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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 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Establishing a process of irradiating small animal brain using a CyberKnife and a microCT scanner

Purpose: Establish and validate a process of accurately irradiating small animals using the CyberKnife G4 System (version 8.5) with treatment plans designed to irradiate a hemisphere of a mouse brain based on microCT scanner images. Methods: These experiments consisted of four parts: (1) building a mouse phantom for intensity modulated radiotherapy (IMRT) quality assurance (QA), (2) proving usability of a microCT for treatment planning, (3) fabricating a small animal positioning system for use with the CyberKnife's image guided radiotherapy (IGRT) system, and (4)in vivo verification of targeting accuracy. A set of solid water mouse phantoms was designed and fabricated, with radiochromic films (RCF) positioned in selected planes to measure delivered doses. After down-sampling for treatment planning compatibility, a CT image set of a phantom was imported into the CyberKnife treatment planning system—MultiPlan (ver. 3.5.2). A 0.5 cm diameter sphere was contoured within the phantom to represent a hemispherical section of a mouse brain. A nude mouse was scanned in an alpha cradle using a microCT scanner (cone-beam, 157 × 149 pixels slices, 0.2 mm longitudinal slice thickness). Based on the results of our positional accuracy study, a planning treatment volume (PTV) was created. A stereotactic body mold of the mouse was “printed” using a 3D printer laying UV curable acrylic plastic. Printer instructions were based on exported contours of the mouse's skin. Positional reproducibility in the mold was checked by measuring ten CT scans. To verify accurate dose delivery in vivo, six mice were irradiated in the mold with a 4 mm target contour and a 2 mm PTV margin to 3 Gy and sacrificed within 20 min to avoid DNA repair. The brain was sliced and stained for analysis. Results: For the IMRT QA using a set of phantoms, the planned dose (6 Gy to the calculation point) was compared to the delivered dose measured via film and analyzed using Gamma analysis (3% and 3 mm). A passing rate of 99% was measured in areas of above 40% of the prescription dose. The final inverse treatment plan was comprised of 43 beams ranging from 5 to 12.5 mm in diameter (2.5 mm size increments are available up to 15 mm in diameter collimation). Using the Xsight Spine Tracking module, the CyberKnife system could not reliably identify and track the tiny mouse spine; however, the CyberKnife system could identify and track the fiducial markers on the 3D mold.In vivo positional accuracy analysis using the 3D mold generated a mean error of 1.41 mm ± 0.73 mm when fiducial markers were used for position tracking. Analysis of the dissected brain confirmed the ability to target the correct brain volume. Conclusions: With the use of a stereotactic body mold with fiducial markers, microCT imaging, and resolution down-sampling, the CyberKnife system can successfully perform small-animal radiotherapy studies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Ultrafast Photoluminescence in Quantum-Confined Silicon Nanocrystals Arises from an Amorphous Surface Layer

Here, we examine ultrafast photoluminescence produced from plasma-grown, colloidal silicon nanocrystals as a function of both particle size and lattice crystallinity. In particular, we quantify the decay time and spectral profiles of nominally few-picosecond direct-gap emission previously attributed to phononless electron–hole recombination. We find that the high-energy (400–600 nm, 2–3 eV) photoluminescence component consists of two decay processes with distinct time scales. The fastest photoluminescence exhibits an ~30 ps decay constant largely independent of emission energy and particle size. Importantly, nearly identical temporal components and blue spectral features appear for amorphous particles. We thus associate high-energy, rapid emission with an amorphous component in all measured samples, as supported by Raman analysis and molecular dynamics simulation. Based on these observations, we advise that the observed dynamics proceed too slowly to originate from intraband carrier thermalization and instead suggest a nonradiative origin associated with the amorphous component.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Ice Nucleating Particles, Aerosols and Clouds over the Higher Latitude Southern Ocean

Improved understanding of aerosol-cloud-precipitation interactions is a key goal of the DOE-ASR program. Ice Nucleating Particles (INPs) are rare aerosol particles that trigger ice formation in clouds. By doing so they may initiate precipitation in clouds, and this impacts cloud lifetime. Nowhere may the role of INPs be manifested so dramatically as in the Southern Ocean (SO). This vast region was the focus of the DOE-ARM MARCUS (Measurement of Aerosols, Radiation and CloUds over the Southern Oceans) and MICRE (Macquarie Island Cloud and Radiation Experiment) campaigns. In the SO, a deficit of INPs has been a leading hypothesis for why liquid clouds persist, which underlays the bias of global climate models in predicting excess shortwave radiation reaching the ocean surface between 55°S and Antarctica. In this study, we used the 6-month acquisition of INP data on four MARCUS cruises from Hobart, Tasmania, to Antarctica, and the single-location full annual INP cycle observed in MICRE, to gain a holistic, quantitative picture of the INP number concentrations as a function of temperature and their variability over SO latitudes from 43°S to Antarctica. Augmenting initial processing of filter collections of aerosol particles during MARCUS and MICRE, additional freezing studies following thermal treatment (to removes INPs associated with microbes) and peroxide treatment (to remove all organics), as well as ionic chemistry and total organic carbon analysis, were applied to samples to improve time and space resolution, and differentiate marine from terrestrial contributions. We also performed Next Generation Sequencing to determine that bacterial composition can tag periods of enhanced and degraded marine organic INPs and the relative lack of occurrence of land-sourced bio-particles. Through these and other analyses, INP data were categorized into representative source types (e.g., marine versus terrestrially-influenced). The products of our analyses are being used to parameterize ice formation for use in numerical modeling studies to determine if, and when, ocean-derived INPs control the microphysical composition and radiative balance of SO clouds in a manner not presently captured by global models. The specific objectives and approaches proposed were largely accomplished, including: 1) Additional and value-added chemical and biological analyses of archived samples of aerosols were completed to categorize and quantify INP types and concentrations over the SO. 2) Analyses were completed to place INP data in meteorological and aerosol context. 3) Sea spray aerosol INPs were demonstrated to dominate the SO region in all but episodic events. 4) New parameterizations for INP sources relevant to the SO were constructed. 5) Collaborative modeling studies demonstrating the crucial role of INPs in determining cloud radiative and precipitation properties were conducted with MARCUS and MICRE partners. Collaborative publication submissions in this regard ensued within the two year study. This work will advance the science of interactions of aerosols, clouds and precipitation, to improve their representation in regional and global climate models. Results have informed representation of primary ice crystal nucleation, give inference to the role of secondary processes, and improve investigations of aerosol influences on clouds via ice nucleation over SO high latitudes and similar vast ocean regions. Application will improve representation of such interactions for clouds in both regional and global climate models. The data base and analyses methods applied will continue to serve research studies in the future.

58 GEOSCIENCES↗
DOE OSTI2023

Effect of Mn on eutectic phase equilibria in Al-rich Al-Ce-Ni alloys

Microstructural analysis of additively manufactured (AM) Al-Ce-Ni-Mn alloys has identified phases not predicted from existing ternary liquidus projections in the Al-Ce-Ni system. Because the rapid cooling rate of AM is orders of magnitude above that of traditional casting, it is unclear if these additional phases arose from the non-equilibrium processing conditions of AM, a drastic shift in phase stability in the system due to the addition of 1 wt% Mn, or some combination of these two influences. The phases and microstructure of cast samples of Al-Ce-Ni and Al-Ce-Ni-Mn alloys were characterized for several annealing conditions which revealed the equilibrium phases at different temperatures. Phase analysis confirmed that minute levels of Mn substituted for Ni in the system drastically shifts the liquidus projection in the Al-rich corner of the ternary phase diagram such that the eutectic Al 3 Ni phase is suppressed in favor of the Al 23 Ni 6 (Ce,Mn) 4 phase. Further addition of Mn promotes the formation of Al 20 Mn 2 Ce and Al 10 Mn 2 Ce phases. The phase analysis data was then used to improve the CALPHAD modeling of the liquidus projection and isothermal sections for the Al-rich Al-Ce-Ni-Mn quaternary system. Thermodynamic modeling and experimental analysis on phases in the AM sample of Al-Ce-Ni with Mn confirmed that the phases present are consistent with Mn-containing Al-Ce-Ni cast samples. Here, this investigation demonstrates the potential for using secondary alloying elements to drastically alter phase stability and microstructure in alloy systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Process-microstructure relationship of laser processed thermoelectric material Bi2Te3

Additive manufacturing allows fabrication of custom-shaped thermoelectric materials while minimizing waste, reducing processing steps, and maximizing integration compared to conventional methods. Establishing the process-structure-property relationship of laser additive manufactured thermoelectric materials facilitates enhanced process control and thermoelectric performance. This research focuses on laser processing of bismuth telluride (Bi 2 Te 3 ), a well-established thermoelectric material for low temperature applications. Single melt tracks under various parameters (laser power, scan speed and number of scans) were processed on Bi 2 Te 3 powder compacts. A detailed analysis of the transition in the melting mode, grain growth, balling formation, and elemental composition is provided. Rapid melting and solidification of Bi 2 Te 3 resulted in fine-grained microstructure with preferential grain growth along the direction of the temperature gradient. Experimental results were corroborated with simulations for melt pool dimensions as well as grain morphology transitions resulting from the relationship between temperature gradient and solidification rate. Samples processed at 25 W, 350 mm/s with 5 scans resulted in minimized balling and porosity, along with columnar grains having a high density of dislocations.

Oztan, Cagri↗
DOE OSTI2013

Fourier Transform Infrared Spectroscopy and Multivariate Analysis for Online Monitoring of Dibutyl Phosphate Degradation Product in Tributyl Phosphate/n-Dodecane/Nitric Acid Solvent

In liquid–liquid extraction separation processes, accumulation of organic solvent degradation products is detrimental to the process robustness, and frequent solvent analysis is warranted. Our research explores the feasibility of online monitoring of the organic solvents relevant to used nuclear fuel reprocessing. This paper describes the first phase of developing a system for monitoring the tributyl phosphate (TBP)/n-dodecane solvent commonly used to separate used nuclear fuel. In this investigation, the effect of extraction of nitric acid from aqueous solutions of variable concentrations on the quantification of TBP and its major degradation product dibutylphosphoric acid (HDBP) was assessed. Fourier transform infrared (FTIR) spectroscopy was used to discriminate between HDBP and TBP in the nitric acid-containing TBP/n-dodecane solvent. Multivariate analysis of the spectral data facilitated the development of regression models for HDBP and TBP quantification in real time, enabling online implementation of the monitoring system. The predictive regression models were validated using TBP/n-dodecane solvent samples subjected to high-dose external ?-irradiation. The predictive models were translated to flow conditions using a hollow fiber FTIR probe installed in a centrifugal contactor extraction apparatus, demonstrating the applicability of the FTIR technique coupled with multivariate analysis for the online monitoring of the organic solvent degradation products.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2016

Hydrothermal Liquefaction and Upgrading of Municipal Wastewater Treatment Plant Sludge: A Preliminary Techno-Economic Analysis, Rev.1

A preliminary process model and techno-economic analysis (TEA) was completed for fuel produced from hydrothermal liquefaction (HTL) of sludge waste from a municipal wastewater treatment plant (WWTP) and subsequent biocrude upgrading. The model is adapted from previous work by Jones et al. (2014) for algae HTL, using experimental data generated in fiscal year 2015 (FY15) bench-scale HTL testing of sludge waste streams. Testing was performed on sludge samples received from Metro Vancouver’s Annacis Island WWTP (Vancouver, B.C.) as part of a collaborative project with the Water Environment and Reuse Foundation (WERF). The full set of sludge HTL testing data from this effort will be documented in a separate report to be issued by WERF. This analysis is based on limited testing data and therefore should be considered preliminary. In addition, the testing was conducted with the goal of successful operation, and therefore does not represent an optimized process. Future refinements are necessary to improve the robustness of the model, including a cross-check of modeled biocrude components with the experimental GCMS data and investigation of equipment costs most appropriate at the relatively small scales used here. Environmental sustainability metrics analysis is also needed to understand the broader impact of this technology pathway. The base case scenario for the analysis consists of 10 HTL plants, each processing 100 dry U.S. ton/day (92.4 ton/day on a dry, ash-free basis) of sludge waste and producing 234 barrel per stream day (BPSD) biocrude, feeding into a centralized biocrude upgrading facility that produces 2,020 barrel per standard day of final fuel. This scale was chosen based upon initial wastewater treatment plant data collected by PNNL’s resource assessment team from the EPA’s Clean Watersheds Needs Survey database (EPA 2015a) and a rough estimate of what the potential sludge availability might be within a 100-mile radius. In addition, we received valuable feedback from the wastewater treatment industry as part of the WERF collaboration that helped form the basis for the selected HTL and upgrading plant scales and feedstock credit (current cost of disposal). It is assumed that the sludge is currently disposed of at $16.20/wet ton ($46/dry ton at 35% solids; $50/ton dry, ash-free basis) and this is included as a feedstock credit in the operating costs. The base case assumptions result in a minimum biocrude selling price of $3.8/gge and a minimum final upgraded fuel selling price of $4.9/gge. Several areas of process improvement and refinements to the analysis have the potential to significantly improve economics relative to the base case: •Optimization of HTL sludge feed solids content •Optimization of HTL biocrude yield •Optimization of HTL reactor liquid hourly space velocity (LHSV) •Optimization of fuel yield from hydrotreating •Combined large and small HTL scales specific to regions (e.g., metropolitan and suburban plants) Combined improvements believed to be achievable in these areas can potentially reduce the minimum selling price of biocrude and final upgraded fuel by about 50%. Further improvements may be possible through recovery of higher value components from the HTL aqueous phase, as being investigated under separate PNNL projects. Upgrading the biocrude at an existing petroleum refinery could also reduce the MFSP, although this option requires further testing to ensure compatibility and mitigation of risks to a refinery. And finally, recycling the HTL aqueous phase product stream back to the headworks of the WWTP (with no catalytic hydrothermal gasification treatment) can significantly reduce cost. This option is uniquely appropriate for application at a water treatment facility but also requires further investigation to determine any technical and economic challenges related to the extra chemical oxygen demand (COD) associated with the recycled water.

09 BIOMASS FUELS↗
DOE OSTI2021

Evaluation of Nuclear Spent Fuel Disposal in Clay-Bearing Rock - Process Model Development and Experimental Studies (M2SF-21SN010301072)

The DOE R&D program under the Spent Fuel Waste Science Technology (SFWST) campaign has made key progress in modeling and experimental approaches towards the characterization of chemical and physical phenomena that could impact the long-term safety assessment of heatgenerating nuclear waste disposition in deep-seated clay/shale/argillaceous rock. International collaboration activities such as heater tests, continuous field data monitoring, and postmortem analysis of samples recovered from these have elucidated key information regarding changes in the engineered barrier system (EBS) material exposed to years of thermal loads. Chemical and structural analyses of sampled bentonite material from such tests as well as experiments conducted on these are key to the characterization of thermal effects affecting bentonite clay barrier performance and the extent of sacrificial zones in the EBS during the thermal period. Thermal, hydrologic, and chemical data collected from heater tests and laboratory experiments has been used in the development, validation, and calibration of THMC simulators to model near-field coupled processes. This information leads to the development of simulation approaches (e.g., continuum and discrete) to tackle issues related to flow and transport at various scales of the host-rock, its interactions with barrier materials, and EBS design concept.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2018

Systematic search for tidal features around nearby galaxies: I. Enhanced SDSS imaging of the Local Volume

In hierarchical models of galaxy formation, stellar tidal streams are expected around most, if not all, galaxies. Although these features may provide useful diagnostics of the Λ CDM model, their observational properties remain poorly constrained because they are challenging to detect and interpret and have been studied in detail for only a sparse sampling of galaxy population. More quantitative, systematic approaches are required. We advocate statistical analysis of the counts and properties of such features in archival wide-field imaging surveys for a direct comparison against results from numerical simulations. We aim to study systematically the frequency of occurrence and other observational properties of tidal features around nearby galaxies. The sample we construct will act as a foundational dataset for statistical comparison with cosmological models of galaxy formation. Our approach is based on a visual classification of diffuse features around a volume-limited sample of nearby galaxies, using a post-processing of Sloan Digital Syk Survey (SDSS) imaging optimized for the detection of stellar structure with low surface brightness. At a limiting surface brightness of 28 mag arcsec –2 , 14% of the galaxies in our sample exhibit evidence of diffuse features likely to have arisen from minor merging events. Our technique recovers all previously known streams in our sample and yields a number of new candidates. Consistent with previous studies, coherent arc-like features and shells are the most common type of tidal structures found in this study. Here, we conclude that although some detections are ambiguous and could be corroborated or refuted with deeper imaging, our technique provides a reliable foundation for the statistical analysis of diffuse circumgalactic features in wide-area imaging surveys, and for the identification of targets for follow-up studies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Evidence for composition variations and impurity segregation at grain boundaries in high current-density polycrystalline K- and Co-doped BaFe{sub 2}As{sub 2} superconductors

Some polycrystalline forms of the K- and Co-doped BaFe{sub 2}As{sub 2} and SrFe{sub 2}As{sub 2} superconductors now have a critical current density (J{sub c}) within a factor of ∼5 of that required for real applications, even though it is known that some grain boundaries (GBs) block current, thus, raising the question of whether this blocking is intrinsic or extrinsically limited by artefacts amenable to improvement by better processing. Herein, we utilize atom-probe tomography (APT) to study the grain and GB composition in high J{sub c} K- and Co-doped BaFe{sub 2}As{sub 2} polycrystals. We find that all GBs studied show significant compositional variations on the scale of a few coherence lengths (ξ), as well as strong segregation of oxygen impurities, which we believe are largely introduced in the starting materials. Importantly, these findings demonstrate that APT enables quantitative analysis of the highest J{sub c} K-doped BaFe{sub 2}As{sub 2} samples, where analytical transmission electron microscopy (TEM) fails because of the great reactivity of thin TEM samples. The observations of major chemical perturbations at GBs make us cautiously optimistic that there is a large extrinsic component to the GB current blocking, which will be ameliorated by better processing, for which APT will likely be a crucial instrument.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Direct observation of Mn distribution/speciation within and surrounding a basidiomycete fungus in the production of Mn-oxides important in toxic element containment

Biogenic manganese (Mn) oxides occur ubiquitously in the environment including the uranium (U) mill tailings at the Ningyo-toge U mine in Okayama, Japan, being important in the sequestration of radioactive radium (Ra). To understand the nanoscale processes in Mn oxides formation at the U mill tailings site, Mn 2+ absorption by a basidiomycete fungus, Coprinopsis urticicola, isolated from Ningyo-toge mine water samples, was investigated in the laboratory under controlled conditions utilizing electron microscopy, synchrotron-based X-ray analysis, and fluorescence microscopy with molecular pH probe. The fungus’ growth was first investigated in an agar-solidified medium supplemented with 1.0 mmol/L of Mn 2+ , ± Cu 2+ (50 – 200 µM), ± Zn 2+ (50 – 200 µM), or ± diphenyleneiodonium chloride (DPI) (50 – 100 µM) at 25 °C. The results revealed that Zn 2+ has no significant effects on the Mn oxides formation, whereas Cu 2+ and DPI significantly inhibit both fungal growth and Mn oxidation, indicating superoxide-mediated Mn oxidation. During the interaction of Mn 2+ with the fungi in solution medium at the initial pH of 5.67, a small fraction of Mn 2+ infiltrated into the fungal hyphae within 8 h, forming a few tens nm-sized concentrates of soluble Mn2+ in the intracellular pH of ~6.5, which can be released back to solution within a day as shown in a subsequent releasing experiment. After 1 day of incubation, Mn oxides began to precipitate on the hyphae, which were characterized to be fibrous nanocrystals with a hexagonal birnessite-structure, these forming spherical aggregates with a diameter of ~1.5 µm. When the fungi were reacted using the Ningyo-toge mine water, the Mn concentration decreased at a rate of 1.0 mmol·day-1 per unit dry weight. The nanoscale processes associated with the fungi derived from the Ningyo-toge mine area provides additional insights into the existing mechanisms of Mn oxidation by filamentous fungi at other U mill tailings sites under circumneutral pH conditions. Such processes add to the class of reactions important to the sequestration of toxic elements.

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

A graph theoretic framework for representation, exploration and analysis on computed states of physical systems

A graph theoretic perspective is taken for a range of phenomena in continuum physics in order to develop representations for analysis of large scale, high-fidelity solutions to these problems. Of interest are phenomena described by partial differential equations, with solutions being obtained by computation. The motivation is to gain insight that may otherwise be difficult to attain because of the high dimensionality of computed solutions. We consider graph theoretic representations that are made possible by low-dimensional states defined on the systems. These states are typically functionals of the high-dimensional solutions, and therefore retain important aspects of the high-fidelity information present in the original, computed solutions. Our method is rooted in regarding each state as a vertex on a graph and identifying edges via processes that are induced either by numerical solution strategies, or by the physics. Correspondences are drawn between the sampling of stationary states, or the time evolution of dynamic phenomena, and the analytic machinery of graph theory. A collection of computations is examined in this framework and new insights to them are presented through analysis of the corresponding graphs.

42 ENGINEERING↗
DOE OSTI2015

The oceanographic toolbox for the collection of sinking and suspended marine particles

Marine particles play a central role in controlling the transport, cycling, and inventories of many major elements and trace elements and isotopes throughout the oceans. Studies seeking to elucidate the biogeochemical roles of marine particles often require reliable ways to collect them from the ocean. Here, we review the oceanographic toolbox of techniques and instrumentation that are employed to collect both suspended and sinking particles. With these tools, it is possible to determine both the concentrations and vertical fluxes of important elements and individual particle types. We describe the various methods for quantifying the concentrations of particulate matter with in situ pumps, towed sampling devices, bottle collectors, and large volume capture devices. The uses of various types of flux collection platforms are discussed including surface tethered, neutrally buoyant, and bottom moored devices. We address the issues of sediment trap collection biases and the apparent inconsistencies that can arise due to differences in the temporal and spatial scales sampled by the various methodologies. Special attention is given to collection considerations made for the analysis of trace metals and isotopes, as these methodologies are of high importance to the ongoing GEOTRACES program which seeks to identify the processes and quantify fluxes that control the distributions of key trace elements and isotopes in the ocean. With the emergence of new particle collection methodologies and the continued reliance on traditional collection methods, it is imperative that we combine these multiple approaches in ways that will help improve their accuracy and precision while enhancing their utility in advancing understanding of the biogeochemical and ecological roles of marine particles.

58 GEOSCIENCES↗
DOE OSTI2026

Lead Isotope Fingerprinting of Nanoscale Mineral Particles via Single Particle Inductively Coupled Plasma Mass Spectrometry

Determining lead (Pb) isotopic ratios is of broad interest across chemical disciplines for source tracing and age determinations, but the technique is inherently limited when multiple sources of Pb are present in a single sample. Single particle methods offer a solution to directly resolve multiple distinct isotopic ratios within individual samples. In this study, single particle inductively coupled plasma-mass spectrometry (spICP-MS) was performed using time-of-flight (TOF) and multicollector (MC)-based platforms to measure the Pb isotopic composition of individual nanoscale particles. Distinct Pb isotope ratios were measured in particles from four powdered galena samples of different origins (average single-particle 206Pb/207Pb ratios ranging from 0.91 to 1.28) using both the TOF and the MC-based platforms. Differentiation of galena particles in a mixture (liberated grains and those hosted in a silicate matrix) was possible due to detecting their unique multielemental fingerprints. The differing behavior of the two galena samples during digestion was investigated; undigested galena particles trapped within silicate minerals were detected using spICP-MS, which has implications for Pb recovery in bulk-scale isotopic analysis. The multinuclide detection capability of the ICP-TOF-MS instrument allowed for the simultaneous detection of secondary constituent elements within the nanoparticles and the identification of multiple populations of isotopically distinct Pb-bearing particles in a copper ore sample, whereas the increased sensitivity of the MC instrument enabled quantification of 204Pb, allowing differentiation using multiple isotopic ratios. A single particle isotope ratio analysis module was developed within an open-source spICP-TOF-MS data processing platform, enabling its adoption across chemical disciplines.

Goodman, Aaron J. [University of Montreal, Quebec,↗
DOE OSTI2014

Soft x-ray ionization induced fragmentation of glycine

X-ray absorption commonly involves dissociative core ionization producing not only momentum correlated charged fragments but also low- and high-energy electrons capable of inducing damage in living tissue. This gives a natural motivation for studying the core ionization induced fragmentation processes in biologically important molecules such as amino acids. Here the fragmentation of amino acid glycine following carbon 1s core ionization has been studied. Using photoelectron-photoion-photoion coincidence technique, a detailed analysis on fragmentation of the sample molecule into pairs of momentum correlated cations has been carried out. The main characteristics of core ionization induced fragmentation of glycine were found to be the rupture of the C–C{sub α} bond and the presence of the CNH{sub 2}{sup +} fragment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Synthesis and field emission behaviour of well faceted In{sub 2}Se{sub 3} micro-crystals

Here in, we report synthesis of crystalline Indium Selenide (In{sub 2}Se{sub 3}) elegant microcrystals on Au coated Si substrates using one-step facile thermal evaporation route and their field emission investigations. The as-synthesized In{sub 2}Se{sub 3} micro-crystals were subjected to structural and morphological analysis prior to the field emission studies. The XRD spectrum of the as-synthesized product reveals formation of crystalline hexagonal phase of In{sub 2}Se{sub 3} under the prevailing experimental conditions. Under optimized process variables, the morphology of the as-synthesized product is characterized by presence of well facetted micron size particles of In2Se3. Furthermore, the EDAX analysis confirms the presence of In and Se in the as-synthesized sample. The field emission characteristic of the In{sub 2}Se{sub 3} micro-crystal emitter is found to be superior to the other metal chalcogenides micro-crystal based emitters. The synthesized In{sub 2}Se{sub 3} micro-crystals emitter delivers current density of ∼ 225 µA/cm{sup 2} at an applied electric field of ∼ 7.44 V/µm. The emission current stability investigated at pre-set value of ∼ 3 µA is observed to be fairly good. These observed results demonstrate potential of the In{sub 2}Se{sub 3} cathode as an electron source for practical applications in vacuum microelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2018

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ESS-DIVE Reporting Format for Amplicon Abundance Table

While standardized sequencing data is available in public repositories and efforts such as MIxS for common sample collection and processing metadata are well established, the lack of common bioinformatic processing metadata has hindered the ability to do large-scale metaanalyses and the potential for data re-use by non-experts such as ecosystem, watershed, or earth system modelers. To address this need for Department of Energy researchers, we have developed an amplicon reporting format which captures both sample preparation and bioinformatic processing metadata and stores processed amplicon data as a paired abundance table and sequencing file to maximize the potential for re-use of these data. To aid in the adoption of accessible and reproducible analysis workflows, this reporting format was developed in concert with amplicon functionality within the Department of Energy’s Systems Biology Knowledgebase (KBase) to ensure common data and metadata requirements and facilitate seamless transfer between these platforms.This dataset contains support documentation for the amplicon reporting format (README.md and instructions.md), templates for both bioinformatic and sequencing metadata (amplicon_bioinformatic_metadata_template_2021_10_03.csv and amplicon_sequencing_metadata_template_2021_10_03.csv), a crosswalk indicating how this reporting format relates to the current MIxS format (ESSDIVE-MIxS_crosswalk.csv), a list of available instrument terms (amplicon_seq_instrument_terms_2021_10_03.csv), a map between QIIME2 parameter settings and metadata fields (amplicon_qiime2_plugin_metadata_map.csv), a data dictionary (amplicon_CSV_dd.csv), and file-level metadata (amplicon_FLMD.csv).

54 ENVIRONMENTAL SCIENCES↗