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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

RF-Net 2: fast inference of virus reassortment and hybridization networks

Abstract Motivation A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. Results Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. Availability and implementation RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. Supplementary information Supplementary data are available at Bioinformatics online.

Markin, Alexey (ORCID:0000000332809050)↗
DOE OSTI2022

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dwarf AGNs from Optical Variability for the Origins of Seeds (DAVOS): insights from the dark energy survey deep fields

ABSTRACT We present a sample of 706, z < 1.5 active galactic nuclei (AGNs) selected from optical photometric variability in three of the Dark Energy Survey (DES) deep fields (E2, C3, and X3) over an area of 4.64 deg2. We construct light curves using difference imaging aperture photometry for resolved sources and non-difference imaging PSF photometry for unresolved sources, respectively, and characterize the variability significance. Our DES light curves have a mean cadence of 7 d, a 6-yr baseline, and a single-epoch imaging depth of up to g ∼ 24.5. Using spectral energy distribution (SED) fitting, we find 26 out of total 706 variable galaxies are consistent with dwarf galaxies with a reliable stellar mass estimate ($M_{\ast }\lt 10^{9.5}\, {\rm M}_\odot$; median photometric redshift of 0.9). We were able to constrain rapid characteristic variability time-scales (∼ weeks) using the DES light curves in 15 dwarf AGN candidates (a subset of our variable AGN candidates) at a median photometric redshift of 0.4. This rapid variability is consistent with their low black hole (BH) masses. We confirm the low-mass AGN nature of one source with a high S/N optical spectrum. We publish our catalogue, optical light curves, and supplementary data, such as X-ray properties and optical spectra, when available. We measure a variable AGN fraction versus stellar mass and compare to results from a forward model. This work demonstrates the feasibility of optical variability to identify AGNs with lower BH masses in deep fields, which may be more ‘pristine’ analogues of supermassive BH seeds.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Dose Coefficient Calculation for Use in Dosimetry Assessment of a Fission-Based Weapon

In the event of a fission-based weapon or improvised nuclear device (IND) detonation, dose coefficients can be harnessed to provide dose assessments for defense, emergency preparedness, and consequence management, as well as to prospectively inform the assessment of radiation biomarkers and development of medical prophylaxis countermeasures for defense and homeland security stakeholders and decision-makers. Although dose coefficients have previously been calculated for this group, they would apply specifically to the studied population, the 1945 Japanese cohort, after which their anthropomorphic computational phantoms were modeled. For this reason, applications to other populations may be limited, and instead, an assessment of a more standardized population is desired. We employed a series of computational human phantoms representing international reference individuals: UF/NCI voxel phantom series containing newborn, 1-, 5-, 10-, 15-, and 35-year-old males and females. Irradiation of the phantoms was simulated using the Monte Carlo N-Particle transport code to determine organ dose coefficients under four idealized irradiation geometries at three distances from the detonation hypocenter at Hiroshima and Nagasaki using DS02 free-in-air prompt neutron and photon fluence spectra. Through these simulations, age-specific dose coefficients were determined for individual organs. Various articulated PIMAL stylized phantoms were simulated as well to estimate the effect of body posture on dose coefficients and determine the effect of posture on dosimetric estimation and reconstruction. Results additionally demonstrate that 137 Cs and the Watt fission spectra are not ideal general surrogate sources for fission weapons, which may be considered for experimental testing of medical countermeasures. Supplementary data provided tabulates the compilation of organ dose-rate coefficients in this study.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2026

Wire-arc Additive Manufacturing Benchmark

This is the dataset associated with the 2022 SRP Additive Manufacturing Prediction Challenge, originally hosted on Github at https://github.com/SRP-AM/SRP_AM_Prediction_Challenge. The benchmark was designed for validating prediction for the temperature history, residual stress, and distortion of an additively manufactured metal part with relatively simple geometry. A calibration problem with the same as-built geometry is provided with measured quantities of interest; including temperature histories at selective locations, post-build residual stress at selective locations, and overall distortion measurements. The challenge problem is presented with a different build sequence (i.e. thermal history). In this dataset, we include the actual recorded calibration and challenge measurements, as well as benchmark template files for testing predictions without incorporating the challenge data. Supplementary files around the materials and setup are available for transparency and reproducibility.

Bachus, Nicholas [UC Davis, Davis, CA]↗
DOE OSTI2023

MODFLOW6 models used to evaluate potential stresses and hydrologic conditions driving water-level fluctuations in well ER-5-3-2, Frenchman Flat, Southern Nevada

The hydrograph for well ER-5-3-2 in Frenchman Flat, southern Nevada, has previously unexplained water-level fluctuations. Four, three-dimensional, groundwater models (MODFLOW 6) were developed to evaluate potential stresses and hydrologic conditions affecting the well ER-5-3-2 hydrograph. Four model scenarios were developed that simulated: (1) wellbore leakage without recharge, (2) wellbore leakage with recharge, (3) shallow (low transmissivity) and deep (high transmissivity) carbonate rocks, and (4) lateral heterogeneity of carbonate rocks. Input and output files for the four model scenarios are in the model and output directories, respectively. Hydraulic conductivity, specific storage, and wellbore-leakage rates (when simulated) were estimated with parameter estimation (PEST) by minimizing a weighted composite, sum-of-squares objective function. The objective function was informed by measurement and Tikhonov regularization observations. Measurement observations included drawdowns from the constant-rate aquifer test and water-level altitudes measured in well ER-5-3-2 from 2001-2021. Tikhonov regularization informed hydraulic conductivity and specific storage parameters that were insensitive to measurement observations, where homogeneity was the preferred relation. Batch files, executables, and MODFLOW 6, PEST, and post-processing utilities are in the ancillary directory. Supplementary data also are included in the ancillary directory, including site information, high-frequency water-level and aquifer-test data, transmissivity estimates, water-chemistry data, and water-temperature analyses. This USGS data release contains data, analyses, and model files for the simulations and analysis results described in U.S. Geological Survey Scientific Investigations Report (https://doi.org/10.3133/sir20225132).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

YeastConvergence2025

Supplementary data for Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

convergent evolution↗
DOE OSTI2025

YeastWGD2025

Supplementary data for Discovery of additional ancient genome duplications in yeasts wgd_syn / - directory containing wgd syn output for all contiguous genomes [dataset] Tree - phylogeny [dataset]Duplications - duplication table from OrthoFinder output KOannotations - KEGG annotations used for enrichment analysis IPRannotations - InterPro annotations used for enrichment analysis DipodascalesOrthogroups - formatted orthogroup assignments for Dipodascales genes.fa and .gff3 files for each new genome assembly are also provided, those these are not required to replicate the analysis

Genomics↗
DOE OSTI2025

EVT 16s Data and Large Supplementary Files

Soil microorganisms often interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat has posed a challenge to elucidating such interactions between soil microorganisms. Here, we seek to address this challenge through analysis of a model soil consortium (MSC-2) of eight soil bacterial species. Our aim was to elucidate specific roles of the member species during chitin metabolism. Samples were collected from MSC-2 incubated in chitin-enriched soil over three months. Multi-omics was used to understand how the community composition, transcripts, proteins and chitin decomposition shifted over time. The data clearly and consistently revealed a temporal shift during chitin decomposition with defined contributions by individual species. A Streptomyces genus member (sp001905665) was a key player in early steps of chitin decomposition, with other MSC-2 members being central in carrying out later steps. These results illustrate how multi-omics applied to a defined consortium untangles interactions between soil microorganisms.

McClure, Ryan [Pacific Northwest National Laborato↗
DOE OSTI2022

Modeling of Supercritical CO2 Shell-and-Tube Heat Exchangers Under Extreme Conditions. Part I: Correlation Development

Abstract High-temperature supercritical CO2 Brayton cycles are promising possibilities for future stationary power generation and hybrid electric propulsion applications. Heat exchangers are critical components in supercritical CO2 thermal cycles and require accurate correlations and comprehensive performance modeling under extreme temperatures and pressures. In this paper (Part I), new Colburn and friction factor correlations are developed to quantify shell-side heat transfer and friction characteristics of flow within heat exchangers in the shell-and-tube configuration. Using experimental and computational fluid dynamics (CFD) data sets from existing literature, multivariate regression analysis is conducted to achieve correlations that capture the effect of multiple critical geometric parameters. These correlations offer superior accuracy and versatility as compared to previous studies and predict the thermohydraulic performance of about 90% of the existing experimental and CFD data within ±15%. Supplementary thermohydraulic performance data are acquired from CFD simulations with supercritical CO2 as working fluid to validate the developed correlations and demonstrate its capability to be applied to supercrtical CO2 heat exchangers.

Engineering↗
DOE OSTI2024

Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species

This dataset contains all data and supplementary materials from "Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species". An Excel file a list of all QTLs and linkage group length (in cM) obtained with two different SNP-calling methods (Tassel-Uneak and Tassel-GBS), genetic map-construction method (linkage-only and reference order-corrected) and depth filters (12x, 20x, 30x and 40x) for genetic mapping of 18 biomass yield traits in a biparental Miscanthus sinensis population using RAD-Seq SNPs is provided as "Supplementary file 1". A Perl script with the code for filtering VCF and HapMap-formatted data files is provided as “Supplementary file 2”. Phenotype data used for QTL mapping is provided as “Supplementary File 3”. A Perl script with the code for the simulation study is provided as “Supplementary file 4”.

GenotypingSimulator↗
DOE OSTI2026

Data for "Genetics of flooding tolerance in an F2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis population"

This dataset contains all data and supplementary materials from "Genetics of flooding tolerance in an F2 Miscanthus sacchariflorus ssp. lutarioriparius × M. sinensis population". 1. The dataset S1 table contains the raw phenotypic data collected during the experiment. 2. The dataset S2 table contains the LSmean values for the 24 traits studied. 3. The dataset S3 table contains the TASSEL GBSv2 map, marker information, and genotype data used for mapping. 4. The dataset S4 table contains information on candidate genes found in each of the QTL intervals. 5. The dataset S5 table contains the GO annotations and KEGG enrichment analyses for those candidate genes. 6. The dataset S6 table contains information on the sequences used to classify AP2 ERF transcription factors. 7. The dataset S7 table contains information on AP2 ERF orthologs between Miscanthus and rice based on synteny. 8. Supplementary file 1 contains the ANOVA results using the raw phenotypic data collected from protocol "A". 9. Supplementary file 2 contains the ANOVA results using the raw phenotypic data collected from protocol "B". 10. Supplementary file 3 contains notes on the comparison of SNP calling methods. 11. Supplementary file 4 is a script for analyzing candidate genes found in QTL intervals.

Miscanthus, flood, partial submergence, complete s↗
DOE OSTI2022

Baseline Characterization Database Verification Report – 2114 Billet A20568

This ECAR provides the results of a validity evaluation of the physical and mechanical property data collected on a billet of nuclear-grade graphite (i.e., 2114 Billet A20568) in support of the ART Baseline Graphite Characterization Program.1,2 Millions of raw data points have been collected during testing and quantification analyses for these billets. The summary scalar property values and supplementary traceability data are collected into comprehensive spreadsheets. Data sets are composed of single billets of graphite for any given grade, organized by mechanical test-specimen type, and further subdivided into individual spreadsheet tabs according to the specific test or evaluation being performed. A direct analysis of properties was not conducted, and this report does not provide information on the validity or performance characteristics of the graphite itself. Rather, this report is intended as a verification of the completeness of actual data collected in accordance with PLN-3467, “Baseline Graphite Characterization Plan: Electromechanical Testing,”3 and their representation of the measurement and test results with sole regard to the graphite billets under evaluation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Baseline Characterization Database Verification Report ? NBG-17 Billet V104

The purpose of this report is to present data collected in the Baseline Graphite Characterization Program, which is directly tasked with supporting the Idaho National Laboratory’s (INL’s) research and development efforts on the Advanced Reactor Technologies (ART) Program. This program populates a comprehensive database that reflects the baseline properties of nuclear-grade graphite regarding individual grade, billet, and position within individual billets. The physical- and mechanical-property information being collected will be transferred to the Nuclear Data Management and Analysis System (NDMAS), and that database will help populate the handbook of property data available to member nations of the Generation-IV International Forum. Transfer of these data from the applicable technical lead to the dissemination databases available to other end users requires a full review of the test procedures and data-collection efforts through an analysis of the multiple summary spreadsheets and values being collected. This report represents the analysis for NBG-17 Billet V104 and facilitates release of associated data to the NDMAS custodians. Millions of raw data points have been collected during testing and quantification analyses for these billets. The summary scalar property values and supplementary traceability data are collected into comprehensive spreadsheets. Data sets are composed of single billets of graphite for any given grade, organized by mechanical test-specimen type, and further subdivided into individual spreadsheet tabs according to the specific test or evaluation being performed. A direct analysis of properties was not conducted, and this report does not provide information on the validity or performance characteristics of the graphite itself. Rather, this report is intended as a verification of the completeness of actual data collected in accordance with PLN-3467, “Baseline Graphite Characterization Plan: Electromechanical Testing,” [1] and PLN-3348 “Graphite Mechanical Testing” [2] and their representation of the measurement and test results with sole regard to the graphite billets under evaluation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗