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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 OSTI2017

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Chain, Patrick↗
DOE OSTI2017

High-Throughput Computational Screening of Multivariate Metal–Organic Frameworks (MTV-MOFs) for CO 2 Capture

Multivariate metal–organic frameworks (MTV-MOFs) contain multiple linker types within a single structure. Arrangements of linkers containing different functional groups confer structural diversity and surface heterogeneity and result in a combinatorial explosion in the number of possible structures. Here, we carried out high-throughput computational screening of a large number of computer-generated MTV-MOFs to assess their CO 2 capture properties using grand canonical Monte Carlo simulations. The results demonstrate that functionalization enhances CO 2 capture performance of MTV-MOFs when compared to their parent (unfunctionalized) counterparts, and the pore size plays a dominant role in determining the CO 2 adsorption capabilities of MTV-MOFs irrespective of the combinations of the three functional groups (-F, -NH 2 , and -OCH 3 ) that we explored. We also found that the functionalization of parent MOFs with small pores led to larger enhancements in CO 2 uptake and CO 2 /N 2 selectivity than functionalization in larger-pore MOFs. Free energy contour maps are presented to visually compare the influence of linker functionalization between frameworks with large and small pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Chapter 21: The Utility of Virtual Reality for Science and Engineering

In our daily usage of the large-scale immersive virtual environment at the National Renewable Energy Laboratory (NREL), we have observed how this VR system can be a useful tool to enhance scientific and engineering workflows. On multiple occasions, we have observed scientists and engineers discover features in their data using immersive environments that they had not seen in prior investigations of their data on traditional desktop displays. We have embedded more information into our analytics tools, allowing engineers to explore complex multivariate spaces. We have observed natural interactions with 3D objects and how those interactions seem to catalyze understanding. And we have seen improved collaboration with groups of stakeholders. In this chapter, we discuss these practical advantages of immersive visualization in the context of several real-world examples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Metaoptics Enabled Multifunctional Imaging

Despite the fact that most microorganisms occupy two- and three-dimensional space in heterogeneous arrangements and in proximity to other microorganisms of different species, much of our current knowledge about their metabolic processes is derived from homogenizing, then analyzing, the chemical content of cultures containing a single microbial species. This project addressed this fundamental dichotomy by developing a set of optical imaging principles combining multiple new technologies. The imaging strategies developed in this project combine metaoptics structures with active in situ nanoscale control of the chemical environment and applied them to a microbial system, Myxococcus xanthus, with particular relevance to the DoE mission. The combination of metaoptical architectures and nanoscale control over the molecular environment enables: (a) precise control over the electromagnetic (EM) field at length scales smaller than the wavelength of light; (b) control of the interaction of the EM field with critical molecular systems in DOE relevant microbes; (c) control over the chemical environment – especially the presence and quantity of reactive oxygen species (ROS) that can affect redox homeostasis; and (d) the ability to ask new kinds of questions not accessible to ‘omics’ approaches or standard methods of biological imaging. These capabilities are applicable to detailed studies of metabolic pathways in microbes and to lignocellulosic biomass deconstruction. To accomplish these objectives, we pursued two over-arching technical goals: (1) the development of new metaoptics-enabled approaches to imaging and spectroscopic characterization; and (2) the development of tools to control the chemical environment of a microbial sample with nanometer-scale precision. Goal 1 was addressed through the design, fabrication, and characterization of new metasurfaces capable of super-resolution imaging through extreme confinement of the optical field. Goal 2 was addressed by controlling the redox potential on the nanoscale in microbial communities and characterizing their effect on intrinsic bacterial fluorophores which act as molecular sentinels and through characterization of soluble factors secreted by Myxococcus xanthus by confocal Raman imaging. The optical imaging/sensing approaches developed here make it possible to use these powerful new imaging and sensing modalities in metabolic studies by making it possible to visualize and track the spatial and temporal expression patterns of natural or engineered pathways in microorganisms.

09 BIOMASS FUELS↗
DOE OSTI2016

AFIP-7 Post-irradiation Examination Summary Report

The following report contains the results and conclusions from post irradiation examinations performed on the fuel plates irradiated as part of the AFIP-7 experiment, the first test of base monolithic fuel in a fuel assembly consisting of curved, constrained fuel plates. These examinations include visual examination; eddy-current testing to measure oxide growth; profilometry to measure dimensional changes of the fuel plates; neutron radiography for evaluating fuel condition prior to sectioning; gamma scanning to provide relative measurements of burn-up and indication of fission-product relocation; analytical chemistry to benchmark the physics burn-up calculations; metallographic examination to identify microstructural changes in the fuel, interlayer and cladding; and blister threshold testing. These characterization activities were conducted to demonstrate that the fuel meets irradiation performance requirements for mechanical integrity, geometric stability, and stable and predictable behavior. Revision 1 being reviewed for share publicly.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Human and Technology Integration Evaluation of Advanced Automation and Data Visualization

While the existing United States (U.S.) light water reactors are highly reliable, safe, and provide a significant proportion of carbon-free electricity, the cost of operating and maintaining them has become less competitive compared to other electricity generating sources. The reason for the gap in operating and maintenance (O&M) costs can be at least in part attributed to the advent of new digital technologies that other electricity generating industries are currently using. Advanced capabilities including digital instrumentation and control (I&C) systems, advanced automation and analytics, and greater span of data integration (i.e., connectedness) across these non-nuclear plants has transformed the way work is performed and ultimately given them a competitive advantage in terms of the cost required for operating, maintaining, and supporting them. To reduce O&M cost and address obsolescence of the aging I&C infrastructure of the existing U.S. light water reactors, the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program Plant Modernization Pathway is conducting targeting multidisciplinary research that 1) delivers a sustainable business model to enable a cost-competitive U.S. nuclear industry and 2) is developing technology modernization solutions that address aging and obsolescence challenges. The work described in this report supports these two objectives and describes the demonstration of human and technology integration across recent industry collaborations to support their large-scale digital I&C modifications. This technical report describes the demonstration of the human and technology integration methodology in performing full-scale performance-based human-in-the-loop tests to evaluate plant-specific advanced automation and data visualization applications within these collaborators’ digital modifications. This technical report also documents future applications of human and technology integration that expand beyond main control room modernization and digital I&C upgrades, which have been a central focus to date. Thus, this technical report discusses how to implement human and technology integration across new business opportunities and how to develop an evaluation plan that defines measures and criteria, and documents key assumptions to support full plant modernization.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

NanoSIP: NanoSIMS Applications for Microbial Biology

High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling—an approach we refer to as nanoSIP—nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15 N and 13 C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. Further, NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and ‘omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2019

Scalable Contour Tree Computation by Data Parallel Peak Pruning

As data sets grow to exascale, automated data analysis and visualization are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this form of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Furthermore, we report the first shared SMP algorithm for fully parallel contour tree computation, with formal guarantees of O(lg V lg t) parallel steps and O(V lg V) work for data with V samples and t contour tree supernodes, and implementations with more than 30× parallel speed up on both CPU using TBB and GPU using Thrust and up 70× speed up compared to the serial sweep and merge algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Water Innovation and R&D Concept Exploration and Preliminary Assessment: Water Scoping Project Report Deliverable

Pacific Northwest National Laboratory and Idaho National Laboratory produced a cursory review and initial framework to support the US Department of Energy’s Water Power Technologies Office (WPTO) in considering options for program development related to water. The laboratories provided a suite of tools – rationales, evaluation criteria, and visual maps – as well as R&D concepts that could be applied at various scales over short- and long-term time horizons. The effort is, by DOE request, largely the result of the authors’ creative efforts and not intended to be a comprehensive or detailed analytical exercise. This report summarizes the work provided to WPTO and is not intended for broad distribution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Computational and analytical comparison of flux discretizations for the semiconductor device equations beyond Boltzmann statistics

We compare three thermodynamically consistent numerical fluxes known in the literature, appearing in a Voronoï finite volume discretization of the van Roosbroeck system with general charge carrier statistics. Our discussion includes an extension of the Scharfetter–Gummel scheme to non-Boltzmann (e.g. Fermi–Dirac) statistics. It is based on the analytical solution of a two-point boundary value problem obtained by projecting the continuous differential equation onto the interval between neighboring collocation points. Hence, it serves as a reference flux. The exact solution of the boundary value problem can be approximated by computationally cheaper fluxes which modify certain physical quantities. One alternative scheme averages the nonlinear diffusion (caused by the non-Boltzmann nature of the problem), another one modifies the effective density of states. To study the differences between these three schemes, we analyze the Taylor expansions, derive an error estimate, visualize the flux error and show how the schemes perform for a carefully designed p-i-n benchmark simulation. We present strong evidence that the flux discretization based on averaging the nonlinear diffusion has an edge over the scheme based on modifying the effective density of states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Failure Analysis of Gas Spray Atomization Crucible Materials

An attempted induction melt for gas spray atomization of a Pd alloy at Savannah River National Laboratory experienced a series of faulty thermocouple readings leading to failure of multiple alumina ceramic components and the loss of the metal charge. The spherical powders are used in research and development efforts for hydrogen storage applications. The failure of the thermocouples led to high operating temperatures exceeding the expected operating temperatures. Estimated temperatures of the liquid metal were established by the comparison of the radio frequency power output and multiple temperature readings and determined to have exceeded the functional temperature range of the alumina components. Failure analyses of the event included characterization of the components using visual observation and X-Ray computed tomography of the frozen ingot.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Small-Angle Neutron Scattering Reveals Energy Landscape for Rhodopsin Photoactivation

Here, knowledge of the activation principles for G-protein-coupled receptors (GPCRs) is critical to development of new pharmaceuticals. Rhodopsin is the archetype for the largest GPCR family, yet the changes in protein dynamics that trigger signaling are not fully understood. Here we show that rhodopsin can be investigated by small-angle neutron scattering (SANS) in fully protiated detergent micelles under contrast matching to resolve light-induced changes in the protein structure. In SANS studies of membrane proteins, the zwitterionic detergent [(cholamidopropyl)dimethylammonio]-propanesulfonate (CHAPS) is advantageous because of the low contrast difference between the hydrophobic core and hydrophilic head groups as compared with alkyl glycoside detergents. Combining SANS results with quasielastic neutron scattering reveals how changes in volumetric protein shape are coupled (slaved) to the aqueous solvent. Upon light exposure, rhodopsin is swollen by the penetration of water into the protein core, allowing interactions with effector proteins in the visual signaling mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Probing atom dynamics of excited Co-Mo-S nanocrystals in 3D

Advances in electron microscopy have enabled visualizations of the three-dimensional (3D) atom arrangements in nano-scale objects. The observations are, however, prone to electron-beam-induced object alterations, so tracking of single atoms in space and time becomes key to unravel inherent structures and properties. Here, we introduce an analytical approach to quantitatively account for atom dynamics in 3D atomic-resolution imaging. The approach is showcased for a Co-Mo-S nanocrystal by analysis of time-resolved in-line holograms achieving ~1.5 Å resolution in 3D. The analysis reveals a decay of phase image contrast towards the nanocrystal edges and meta-stable edge motifs with crystallographic dependence. These findings are explained by beam-stimulated vibrations that exceed Debye-Waller factors and cause chemical transformations at catalytically relevant edges. This ability to simultaneously probe atom vibrations and displacements enables a recovery of the pristine Co-Mo-S structure and establishes, in turn, a foundation to understand heterogeneous chemical functionality of nanostructures, surfaces and molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Teaching Nonradiative Transitions with MATLAB and Python

Nonradiative transitions are changes in energy states of atoms, ions, or molecules that do not involve the emission or absorption of photons. Despite their importance in understanding luminescent properties and photochemical reaction mechanisms, nonradiative transitions are rarely given more than a qualitative overview in undergraduate and even graduate physical chemistry curricula. To supplement the coverage of nonradiative transition topics, we provide here a set of active learning exercises to help students develop an intuitive understanding of the factors that determine the rate of nonradiative transitions. Here, we start by outlining the theoretical background through the formulations of the Franck–Condon factor and its relation to the rate of nonradiative transition. We then introduce three teaching modules, with associated MATLAB and Python codes, to explore how (1) the excited state nuclear displacement, (2) the electronic energy gap between excited and ground state and (3) the excited/ground state vibrational mode frequencies affect the magnitude of the Franck–Condon factor and thereby the rate of nonradiative transitions. The wave function overlap plots that accompany all teaching modules provide direct visualization of the effect of input parameters on the magnitude of Franck–Condon overlap integral.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Colloidal quantum dot based infrared detectors: extending to the mid-infrared and moving from the lab to the field

Quantum dots (QDs) that absorb in the mid-wave infrared (MWIR) regime (3–5 μm) have recently generated significant interest as possible detector materials for MWIR cameras, with promises to reduce materials and device fabrication costs and potentially increase device operating temperatures. However, these materials have been primarily explored in single pixel devices – not multi-pixel cameras – and their current performance lags behind that of commercially available MWIR cameras based on single crystalline materials. To realize the potential of QD MWIR photodetectors with imaging capabilities, improvements are needed in the quality of the MWIR-absorbing QD materials, ligands dictating inter-QD charge transport, ordering of QD films, device architectures, and scalability of these methods to larger areas. With three families of QDs being researched – lead-, silver-, and mercury-based chalcogenides – as well as a multitude of possible capping ligands and film deposition techniques, the experimental phase space for MWIR QDs is vast. Here, we provide a roadmap, considering the pros and cons of various film deposition and ligand exchange techniques, as well as reintroduce lessons learned over years of research on QD film formation. We also extracted and created a database of reported quantum dot photodetectors’ performance and fabrication methods and have developed an interactive data visualization dashboard for this database, which provides researchers in the field a quick snapshot of the existing state of the art. Finally, we outline figures of merit and information that should be presented in papers moving forward which would help to clarify the reported results, as well as offer ideas for future steps. We provide a database visualization of the QD photodetector literature at https://public.tableau.com/app/profile/tom.nakotte/viz/IRQDphotodetectors_16384709473480/Dashboard1#1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ultraintense, ultrashort pulse X-ray scattering in small molecules

In this work, we examine X-ray scattering from an isolated organic molecule from the linear to nonlinear absorptive regime. In the nonlinear regime, we explore the importance of both the coherent and incoherent channels and observe the onset of nonlinear behavior as a function of pulse duration and energy. In the linear regime, we test the sensitivity of the scattering signal to molecular bonding and electronic correlation via calculations using the independent atom model (IAM), Hartree–Fock (HF) and density functional theory (DFT). Finally, we describe how coherent X-ray scattering can be used to directly visualize femtosecond charge transfer and dissociation within a single molecule undergoing X-ray multiphoton absorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗