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440 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sage: parallel semi-asymmtric graph algorithms for NVRAMs

Non-volatile main memory (NVRAM) technologies provide an attractive set of features for large-scale graph analytics, including byte-addressability, low idle power, and improved memory-density. NVRAM systems today have an order of magnitude more NVRAM than traditional memory (DRAM). NVRAM systems could therefore potentially allow very large graph problems to be solved on a single machine, at a modest cost. However, a significant challenge in achieving high performance is in accounting for the fact that NVRAM writes can be much more expensive than NVRAM reads. In this paper, we propose an approach to parallel graph analytics using the Parallel Semi-Asymmetric Model (PSAM), in which the graph is stored as a read-only data structure (in NVRAM), and the amount of mutable memory is kept proportional to the number of vertices. Similar to the popular semi-external and semi-streaming models for graph analytics, the PSAM approach assumes that the vertices of the graph fit in a fast read-write memory (DRAM), but the edges do not. In NVRAM systems, our approach eliminates writes to the NVRAM, among other benefits. To experimentally study this new setting, we develop Sage, a parallel semi-asymmetric graph engine with which we implement provably-efficient (and often work-optimal) PSAM algorithms for over a dozen fundamental graph problems. We experimentally study Sage using a 48--core machine on the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) equipped with Optane DC Persistent Memory, and show that Sage outperforms the fastest prior systems designed for NVRAM. Importantly, we also show that Sage nearly matches the fastest prior systems running solely in DRAM, by effectively hiding the costs of repeatedly accessing NVRAM versus DRAM.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Modeling and Simulation of Fuel Dispersal During the Loss-of-Coolant Accident

This document is the compilation of the milestone portion to a larger end of project NEUP report. The executive summary of the modeling portion is provided below: In the event of cladding rupture during a postulated LOCA in a pressurized water reactor, fuel particles, along with fission gases, can be expelled into the reactor core from the fractured fuel rod, a phenomenon referred to as fuel dispersal. The initial stage of fuel dispersal is strongly influenced by the high-pressure ejection of fuel fragments, the size and geometry of the ruptured cladding, and the depressurization history of the fuel rod during the postulated LOCA transient. Depending on the location of the burst orifice relative to the quench front, the dispersal event represents an intricate three-phase flow and heat transfer phenomenon, where high-temperature fuel particles carried by the fission gases interact with the coolant within the narrow subchannels of the fuel assemblies, inducing localized phase change. Given the unique multiphysics nature of this phenomena, the current study develops a dedicated computational framework to predict the mass distribution and cooling of dispersing fuel particles, facilitating post-accident assessment and management of the fuel assemblies. Considering the scale of nuclear reactor applications, a continuum three-fluid model is proposed for simulating the transport of solids within the reactor core. With high-temperature fuel fragments within the liquid media, nucleation sites inducing phase changes are dispersed within the flow domain. Coupled with the fact that the transient dispersal event occurs on different time scales than other three-phase flow applications, this study derives a time-averaged three-fluid flow model without losing generality. The assumptions regarding the continuum treatment of the solid phase and the modeling of fuel dispersal behavior are incorporated to simplify the governing equations and derive applicable closure relations. The computational validation of the model was conducted using adiabatic experimental results obtained from ongoing research at Oregon State University, focusing on characterizing fuel dispersal behavior during simulated LOCA conditions. Settlement characteristics of the solids, quantified by the probability distribution of equivalent particles, closely matched the probability density functions reported in experimental studies. The transport of fuel particles within a scaled 5 × 5 lattice of a pressurized-water reactor rod bundle geometry was modeled through a two-fluid Eulerian framework. The required boundary conditions were evaluated from the fuel performance code BISON in a postulated large-break LOCA scenario. The modeling framework considered solid fuel particles as granular matter, interacting with the gaseous dry steam phase and fission gases through the governing interfacial momentum exchange between the participating fluids. The simulation results provided the volume fraction of the solids obtained at the bottom surface of the enclosing tank geometry. Postulated LOCA leading to fuel dispersal phenomena involves the strong coupling between fuel thermomechanics, cladding deformation, thermal-hydraulics, and fuel particle transport. Incorporation of such a strong coupling in numerical simulation is performed by coupling the multiphysics solvers. In the case of fuel dispersal, a strong coupled simulation can be performed by coupling the BISON code for fuel performance, the TRACE code for system-level thermal hydraulics, and fuel particle transport in Multiphysics Object-Oriented Simulation Environment (MOOSE). For such intricate infrastructure, the MOOSE Framework eases the data transfer between codes. The recent version of MOOSE has incorporated the Navier-Stokes module for the fluid flow. An exploratory exercise was done to gain familiarity with finite volume capabilities in the MOOSE framework to incorporate the Spalart-Allmaras (SA) turbulence model. New finite-volume and auxiliary kernels were introduced to assemble the SA transport equation, compute turbulent viscosity, and evaluate wall distance and diagnostic turbulence terms, fully integrated with existing Navier-Stokes modules. A turbulent lid-driven cavity at a Reynolds number of approximately 10,000 is used for verification. MOOSE shows the robust solver convergence and produces the turbulent features. But it underpredicts the velocity profile and turbulent quantities, emphasizing the need to develop improved SA near-wall treatments (e.g., low-Re corrections or wall functions) as a key direction for future work.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Reservoir Sediment Management and Monitoring Database

Overview This dataset compiles dam sediment management and monitoring information from surveys, case studies, and journal articles. Additionally, features described by the National Inventory of Dams (i.e., presence of sluice gates) are included to indicate known infrastructure features that may address sediment releases. The location and description of records from downstream monitoring gages are catalogued in order to help with tracking conditions over time (e.g., before and after management actions, as operations change, etc.). The data help address national scale understanding of challenges and solutions related to the accumulation of sediment behind a dam as well as downstream passage. Sediment trapping causes problems as it reduces storage capacity, disrupts dam and reservoir function, impedes access for recreation, alters water quality/habitat conditions, and contributes to riverbank and coastal erosion within the reservoir. Data compilation from a variety of sources is a first step towards assessing system-wide efficacy of management solutions. This dataset was developed under the Water Power Technologies Office funded effort which began as a Seedling on Reservoir Sedimentation Data, and was supported by the Reservoir Sedimentation Modeling Framework and Data Analysis project. These projects have addressed challenges in describing sediment transport, trapping, and management at dams throughout the US. Methodology An outer join on dams/reservoirs with surveys and survey reports (documented in the RESSED database, USBR or USACE databases, project websites, etc.) with the National Inventory of Dams, based on the NIDID to determine dams with documented management and/or sluice gates. Additional dams with documented management activity were identified through review of technical articles from the past 25 years in Journal of Hydrology, Journal of Water Resources Planning and Management, Geomorphology, Journal of Hydraulic Engineering, Water, Journal of Cleaner Production, International Journal of Sediment Research, Nature Scientific Reports, Earth Surface Processes and Landforms, and Environmental Science and Pollution Research. Individual records were created for each survey or management activity documented. To evaluate downstream sediment monitoring records, the nhdPlusTools and dataRetrieval packages in R were used to find gages within 10km of each dam in the management database. Length of record and location of matched gages were retrieved for those parameters relevant to sediment concentration or total sediment discharge.

Hansen, Carly [ORNL] (ORCID:0000000193280838)↗
DOE OSTI2020

Planck intermediate results

We present the NPIPE processing pipeline, which produces calibrated frequency maps in temperature and polarization from data from the Planck Low Frequency Instrument (LFI) and High Frequency Instrument (HFI) using high-performance computers. NPIPE represents a natural evolution of previous Planck analysis efforts, and combines some of the most powerful features of the separate LFI and HFI analysis pipelines. For example, following the LFI 2018 processing procedure, NPIPE uses foreground polarization priors during the calibration stage in order to break scanning-induced degeneracies. Similarly, NPIPE employs the HFI 2018 time-domain processing methodology to correct for bandpass mismatch at all frequencies. In addition, NPIPE introduces several improvements, including, but not limited to: inclusion of the 8% of data collected during repointing manoeuvres; smoothing of the LFI reference load data streams; in-flight estimation of detector polarization parameters; and construction of maximally independent detector-set split maps. For component-separation purposes, important improvements include: maps that retain the CMB Solar dipole, allowing for high-precision relative calibration in higher-level analyses; well-defined single-detector maps, allowing for robust CO extraction; and HFI temperature maps between 217 and 857 GHz that are binned into 0'.9 pixels (Nside = 4096), ensuring that the full angular information in the data is represented in the maps even at the highest Planck resolutions. The net effect of these improvements is lower levels of noise and systematics in both frequency and component maps at essentially all angular scales, as well as notably improved internal consistency between the various frequency channels. Based on the NPIPE maps, we present the first estimate of the Solar dipole determined through component separation across all nine Planck frequencies. The amplitude is (3366.6 ± 2.7) μK, consistent with, albeit slightly higher than, earlier estimates. From the large-scale polarization data, we derive an updated estimate of the optical depth of reionization of τ = 0.051 ± 0.006, which appears robust with respect to data and sky cuts. There are 600 complete signal, noise and systematics simulations of the full-frequency and detector-set maps. As a Planck first, these simulations include full time-domain processing of the beam-convolved CMB anisotropies. The release of NPIPE maps and simulations is accompanied with a complete suite of raw and processed time-ordered data and the software, scripts, auxiliary data, and parameter files needed to improve further on the analysis and to run matching simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Shape-Controlled Synthesis of Copper Nanocrystals for Plasmonic, Biomedical, and Electrocatalytic Applications

As a metal that can occur in nature in the elemental form, copper (Cu) has been used by humans since ca. 8000 BC. With most properties matching those of Ag and Au, Cu has played a more significant role in commercial applications owing to its much higher (the 25th among all elements) abundance in Earth’s crust and thus more affordable price. In addition to its common use as a conductor of heat and electricity, it is a constituent of various metal alloys for hardware, coins, strain gauges, and thermocouples. Bulk Cu is also widely utilized as a building material. When downsized to the nanoscale, Cu and Cu-based structures have found widespread use in applications ranging from electronics to optoelectronics, plasmonics, catalysis, sensing, and biomedicine. Besides Ag and Au, for example, Cu is another metal known for its localized surface plasmon resonance (LSPR) in the visible and near-infrared regions when prepared as nanocrystals. As a potential replacement for indium–tin oxide (ITO) films, polymer coatings containing Cu nanowires are strong candidates for the fabrication of transparent and flexible electrodes key to touchscreen display and related applications. The commercial catalysts for water–gas shift and gas detoxification reactions are also based on Cu nanoparticles. Most recently, Cu nanocrystals have attracted considerable interest for their superior selectivity toward hydrocarbons and multicarbon species during the electrochemical reduction of CO 2 . The success of all these applications critically depends on our ability to control the shape and surface structure of the nanocrystals. Relative to Ag and Au, it is more challenging to generate Cu-based nanocrystals using colloidal methods due to its lower reduction potential and greater vulnerability to oxidation. Here, in this account, we discuss recent progress in the colloidal synthesis of Cu nanocrystals with controlled shapes for plasmonic, biomedical, and catalytic applications. With glucose serving as a reducing agent, Cu nanocrystals bearing a twinned or single-crystal structure can be synthesized using an aqueous system with the assistance of hexadecylamine (HDA). In this synthetic protocol, HDA not only passivates the surface to protect the nanocrystals from oxidation but also manipulates the reduction kinetics of Cu(II) precursor through coordination and an increase of solution pH. Typical products include nanocubes and penta-twinned nanowires whose surfaces are dominated by {100} facets. When seeds produced either in situ or ex situ are introduced, Cu-based nanocrystals featuring a singly twinned, core–shell, or Janus structure can be readily synthesized. Aside from segmented structures, Cu-based alloys with various noble metals can be synthesized through coreduction or a galvanic replacement reaction with preformed Cu nanocrystals. By controlling the size and/or shape of Cu nanocrystals, their LSPR peaks can be tuned into the near-infrared region, making them promising candidates for optical imaging contrast enhancement and photothermal treatment. The inclusion of the 64 Cu isotope makes them immediately useful in positron emission tomography and thus image-guided therapy. The surface structure, elemental distribution, and valence state of Cu-based nanocrystals can all be tailored to augment their electrocatalytic performance. It is hoped that this Account will inspire more studies into the development of rational methods capable of producing Cu-based nanocrystals with diverse and well-controlled shapes, internal structures, and compositions for a broader range of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Digital Twin Model for Advanced Manufacture of a Rotating Detonation Engine Injector

A digital twin material model (DTMM) of an additive manufacturing (AM) process was created to advance the state of the art in rotating detonation engine (RDE) injector design. Current RDE injectors are designed with large pressure drops, enabling a stable and repeatable combustion process. However, this comes at the cost of system efficiency. For the technology to transition to commercial fossil-based power generation, it is important to develop injectors with reduced flow losses. Low-loss injectors are difficult to design and manufacture with conventional manufacturing techniques. AM enables new design options, but the AM manufacturing process must be thoroughly understood to result in a robust design. A DTMM provides the necessary insight by defining the cause-effect relationships between process parameters, microstructure features, and properties. Therefore, a DTMM to support the design and manufacturing process was developed and applied to the design of a new additively manufactured low-loss injector. The injector combustion behavior was characterized through hot-fire tests, and mechanical performance was compared to the DTMM predictions. The two project goals were the successful development of the DTMM and the demonstration of an improved RDE injector design. The RDE injector design and DTMM developments occurred on parallel but dependent paths. The injector was designed to reduce pressure drop by increasing the cross-sectional flow area ratio between the injector air passages and the combustor annulus. This resulted in less structural material, raising the concern that thin members would be susceptible to high-cycle fatigue (HCF) under the periodic loading inherent to an RDE. It was most important for the DTMM to predict behavior in these features; therefore, the injector design concept guided the material thicknesses used in fatigue tests. The DTMM development started by manufacturing a series of coupons over the range of possible AM process variations. A design-of-experiment approach was used to select which process variable combinations gave the most efficient coverage relevant to the injector design space. The microstructure in each of these coupons was characterized, and then computational methods were used to create a numerical model of the correlation between process variables and microstructure. Next, a set of HCF samples were tested to calibrate existing models that map microstructure to HCF performance. Together, these two links formed the DTMM that calculates HCF behavior from AM process variables. Two injector prototypes were additively manufactured. The first injector design strategy aggressively pursued low-loss performance by substantially increasing the oxidizer flow area. The combination of manufacturing lead times and the fatigue testing schedule meant that the DTMM was not available when building this first prototype. Therefore, its process parameters were chosen based on a manual review of the available coupon data. This prototype was built successfully and evaluated in 58 combustion tests. Sustained detonation was achieved with remarkably reduced pressure loss, and some tests even displayed pressure loss characteristics similar to conventional gas turbine combustors. This achieved the project goal of improving RDE injector design. The second injector was manufactured according to the optimized parameters predicted by the DTMM. The flow area modifications of this injector were less aggressive than the first injector since demonstrating low pressure loss was not an objective of the second hot-fire test series. Rather, the test objective was to cause high cycle fatigue failure in the part due to periodic loading from the rotating detonation wave. The observed number of cycles to failure was to be compared to the number predicted by the DTMM and thereby assess the utility of the DTMM in component design. However, the required level of vibration was not obtained during combustion. Therefore, high cycle fatigue was not experienced in the hot-fire tests of the second injector. Fatigue data was obtained by further testing the second injector in a conventional HCF test apparatus. The injector demonstrated HCF strength above the DTMM prediction. In fact, it did not fail and testing was only discontinued due to reaching the end of the period of performance. This points to some success in the project’s primary goal of successfully developing and applying the DTMM to a component design. Implementing the DTMM recommendations for optimal processing parameters led to a part with acceptable properties. The DTMM was also shown to be an efficient correlator of data and to provide insight into the relationship between process settings, microstructure, and property performance. However, the failure of the DTMM prediction to match the experimental result of the injector fatigue test also points to the need to include significantly more data in the model development. In this project, coupons made with identical processing parameters exhibited drastically different properties from each other and from the injector part, which clearly influences the accuracy of a model that predicts performance based on parameters. Uncertainties in the build process must be quantified to develop more robust models. A denser and broader matrix of coupon process and geometry variations, several repeated builds of every point, more in-situ build process measurements, and direct observation of tensile and HCF sample microstructure (as opposed to separate microstructure specimens) are recommendations to improve future AM modeling efforts.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2025

Dataset: "Widespread Drought-driven Declines in Streamflows and Water quality in the Upper Colorado River Basin (1998-2022)"

This data package contains the associated data and scripts for Nagamoto, E., Ombadi, M., Ciulla, F. et al. Widespread drought-driven declines in streamflows and water quality in the Upper Colorado River Basin during 1998-2022. Commun Earth Environ 7, 734 (2026). https://doi.org/10.1038/s43247-026-03890-5. This purpose of this study was to investigate the impact of the 21st century drought on water quantity and quality at catchments throughout the Upper Colorado River Basin (UCRB). We used stream flow, water temperature, specific conductance, air temperature, precipitation, and catchment attribute data for over 200 sites in the UCRB, collected from the National Water Information System using Basin3D (Varadharajan, 2023), GAGESII (Falcone, 2010), and the Google Earth Engine. We identified years of severe drought between 1998 and 2022 using the Standardized Precipitation Evaporation Index (SPEI), then calculated the relative change percentage of the stream flow, water temperature, and specific conductance from drought versus non-drought years. We used the attribute information from GAGESII to investigate what physical traits of catchments are associated streamflow vulnerability (greater relative change) or resilience to drought. We used land cover data from the National Land Cover Database (USGS, 2024) to assess any changes to physical attributes that may not be represented in the static attributes information in GAGESII. To increase data availability, we modeled stream temperature using methods from Willard, 2023. While the study period is water years 1998 to 2022, the raw water quantity and quality data extends to 1950 and the meteorological data extends to 1980. The data and code can be downloaded via the UCRB_drought.zip. Within the zip, the files are organized as follows: - INPUTS: Contains all input data used in UCRB_Drought_Workflow.ipynb - OUTPUTS: Contains all intermediate data created from UCRB_Drought_Workflow.ipynb as well as final products including the calculated Standardized Evapotranspiration Index (SPEI) - climatic_variables: The code used to collect meteorologic data from Google Earth Engine - feature_importance: The code used for the catchment attributes analysis - preprocessing: Code used in UCRB_Drought_Workflow_Preprocessing.ipynb - pyeto: Code used in UCRB_Drought_Workflow_Preprocessing.ipynb - calculations: Code used in UCRB_Drought_Workflow_Impacts.ipynb - plotting: Code used in UCRB_Drought_Workflow_Impacts.ipynb - README.md - UCRB_Drought_Workflow_Preprocessing.ipynb: The code used to prep raw data for the analysis - UCRB_Drought_Workflow_Impact.ipynb: The code which uses the prepped raw data for analysis, and plots all figures - requirements_ucrb-drought_v2.yml: The requirements file to create a virtual environment and Jupyter Lab kernel to run the code The INPUTS folder is organized into the following major directories and sub-directories. The "RDC_WT_SC_RAW" folder contains raw data for streamflow, water temperature, and specific conductance in a ".h5" file. The "NLCD_RAW" folder contains ".csv" files with annual land cover percentages for counties within the UCRB. The "MET_RAW" folder contains a ".csv" file with monthly meteorological data (air temperature and precipitation) for the sites in the UCRB which was obtained from code in the climatic_variables folder. The "GAGESII" folder contains ".csv" files with physical catchment attribute variables for catchments across the country. The "WT_LSTM_data" folder contains ".csv" files with calculated WT (Willard, 2023) and the associated RMSEs. The "Upper_Colorado_River_Basin_Boundary" folder contains geographic data including a shapefile for plotting in the UCRB_Drought_Workflow.ipynb. The "RESERVOIRS_RAW" folder contains ".csv" files for each reservoir in the UCRB with daily reservoir storage. There are also two files in the INPUTS folder that have combined reservoir storage data and reservoir metadata. The OUTPUTS folder is organized into the following major directories and sub-directories. The "RDC_WT_SC_data" folder contains a folder "Water_year" with the associated cleaned data, metadata, and data availability information in ".csv" files, a folder "Median_Relchange" with the relative change comparing drought to non-drought years in ".csv" files, and a folder "Peak95_Min5_Relchange" that has ".csv" files for the relative change in peak (95th %) and minimum (5th %) variables. The "NLCD_data" folder contains the difference in land cover from the beginning to end of the study period and the percentage of the county that is within UCRB bounds can be found in Nagamoto et al (2025)). The "MET_data" folder contains separated monthly air temperature and precipitation data and the calculated PET in ".csv" files. The "SPEI_data" folder contains ".csv" files with calculated SPEI values (one restricted to the study period and the other with information from the entire MET data period). The "Paper_Tables" folder contains two ".csv" files containing site information and data availability and information about the GAGESII trait aggregated categories. The base directory includes the file “flmd.csv” for a list and description of all files and the file “dd.csv” for data dictionaries. Scripts for preprocessing, analysis, and figure generation are located in the associated GitHub repository found at [https://github.com/iNAIADS/drought-impacts/tree/develop/UCRB-drought]. UPDATE 1: Title and code file updated to match submitted manuscript 10-15-2025. UPDATE 2: Code and data files updated to match revised manuscript 3-4-2026. UPDATE 3: Code and data files updated to match revised manuscript 6-7-2026. ** NOTE: DD and FLMD have not been updated yet. UPDATE 4: Added associated Manuscript information and DD and FLMD have been updated. To cite this code, please use the following BibTeX: @misc{nagamoto2025drought, author = {Emily Nagamoto and Fabio Ciulla and Mohammad Ombadi and Jared Willard and Rosemary Carroll and Charuleka Varadharajan}, title = {Dataset: "Widespread Drought-driven Declines in Streamflows and Water quality in the Upper Colorado River Basin (1998-2022)"}, year = {2025}, doi = {10.15485/2551894}, publisher = {ESS-DIVE Repository}, url = {https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2551894} }

54 ENVIRONMENTAL SCIENCES↗