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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Simple and Flexible Infusion Platform for Automated Native Mass Spectrometry Analysis

High throughput native mass spectrometry analysis of proteins and protein complexes has been enabled by recent development of infusion and liquid chromatography (LC) systems, which often include complete LC pumps without fully utilizing their gradient flows. We demonstrated a lower-cost infusion cart for native mass spectrometry applications using a single isocratic solvent pump that can operate at both nano- and high-flow configurations (0.05-150 $μ$L/min) for both infusion and online buffer exchange experiments. In conclusion, the platform is controlled via open-source software and can potentially be expanded for customized experimental designs, offering a lower cost alternative to laboratories with limited budgets and/or needs in student training.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

Abstract The PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

Chemistry↗
DOE OSTI2023

Electron–phonon physics from first principles using the EPW code

EPW is an open-source software for ab initio calculations of electron–phonon interactions and related materials properties. The code combines density functional perturbation theory and maximally localized Wannier functions to efficiently compute electron–phonon coupling matrix elements, and to perform predictive calculations of temperature-dependent properties and phonon-assisted quantum processes in bulk solids and low-dimensional materials. Here, we report on significant developments in the code since 2016, namely: a transport module for the calculation of charge carrier mobility under electric and magnetic fields using the Boltzmann transport equation; a superconductivity module for calculations of phonon-mediated superconductors using the anisotropic multi-band Eliashberg theory; an optics module for calculations of phonon-assisted indirect transitions; a module for the calculation of small and large polarons without supercells; and a module for calculating band structure renormalization and temperature-dependent optical spectra using the special displacement method. For each capability, we outline the methodology and implementation and provide example calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Qiita: rapid, web-enabled microbiome meta-analysis

Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.

microbiome, bioinformatics software, open source s↗
DOE OSTI2022

USEEIO v2.0, The US Environmentally-Extended Input-Output Model v2.0

USEEIO v2.0 is an environmental-economic model of US goods and services that can be used for life cycle assessment, footprinting, national prioritization, and related applications. This paper describes the development of the model and accompanies the release of a full model dataset as well as various supporting datasets of national environmental totals by US industry. Novel methodological elements since USEEIO v1 models include waste sector disaggregation, final demand vectors for US consumption and production, a domestic form of the model that can be used to separate domestic and foreign impacts, and price adjustment matrices for converting outputs to purchaser price and in various US dollar years. Improvements in modeling national totals of industry and environmental flows are described. The model is validated through reproduction of national totals from input data sources and through analysis of changes from the most recent complete USEEIO model that can be explained based on data updates or method changes. The model datasets can all be reproduced with open source software packages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Integrative Quantitative-Phase and Airy Light-Sheet Imaging

Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free organelle recognition and metabolic information that are inaccessible by conventional methods. We report the fusion of these two modalities onto a standard inverted microscope that retains compatibility with microfluidics. We describe the utilization of an accelerating Airy-beam light-sheet yielding identical imaging areas with interferometry, and an application in unmasking the effects of cellular noise on metabolic compartmentalization.

Biological sciences, Biological techniques, Micros↗
DOE OSTI2021

Implementation and analysis of quantum computing application to Higgs boson reconstruction at the large Hadron Collider

With the advent of the High-Luminosity Large Hadron Collider (HL-LHC) era, high energy physics (HEP) event selection will require new approaches to rapidly and accurately analyze vast databases. The current study addresses the enormity of HEP databases in an unprecedented manner—a quantum search using Grover’s Algorithm (GA) on an unsorted database, ATLAS Open Data, from the ATLAS detector. A novel method to identify rare events at 13 TeV in CERN’s LHC using quantum computing (QC) is presented. As indicated by the Higgs boson decay channel H→ZZ*→4l , the detection of four leptons in one event may be used to reconstruct the Higgs boson and, more importantly, evince Higgs boson decay to some new phenomena, such as H→ZZ d →4l . Searching the dataset for collisions resulting in detection of four leptons using a Jupyter Notebook, a classical simulation of GA, and several quantum computers with multiple qubits, the current application was found to make the proper selection in the unsorted dataset. Quantum search efficacy was analyzed for the incoming HL-LHC by implementing the QC method on multiple classical simulators and IBM’s quantum computers with the IBM Qiskit Open Source Software. The current QC application provides a novel, high-efficiency alternative to classical database searches, demonstrating its potential utility as a rapid and increasingly accurate search method in HEP.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Over the past several decades, electron and scanning probe microscopes have become critical components of condensed matter physics, materials science and chemistry research. At the same time, the infrastructure for establishing a connection between microscopy observations and materials behaviour over a broader parameter space is lacking. In this work, we introduce AtomAI, an open-source software package bridging instrument-specific Python libraries, deep learning and simulation tools into a single ecosystem. AtomAI allows direct applications of deep neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders for disentangling structural factors of variation and im2spec type of encoder–decoder models for mapping structure–property relationships. Finally, our framework allows seamless connection to the first principles modelling with a Python interface on the inferred atomic positions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Ptychography at all wavelengths

Ptychography is a computational imaging technique that operates across multiple wavelength regimes, from electron (picometres) to X-ray (~0.1 nm), extreme ultraviolet (~10 nm) and visible light (micrometres). By reconstructing both amplitude and phase from diffraction patterns, ptychography enables high-resolution, quantitative imaging without conventional limitations imposed by lens-based optics. Ptychography has enabled advances across a range of scales: achieving deep-sub-angstrom resolution with electron microscopy, becoming an indispensable tool at X-ray synchrotron facilities worldwide and overcoming the trade-offs between resolution and field-of-view in optical imaging. This Primer provides a unified treatment of ptychography across these wavelength regimes. First, we discuss theoretical foundations, reconstruction algorithms, experimental considerations and wavelength-specific challenges. We then give examples of raw and processed data from various configurations and wavelengths. Next, we highlight key applications of ptychography in life sciences, materials science and industry. We also discuss data standards, open-source software implementations and best practices for ensuring reproducibility across different wavelength regimes. Finally, we consider limitations and future opportunities for ptychography. Together with accompanying datasets and code implementations, this Primer aims to serve newcomers and experienced practitioners in the field, facilitating broader adoption of ptychography across different disciplines.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Spectrum and extension of the inverse-Compton emission of the Crab Nebula from a combined Fermi -LAT and H.E.S.S. analysis

The Crab Nebula is a unique laboratory for studying the acceleration of electrons and positrons through their non-thermal radiation. Observations of very-high-energy γ rays from the Crab Nebula have provided important constraints for modelling its broadband emission. We present the first fully self-consistent analysis of the Crab Nebula’s γ-ray emission between 1 GeV and ∼100 TeV, that is, over five orders of magnitude in energy. Using the open-source software package GAMMAPY, we combined 11.4 yr of data from the Fermi Large Area Telescope and 80 h of High Energy Stereoscopic System (H.E.S.S.) data at the event level and provide a measurement of the spatial extension of the nebula and its energy spectrum. We find evidence for a shrinking of the nebula with increasing γ-ray energy. Furthermore, we fitted several phenomenological models to the measured data, finding that none of them can fully describe the spatial extension and the spectral energy distribution at the same time. Especially the extension measured at TeV energies appears too large when compared to the X-ray emission. Our measurements probe the structure of the magnetic field between the pulsar wind termination shock and the dust torus, and we conclude that the magnetic field strength decreases with increasing distance from the pulsar. We complement our study with a careful assessment of systematic uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

dCache - Keeping up With the Evolution of Science

The dCache project provides open-source software deployed internationally to satisfy ever more demanding storage requirements of various scientific communities. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, through wide access and easy integration with existing systems, including event driven workflow management. With this presentation, we will show some of the recent developments that optimize data management and access to maximise the gain from stored data.

Mkrtchyan, Tigran↗
DOE OSTI2021

dCache: Inter-disciplinary storage system

The dCache project provides open-source software deployed internationally to satisfy ever more demanding storage requirements. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, data sharing over wide area networks, efficient access from HPC clusters and long term data persistence on a tertiary storage. Though it was originally developed for the HEP experiments, today it is used by various scientific communities, including astrophysics, biomed, life science, which have their specific requirements. In this paper we describe some of the new requirements as well as demonstrate how dCache developers are addressing them.

Mkrtchyan, Tigran↗
DOE OSTI2014

Concept, implementation and commissioning of the automation system for the accelerator module test facility AMTF

The European XFEL project launched on June 5, 2007 will require about 103 accelerator modules as a main part of the XFEL linear accelerator. All superconducting components constituting the accelerator module like cavities and magnets have to be tested before the assembly. For the tests of the individual cavities and the complete modules an XFEL Accelerator Module Test Facility (AMTF) has been erected at DESY. The process control system EPICS (Experimental Physics and Industrial Control System) is used to control and operate the cryogenic plant and all its subcomponents. A complementary component of EPICS is the Open Source software suit CSS (Control System Studio). CSS is an integrated engineering, maintenance and operating tool for EPICS. CSS enables local and remote operating and monitoring of the complete system and thus represents the human machine interface. More than 250 PROFIBUS nodes work at the accelerator module test facility. DESY installed an extensive diagnostic and condition monitoring system. With these diagnostic tools it is possible to examine the correct installation and configuration of all PROFIBUS nodes in real time. The condition monitoring system based on FDT/DTM technology shows the state of the PROFIBUS devices at a glance. This information can be used for preventive maintenance which is mandatory for continuous operation of the AMTF facility. The poster will describe all steps form engineering to implementation and commissioning.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

Embedded image processing engine using ARM cortex-M4 based STM32F407 microcontroller

Due to advancement in low cost, easily available, yet powerful hardware and revolution in open source software, urge to make newer, more interactive machines and electronic systems have increased manifold among engineers. To make system more interactive, designers need easy to use sensor systems. Giving the boon of vision to machines was never easy, though it is not impossible these days; it is still not easy and expensive. This work presents a low cost, moderate performance and programmable Image processing engine. This Image processing engine is able to capture real time images, can store the images in the permanent storage and can perform preprogrammed image processing operations on the captured images.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Heliostat Aiming Strategies for Arbitrary Flux Profiles for High Temperature Gas-Based Receivers

High temperature gas-based receivers are seen as one potential path toward achieving the next generation of concentrated solar power tower systems. A key challenge associated with high temperature, high pressure heat transfer fluids is the lifetime of receiver containment materials. Achieving the desired lifetime while also designing an efficient receiver requires implementation of unique flux profiles, tailored to place high fluxes at cold fluid injection points. An aimpoint selection methodology was developed in the present study to allow user-defined flux profiles to be prescribed for a receiver. The methodology was implemented in NREL's open-source software SolarPILOT, modifying the existing “image size priority” aimpoint strategy. A case study for a tubular gas-based receiver is presented, examining the effect of various parameters on the ability to replicate the desired flux profile.

41 EE - Solar Energy Technologies Office (EE-4S)↗
DOE OSTI2023

Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration

The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application (“Fragme∩t”), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.

Chemistry↗