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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Fully synthetic platform to rapidly generate tetravalent bispecific nanobody–based immunoglobulins

Nanobodies bind a target antigen with a kinetic profile similar to a conventional antibody, but exist as a single heavy chain domain that can be readily multimerized to engage antigen via multiple interactions. Presently, most nanobodies are produced by immunizing camelids; however, platforms for animal-free production are growing in popularity. Here, we describe the development of a fully synthetic nanobody library based on an engineered human V H 3-23 variable gene and a multispecific antibody-like format designed for biparatopic target engagement. To validate our library, we selected nanobodies against the SARS-CoV-2 receptor–binding domain and employed an on-yeast epitope binning strategy to rapidly map the specificities of the selected nanobodies. We then generated antibody-like molecules by replacing the V H and V L domains of a conventional antibody with two different nanobodies, designed as a molecular clamp to engage the receptor-binding domain biparatopically. The resulting bispecific tetra-nanobody immunoglobulins neutralized diverse SARS-CoV-2 variants with potencies similar to antibodies isolated from convalescent donors. Subsequent biochemical analyses confirmed the accuracy of the on-yeast epitope binning and structures of both individual nanobodies, and a tetra-nanobody immunoglobulin revealed that the intended mode of interaction had been achieved. This overall workflow is applicable to nearly any protein target and provides a blueprint for a modular workflow for the development of multispecific molecules.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

ENDF/B-VIII.1

The ENDF/B-VIII.1 release is the newest evaluated nuclear data library produced, distributed, and recommended by CSEWG for use in nuclear science and technology applications. Among the many key advances, relative to the previous version ENDF/B-VIII.0, are: re-evaluation of 239Pu file by a joint international effort; updated 16,18O, 19F, 28-30Si, 50-54Cr, 55Mn, 54,56,57Fe, 63,65Cu, 139La, 233,235,238U, and 240,241Pu neutron nuclear data by the IAEA-coordinated INDEN collaboration; significant changes for 3He, 6Li, 9Be, 51V, 88Sr, 103Rh, 140,142Ce, Dy, 181Ta, Pt, 206-208Pb, and 234,236U neutron data; new nuclear data for the photo-nuclear, being 196 adopted from the IAEA2019 Photonuclear Data Library and one new file from JENDL-5; and new evaluations for the charged-particle and atomic sublibraries. Numerous thermal neutron scattering kernels were re-evaluated or provided for the very first time. Additionally, new covariance testing was implemented. ENDF/B-VIII.1 reduced bias in the simulations of many integral experiments with particular progress noted for fluorine, copper and stainless steel containing benchmarks. Data issues which had hindered the deployment of ENDF/B-VIII.0 for commercial nuclear power applications in high burn-up situations, were addressed. ENDF/B-VIII.1 data are distributed in both ENDF-6 and GNDS formats.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling

Though chemical exposures are known to potentially have negative impacts on health, including contributing to chronic diseases such as cancer, the quantitative contribution of risk is not fully understood for every chemical. A commonly used approach to quantify levels of risk is to measure the proportion of organisms (such as a total number of zebrafish on a plate or mice in a cage) with abnormal behavioral responses or morphology at increasing concentrations of chemical exposure. A particular challenge with processing the proportional data from these assays is the appropriate estimation of chemical concentration levels that result in malformations or acute toxicity, as these values typically vary between experimental measurements. The recommended approach by the Environmental Protection Agency (EPA) is to fit benchmark dose curves with specific filters and model fitting steps, which are crucial to properly processing the proportional data. Several tools exist for the fitting of benchmark dose response curves, but none are standalone Python libraries built to process both morphological and behavioral data as proportions with all the EPA recommended filters, filter parameters, models, and model parameters. Thus, here we present the benchmark dose response curve (bmdrc) Python library, which was built to closely follow these EPA guidelines with helpful visualizations of filters and fitted model curves, and reports for reproducibility purposes. bmdrc is open-source and has demonstrated utility as a support package to an existing web portal for information on chemicals (https://srp.pnnl.gov). Our package will support any toxicology analysis where the response is a proportional value at increasing levels of a concentration of a chemical or chemical mixture.

Superfund↗
DOE OSTI2020

Thermal Neutron Scattering Law Benchmark and Validation at NCSU [Slides]

The presentation discusses how the NCSU graphite SDT ORELA experiment is under development as a benchmark. It discusses the testing of various ENDF/B-VII.1 and ENDF/B-VIII.0 graphite libraries that have been performed using the PROTEUS benchmark. The presentation demonstrates that the NSCU Polyethylene ENDF/B-VIII.0 TSL improves agreement with total cross section measurements. The presentation concludes by stating that the NCSU single crystal sapphire TSL library is based on realistic data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

VALID Past, Present, and Future [Slides]

This presentation discusses the Verified, Archived Library of Inputs and Data (VALID) procedure which is managed per computational procedure under the overall SCALE quality assurance plan. The principle behind VALID is that two independent, qualified people prepare and review the model, while a dual, independent check acts as a primary barrier to prevent errors in the library. A final check by VALID QAC of procedural compliance is then performed. The future for VALID includes plans to add more experiments, a review for all ICSBEP cases containing Deuterium, ZEUS intermediate and fast spectrum evaluations, intermediate enrichment experiments, other cases of interest to sponsors, and mixed/intermediate spectrum experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Updated Gadolinium Validation in SCALE 6.3.0 using ENDF/B-VIII.0 Data [Slides]

This presentation provides a brief recap of the ANS Summer meeting in 2018 with a discussion of the results. The presentation also provides an overview of new models and states that all new models have been checked but have not yet been added to the VALID library. It also states that the models were originally created as part of a master's thesis or summer internships. Additionally, all models have been rerun in SCALE 6.3.0 using CE ENDF/B-VIII.0 library. In conclusion, this project has facilitated a significant expansion of validation set containing gadolinium, including 13 cases previously in VALID plus 99 new cases. The completion of IPPE HST experiments confirm no clear trend as a function of concentration or spectrum. Solid absorber cases also show no clear trends and LANL HMT experiments have significant discrepancies in Gd alloy cases. While almost half of the total gadolinium-bearing cases from the ICSBEP Handbook are considered here, the presentation recognizes that there is more work to be done.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Evaluated Nuclear Data Requirements in Support of Fission and Fusion Applications [Slides]

This presentation touches on thermal scattering cross section and scattering lengths including criticality benchmarks (fission). Secondly, development and completeness of charged ­particle libraries: criticality benchmarks (fission), neutron source (fission/fusion), simulation benchmarks and light elements generation (fusion). Additionally, this presentation details on the covariances (methodology and completeness) with adjustment and optimization of nuclear data libraries (fission/fusion). Finally nuclear data reproducibility and conclusions are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

A Case Study on Condenser Water Supply Temperature Optimization with a District Cooling Plant

District cooling (DC) continues to proliferate due to increasing global cooling demands and economies of scale benefits; however, most district-scale modeling has focused on heating, and to the best of our knowledge, researchers have yet to model cooling plants featuring waterside economizers in DC settings. With the popular Modelica Buildings library expanding its capabilities to district scale, this study is one of the first to demonstrate how the open-source models can be used for detailed energy and control analysis of a DC plant. For a real-world case study, we developed and calibrated high-fidelity models for a DC system central plant at a college campus in Colorado, USA, and we optimized the condenser water supply temperature (CWST) setpoint for a DC plant across multiple time horizons using the Optimization library in Dymola. Results indicate that annual CWST optimization saves 4.7% annual plant energy, with less than 1% of additional energy savings gained through daily optimization. This confirms previous studies' findings that high frequency CWST optimizations are not necessary for the studied system.

chiller plant↗
DOE OSTI2026

Multibody for Everybody (M4E): A Symbolic Dynamics Modeling Tool with Applications in Simulation, Control, and Optimization

Developing the analytical model of a multibody system is often the initial step in control and optimization. The analytical model (equations of motion) describes a system’s time evolution under specified forcing conditions. Although developing these equations is easy for simple systems, this process becomes more complex for systems composed of multiple bodies. Deriving equations of motion for complex multibody systems requires specialized expertise in multibody dynamics, is time-consuming, and is susceptible to error. To address this issue, this paper presents an open-source, easy-to-use, systematic framework to derive symbolic equations of motion in both Python and MATLAB using the joint coordinate formulation. This formulation results in a set of ordinary differential equations that use the minimum set of coordinates needed to model a system. The symbolic representation provides better insight into the influence of design parameters on system performance, facilitates sensitivity analysis and parameter studies, and supports direct implementation of control and optimization routines. The tool enables numerical simulation for specified parameter sets, is modular for straightforward integration with other tools and libraries, and allows incorporation of hydrodynamics, mooring, and other external forces. The result is a reproducible, extensible pipeline for modeling, simulation, and design of complex multibody systems. The proposed tool is versatile and can be applied to domains such as robotics, control, and design. In addition, we integrated external libraries that provide capabilities for modeling offshore systems such as underwater robots and marine energy converters.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

Uncovering Where Compensating Errors Could Hide in ENDF/B-VIII.0

Unconstrained physics spaces between two or more nuclear data observables in a library occur when their values can be simultaneously adjusted without violating the uncertainties in either differential information or simulations of relevant integral experiments. Differential data are often too imprecise to fully bound all nuclear data observables of interest for application simulations. Integral data are simulated with combinations of nuclear data so that an error in one observable may be hidden by a counterbalancing error in another. In this manner compensating errors may lurk within nuclear data libraries and these errors have the potential to undermine the predictive power of neutron transport simulations, particularly in situations where there is no conclusive validation experiment that resembles the application of interest. The EUCLID project (Experiments Underpinned by Computational Learning for Improvements in Nuclear Data) developed a preliminary workflow to identify these unconstrained physics spaces by bringing together results from a large collection of integral experiments with their simulated counter-parts as well as differential information that have a one-to-one correspondence to nuclear data. This wealth of information is processed by machine learning tools for subsequent refinement by human experts. Here, we show how the EUCLID work-flow is executed by applying it first to 239 Pu and then to 9 Be nuclear data in ENDF/B-VIII.0.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

RNAseq-based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery

Accurate genome annotations are essential in modern biology and biotechnology, yet they are still largely based on genome sequencing and comparative analyses. We show that the Clostridium acetobutylicum genome annotation can be markedly improved by integrating bioinformatic predictions with RNA sequencing (RNAseq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth conditions. Analysis of an initial assembly revealed errors due to background signals and limitations of assembly algorithms. Hurdles for RNAseq transcriptome mapping include optimizing library complexity and sequencing depth, yet most studies report low sequencing depth and ignore the effect of ribosomal RNA abundance. An integrative analysis was developed to combine motif predictions, single-nucleotide resolution sequencing depth, and library complexity to resolve difficulties in assembly curation. This minimized false positive error and determined gene boundaries, in some cases, to the exact base-pair of prior studies. This will be the first strand-specific transcriptome assembly in a Clostridium organism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes

Abstract The discovery of new compounds with pharmacological properties is usually a lengthy, laborious and expensive process. Thus, there is increasing interest in developing workflows that allow for the rapid synthesis and evaluation of libraries of compounds with the aim of identifying leads for further drug development. Herein, we apply combinatorial synthesis to build a library of 90 iridium(III) complexes (81 of which are new) over two synthesise‐and‐test cycles, with the aim of identifying potential agents for photodynamic therapy. We demonstrate the power of this approach by identifying highly active complexes that are well‐tolerated in the dark but display very low nM phototoxicity against cancer cells. To build a detailed structure–activity relationship for this class of compounds we have used density functional theory (DFT) calculations to determine some key electronic parameters and study correlations with the experimental data. Finally, we present an optimised semi‐automated synthesise‐and‐test protocol to obtain multiplex data within 72 hours.

Kench, Timothy↗
DOE OSTI2024

A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes

Abstract The discovery of new compounds with pharmacological properties is usually a lengthy, laborious and expensive process. Thus, there is increasing interest in developing workflows that allow for the rapid synthesis and evaluation of libraries of compounds with the aim of identifying leads for further drug development. Herein, we apply combinatorial synthesis to build a library of 90 iridium(III) complexes (81 of which are new) over two synthesise‐and‐test cycles, with the aim of identifying potential agents for photodynamic therapy. We demonstrate the power of this approach by identifying highly active complexes that are well‐tolerated in the dark but display very low nM phototoxicity against cancer cells. To build a detailed structure–activity relationship for this class of compounds we have used density functional theory (DFT) calculations to determine some key electronic parameters and study correlations with the experimental data. Finally, we present an optimised semi‐automated synthesise‐and‐test protocol to obtain multiplex data within 72 hours.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Evaluating integration and performance of containerized climate applications on a Hewlett Packard Enterprise Cray system

Containers have taken over large swaths of cloud computing as the most convenient way of packaging and deploying applications. The features that containers offer for packaging and deploying applications translate to high performance computing (HPC) as well. At The National Oceanic and Atmospheric Administration, containers provide an easy way to build and distribute complex HPC applications, allowing faster collaboration, portability, and experiment computer environment reproducibility amongst the scientific community. The challenge arises when applications rely on message passing interface (MPI). This necessitates investigation into how to properly run these applications with their own unique requirements and produce performance on par with native runs. We investigate the MPI performance for benchmarks and containerized climate models for various containers covering selection of compiler and MPI library combinations from the Cray provided programming environments on the Cray XC supercomputer GAEA. Performance from the benchmarks and the climate models shows that for the most part containerized applications perform on par with the natively built applications when the system optimized Cray MPICH libraries are bound into the container, and the hybrid model containers have poor performance in comparison. We also describe several challenges and our solutions in running these containers, particularly challenges with heterogeneous jobs for the containerized model runs.

Abraham, Subil↗
DOE OSTI2024

ReactionMechanismSimulator.jl: A modern approach to chemical kinetic mechanism simulation and analysis

Abstract We present ReactionMechanismSimulator.jl (RMS), a modern differentiable software for the simulation and analysis of chemical kinetic mechanisms, including multiphase systems. RMS has already been applied to problems in combustion, pyrolysis, polymers, pharmaceuticals, catalysis, and electrocatalysis. RMS is written in Julia, making it easy to develop and allowing it to take advantage of Julia's extensive numerical computing ecosystem. In addition to its extensive library of optimized analytic Jacobians, RMS can generate and use Jacobians computed using automatic differentiation and symbolically generated analytic Jacobians. RMS is demonstrated to be faster than Cantera and Chemkin in several benchmarks. RMS also implements an extensive set of features for analyzing chemical mechanisms, including a library of easy‐to‐call plotting functions, molecular structure resolved flux diagram generation, crash analysis, traditional sensitivity analysis, transitory sensitivity analysis, and an automatic mechanism analysis toolkit. RMS implements efficient adjoint and parallel forward sensitivity analyses. We also demonstrate the ease of adding new features to RMS.

Johnson, Matthew S.↗
DOE OSTI2021

Metagenomic strategies identify diverse integron–integrase and antibiotic resistance genes in the Antarctic environment

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Hypergraph Analytics of Domain Name System Relationships

We report on the use of novel mathematical methods in hypergraph analytice over a large quantity of DNS data. Hypergraphs generalize graphs, as used in network science, to better model complex multiway relations in cyber data. Specifically, casting DNS data from Georgia Tech's ActiveDNS repository as hypergraphs allows us to fully represent the interactions between {\em collections} of domains and IP addresses. To facilitate large-scale analytics, we fielded an analytical pipeline of two capabilities. HyperNetX (HNX) is a Python package for the exploration and visualization of hypergraphs, acting as a frontend. For the backend, the Chapel HyperGraph Library (CHGL) is a library for high performance hypergraph analytics written in the exascale programming language Chapel. CHGL was used to process gigascale DNS data, performing compute-intensive calculations for data reduction and segmentation. Identified portions are then sent to HNX for both exploratory analysis and knowledge discovery targeting known tactics, techniques, and procedures.

Joslyn, Cliff A.↗
DOE OSTI2024

MatRIS: Addressing the Challenges for Portability and Heterogeneity Using Tasking for Matrix Decomposition (Cholesky)

The ubiquitous in-node heterogeneity of HPC and cloud computing platforms makes software portability and performance optimization extremely challenging. Described here, the MatRIS multilevel math library abstraction framework employs tasking to alleviate these difficulties. MatRIS includes the IRIS task-based runtime on the bottom level and exposes different layers of abstraction to render algorithms architecturally agnostic. MatRIS ensures the decomposition and creation of tasks that represent the necessary encapsulation of the optimized kernels from both vendor and open-source math libraries. Once built, MatRIS can select different combinations of accelerators at runtime, making it portable even on diverse heterogeneous architectures. By leveraging the IRIS runtime’s features for managing heterogeneity, MatRIS deploys algorithms that remove the need to specify orchestration and data transfer. This study describes how the serial task abstraction of a tiled Cholesky factorization is made portable and scalable in the case of multi-device and multi-vendor heterogeneity on a node with NVIDIA and AMD GPUs by using MatRIS. First, we demonstrate that Cholesky in MatRIS provides multi-GPU scalability that offers competitive performance versus cuSolverMG. Then, we present the challenges and opportunities for heterogeneous execution.

Monil, M. A. H.↗