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

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗
DOE OSTI2023

malbacR: A Package for Standardized Implementation of Batch Correction Methods for Omics Data

Mass spectrometry is a powerful tool for identifying and analyzing small molecules, such as metabolites and lipids, in com-plex biological samples. Liquid chromatography and gas chromatography mass spectrometry studies quite commonly in-volve large numbers of samples, which can require significant time for sample preparation and analyses. To accommodate such studies, the samples are commonly split into batches. Inevitably, variations in sample handling, temperature fluctua-tion, imprecise timing, column degradation and other factors result in systematic errors or biases of the measured abundances between the batches. Numerous methods are available via R packages to assist with batch correction for small molecule om-ics data; however, since these methods were developed by different research teams, the algorithms are available in separate R packages, each with different data input and output formats. We introduce the malbacR package which consolidates eleven common batch effect correction methods for small molecule omics data into one place so users can easily implement and compare: pareto scaling, power scaling, range scaling, ComBat, EigenMS, NOMIS, RUV-random, QC-RLSC, WaveI-CA2.0, TIGER, and SERRF. The malbacR package standardizes data input and output formats across these batch correction methods. The package works in conjunction with the pmartR package, allowing users to seamlessly include batch effect cor-rection in a pmartR workflow without needing any additional data manipulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Quantitative 14 N NMR with Monte Carlo Uncertainty Analysis of Nitrate/Nitrite in Alkaline Nuclear Waste

While monitoring of nitrate and nitrite concentrations is important for managing corrosion in nuclear waste systems, existing analytical methods are hindered by turbidity, spectral interference, and delays from sample handling. Here, we demonstrate quantitative 14 N nuclear magnetic resonance (qNMR) spectroscopy as a direct, matrix-tolerant approach for nitrate and nitrite detection at natural abundance. Monte Carlo resampling was integrated into the workflow to quantify random error, establish precision–time tradeoffs, and separate noise-limited uncertainty from systematic bias arising from shimming, transmitter offset, or excitation pulse conditions. Quantification of nitrate and nitrite were validated in controlled alkaline matrix challenges and in 18-component Hanford-type simulants. These results establish 14 N qNMR as a practical, uncertainty-bounded tool for monitoring redox-active nitrogen species in chemically complex environments and provide a generalizable framework for quantitative analysis of quadrupolar nuclei.

Graham, Trent R. [Pacific Northwest National Labor↗
DOE OSTI2021

Directly Probing the Fracture Behavior of Ultrathin Polymeric Films

Understanding fracture mechanics of ultrathin polymeric films is crucial for modern technologies, including semiconductor and coating industries. However, up to now, the fracture behavior of sub-100 nm polymeric thin films is rarely explored due to challenges in handling samples and limited testing methods available. In this work, we report a new testing methodology that can not only visualize the evolution of the local stress distribution through wrinkling patterns and crack propagation during the deformation of ultrathin films but also directly measure their fracture energies. Using ultrathin polystyrene films as a model system, we both experimentally and computationally investigate the effect of the film thickness and molecular weight on their fracture behavior, both of which show a ductile-to-brittle transition. Furthermore, we demonstrate the broad applicability of this testing method in semicrystalline semiconducting polymers. We anticipate our methodology described here could provide new ways of studying the fracture behavior of ultrathin films under confinement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Imaging from Macro to Nanoscale: Multimodal Advances in Chemical and Biomedical Imaging

Imaging increasingly serves as a multiscale framework for linking molecular mechanisms to cellular behavior, tissue architecture, and organ phenotypes in biology and unraveling fundamental processes in chemistry, physics and materials science. This Perspective highlights recent advances in chemical and biomedical imaging across macro-, micro-, and nanoscales, using representative examples published in Chemical and Biomedical Imaging (CBMI). At the macroscale, we discuss chemically selective MRI, including endogenous and exogenous CEST strategies, together with photoacoustic imaging as a hybrid modality with functional and chemical contrast. At the microscale, we consider fluorescence, label-free optical and vibrational imaging, and selected X-ray approaches that expand sensitivity, specificity, and temporal resolution in biological and materials systems. At the nanoscale, we highlight super-resolution fluorescence microscopy, single-molecule methods, tip-enhanced Raman spectroscopy, and correlative imaging strategies that resolve local heterogeneity and molecular organization. Across scales, a common theme emerges that advances in probes, contrast mechanisms, instrumentation, and sample handling are enabling chemically informed imaging that connects molecular specificity with biological context.

multiscale imaging↗
DOE OSTI2025

Scalable fabrication of an array-type fixed-target device for automated room temperature X-ray protein crystallography

X-ray crystallography is one of the leading tools to analyze the 3-D structure, and therefore, function of proteins and other biological macromolecules. Traditional methods of mounting individual crystals for X-ray diffraction analysis can be tedious and result in damage to fragile protein crystals. Furthermore, the advent of multi-crystal and serial crystallography methods explicitly require the mounting of larger numbers of crystals. To address this need, we have developed a device that facilitates the straightforward mounting of protein crystals for diffraction analysis, and that can be easily manufactured at scale. Inspired by grid-style devices that have been reported in the literature, we have developed an X-ray compatible microfluidic device that can be used to trap protein crystals in an array configuration, while also providing excellent optical transparency, a low X-ray background, and compatibility with the robotic sample handling and environmental controls used at synchrotron macromolecular crystallography beamlines. At the Stanford Synchrotron Radiation Lightsource (SSRL), these capabilities allow for fully remote-access data collection at controlled humidity conditions. Furthermore, we have demonstrated continuous manufacturing of these devices via roll-to-roll fabrication to enable cost-effective and efficient large-scale production.

chemical engineering↗
DOE OSTI2023

A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening

Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS “barcodes” (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Ion beam analysis of fusion plasma-facing materials and components: facilities and research challenges

Following the IAEA Technical Meeting on 'Advanced Methodologies for the Analysis of Materials in Energy Applications Using Ion Beam Accelerators', our work reviews the current status of ion beam analysis (IBA) techniques and some aspects of ion-induced radiation damage in materials for the field of materials relevant to fusion. Available facilities, apparatus development, future research options and challenges are presented and discussed. The analysis of beryllium and radioactivity-containing samples from future experiments in JET or ITER represents not only an analytical but also a technical challenge. A comprehensive list of the facilities, their current status, and analytical capabilities comes alongside detailed descriptions of the labs. A discussion of future issues of sample handling and the current status of facilities at JET complete the technical section. To prepare the international IBA community for these challenges, the IAEA technical meeting finalizes the necessity for determining new nuclear reaction cross-sections and improving the inter-laboratory comparability by defining international standards and testing these via a round-robin test.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

The XFP (17-BM) beamline for X-ray footprinting at NSLS-II

Hydroxyl-radical mediated synchrotron X-ray footprinting (XF) is a powerful solution-state technique in structural biology for the study of macromolecular structure and dynamics of proteins and nucleic acids, with several synchrotron resources available to serve the XF community worldwide. The XFP (Biological X-ray Footprinting) beamline at the NSLS-II was constructed on a three-pole wiggler source at 17-BM to serve as the premier beamline for performing this technique, providing an unparalleled combination of high flux density broadband beam, flexibility in beam morphology, and sample handling capabilities specifically designed for XF experiments. The details of beamline design, beam measurements, and science commissioning results for a standard protein using the two distinct XFP endstations are presented here. XFP took first light in 2016 and is now available for general user operations through peer-reviewed proposals. Currently, beam sizes from 450 µm × 120 µm to 2.7 mm × 2.7 mm (FWHM) are available, with a flux of 1.6 × 10 16 photons s −1 (measured at 325 mA ring current) in a broadband (∼5–16 keV) beam. This flux is expected to rise to 2.5 × 10 16 photons s −1 at the full NSLS-II design current of 500 mA, providing an incident power density of >500 W mm −2 at full focus.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Fixed-target serial crystallography at the Structural Biology Center

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A standardized quantitative analysis strategy for stable isotope probing metagenomics

ABSTRACT Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg , an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, “who is eating what?” and “who is active?” within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism’s taxonomic identity and genome composition while providing quantitative estimates of the microorganism’s isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

NSUF Rad-AFM: Nanoscale Material Property Measurements of Radioactive Materials

Many advances in our understanding of radiation induced damage mechanisms are due to imaging techniques including transmission electron microscopy and scanning electron microscopy. However, the effect of these radiation induced defects characterized on the atomic to micrometer scale are often interpreted by changes in bulk material properties measured in the hundreds of microns to cm scale. In order to bridge this gap, additional tools need to be developed for use with radioactive materials. To this end a new Asylum Infinity multimodal atomic force microscope (AFM) has been added to the library of Nuclear Science User Facility (NSUF) instruments for use on radioactive materials. This instrument is housed in the Radiochemical Processing Laboratory (RPL) which is a Department of Energy Hazard Category II Non-Reactor Nuclear Facility operated by Battelle at Pacific Northwest National Laboratory. This allows for the handling, sample preparation, and characterization of highly radioactive materials providing a unique capability to understand fundamental properties of nuclear materials and the effects of radiation induced damage.

Riechers, Shawn L.↗
DOE OSTI2017

Scoping study to expedite development of a field deployable and portable instrument for UF6 enrichment assay

The primary objective of the present study is to identity the most promising, viable technologies that are likely to culminate in an expedited development of the next-generation, field-deployable instrument for providing rapid, accurate, and precise enrichment assay of uranium hexafluoride (UF6). UF6 is typically involved, and is arguably the most important uranium compound, in uranium enrichment processes. As the first line of defense against proliferation, accurate analytical techniques to determine the uranium isotopic distribution in UF6 are critical for materials verification, accounting, and safeguards at enrichment plants. As nuclear fuel cycle technology becomes more prevalent around the world, international nuclear safeguards and interest in UF6 enrichment assay has been growing. At present, laboratory-based mass spectrometry (MS), which offers the highest attainable analytical accuracy and precision, is the technique of choice for the analysis of stable and long-lived isotopes. Currently, the International Atomic Energy Agency (IAEA) monitors the production of enriched UF6 at declared facilities by collecting a small amount (between 1 to 10 g) of gaseous UF6 into a sample bottle, which is then shipped under chain of custody to a central laboratory (IAEA’s Nuclear Materials Analysis Laboratory) for high-precision isotopic assay by MS. The logistics are cumbersome and new shipping regulations are making it more difficult to transport UF6. Furthermore, the analysis is costly, and results are not available for some time after sample collection. Hence, the IAEA is challenged to develop effective safeguards approaches at enrichment plants. In-field isotopic analysis of UF6 has the potential to substantially reduce the time, logistics and expense of sample handling. However, current laboratory-based MS techniques require too much infrastructure and operator expertise for field deployment and operation. As outlined in the IAEA Department of Safeguards Long-Term R&D Plan, 2012–2023, one of the IAEA long-term R&D needs is to “develop tools and techniques to enable timely, potentially real-time, detection of HEU (Highly Enriched Uranium) production in LEU (Lowly Enriched Uranium) enrichment facilities” (Milestone 5.2). Because it is common that the next generation of analytical instruments is driven by technologies that are either currently available or just now emerging, one reasonable and practical approach to project the next generation of chemical instrumentation is to track the recent trends and to extrapolate them. This study adopted a similar approach, and an extensive literature review on existing and emerging technologies for UF6 enrichment assay was performed. The competitive advantages and current limitations of different analytical techniques for in-field UF6 enrichment assay were then compared, and the main gaps between needs and capabilities for their field use were examined. Subsequently, based on these results, technologies for the next-generation field-deployable instrument for UF6 enrichment assay were recommended. The study was organized in a way that a suite of assessment metric was first identified. Criteria used in this evaluation are presented in Section 1 of this report, and the most important ones are described briefly in the next few paragraphs. Because one driving force for in-field UF6 enrichment assay is related to the demanding transportation regulation for gaseous UF6, Section 2 contains a review of solid sorbents that convert and immobilized gaseous UF6 to a solid state, which is regarded as more transportation friendly and is less regulated. Furthermore, candidate solid sorbents, which show promise in mating with existing and emerging assay technologies, also factor into technology recommendations. Extensive literature reviews on existing and emerging technologies for UF6 enrichment assay, covering their scientific principles, instrument options, and current limitations are detailed in Sections 3 and 4, respectively. In Section 5, the technological gaps as well as start-of-the-art and commercial off-the-shelf components that can be adopted to expedite the development of a fieldable or portable UF6 enrichment-assay instrument are identified and discussed. Finally, based on the results of the review, requirements and recommendations for developing the next-generation field-deployable instrument for UF6 enrichment assay are presented in Section 6.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structural Stability Study of Crystalline Silicotitanate Dispersed in Caustic Solutions for Extended Periods

The purpose of this study was to determine if pretreated engineered crystalline silicotitanate (CST) utilized in the Tank Cesium Closure Removal (TCCR) process would aggregate when contacted with sodium hydroxide (NaOH) or simulated tank waste solutions over an extended period. The aggregation of CST could be problematic for the TCCR process as it may lead to increased pressure drops across the columns, due to column plugging. Multiple prior studies have been completed on the agglomeration of CST stored in caustic simulants for prolonged periods showing evidence of clumping especially at elevated temperatures. For this study, pretreated CST was combined with various concentrations of sodium hydroxide and SRS simulant, in both glass and plastic storage containers, and monitored for an extended period. The samples were monitored for signs of agglomeration for a period of 8 months. After 7 months weak agglomeration was observed in the sample stored in SRS simulant, while no signs of clumping were observed in the samples stored in 2, 3, or 4 M NaOH. This is consistent with previous work where agglomeration of CST was not observed in simple salt solutions, only in simulants containing Al. In addition, the clumping observed for the sample stored in SRS simulant was not replicated in the duplicate sample stored in a plastic (as opposed to glass) vial, indicating leaching of Si from the glass may have contributed. It was also noted during the study that the solution above the CST stored in 4 M NaOH became opaque. The most likely cause of the opaque solution is the presence of micro-CST particles that may have been generated through sample handling, although this has not been confirmed by analysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Resurgence of a Nation’s Radiation Science Driven by Its Nuclear Industry Needs

This article describes the radiation facilities and associated sample preparation, management, and analysis equipment currently in place at the Dalton Cumbrian Facility, a facility which opened in 2011 to support the UK’s nuclear industry. Examples of measurements performed using these facilities are presented to illustrate their versatility and the breadth of research they make possible. Results are presented from research which furthers our understanding of radiation damage to polymeric materials, radiolytic yield of gaseous products in situations relevant to nuclear materials, radiation chemistry in light water reactor cooling systems, material chemistry relevant to immobilization of nuclear waste, and radiation-induced corrosion of fuel cladding elements. Applications of radiation chemistry relevant to health care are also described. Research concerning the mechanisms of radioprotection by dietary carotenoids is reported. An ongoing open-labware project to develop a suite of modular sample handling components suited to radiation research is described, as is the development of a new neutron source able to provide directional beams of neutrons.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS1983

Electronic Dilatometer

Nonclamping micrometer measures small strains. Electronic dilatometer measures minute dimensional changes caused by moisture absorption in graphite/ epoxy composites. Instrument handles sample 6 inches (15 cm) long and has strain resolution of 0.1 micro-inch/inch (0.1 micron/meter). Possible to predict humidity-induced dimensional changes in items constructed of sample material.

Stroope, C. R.↗
NASA NTRS1984

High pressure cosmochemistry applied to major planetary interiors: Experimental studies

Progress is reported on a project to determine the properties and boundaries of high pressure phases of the H2-He-H2O-NH3-CH4 system that are needed to constrain theoretical models of the interiors of the major planets. This project is one of the first attempts to measure phase equilibria in binary fluid-solid systems in diamond anvil cells. Vibrational spectroscopy, direct visual observations, and X-ray diffraction crystallography of materials confined in externally heated cells are the primary experimental probes. Adiabats of these materials are also measured in order to constrain models of heat flow in these bodies and to detect phase transitions by thermal anomalies. Initial efforts involve the NH3-H2O binary. This system is especially relevant to models for surface reconstruction of the icy satellites of Jupiter and Saturn. Thermal analysis experiments were completed for the P-X space, p4GPa:0 or = 0.50, near room temperature. The cryostat, sample handling equipment, and optics needed to extend the optical P-T-X work below room temperature was completed.

Nicol, M. F.↗