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DOE OSTI2019

The formation of spinel-group minerals in contaminated soils: the sequestration of metal(loid)s by unexpected incidental nanoparticles

Mineralogical studies of contaminated soils affected by smelter emission and dust from mining activities indicate that minerals of the spinel group are one of the common hosts of metal-bearing contaminants. Spinel group minerals typically originate from high temperature processes, but an increasing number of studies indicate that metal-bearing spinel group minerals can also form under ambient Earth surface conditions in surficial soils. In this contribution to honor Donald Sparks, we show that the spinels Zn-bearing magnetite (Zn 0.5 Fe 2.5 O 4 ) and minium (Pb 3 O 4 ) form during low temperature alteration of Pb-bearing silica glass in surficial organic rich soils in proximity to a former Cu-smelter in Timmins, Ontario, Canada. The glass most likely formed during high-temperature processes and has been either emitted by the smelter or wind-blown from waste rock piles to near-by soils. The alteration of the glass by percolating pore solutions has resulted in the formation of large micrometer-size dendritic etch features and in nanometer-size dendritic alteration halos composed of nano-size prismatic crystals of Zn-rich magnetite and spherical nanoparticles of minium. Both spinel-type phases are embedded in an amorphous silica matrix which formed during the alteration of the glass at low temperature. A review on the occurrence of spinel-group minerals in smelter-affected soils or mine tailings indicates that the formation of these minerals under ambient Earth surface conditions is quite common and often results in the sequestration of contaminants such as Cu, Ni, Zn and Sb. The pedogenic spinels often occur as euhedral crystals in nano-size mineral assemblages within alteration features such as dendritic etch patterns, mineral surface coatings and mineralized organic matter. Their well-developed crystal forms indicate that (a) they have not formed during a rapid cooling process in a smelter or refinery which typically creates spherical particulate matter, and (b) they have not been part of particulate matter added via fluvial or Aeolian processes which most commonly yield anhedral morphologies. The formation of nano-size spinel-group minerals in low temperature environmental settings may lead to the long-term storage of metal(loid)s in mineral phases and their transport over vast distances via fluvial, alluvial and Aeolian processes.

58 GEOSCIENCES↗

DOE OSTI2023

Data Analytics for Residential PV from Permit to Interconnect (Final Technical Report)

The main objective of this research is to provide novel insights into the effects of permitting, inspection, and interconnection (PII) processes on PV system installations—and in particular, into the relationship between PII processes and adoption timelines. This research can then be used to clarify the potential effect of various process changes on reducing PII timelines, customer cancellation rates, and related costs nationwide. NREL completed this research by assembling a data set of distributed, largely residential rooftop solar systems less than 50 kilowatts in size from participating solar installers. NREL produced five publications describing the effects that PII processes can have on adoption timelines nationwide, in addition to publishing an interactive data viewer with five years of PII cycle time data. This tool can be used by stakeholders to identify potential adoption timelines by local government.

14 SOLAR ENERGY↗

DOE OSTI2022

The Influence of Dust-Smoke Mixtures on Boundary Layer Processes and Nocturnal Warming in the Sahel

Using a single column model with ground-based, aircraft, and satellite data sets we assess the combined role of smoke and dust aerosols, land degradation/aridization (LDA), and their impact on the planetary boundary layer (PBL) in influencing near-surface air temperature over the Sahel. Our study is unique because it assesses the combined role of smoke and dust aerosols on PBL evolution and near-surface air temperatures during both day and nighttime. More importantly, using a theoretical framework, we provide a careful explanation of the geophysical processes responsible for the changes in PBL and near-surface air temperature. Our results indicate that during northern hemisphere winter months, dust, and smoke over Sahel radiatively combine to impact the PBL. We show that aerosol mixtures dominated by dust modify PBL height in a manner that minimizes/maximizes surface layer cooling/warming at times when daytime maximum/nocturnal minimum temperatures occur. Furthermore, we find that increasing smoke contribution to total column aerosol optical extinction counteracts nighttime warming through daytime cooling. When smoke constitutes half or more of to the total column aerosol optical extinction, the ratio of longwave to shortwave radiative forcing is less than 10%, and nighttime cooling ensues. Minimum temperature is most sensitive to changes in mid-visible aerosol optical depth (AOD) values <1 and doubling of dust AOD within this range during the 1950–1980 Sahelian LDA event is estimated to have a nocturnal warming potential of 0.6°C.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

A Standardized Analysis Process Using Digital Image Correlation to Calculate In Situ Cladding Strain from Modified Burst Tests for Fuel Performance Code Validation

Historical data collection on nuclear fuel cladding materials has focused on generating a statistically significant amount of data to assess the material and its failure behavior. Furthermore, data generated to support material model and failure criteria development were previously posttest evaluations, so a large number of tests was required to gain new understanding. A way to expedite this process is to develop techniques capable of generating large, high-fidelity data sets from a single test with lower uncertainty or quantified uncertainty. One such example of this approach is Oak Ridge National Laboratory’s use of modified burst tests (MBTs) to analyze the mechanical behavior and failure conditions of cladding during a simulated reactivity-initiated accident (RIA). Each test incorporates digital image correlation (DIC) analysis techniques that are used to assess the accumulated strain in situ, as well as eventual cladding failure. This work has been fruitful in defining strain-to-failure conditions for materials like silicon carbide (SiC) fiber–reinforced/SiC matrix composite tubes (SiC/SiC), iron-chromium-aluminum (FeCrAl) alloy tubes, and chromium-coated Zircaloy-4 tubes. However, there are numerous DIC software available, including open-source and proprietary software. The different DIC software use various algorithms to process images and calculate displacement values. Using these different software and algorithms can lead to varying results, and perhaps larger-than-expected uncertainties. In the present study, previously published MBT data encompassing a variety of test conditions were reanalyzed with two different DIC software to assess the variance in the calculated strain results. The data consisted of SiC/SiC, FeCrAl, and chromium-coated Zircaloy-4 tubes. Plots of the calculated strains during the transient revealed good agreement between the two DIC software. The average root-mean-square errors between the two software was 0.20% strain, which is slightly larger than a previously reported error value for these tests. In conclusion, this variance in results is low enough that this analysis method can be used for code validation.

Reactivity-initiated accident↗

DOE OSTI2024

Electrophoretic deposition for improved trace element homogeneity in silica reference materials

Spatially-resolved analysis requires homogeneous reference materials (RMs) to make reliable quantitative measurements. Here we previously developed an electrophoretic deposition (EPD) method for fabrication of glassy microanalytical RMs with superior platinum-group element homogeneity **[1], and now include further dopants. For 39 trace elements, we analyzed dopant homogeneity in sintered silica (SiO 2 ) samples consolidated either mechanically by die-pressing (DP) or by EPD. A set of EPD and DP samples was made from each of two nanoparticle feedstocks produced by variations of the Stöber process **[2]. Spatially-resolved dopant distribution was characterized in all samples by laser-ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS). In both sample sets, homogeneity of most trace elements was substantially improved by EPD relative to their DP counterpart.

36 MATERIALS SCIENCE↗

DOE OSTI2015

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra

De novo sequencing of proteins and peptides is one of the most important problems in mass spectrometry-driven proteomics. A variety of methods have been developed to accomplish this task from a set of bottom-up tandem (MS/MS) mass spectra. However, a more recently emerged top-down technology, now gaining more and more popularity, opens new perspectives for protein analysis and characterization, implying a need in efficient algorithms for processing this kind of MS/MS data. Here we describe a method that allows to retrieve from a set of top-down MS/MS spectra long and accurate sequence fragments of the proteins contained in a sample. To this end, we outline a strategy for generating high-quality sequence tags from top-down spectra, and introduce the concept of a T-Bruijn graph by adapting to the case of tags the notion of an A-Bruijn graph widely used in genomics. The output of the proposed approach represents the set of amino acid strings spelled out by optimal paths in the connected components of a T-Bruijn graph. We illustrate its performance on top-down datasets acquired from carbonic anhydrase 2 (CAH2) and the Fab region of alemtuzumab.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2021

DOE JGI Metagenome Workflow

The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723–D733, 2021, https://doi.org/10.1093/nar/gkaa983).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Operation of Argonne's Liquid Salt-Liquid Metal Separation Testbed for U/TRU Product Processing

Argonne National Laboratory has constructed a liquid salt-liquid metal separation testbed for use in the development and advancement of cathode processing of U/TRU co‑deposits generated by pyroprocessing of used nuclear fuel. The U/TRU product recovered from the electrorefiner contains adhered and entrained salt that must be removed prior to consolidation of the U/TRU alloy for use in advanced reactor fuel fabrication. The bottom pour operation utilizes the low melting points of U/TRU co‑deposits and higher densities of molten metals compared to molten salts to separate and consolidate the U/TRU product. Argonne’s testbed is designed to support the development and optimization of bottom-pouring configurations for batch and semi-continuous operations, integration of process monitoring and control technologies, and determination of operational requirements for implementing in an industrial setting. Scoping tests were performed to demonstrate operational aspects of the testbed, including operation using single-pour spout and dual-pour spout configurations, effectiveness of salt containment and extent of salt vaporization, and the use of sensor probes to detect the location of the interface between the metal and salt phases during pouring. Recommendations for process optimization testing for further development of bottom pour processing to separate U/TRU alloys from adhered salt were made based on the results of scoping tests. Completing the recommended activities will increase the technical readiness level (TRL) of the liquid salt-liquid metal separation operation and consolidation of U/TRU alloys to support industrialization of pyroprocessing.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

A new primer set for Clade I nosZ that recovers genes from a broader range of taxa

Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N 2 O) to N 2 has been widely used as a biomarker to study denitrifying communities. However, conventional PCR primers target a limited range of the genetically diverse Clade I nosZ, and the amplicons are too long for sequencing on current NGS platforms. To address these issues, here we developed a new PCR primer set that amplifies a 355-bp region of Clade I nosZ and captures broader taxonomic coverage than conventional primers in in silico tests. When compared with the widely used nosZF_nosZR_Rich_2003 set using the same soil samples and the same sequencing depth, the new set retrieved genes from four times more unique species, with consistently higher general diversity-based metrics. The new primer set performed well with different sequencing platforms (Ion Torrent and Illumina), and among a wide variety of soils from polar to tropical, desert to agricultural, and surface to a very low biomass subsoil, with significant differences in denitrifying community diversity and composition. This new primer set for Clade I together with the primers recently reported for Clade II by Chee-Sanford et al. provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ~40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A laser-assisted chlorination process for reversible writing of doping patterns in graphene

Chemical doping can be used to control the charge-carrier polarity and concentration in two-dimensional van der Waals materials. However, conventional methods based on substitutional doping or surface functionalization result in the degradation of electrical mobility due to structural disorder, and the maximum doping density is set by the solubility limit of dopants. Here we show that a reversible laser-assisted chlorination process can be used to create high doping concentrations (above 3 × 10 13 cm -2 ) in graphene monolayers with minimal drops in mobility. The approach uses two lasers—with distinct photon energies and geometric configurations—that are designed for chlorination and subsequent chlorine removal, allowing highly doped patterns to be written and erased without damaging the graphene. To illustrate the capabilities of our approach, we use it to create rewritable photoactive junctions for graphene-based photodetectors.

42 ENGINEERING↗

DOE OSTI2018

Revealing the Impact of F4‐TCNQ as Additive on Morphology and Performance of High‐Efficiency Nonfullerene Organic Solar Cells

Abstract Fluorinated molecule 2,3,5,6‐tetrafluoro‐7,7,8,8‐tetracyanoquinodimethane (F4‐TCNQ) and its derivatives have been used in polymer:fullerene solar cells primarily as a dopant to optimize the electrical properties and device performance. However, the underlying mechanism and generality of how F4‐TCNQ affects device operation and possibly the morphology is poorly understood, particularly for emerging nonfullerene organic solar cells. In this work, the influence of F4‐TCNQ on the blend film morphology and photovoltaic performance of nonfullerene solar cells processed by a single halogen‐free solvent is systematically investigated using a set of morphological and electrical characterizations. In solar cells with a high‐performance polymer:small molecule blend FTAZ:IT‐M, F4‐TCNQ has a negligibly small effect on the molecular packing and surface characteristics, while it clearly affects the electronic properties and mean‐square composition variation of the bulk. In comparison to the control devices with an average power conversion efficiency (PCE) of 11.8%, inclusion of a trace amount of F4‐TCNQ in the active layer has improved device fill factor and current density, which has resulted into a PCE of 12.4%. Further increase in F4‐TCNQ content degrades device performance. This investigation aims at delineating the precise role of F4‐TCNQ in nonfullerene bulk heterojunction films, and thereby establishing a facile approach to fabricate highly optimized nonfullerene solar cells.

Xiong, Yuan↗

DOE OSTI2017

Systematic Parameterization of Lignin for the CHARMM Force Field

Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization for emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between disparate feedstocks, and guide further lignin engineering efforts.

09 BIOMASS FUELS↗

DOE OSTI2019

The Influenza A Virus Endoribonuclease PA-X Usurps Host mRNA Processing Machinery to Limit Host Gene Expression

Often, many viruses shut off host gene expression to inhibit antiviral responses. Viral proteins and host proteins required for viral replication are typically spared in this process, yet the mechanisms of target selectivity during host shutoff remain poorly understood. Using transcriptome-wide and targeted reporter experiments, we demonstrate that the influenza A virus endoribonuclease PA-X usurps RNA splicing to selectively target host RNAs for destruction. Proximity-labeling proteomics reveals that PA-X interacts with cellular RNA processing proteins, some of which are partially required for host shutoff. Thus, PA-X taps into host nuclear pre-mRNA processing mechanisms to destroy nascent mRNAs shortly after their synthesis. This mechanism sets PA-X apart from other viral host shutoff proteins that target actively translating mRNAs in the cytoplasm. Our study reveals a unique mechanism of host shutoff that helps us understand how influenza viruses suppress host gene expression.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Characteristic constitution model and microstructure of an Al-3.5Cu-1.5Li alloy subjected to thermal deformation

The constitution model and microstructure of 2A97 Al-Li alloy during thermal deformation were investigated. The thermal deformation behavior was dominated by the interaction between work hardening and dynamic softening. The constitution model was constructed to predict the rheology behavior, in which Zener-Holloman equation with a fifth-order polynomial was set to describe the effect of various strains on the material parameters. Processing maps displayed to exist two unstable domains in microstructure (one domain with the temperature range from 300 °C to 370 °C and the strain rate range from 10{sup 0.5} s{sup −1} to 10s{sup −1}, and the other with the temperature range from 380 °C to 500 °C and the strain rate range from 0 s{sup −1} to 10 s{sup −1}). Microstructural characteristics of dynamic recovery (DRV) and dynamic recrystallization (DRX) in the stable domain and local rheology in the unstable domain were observed, respectively. The dynamic precipitation (DPN) of T{sub 1} phases and the interaction between dislocations and Al{sub 20}Cu{sub 2}Mn{sub 3} and Al{sub 3}Zr phases were concluded by high resolution transmission electron microscopy (HRTEM), which was the first experimental evidence for the DPN in 2A97 Al-Li alloy. All these confirmed the occurrence of the continuous dynamic recrystallization during thermal deformation.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Effect of temperature on the fatigue cracking mechanisms in A356 Al alloy

This work builds on our previous investigation of the room temperature fatigue cracking mechanisms of an A356 Al alloy. Here, we analyze the elevated temperature fatigue cracking mechanisms in cast and friction stir processed (FSP) A356, and contrast them with the room temperature behavior. Two sets of FSP parameters were used to modify the microstructure of the cast alloy. After heat treatment, both the FSPed microstructures exhibited severe abnormal grain growth (AGG) leading to a very wide grain size distribution (from a few microns to a few millimeters). During room temperature fatigue tests, the FSP conditions exhibited significant improvements in fatigue lives, even up to an order of magnitude. However, with increasing temperature, the difference in the performance of the FSPed and Cast microstructures decreased until, at 200 °C, all three microstructural conditions exhibited similar fatigue response. Detailed electron back scattered diffraction (EBSD) imaging of failed fatigue specimens was used to study crack behavior. At room temperature, cracks initiated at defect sites or along persistent slip bands (PSBs) and propagated transgranularly. The grain boundaries acted as barriers to crack growth. At elevated temperatures, there was a complete role reversal of the grain boundaries. Cracks initiated along grain boundaries and propagated intergranularly in all microstructures. Below, we explore this transition of the cracking mechanism in detail.

Nelaturu, Plalgun↗

DOE OSTI2021

The Rise of Neural Networks for Materials and Chemical Dynamics

Machine learning (ML) is quickly becoming a premier tool for modeling chemical processes and materials. ML-based force fields, trained on large data sets of high-quality electron structure calculations, are particularly attractive due their unique combination of computational efficiency and physical accuracy. This Perspective summarizes some recent advances in the development of neural network-based interatomic potentials. Designing high-quality training data sets is crucial to overall model accuracy. One strategy is active learning, in which new data are automatically collected for atomic configurations that produce large ML uncertainties. Another strategy is to use the highest levels of quantum theory possible. Transfer learning allows training to a data set of mixed fidelity. A model initially trained to a large data set of density functional theory calculations can be significantly improved by retraining to a relatively small data set of expensive coupled cluster theory calculations. These advances are exemplified by applications to molecules and materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Microseismicity cloud can be substantially larger than the associated stimulated fracture volume: the case of the Paralana Enhanced Geothermal System

Here, the goal of hydraulic stimulation is to increase formation permeability in the near vicinity of a well. However, there remain technical challenges around measuring the outcome of this operation. During two Enhanced Geothermal System (EGS) stimulations in South Australia, Paralana in 2011 and Habanero in 2003, extensive catalogs of microseismicity were recovered. It is often assumed that shear failure of existing fractures is the main mechanism behind both the induced earthquakes and any permeability enhancement. This underpins a common notion, that the seismically active volume is also the stimulated reservoir. In this paper, we compute the density of earthquake hypocenters and provide evidence that, under certain conditions, this spatiotemporal quantity is a reasonable proxy for pore pressure increase. We then apply an inverse modeling approach that uses the earthquake observations and a modified reservoir simulator to estimate the parameters of a permeability evolution relation. The regime implied by the data indicates that most permeability enhancement occurred very near to the wellbore and was not coincident with the bulk of the seismicity, whose volume was about two orders of magnitude larger. Thus, we conclude that, in some cases, it is possible for permeability enhancement and induced seismicity to be decoupled, in which case the seismically active volume is a poor indicator of the stimulated reservoir. Our results raise serious questions about the effectiveness of hydroshearing as a stimulation mechanism in EGS. Finally, this study extends our understanding of the complex processes linking earthquakes, fluid pressure, and permeability in both natural and engineered settings.

58 GEOSCIENCES↗