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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Impacts of Guanidine Degradation Products on Next Generation Solvent (NGS) Caustic Side Solvent Extraction (CSSX) Processing

Savannah River National Laboratory researchers have been requested to perform testing to assess the potential for build-up of guanidine degradation compounds in the Next Generation Solvent Caustic Side Solvent Extraction process. Testing was also requested to determine the impact of guanidine degradation compounds [3,7-dimethyloctylamine (iDA) and Bis-N,N’-(3,7-dimethyloctyl)urea (DiDU)] on cesium behavior in the flowsheet. Twelve partitioning experiments were performed to quantify the partitioning coefficient of identified guanidine degradation compounds in various organic-aqueous mixtures. Six Extraction, Scrub, and Strip (ESS) experiments were performed to quantify the impact of degradation products on cesium behavior.

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

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality (“greenness”) as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Literature Review on Next Generation Solvent Isopar ® L Vapor Pressure Curve and the Partitioning of its Modifier and Extractant

The Next Generation Solvent (NGS) is set to replace the Original Caustic Side Solvent Extractant (CSSX) at the Salt Waste Processing Facility (SWPF). The Savannah River National Laboratory (SRNL) was requested by Savannah River Mission Completion (SRMC), formerly Savannah River Remediation (SRR), to perform a literature review on the following topics to address flammability concerns with the current solvent: Isopar ® L vapor pressure curve for NGS, partitioning ratio for the extractant MaxCalix and the modifier Cs-7SB, and high cesium concentration impacts on NGS radiolysis and potential solvent degradation rates in high cesium concentrations. The following conclusions and recommendations are made based on previous experimental work and literature: (1) Current SWPF flammable gas generation calculations use an Isopar ® L vapor pressure curve based on experimental testing with the Original CSSX solvent. No such testing to date has been performed with NGS. It is suggested that the decrease in Cs-7SB concentration for NGS compared to the Original CSSX solvent would lead to a slightly higher vapor pressure at all temperatures in SWPF vessels. A bounding NGS vapor pressure curve has been provided; it is recommended to see if these values would challenge current flammability controls and to perform testing if needed.(2) The partitioning ratio for Cs-7SB is known in the Original CSSX solvent with dilute nitric acid and caustic solutions. No tests could be found for the partitioning of Cs-7SB to dilute boric acid solutions; however, a similar partitioning ratio is expected. Due to the lipophilic alkyl chains on MaxCalix, it is expected to be even less soluble than BOBCalixC6 in the aqueous phase and should not be considered a significant contributor to the f organic term. Additionally, the reaction rate of N,N’,N’’-Tris(3,7-dimethyloctyl)guanidine (TiDG) or its degradation products with a hydrogen radical should be estimated/determined if they are found to be significant contributors to the f organic term. (3) NGS is expected to see much higher Cs concentrations at SWPF in comparison to its use at the Modular CSSX Unit (MCU). These higher Cs concentrations could influence radiolytic degradation rates of the solvent. NGS appears to be fairly stable to radiolytic degradation based on previous testing and its use at MCU. However, there has not been radiolytic flammable gas generation testing with NGS to date. There is a risk that the continued use of G-values obtained for flammable gases produced from the irradiation of the Original CSSX solvent is not bounding for NGS, but this is considered a very low risk due to the similarities in the composition of the solvents, as well as the conservatisms in the experimental design of the Original CSSX testing.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Next Generation Solvent Vapor Pressure Testing

Previous work by Savannah River National Laboratory (SRNL) indicated that the actual Next Generation Solvent vapor pressure would be higher than the Original Caustic Side Solvent Extraction (CSSX) solvent vapor pressure, but below a bounding vapor pressure using Raoult’s Law. Since solvent vapor pressure has a significant impact on Composite Lower Flammability Limits (CLFL) and attendant accident analyses, obtaining an additional margin from the bounding NGS vapor pressure would be valuable. In order to quantify how much margin might be gained from the NGS bounding solvent, SRNL researchers were requested to perform vapor pressure testing with the Next Generation Solvent (NGS) by Savannah River Mission Completion (SRMC). The vapor pressure curve for the NGS formulation set to be deployed at the Salt Waste Processing Facility (SWPF) has been determined by SRNL up to 55°C (131°F) using headspace Gas Chromatography (GC). It was expected that NGS would have a higher vapor pressure than the Original CSSX solvent; however, experimental results indicate a lower vapor pressure. At this time, it is uncertain if this difference is due to the 7x increase in concentration of the large calixarene in the solvent (0.007M BOBCalix in Original CSSX solvent vs. 0.05M MaxCalix in NGS) or to minor batch-to-batch variations in Isopar-L constituents. The NGS and the Original CSSX solvent vapor pressure data were fitted to the Antoine Equation. The Antoine equation gives a more accurate representation of the expected vapor pressure of the solvents outside of the temperature range tested. The Antoine equation fitting for NGS is given below: $P=10^{6.364⁻\frac{1788.4}{T+219.3}}$. Where, p is the vapor pressure (partial pressure) of NGS in mmHg and T is the temperature in °C. It is recommended that SRMC either continue using the more conservative Isopar-L vapor pressure calculations at SWPF with the equation developed for the Original CSSX solvent, or the equation presented above for the NGS solvent. Additionally, it is recommended to study the variability in Isopar-L vapor pressure between lots.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Non-growing season plant nutrient uptake controls Arctic tundra vegetation composition under future climate

Abstract Plant growth and distribution in high-latitude tundra ecosystems is strongly limited by nutrient availability and is critical for quantifying centennial-scale carbon-climate interactions. However, land model representations of plant–nutrient interactions are uncertain, leading to poor comparisons with high-latitude observations. Although it has been recognized for decades in the observational community that plants continue to acquire nutrients well past when aboveground activity has ceased, most large-scale land models ignore this process. Here we address the role tundra plant nutrient acquisition during the non-growing season (NGS) has on centennial-scale vegetation growth and dynamics, with a focus on shrub expansion. We apply a well-tested mechanistic model of coupled plant, microbial, hydrological, and thermal dynamics that explicitly represents nutrient acquisition based on plant and microbial traits, thereby allowing a prognostic assessment of NGS nutrient uptake. We first show that the model accurately represents observed seasonality of NGS plant nutrient uptake in a northern Alaskan tundra site. Applying the model across the North America tundra indicates that NGS nutrient uptake is consistent with observations and ranges between ∼5% and 50% of annual uptake, with large spatial variability and dependence on plant functional type. We show that NGS plant nutrient acquisition strongly enhances modeled 21 st century tundra shrub growth and expansion rates. Our results suggest that without NGS nutrient uptake, total shrub aboveground dominance would be ∼50% lower, limited primarily by their inability to grow tall enough to maximize their inherent capacity for light competition. Evergreen shrubs would be more strongly affected because of their relatively lower capacity for nutrient remobilization and acquisition compared to deciduous shrubs. Our results highlight the importance of NGS plant and soil processes on high-latitude biogeochemistry and vegetation dynamics and motivate new observations and model structures to represent these dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).

Parris, D. Joshua↗
DOE OSTI2023

Scripts and data associated with a manuscript linking soil and sediment elemental composition with dissolved organic matter chemistry across CONUS

This data package provides scripts and geochemical data for a manuscript titled “Linkages between mineral element composition of soils and sediments with hyporheic zone dissolved organic matter chemistry across the contiguous United States” (preprint: doi: 10.22541/essoar.169447343.31694990/v1). This data is associated with the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS, https://whondrs.pnnl.gov) and is an extension of the Summer 2019 Sampling campaign which crowdsourced samples from rivers and sediment across the continental United States. Data from this study can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1603775 and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719. The main objective of this manuscript was to couple sediment water extractable dissolved organic matter chemistry, defined by ultra-high resolution mass spectrometry, with localized sediment elemental composition and watershed scale soil elemental characteristics. This data package contains one main folder with four subfolders. The main data folder contains (1) readme; (2) data dictionary (dd); (3) file-level metadata (flmd); (4) an R markdown to reproduce manuscript figures and analyses; (5) a pdf of instructions to reproduce NGS interpolations with ArcGIS software; and (6) a python script to reproduce NGS extrapolations with python. The four subfolders contain files required to reproduce NGS extrapolations include (1) ‘CONUS_boundaries’ containing boundary layers (.shp) for the Continental United States; (2) ‘ngs_project’ containing files (.shp) with point level NGS soil elemental data (Grossman et al., 2004); (3) ‘raster_outputs’ containing the interpolated raster output files for various soil elements; and (4) ‘NGS_Chemistry_Final’ contain final extracted soil elemental data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Density of Next-Generation Caustic-Side Solvent Extraction Solvent

This report recommends the appropriate modifier concentration to employ in the Next Generation Solvent (NGS) to be used in the Salt Waste Processing Facility (SWPF) at the Savannah River Site for removal of cesium from legacy tank waste. The Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process employing the NGS is a marked improvement over the original Caustic-Side Solvent Extraction (CSSX) process, as it provides more effective removal of cesium from highly alkaline radioactive wastes and concentrates this removed cesium into an aqueous solution that is easy to vitrify for final disposal. Considerable effort has been devoted to optimizing the chemistry and process conditions of both systems, and their effectiveness has been demonstrated at the pilot scale at the Modular CSSX Unit (MCU). Due to the success of the demonstration and pilot-scale tests, the Salt Waste Processing Facility (SWPF) has been built to process larger volumes of waste with the CSSX process. To accelerate the waste-processing rate of the SWPF beyond its design throughput, plans call for the replacement of the CSSX process by the NG-CSSX process. To implement the NG-CSSX process in equipment optimized for CSSX, adjusting the density of the NGS to match the CSSX solvent density of 0.851 ± 0.0008 g/mL is considered advisable to obtain comparable hydraulic performance. Toward this objective, the density of the NGS has been measured at different temperatures and modifier concentrations to determine that a concentration of 0.650 M Cs-7SB modifier provides the best match for the desired density.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Atomistic simulations of nanoindentation on nanoglasses: Effects of grain size and gradient microstructure on the mechanical properties

The use of nanoglass (NG) microstructures has been shown as an effective strategy to improve the ductility of rather brittle metallic glass alloys. To evaluate the effects of grain size and gradient design on the mechanical properties of NGs, we perform molecular dynamics simulations of nanoindentation on Cu 64 Zr 36 NGs. We consider samples with uniform 3 and 7 nm grain sizes as well as gradient microstructures with gradient grain sizes varying from 3 to 7 nm. Here, the results show that the deformation mechanism in NGs with small grain sizes is dominated by the activation and evolution of multiple shear transformation zones. Increasing grain sizes enhances the elastic modulus and hardness at the cost of reduced abrasion resistance. Though the average grain size at the indentation surface plays a crucial role in the deformation behavior of gradient NG models, their strain localization and plastic deformation states are affected by the grain sizes far from the indenter. Desired combinations of mechanical properties can be realized by different NG microstructure designs.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Excess free volume and structural properties of inert gas condensation synthesized nanoparticles based CuZr nanoglasses

Abstract Nanoglass (NG) as a new structure-tunable material has been investigated using both experiments and computational modeling. Experimentally, inert gas condensation (IGC) is commonly employed to prepare metallic glass (MG) nanoparticles that are consolidated using cold compression to generate an NG. In computational modeling, various methods have been used to generate NGs. However, due to the high computational cost involved, heretofore modeling investigations have not followed the experimental synthesis route. In this work, we use molecular dynamics simulations to generate an NG model by consolidating IGC-prepared Cu 64 Zr 36 nanoparticles following a workflow similar to that of experiments. The resulting structure is compared with those of NGs produced following two alternative procedures previously used: direct generation employing Voronoi tessellation and consolidation of spherical nanoparticles carved from an MG sample. We focus on the characterization of the excess free volume and the Voronoi polyhedral statistics in order to identify and quantify contrasting features of the glass-glass interfaces in the three NG samples prepared using distinct methods. Results indicate that glass-glass interfaces in IGC-based NGs are thicker and display higher structural contrast with their parent MG structure. Nanoparticle-based methods display excess free volume exceeding 4%, in agreement with experiments. IGC-prepared nanoparticles, which display Cu segregation to their surfaces, generate the highest glass-glass interface excess free volume levels and the largest relative interface volume with excess free volume higher than 3%. Voronoi polyhedral analysis indicates a sharp drop in the full icosahedral motif fraction in the glass-glass interfaces in nanoparticle-based NG as compared to their parent MG.

36 MATERIALS SCIENCE↗
DOE OSTI2023

SSGUI v1.0

SSGUI is a web-based application that integrates the integrative genomics browser (IGV) with upstream alignment pipelines enabling rapid analysis of a batch of next-generation sequencing (NGS) samples. The input to SSGUI is an NGS file system directory that is organized by experiment and reference sequence. The output is an online dashboard containing various sequencing statistics for each sample and an integrated IGV plugin enabling rapid analysis of aligned NGS reads.

Kulawik, Mark↗
DOE OSTI2022

Non-growing Season Plant Nutrient Uptake Controls Arctic Tundra Vegetation Composition: Modeling Archive

This Modeling Archive is in support of a NGEE-Arctic publication: Riley et al. (2021) “Non-growing season plant nutrient uptake controls Arctic tundra vegetation composition under future climate” (Riley et al., 2021). The dataset contains “ecosys” model outputs reported in Riley et al. (2021) that examines the role of non-growing season (NGS) nutrient dynamics on 21st century vegetation composition. The study highlighted the importance of these nutrient dynamics on the emergent plant functional type distributions, focusing on their role in shrub expansion. The study showed that ignoring NGS nutrient dynamics led to a dramatic under-prediction of shrub expansion by year 2100, motivating the need to include these processes in Earth System Models. Included are modeled net primary production (NPP) and nitrogen (N) uptake for two scenarios: (1) baseline and (2) no NGS N uptake. The output is provided (1) at 25 km resolution across the North American tundra; (2) for years 2012 through 2100; and (3) PFT-specific. Dataset contains 20 NetCDF files in a zip file and one pdf.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Literature Review on the Impact of Thermolytic Hydrogen Generation Rate from the Next Generation Solvent

A literature review was undertaken to assess the thermolytic hydrogen generation potential of the Next Generation Solvent (NGS) system, which is planned to replace the Original Caustic-Side Solvent Extraction (CSSX) Solvent at the Salt Waste Processing Facility. NGS uses a new extractant and suppressor and the same modifier and organic carrier solvent as the Original CSSX Solvent at different concentrations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

A Review of the Literature on the Radiolytic Stability of the Next-Generation Solvent

The Original Caustic-Side Solvent Extraction (CSSX) solvent (based on the BOBCalixC6 extractant) currently in use at the Salt Waste Processing Facility (SWPF) is set to be replaced by the Next-Generation Solvent (NGS, based on the MaxCalix extractant). Current SWPF flammability safety controls use G-values for volatile gases obtained from radiolysis studies with the Original CSSX solvent. A review of past irradiation tests of both solvent systems was performed to assess the radiolytic stability of NGS with respect to flammable gas generation from radiolysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Linkage map construction using limited parental genotypic information

Abstract Genetic linkage maps based on single nucleotide polymorphisms (SNPs) represent an essential tool for a variety of genomic analyses. Today, next-generation sequencing (NGS) enables rapid genotyping of different mapping populations based on thousands of SNPs and the construction of highly saturated linkage maps. Nevertheless, missing data in the genotyping of the parental lines creates a bottleneck that determines the number of SNPs that can be used for the linkage map. As a proof of concept, a highly saturated genetic linkage map was constructed using the imputed genotypic data of a recombinant inbred line (RIL) population and the limited genotypic information of its parental lines. Two ABH genotype files were created from a pseudo-parental genotypic data set that includes all the SNPs present in the RIL population. In the first ABH file pseudo-parental 1 was considered parental A, while in the second pseudo-parental 1 was considered parental B. These two duplicate ABH genotype files were merged by chromosome and subjected to linkage map analysis. Since the ABH data were duplicated, two mirrored linkage groups were generated per chromosome. The correct linkage map was identified and selected based on the partial genotypic data of the parental lines. This strategy was effective for constructing a highly saturated linkage map of 33,421 SNPs based on the genotyping of 205 RILs and a limited number of 100 SNPs present in the parental lines. This strategy enables the use of all the NGS SNP data obtained from a low-coverage sequencing experiment in the mapping population.

59 BASIC BIOLOGICAL SCIENCES↗