochemical-Argo Floats and the Carbon-Based Productivity Model

Estimates of marine net primary production (NPP) commonly rely on limited in situ 14C incubations or satellite-based algorithms mainly constrained to the surface ocean. Here we combine data from biogeochemical Argo floats with a carbon-based productivity model (CbPM) to compute vertically-resolved estimates of NPP. Inferred NPP profiles derived by informing the CbPM with float-based, depth-resolved, bio-optical data are able to qualitatively reproduce the vertical structure in NPP inferred from in situ 14C incubations at various ocean regions. At station ALOHA, float-based estimates agree within uncertainty with productivity observations at depth, but underestimate surface NPP. We test the ability of the CbPM to infer the depth-resolved structure in NPP from bio-optical properties in the mixed layer, in similar fashion as how remote sensing algorithms of ocean productivity operate. In Southern Ocean waters, the depth-reconstructing implementation of the CbPM overestimates phytoplankton division rates and Chl:C below the mixed layer, resulting in artificially high subsurface NPP when compared with the fully float-informed implementation of the model. The CbPM subsurface extrapolation of phytoplankton Chl, Chl:C division rates, and NPP improves by accounting for deep nutrient (iron) stress impacts on photoacclimation in the Southern Ocean. This improvement is also observed in vertically- integrated NPP, where the mean bias between model implementations in depth-integrated productivity south of 30◦S is reduced by 62 % when account for deep iron limitation. Our results demonstrate that profiling data from biogeochemical Argo floats can serve to inform regional adjustments that lead to the improvement of marine productivity algorithms.

NPP↗
DOE OSTI2022

Phenomenological R -Matrix parameterization of direct, doorway, and compound nuclear reactions [Abstract]

Although formal expressions for scattering matrix accounting for direct, doorway, and compound nuclear (CN) resonant reactions have been derived several decades ago in both the transition ( T -)matrix formalism and the reactance ( K -)matrix formalism, the absence of corresponding expressions in phenomenological R -matrix formalism has limited the application of the latter to CN resonant reactions only. We remove this limitation by parameterizing direct, doorway, and CN resonant reactions in a phenomenological R -matrix scattering matrix, and provide a parameterization for a corresponding Reich-Moore approximation of eliminated capture channels. Direct reactions induce (previously neglected) mixing among the incoming or outgoing R -matrix channel wave functions, parameterized by real and orthonormal channel-rotation matrix, M , whereby the original scattering matrix U is transformed into M T UM . Any real and orthonormal matrix, M , can be equivalently expressed as e η , where η is a real and skew-symmetric 2 rotation-generating matrix that subsequently yields a more intuitive parameterization of eliminated direct capture reactions in Reich-Moore approximation. A phenomenological R -matrix parameterization of doorway reactions is inferred by equating the expression for reactance ( K -)matrix, given in terms of Brune’s alternative R -matrix parameterization, to a corresponding expression derived using Feshbach’s projection operator formalism. Assuming that all doorway states, just like CN states, are confined within spheres defined by R -matrix channel radii, a new R -matrix-like term induced by doorway states is gleaned, wherein each doorway state is parameterized by its energy, width, and the strength of its coupling to each CN state. Since a Reich-Moore approximation for retained-channel scattering matrix ought to approximate the effect of eliminated capture channels taking place via direct, doorway, or CN reactions, each of the three kinds of reactions contributing to the capture entails a corresponding Reich-Moore parameterization in a first-order approximation: direct contribution is parameterized by introducing finite diagonal elements of a retained-channel rotation-generating matrix, doorway contribution is parameterized by doorway capture widths, while CN contribution is parameterized by conventional Reich-Moore capture widths. We will present evidence of direct and doorway reactions observed in recent measurements of resolved resonance cross sections at the Gaerttner LINAC Center at Rensselaer Polytechnic Institute, and will outline a path for implementing this new R -matrix parameterization into the SAMMY nuclear data evaluation code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS2007

Using Remotely-Sensed Estimates of Soil Moisture to Infer Soil Texture and Hydraulic Properties across a Semi-arid Watershed

Near-surface soil moisture is a critical component of land surface energy and water balance studies encompassing a wide range of disciplines. However, the processes of infiltration, runoff, and evapotranspiration in the vadose zone of the soil are not easy to quantify or predict because of the difficulty in accurately representing soil texture and hydraulic properties in land surface models. This study approaches the problem of parameterizing soils from a unique perspective based on components originally developed for operational estimation of soil moisture for mobility assessments. Estimates of near-surface soil moisture derived from passive (L-band) microwave remote sensing were acquired on six dates during the Monsoon '90 experiment in southeastern Arizona, and used to calibrate hydraulic properties in an offline land surface model and infer information on the soil conditions of the region. Specifically, a robust parameter estimation tool (PEST) was used to calibrate the Noah land surface model and run at very high spatial resolution across the Walnut Gulch Experimental Watershed. Errors in simulated versus observed soil moisture were minimized by adjusting the soil texture, which in turn controls the hydraulic properties through the use of pedotransfer functions. By estimating a continuous range of widely applicable soil properties such as sand, silt, and clay percentages rather than applying rigid soil texture classes, lookup tables, or large parameter sets as in previous studies, the physical accuracy and consistency of the resulting soils could then be assessed. In addition, the sensitivity of this calibration method to the number and timing of microwave retrievals is determined in relation to the temporal patterns in precipitation and soil drying. The resultant soil properties were applied to an extended time period demonstrating the improvement in simulated soil moisture over that using default or county-level soil parameters. The methodology is also applied to an independent case at Walnut Gulch using a new soil moisture product from active (C-band) radar imagery with much lower spatial and temporal resolution. Overall, results demonstrate the potential to gain physically meaningful soils information using simple parameter estimation with few but appropriately timed remote sensing retrievals.

Santanello, Joseph A.↗
DOE OSTI2020

Shepherding Metadata Through the Building Lifecycle

Many different digital representations of a building are produced over the course of its lifecycle. These representations contain the metadata required to support different stages of the building, from initial planning and design, to construction and commissioning, through operations, audits, retrofits and maintenance. However, because of differences in the semantics, structure and syntax of these representations, the metadata they contain is not interoperable. We present a novel method for leveraging these representations to create a unified, authoritative Brick metadata model for a building that can be continually maintained over the course of the building lifecycle. A simple synchronization protocol relays inferred Brick metadata from existing metadata sources such as gbXML, BuildingSync, Project Haystack and Modelica to a central integration server, which merges the metadata into a valid Brick model.

Fierro, Gabe↗
DOE OSTI2026

Agentic framework for programmatic crystal structure generation using a fine-tuned worker–supervisor large language model

Platinum group metals (PGMs) underpin many catalytic technologies but face severe supply constraints, motivating the search for alternative materials and computational methods to accelerate discovery. While atomistic simulation tools such as Pymatgen and ASE have streamlined structure manipulation, they require detailed inputs, limiting accessibility for experimentalists and slowing early-stage exploration. Here, in this study, we present an AI-driven agentic framework that orchestrates worker–supervisor large language models (LLMs). The worker translates natural-language prompts of varying abstraction into valid crystallographic structures using a compact LLM fine-tuned with low-rank adaptation on a curated text–code–CIF dataset, emphasizing energy-efficient training. Benchmarking against the baseline CodeGen-350M-mono model shows that fine-tuning reduces hallucination rates from 100% to as low as 5% and improves structural match accuracy to up to 82% for fully specified inputs. Accuracy declines with decreasing prompt detail but remains nontrivial even when only stoichiometry and space group are provided, underscoring the LLM’s capacity for crystallographic inference. The supervisor Claude LLM evaluates the outputs and triggers iterative refinement through the worker’s built-in structure manipulation capabilities (e.g., supercell scaling, strain, vacancy, and substitution operations). We further demonstrate use cases for technologically relevant catalysts, including IrO 2 , pyrochlore Pb 2 Ir 2 O 7 , Ni 2 FeO 4 , and Ni 3 Mo, where the framework generates physically consistent structures that can be refined via geometry optimization. This work introduces a low-energy, language-driven pathway for integrating human and machine intelligence in materials design, paving the way for AI-assisted synthesis planning and high-throughput screening of complex oxides.

AI agent↗
DOE OSTI2025

HEPCloud Operations at Fermilab—The First Five Years

The HEPCloud Facility at Fermilab has now been in production operation for five years. This facility is a unified provisioning gateway to US high performance computing centers, including NERSC, OLCF, and ALCF, other large supercomputers run by the NSF, and commercial clouds. HEPCloud delivers hundreds of millions of core-hours yearly for CMS. HEPCloud also serves other Fermilab experiments including DUNE, Mu2e, Muon g-2, and NOvA. In this paper we present the practical considerations of operating a distributed facility such as HEPCloud. We also mention some of the interesting research and development that HEPCloud has been used for including GPU-based machine learning inference servers, and tests of Quantum Computing.

Timm, Steven [Fermilab]↗
DOE OSTI2021

The Scattered Light Time-history Diagnostic suite at the National Ignition Facility

The Scattered Light Time-history Diagnostic (SLTD) is being implemented at the National Ignition Facility (NIF) to greatly expand the angular coverage of absolute scattered-light measurements for direct- and indirect-drive inertial confinement fusion (ICF) experiments. The SLTD array will ultimately consist of 15 units mounted at a variety of polar and azimuthal angles on the NIF target chamber, complementing the existing NIF backscatter suite. Each SLTD unit collects and diffuses scattered light onto a set of three optical fibers, which transport the light to filtered photodiodes to measure scattered light in different wavelength bands: stimulated Brillouin scattering (350 nm–352 nm), stimulated Raman scattering (430 nm–760 nm), and ω/2 (695 nm–745 nm). SLTD measures scattered light with a time resolution of ~1 ns and a signal-to-noise ratio of up to 500. Currently, six units are operational and recording data. Measurements of the angular dependence of scattered light will strongly constrain models of laser energy coupling in ICF experiments and allow for a more robust inference of the total laser energy coupled to implosions.

47 OTHER INSTRUMENTATION↗
NASA NTRS1983

Landsat-4 on-board ephemeris determination utilizing the Global Positioning System

The Global Positioning System (GPS) is a worldwide system of navigation data satellites currently being deployed by the United States for land, sea, air and space-borne users. Currently several development satellites have been launched for system evaluation. Eventually the system will include 18 operational satellites. The GPS system utilizes precision clocks to allow users to measure the one-way propagation delay of navigational signals from the satellites, so that users can infer their position by decoding the navigation signal and observing the delay from several satellites. Landsat-4 is the first spacecraft to carry a GPS navigation system into orbit. This paper describes the Landsat-4 GPS experiment, Landsat-4 requirements for ephemeris data and the in-flight performance of the system.

Korenstein, D. A.↗
NASA NTRS1993

A comparison of several techniques to assign heights to cloud tracers

Experimental results are presented which suggest that the water-vapor technique of radiance measurement is a viable alternative to the CO2 technique for inferring the height of semitransparent cloud elements. Future environmental satellites will rely on H2O-derived cloud-height assignments in the wind-field determinations with the next operational geostationary satellite. On a given day, the heights from the H2O and CO2 approaches compare to within 60-110 hPa rms.

Nieman, Steven J.↗
NASA NTRS2000

Two Fiber Optical Fiber Thermometry

An optical fiber thermometer consists of an optical fiber whose sensing tip is given a metallic coating. The sensing tip of the fiber is essentially an isothermal cavity, so the emission from this cavity will be approximately equal to the emission from a blackbody. Temperature readings are obtained by measuring the spectral radiative heat flux at the end of the fiber at two wavelengths. The ratio of these measurements and Planck's Law are used to infer the temperature at the sensing tip. Optical fiber thermometers have high accuracy, excellent long-term stability and are immune to electromagnetic interference. In addition, they can be operated for extended periods without requiring re-calibration. For these reasons. it is desirable to use optical fiber thermometers in environments such as the International Space Station. However, it has recently been shown that temperature readings are corrupted by emission from the fiber when extended portions of the probe are exposed to elevated temperatures. This paper will describe several ways in which the reading from a second fiber can be used to correct the corrupted temperature measurements. The accuracy and sensitivity to measurement uncertainty will be presented for each method.

Jones, Mathew R.↗
NASA NTRS2002

Determining the Compositions of Extraterrestrial Lava Flows

The primary purpose of this research project has been to develop techniques that allow the emplacement conditions of volcanic landforms on other planets to be related to attributes that can be remotely detected with available instrumentation. The underlying assumption of our work is that the appearance of a volcano, lava flow, debris avalanche, or exhumed magmatic intrusion can provide clues about the conditions operating when that feature was first emplaced. Magma composition, amount of crustal heat flow, state of tectonic stress, and climatic conditions are among the important variables that can be inferred from the morphology and texture of an igneous body.

Fink, Jonathan H.↗
NASA NTRS1991

The Au Cathode in the System Li2CO3-CO2-CO at 800 to 900 C

Gold is one of several metals being evaluated at NASA Lewis Research Center as positive electrode catalysts for an alkali metal/molten alkali metal carbonate/carbon dioxide electrochemical cell. Such a cell is proposed for CO2-rich planetary atmospheres such as those of Mars and Venus. Its application could be as a primary power supply, as a secondary power supply recharged either 'chemically' by replenishment of the alkali metal or electrochemically from a central station power source, or as a converter of carbon dioxide to oxygen via a complete electrochemical cycle. For the work being reported, lithium was assumed to be the alkali metal of choice for the negative electrode of the cell, and therefore molten lithium carbonate was the electrolyte used in the Au electrode experiments. Cathodic linear sweep voltammetry (LSV) was the primary analytical technique for evaluating the performance of the Au cathode. interest comprised the cell temperature and the total pressure and composition of the reactant gas. In the absence of operational difficulties, the effect of bubbling the reactant gas through the melt was also determined. On the basis of the variation of electrode performance with changes in these parameters, inferences have been made concerning the electrochemical and chemical processes at and near the electrode. The results of post-test micrographic analyses of the Au cathode are also presented. An attempt is then made to project from the experimental results to some relevant conclusions pertaining to a gold cathode in a practical alkali metal - carbon dioxide cell.

Hagedorn, Norman H.↗