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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

JOINT APPOINTEE: Evolution of ferroelectric properties in SmxBi1-xFeO3 via automated Piezoresponse Force Microscopy across combinatorial spread libraries

Combinatorial spread libraries offer a innovative approach to explore the evolution of material properties over broad concentration, temperature, and growth parameter spaces. However, traditional limitation of this approach is the requirement for the read-out of functional properties across the library. Here we develop automated Piezoresponse Force Microscopy (PFM) for the exploration of combinatorial spread libraries and demonstrate its application in the SmxBi1-xFeO3 system with the ferroelectric-antiferroelectric morphotropic phase boundary. This approach relies on the synergy of the quantitative nature of PFM and the implementation of automated experiments that allow PFM-based sampling over macroscopic samples. The concentration dependence of pertinent ferroelectric parameters has been determined and used to develop the mathematical framework based on Ginzburg-Landau theory describing the evolution of these properties across the concentration space. We pose that a combination of automated scanning probe microscope and combinatorial spread library approach will emerge as an efficient research paradigm to close the characterization gap in the high-throughput materials discovery. We make the data sets open to the community and hope that this will stimulate other efforts to interpret and understand the physics of these systems.

Automated Microscopy, Combinatorial Library, Ferro↗
DOE OSTI2024

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗
DOE OSTI2022

Version [OpenIPSL 2.0.0] - [iTesla Power Systems Library (iPSL): A Modelica library for phasor time-domain simulations]

This paper describes Open-Instance Power System Library (OpenIPSL) version 2.0.0 and its most recent enhancements. This new version brings upgrades that include more robust models that are better documented, and example systems that illustrate certain functionalities to users. Repository and library documentations have been enhanced and expanded, and the library is now released under a new license. Changes are meant to foster user and developer communities, while providing more attractive frameworks for collaborative work to be carried out with the library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry

Graph deep learning models, which incorporate a natural inductive bias for atomic structures, are of immense interest in materials science and chemistry. Here, we introduce the Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry. Built on top of the popular Deep Graph Library (DGL) and Python Materials Genomics (Pymatgen) packages, MatGL is designed to be an extensible “batteries-included” library for developing advanced model architectures for materials property predictions and interatomic potentials. At present, MatGL has efficient implementations for both invariant and equivariant graph deep learning models, including the Materials 3-body Graph Network (M3GNet), MatErials Graph Network (MEGNet), Crystal Hamiltonian Graph Network (CHGNet), TensorNet and SO3Net architectures. MatGL also provides several pre-trained foundation potentials (FPs) with coverage of the entire periodic table, and property prediction models for out-of-box usage, benchmarking and fine-tuning. Finally, MatGL integrates with PyTorch Lightning to enable efficient model training.

chemistry↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2026

MassIVE MSV000100641 - Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli: Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.

Explore the source record for details and available documents.

Alexander, William G. [Oak Ridge National Laborato↗
DOE OSTI2026

LibraryX: A Framework for Cross-Library-Call Optimization

Scientific applications utilize performance libraries as a software engineering concept: these libraries encapsulate important and well-understood (mathematical) operations, allow for reuse, and are implemented and tuned by experts. Domain scientists then implement complex algorithms based on these domainspecific libraries. While individual library calls are optimized, larger performance gains across sequences of calls—sometimes spanning multiple libraries—are often unrealized, forcing a trade-off between performance and implementation complexity.To overcome this issue, we propose LibraryX, an approach and a system that allows for cross-library-call optimization even when library calls stem from multiple performance libraries. LibraryX annotates library calls with semantic information and optimizes entire directed acyclic graphs (DAGs) of calls dynamically using the SPIRAL code generation system. We demonstrate its effectiveness across a range of memory bound workloads, achieving significant speedups on Nvidia, AMD, and Intel accelerators compared to code using native libraries without cross-call optimization.

Rao, Sanil [Carnegie Mellon University,Department ↗
DOE OSTI2023

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

With advances in machine learning (ML)-assisted protein engineering, models based on data, biophysics, and natural evolution are being used to propose informed libraries of protein variants to explore. Synthesizing these libraries for experimental screens is a major bottleneck, as the cost of obtaining large numbers of exact gene sequences is often prohibitive. Degenerate codon (DC) libraries are a cost-effective alternative for generating combinatorial mutagenesis libraries where mutations are targeted to a handful of amino acid sites. However, existing computational methods to optimize DC libraries to include desired protein variants are not well suited to design libraries for ML-assisted protein engineering. To address these drawbacks, we present DEgenerate Codon Optimization for Informed Libraries (DeCOIL), a generalized method which directly optimizes DC libraries to be useful for protein engineering: to sample protein variants that are likely to have both high fitness and high diversity in the sequence search space. Using computational simulations and wet-lab experiments, we demonstrate that DeCOIL is effective across two specific case studies, with potential to be applied to many other use cases. DeCOIL offers several advantages over existing methods, as it is direct, easy-to-use, generalizable, and scalable. With accompanying software, DeCOIL can be readily implemented to generate desired informed libraries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Verification of the ENDF/B-VII.1 Based MC 2 -3 Library Rev.1

The MC 2 -3 code, developed by Argonne National Laboratory under the DOE-NE NEAMS program, is a multigroup cross section generation code for fast reactor applications. Last year, the ENDF/B-VII.0 (E70) MC 2 -3 library, which has been extensively used, verified, and validated over a long period, was intensively reverified and updated to support the commercial grade dedication (CGD) requirement of the TerraPower Natrium project. This year, the ENDF/B-VII.1 (E71) MC 2 -3 library, the preliminary version of which was generated several years ago, was regenerated and rigorously verified to support the Natrium project as well as the completion of verification of the E71 library. The E71 library was verified using the process developed during the verification of the E70 library, including comparisons of cross sections with the NJOY-generated cross sections, comparisons of the resolved resonance cross sections with those using the PEDNF library, and comparison of total cross sections with the sum of partial cross sections. Additional verifications were conducted to ensure that the benchmark problem solutions with the E71 library are reasonable compared to the corresponding Monte Carlo solutions. Furthermore, the E71 gamma library was generated, which includes data for prompt gamma, delayed gamma, and delayed beta as well as neutron and gamma heating. The gamma library was verified at the level of individual isotopes. The EBR-II core solutions from MC 2 -3/ DIF3D and MCNP were compared, demonstrating that those solutions in terms of k-effective and assembly powers were in good agreement.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Singe Library Review: XCAP Review Report

Singe is a computational library for simulating thermonuclear reactions written in C++14. It was inspired by the earlier Singe library, developed by Joann Campbell. From the beginning of the Singe project, the goal has been to create a library that provides the necessary functionality, runs efficiently, and is flexible enough to connect to a variety of multi-physics host codes. Such a library allows subject-matter experts to focus on development within the library, while library staff can support host-code staff in integrating Singe into their multi-physics codes. A common library used across multiple multi-physics codes allows those subject-matter experts to roll out new features to all host codes simultaneously, and eases the process of code-to-code comparison between codes that are leveraging the same physics in different ways. The Singe effort was established by Joann Campbell, who provided significant guidance on the goals, requirements, and philosophy of the library. It has been developed by Brendan K. Krueger, CJ Solomon, Jesse Canfield, and Terry Adams, with computer science support from Tyler Reddy and Karen Tsai. Discussions with multiple potential stakeholders have been critical to the planning of such a cross-cutting project, including representatives from multiple host codes and Brian Haines who helped define usage and needs for the inertial confinement fusion (ICF) program. This document is based on the XCAP review process. It is an updated version of the initial document distributed to the reviewers, memo XCP-2:21-005. We want to acknowledge the time and effort of the reviewers who participated in this process: Philipp Edelmann, Alan Harrison, Christopher Malone, Edward Norris, Ryosuke Park, Galen Shipman, CJ Solomon, and any others who may have contributed to the feedback that was provided to us.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Benchmarking of ENDF/B-VIII.1 Thermal Scattering Library for Hydrogen

In correctly characterizing the energy and momentum transfer at thermal and cold energies between neutrons and its interacting medium, thermal scattering libraries, which details energy states due to the intra- and inter-molecular bond effects for the medium materials, are applied in place of free-gas cross section libraries in a particle transport simulation code. They are essential to the neutron performance of a neutron facility like SNS, where thermalized neutrons from 20 K liquid hydrogen and ambient (~300 K) water are transported to the beamlines for neutron scattering experiments in studying materials. Recently, a new version of thermal scattering library for parahydrogen and orthohydrogen at 14-20 K was developed and to be released in ENDF/B-VIII.1. It is, therefore, important to benchmark its impacts on the prediction of moderator performance due to the updates in the thermal scattering library. In this study, the recent ENDF/B-VIII.1 thermal scattering library was compared to the current ENDF/B-VII.1 one in the neutron performance calculations for the decoupled and coupled hydrogen moderators at SNS under theorized and real working conditions. In addition, the predictions using both thermal scattering libraries were benchmarked to the measurements of moderator performance. The consistency between the libraries was observed mostly for parahydrogen and the difference in orthohydrogen at cold neutron energies was noted.

Lu, Wei↗
DOE OSTI2023

Selecting Minimal Motion Primitive Libraries with Genetic Algorithms

Motion primitives allow for application of discrete search algorithms to rapidly produce trajectories in complex continuous space. The maneuver automaton (MA) provides an elegant formulation for creating a primitive library based on trims and maneuvers. However, performance is fundamentally limited by the contents of the primitive library. If the library is too sparse, performance can be poor in terms of path cost, whereas a library that is too large can increase run time. This work outlines new methods for using genetic algorithms to prune a primitive library. The proposed methods balance the path cost and planning time while maintaining the reachability of the MA. The genetic algorithm in this paper evaluates and mutates populations of motion primitive libraries to optimize both objectives. Here, we illustrate the performance of these methods with a simulated study using a nonlinear medium-fidelity F-16 model. We optimize a library with the presented algorithm for obstacle-free navigation and a nap-of-the-Earth navigation task. In the obstacle-free navigation task, we show a tradeoff of a 10.16% higher planning cost for a 96.63% improvement in run time. In the nap-of-the-Earth task, we show a tradeoff of a 9.712% higher planning cost for a 92.06% improvement in run time.

42 ENGINEERING↗
DOE OSTI2025

Solar Energy Demonstration Project for Public Libraries

In this project, the South Hero Library Foundation purchased and installed a 39.95 kW DC roof-mounted solar array on the south-facing roof of the Worthen Library as well as on the south-facing roof of the neighboring 54 Community Lane building. This 94 panel array has a projected output of 39,950 kWh of power which will cover the Library’s annual power usage for heat and lighting. Any power overage will be distributed to other local organizations as designated by the Library. Library programming and added resources will be available to all patrons.

14 SOLAR ENERGY↗
DOE OSTI2023

Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or “suspects,” were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A leaf-level spectral library to support high-throughput plant phenotyping: predictive accuracy and model transfer

Abstract Leaf-level hyperspectral reflectance has become an effective tool for high-throughput phenotyping of plant leaf traits due to its rapid, low-cost, multi-sensing, and non-destructive nature. However, collecting samples for model calibration can still be expensive, and models show poor transferability among different datasets. This study had three specific objectives: first, to assemble a large library of leaf hyperspectral data (n=2460) from maize and sorghum; second, to evaluate two machine-learning approaches to estimate nine leaf properties (chlorophyll, thickness, water content, nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur); and third, to investigate the usefulness of this spectral library for predicting external datasets (n=445) including soybean and camelina using extra-weighted spiking. Internal cross-validation showed satisfactory performance of the spectral library to estimate all nine traits (mean R2=0.688), with partial least-squares regression outperforming deep neural network models. Models calibrated solely using the spectral library showed degraded performance on external datasets (mean R2=0.159 for camelina, 0.337 for soybean). Models improved significantly when a small portion of external samples (n=20) was added to the library via extra-weighted spiking (mean R2=0.574 for camelina, 0.536 for soybean). The leaf-level spectral library greatly benefits plant physiological and biochemical phenotyping, whilst extra-weight spiking improves model transferability and extends its utility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Benchmarking a Proof-of-Concept Performance Portable SYCL-based Fast Fourier Transformation Library

ABSTRACT In this paper, we present an early version of a SYCL-based FFT library, capable of running on all major vendor hardware, including CPUs and GPUs from AMD, ARM, Intel and NVIDIA. The current limitations of our library is it supports single-dimension FFTs up to 211 in length and base-2 input sequences. Although preliminary, the aim of this work is to seed further developments for a rich set of features for calculating FFTs. The library has the advantage over existing portable FFT libraries in that it is single-source, and there- fore removes the complexities that arise due to abundant use of pre-processor macros and auto-generated kernels to target different architectures. We exercise two SYCL-enabled compilers, Codeplay ComputeCpp and Intel's open-source LLVM project, to evaluate performance portability of our SYCL-based FFT on various hetero- geneous architectures.We provide studies comparing our portable library with highly optimized vendor-specific FFT libraries, and discuss potential sources hindering performance.

97 MATHEMATICS AND COMPUTING↗