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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 OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MeerKAT view of the dancing ghosts – peculiar galaxy pair PKS 2130−538 in Abell 3785

ABSTRACT We present MeerKAT L-band (886–1682 MHz) observations of the extended radio structure of the peculiar galaxy pair PKS 2130−538 known as the ‘Dancing Ghosts’. The complex of bending and possibly interacting jets and lobes originate from two active galactic nuclei hosts in the Abell 3785 galaxy cluster, one of which is the brightest cluster galaxy. The radio properties of the PKS 2130−538 – flux density, spectral index, and polarization – are typical for large, bent-tail galaxies. We also investigate a number of thin extended low surface brightness filaments originating from the lobes. South-east from the Dancing Ghosts, we detect a region of low surface brightness emission that has no clear origin. While it could originate from the Abell 3785 radio halo, we investigate the possibility that it is associated with the two PKS 2130−538 hosts. We find no evidence of interaction between the two PKS 2130−538 hosts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Long-lived neutron-star remnants from asymmetric binary neutron star mergers: element formation, kilonova signals and gravitational waves

We present 3D general-relativistic neutrino-radiation hydrodynamics simulations of two asymmetric binary neutron star mergers producing long-lived neutron stars remnants and spanning a fraction of their cooling time scale. The mergers are characterized by significant tidal disruption with neutron rich material forming a massive disc around the remnant. The latter develops one-armed dynamics that is imprinted in the emitted kilo-Hertz gravitational waves. Angular momentum transport to the disc is initially driven by spiral-density waves and enhanced by turbulent viscosity and neutrino heating on longer timescales. The mass outflows are composed by neutron-rich dynamical ejecta of mass ∼10 −3 –10 −2 M ⊙ followed by a persistent spiral-wave/neutrino-driven wind of ≳ 10 −2 M ⊙ with material spanning a wide range of electron fractions, ∼0.1–0.55. Dynamical ejecta (winds) have fast velocity tails up to ∼0.8 (∼0.4) c. The outflows are further evolved to days timescale using 2D ray-by-ray radiation-hydrodynamics simulations that include an online nuclear network. We find complete r-process yields and identify the production of 56 Ni and the subsequent decay chain to 56 Co and 56 Fe. Synthetic kilonova light curves predict an extended (near-) infrared peak a few days postmerger originating from r-process in the neutron-rich/high-opacity ejecta and UV/optical peaks at a few hours (ten minutes) postmerger originating from weak r-process (free-neutron decay) in the faster ejecta components. Additionally, the fast tail of tidal origin generates kilonova afterglows potentially detectable in radio and X band on a few to ten years time scale. Quantitative effects originating from the tidal disruption merger dynamics are reflected in the multimessenger emissions.

abundances↗
DOE OSTI2020

Gravitational-wave signal of a core-collapse supernova explosion of a 15M ⊙ star

In this paper we report on the gravitational-wave signal computed in the context of a three-dimensional simulation of a core-collapse supernova explosion of a 15 M ⊙ star. The simulation was performed with our neutrino hydrodynamics code chimera . We detail the gravitational wave strains as a function of time, for both polarizations, and discuss their physical origins. We also present the corresponding spectral signatures. Gravitational wave emission in our model has two key features: low-frequency emission (less than 200 Hz) emanates from the gain layer as a result of neutrino-driven convection and the standing accretion shock instability (SASI), and high-frequency emission (greater than 600 Hz) emanates from the proto–neutron star due to Ledoux convection within it. The high-frequency emission dominates the gravitational wave emission in our model and emanates largely from the convective layer itself, not from the convectively stable layer above it, due to convective overshoot. Moreover, the low-frequency emission emanates from the gain layer itself, not from the proto–neutron star, due to accretion onto it. We provide evidence of the SASI in our model and demonstrate that the peak of our low-frequency gravitational wave emission spectrum corresponds to it. Given its origin in the gain layer, we classify the SASI emission in our model as p-mode emission and assign a purely acoustic origin, not a vortical–acoustic origin, to it. We compare the results of our three-dimensional model analysis with those obtained from the model’s two-dimensional counterpart and find a significant reduction in the strain amplitudes in the former case, as well as significant reductions in all related quantities. Our dominant proto–neutron star gravitational wave emission is not well characterized by emission from surface g modes, complicating the relationship between peak frequencies observed and the mass and radius of the proto–neutron star expressed by analytic estimates under the assumption of surface g-mode emission. We present our frequency normalized characteristic strain along with the sensitivity curves of current- and next-generation gravitational wave detectors. This simple analysis indicates that the spectrum of gravitational wave emission between approximately 20 Hz and approximately 1 kHz, stemming from neutrino-driven convection, the SASI, accretion onto the proto–neutron star, and proto–neutron star convection, will be accessible for a Galactic event.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Revisiting the dark matter interpretation of excess rates in semiconductors

In light of recent results from low-threshold dark matter detectors, we revisit the possibility of a common dark matter origin for multiple excesses across numerous direct detection experiments, with a focus on the excess rates in semiconductor detectors. We explore the interpretation of the low-threshold calorimetric excess rates above 40 eV in the silicon SuperCDMS Cryogenic Phonon Detector and above 100 eV in the germanium EDELWEISS Surface detector as arising from a common but unknown origin, and demonstrate a compatible fit for the observed energy spectra in both experiments, which follow a power law of index α = 3.4 3 - 0.06 + 0.11 . Despite the intriguing scaling of the normalization of these two excess rates with approximately the square of the mass number A 2 , we argue that the possibility of common origin by dark matter scattering via nuclear recoils is strongly disfavored, even allowing for exotic condensed matter effects in an as-yet unmeasured kinematic regime, due to the unphysically large dark matter velocity required to give comparable rates in the different energy ranges of the silicon and germanium excesses. We also investigate the possibility of inelastic nuclear scattering by cosmic ray neutrons, solar neutrinos, and photons as the origin, and quantitatively disfavor all three based on known fluxes of particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Accelerating accurate simulations of calorimeter showers with normalizing flows and probability density distillation

Recently, we introduced caloflow, a high-fidelity generative model for GEANT4 calorimeter shower emulation based on normalizing flows. Here, we present caloflow v2, an improvement on our original framework that speeds up shower generation by a further factor of 500 relative to the original. The improvement is based on a technique called probability density distillation, originally developed for speech synthesis in the machine learning literature, and which we develop further by introducing a set of powerful new loss terms. We demonstrate that caloflow v2 preserves the same high fidelity as the original using qualitative (average images, histograms of high-level features) and quantitative (classifier metric between geant4 and generated samples) measures. The result is a generative model for calorimeter showers that matches the state of the art in speed (a factor of 10 4 faster than GEANT4) and greatly surpasses the previous state of the art in fidelity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

A Modified Sequence-to-point HVAC Load Disaggregation Algorithm

This paper presents a modified sequence-to-point (S2P) algorithm for disaggregating the heat, ventilation, and air conditioning (HVAC) load from the total building electricity consumption. The original S2P model is convolutional neural network (CNN) based, which uses load profiles as inputs. We propose three modifications. First, the input convolution layer is changed from 1D to 2D so that normalized temperature profiles are also used inputs to the S2P model. Second, a drop-out layer is added to improve adaptability and generalizability so that the model trained in one area can be transferred to other geographical areas without labelled HVAC data. Third, a fine-tuning process is proposed for areas with a small amount of labelled HVAC data so that the pre-trained S2P model can be fine-tuned to achieve higher disaggregation accuracy (i.e., better transferability) in other areas. The model is first trained and tested using smart meter and sub-metered HVAC data collected in Austin, Texas. Then, the trained model is tested on two other areas: Boulder, Colorado and San Diego, California. Simulation results show that the proposed modified S2P algorithm outperforms the original S2P model and the support-vector machine based approach in accuracy, adaptability, and transferability.

Ye, Kai↗
DOE OSTI2024

Sensitivity of modelled passive margin stratigraphy to variations in sea level, sediment supply and subsidence

Abstract We produced a 10 Myr synthetic stratigraphic section using a forward stratigraphic model that generates marine deltaic stratigraphy over geological timescales. We recursively fit the model using a Bayesian inversion algorithm to test: (1) if it could be accurately reconstructed; (2) if the parameters used to create it could be recovered; and (3) the sensitivity of the model output to given model parameters and the attendant physical processes. The original synthetic stratigraphic section was produced with cyclical sea‐level variations of 40 and 30 m with 2.4 and 10 Myr periods respectively. Sediment was also supplied cyclically, in 2.4 and 10 Myr cycles with amplitudes of 30 and 80 tons/100 kyr, respectively, varying from a mean of 232 tons/100 kyr. Parameter values were sampled to fit the model using a Markov chain Monte Carlo algorithm, resulting in a ±5 m (1σ) variation between the experimental output and the original. Sea level varied by ±7 m (1σ) within the posterior distribution of parameters. As a result, both the 10 Myr and 2.4 Myr sea‐level cycles could be extracted from the original output. The variation in sediment supply was approximately ±38 tons/100 kyr (1σ) and, as a result, only the larger long‐term supply variations could be accurately recovered in refitting the model. The variation in thermal, flexural and total subsidence across those parameter sets is less than ±10 m (1σ). The original section experienced 150 m of total subsidence at the depocentre. Our results demonstrate the distinct and interpretable imprint of sea level and subsidence on continental margin stratigraphy can be quantified. Moreover, we conclude that sea‐level change produces a defined effect on the geometries of stratigraphic architecture, and that techniques applied for the purpose of delineating sea‐level variation from continental margin strata have a well‐founded conceptual basis.

Schmelz, William J.↗
DOE OSTI2021

Direct evidence for eoarchean iron metabolism?

Metasedimentary rocks from Isua, West Greenland (> 3,700 million years old) contain carbonaceous compounds, compatible with a biogenic origin. The metamorphic mineral assemblage with garnet and quartz intergrowths contains layers of carbonaceous inclusions contiguous with carbon–rich sedimentary beds in the host rock. Previous studies on Isua rocks focused on testing the biogenic origin of the carbonaceous material, but here we searched for evidence which could provide new insights into the nature of the life that generated this carbonaceous material. We studied material trapped in inclusions armoured within quartz grains inside garnet porphyroblasts by non–destructive ptychographic X–ray nanotomography (PXCT). The 3D electron density maps generated by PXCT were correlated with maps from X–ray fluorescence tomography and micro–Raman spectroscopy. We found that the material trapped inside inclusions in the quartz grains consist of disordered carbon material encasing domains of iron–rich carbonaceous material. These results corroborate earlier claims for biogenic origins and are compatible with relics of metamorphosed biological material originally containing high iron/carbon ratios, comparable to ratios found in most extant organisms. Finally, these iron–rich domains represent the oldest evidence for organic iron complexes in the geologic record and are consistent with Fe–isotopic evidence for metabolic iron fractionation in > 3,700 Ma Isua banded iron formation.

58 GEOSCIENCES↗
DOE OSTI2022

Transmission of Human Influenza A Virus in Pigs Selects for Adaptive Mutations on the HA Gene

Influenza A viruses (FLUAV) cause respiratory diseases in many host species, including humans and pigs. The spillover of FLUAV between swine and humans has been a concern for both public health and the swine industry. With the emergence of the triple reassortant internal gene (TRIG) constellation, establishment of human-origin FLUAVs in pigs has become more common, leading to increased viral diversity. However, little is known about the adaptation processes that are needed for a human-origin FLUAV to transmit and become established in pigs. Here, we generated a reassortant FLUAV (VIC11pTRIG) containing surface gene segments from a human FLUAV strain and internal gene segments from the 2009 pandemic and TRIG FLUAV lineages and demonstrated that it can replicate and transmit in pigs. Sequencing and variant analysis identified three mutants that emerged during replication in pigs, which were mapped near the receptor binding site of the hemagglutinin (HA). The variants replicated more efficiently in differentiated swine tracheal cells compared to the virus containing the wildtype human-origin HA, and one of them was present in all contact pigs. These results show that variants are selected quickly after replication of human-origin HA in pigs, leading to improved fitness in the swine host, likely contributing to transmission.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Characterization of a 2016-2017 Human Seasonal H3 Influenza A Virus Spillover Now Endemic to U.S. Swine

In 2017, the Iowa State University Veterinary Diagnostic Laboratory detected a reverse-zoonotic transmission of a human seasonal H3 influenza A virus into swine (IAV-S) in Oklahoma. Pairwise comparison between the recently characterized human seasonal H3 IAV-S (H3.2010.2) hemagglutinin (HA) sequences detected in swine and the most similar 2016–2017 human seasonal H3 revealed 99.9% nucleotide identity. To elucidate the origin of H3.2010.2 IAV-S, 45 HA and 27 neuraminidase (NA) sequences from 2017 to 2020 as well as 11 whole-genome sequences (WGS) were genetically characterized. Time to most recent common human ancestor was estimated between August and September 2016. The N2 NA was of human origin in all but one strain from diagnostic submissions with NA sequences, and the internal gene segments from WGS consisted of matrix genes originating from the 2009 pandemic H1N1 and another 5 internal genes of triple reassortant swine origin (TTTTPT). Pigs experimentally infected with H3.2010.2 demonstrated efficient nasal shedding and replication in the lungs, mild pneumonia, and minimal microscopic lung lesions and transmitted the virus to indirect contact swine. Antigenically, H3.2010.2 viruses were closer to a human seasonal vaccine strain, A/Hong Kong/4801/2014, than to the H3.2010.1 human seasonal H3 viruses detected in swine in 2012. This was the second sustained transmission of a human seasonal IAV into swine from the 2010 decade after H3.2010.1. Monitoring the spillover and detection of novel IAV from humans to swine may help vaccine antigen selection and could impact pandemic preparedness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

OptiMX

OptiMX is a GUI-oriented program with principal aim to be an easy to use, yet comprehensive, interactive accelerator optics design and analysis tool. It was originally developed starting in the 1990s as an MS Windows centric application using the commercial Borland OWL framework. In the spring of 2014, a decision was made to port OptiM to Qt, a modern, portable and open framework. As much as possible, the original interface was preserved.While a significant amount of refactoring was required, the underlying physics has been for the most, left unchanged. The custom plots of the original application have been replaced with functional equivalents based on a stable and well-established library (qwt). With very few minor exceptions the new refactored OptiMX should be a drop-in replacement for the original OWL version.

Lebedev, ValeriA. [Joint Inst. for Nuclear Researc↗
DOE OSTI2020

An Overview of the State-of-the-Art Reactor Consequence Uncertainty Assessment Accident Progression Insights

The U.S. Nuclear Regulatory Commission (NRC) with Sandia National Laboratories (Sandia) have completed three uncertainty analyses (UAs) as part of the State-of-the-Art Reactor Consequence Analyses (SOARCA) program. The SOARCA UAs included an integrated evaluation of uncertainty in accident progression, radiological release, and offsite health consequence projections. The UA for Peach Bottom, a boiling-water reactor (BWR) with a Mark I containment located in the State of Pennsylvania, analyzed the unmitigated long-term station blackout SOARCA scenario. The UA for Sequoyah, a 4-loop Westinghouse pressurized-water reactor (PWR) located in the State of Tennessee, analyzed the unmitigated short-term station blackout SOARCA scenario, with a focus on issues unique to the ice condenser containment and the potential for early containment failure due to hydrogen deflagration. The UA for Surry, a 3-loop Westinghouse PWR with a sub-atmospheric large dry containment located in the State of Virginia, analyzed the unmitigated short-term station blackout SOARCA scenario including the potential for thermally-induced steam-generator tube rupture. These three UAs are currently documented in three NUREG/CR reports. This report provides input to planned NRC documentation on the insights and findings from the SOARCA UA program. The purpose of the summary report is to provide a useful reference for regulatory applications that require the evaluation of offsite consequence risk from beyond design basis event severe accidents. This report focuses on the accident progression and source term insights developed from the MELCOR analyses. MELCOR is the NRC's best-estimate, severe accident computer code used in the SOARCA UAs. In anticipation of the SOARCA UA insights work, NRC and Sandia benchmarked the response of the Peach Bottom model to selected reference calculations from the Peach Bottom SOARCA UA. Peach Bottom was the first SOARCA UA performed and was completed in 2015 using the MELCOR 1.8.6 code. The PWR SOARCA UAs evolved the original methodology and utilized the updated MELCOR 2.2 computer code. The Peach Bottom model has been systematically updated for other NRC research efforts and has been updated to MELCOR 2.2. computer code. The findings from the new reference calculations using the updated model with the MELCOR 2.2 code are also integrated into the report. A second objective is an assessment of the applicability of the results to the other nuclear reactors in the U.S. As the key findings are reviewed, judgments are presented on the applicability of the results to other U.S. nuclear power plants. An important objective of the SOARCA program relied on high- fidelity plant-specific modeling. However, the nature of the insights and conclusions allowed judgements to be made on the applicability of the various insights to the same general classification of plant (i.e., BWR or PWR) or the entire fleet of plants. Finally, the results from the SOARCA UA accident progression calculations contain a wealth of information not previously documented in the NUREG/CRs. This report includes new but related information that can be used to benchmark past or support future regulatory decisions related to severe accidents. The new work includes a benchmark of the NUREG-1465 licensing source term definitions, the variability of key accident progression events and timing to radionuclide release, and an improved understanding of the timing and source terms from consequential steam generator tube ruptures. iii ACKNOWLEDGEMENTS The Sandia authors gratefully acknowledge the significant technical and programmatic contributions from the NRC SOARCA team which are reflected throughout the report. Dr. Tina Ghosh has been involved throughout the SOARCA UAs, providing the primary managerial and technical oversight. The long lists of NRC and Sandia contributors from the SOARCA UAs are cited in the three NUREG/CRs and are also gratefully acknowledged by the small team of authors compiling the results of their efforts. Significant technical contributions, advice, and reviews were provided by Dr. Hossein Esmaili, Dr. Alfred Hathaway, and Dr. Edward Fuller (retired) of the NRC. Dr. Randal Gauntt (retired), Mr. Patrick Mattie, Mr. Joseph Jones (retired), and Dr. Doug Osborn from Sandia are recognized as the SOARCA UA managers guiding the past efforts. There is a comparable list of project managers at the NRC including Ms. Patricia Santiago, Dr. Salman Haq, and Mr. Jon Barr. Sadly, we have lost Mr. Charlie Tinkler and Mr. Robert Prato, who were important contributors to the original SOARCA project. Finally, Mr. Kyle Ross and Mr. Mark Leonard have also retired but were significant technical contributors. Mr. Kyle Ross was the technical lead on all three SOARCA UAs and the original pressurized water reactor SOARCA study. Mr. Leonard was the technical lead on the original boiling water reactor SOARCA study and a key contributor to the first Peach Bottom SOARCA UA. iv

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Construction Support for New Slab Creek Powerhouse Project (Final Technical Report)

The Sacramento Municipal Utility District (SMUD) has constructed a new powerhouse and Boating Flow Release Facility (BFRF) ¼ mile downstream of the existing Slab Creek Dam with the assistance of grant funding from the Department of Energy in the amount of $1.5 million. Slab Creek Dam impounds 16,600 acre-feet of storage and has a normal full pool elevation of 1850ft. Water is conveyed from Slab Creek Reservoir through a 4.9 mile power tunnel to the 224 MW White Rock Powerhouse which discharges into Chili Bar Reservoir. A small 450 kW powerhouse located at Slab Creek Dam utilizes the original license in-stream flow requirement. The new license (FERC Project No. 2101-084) requires significantly more instream flows immediately below the dam for aquatic preservation and recreational flows over the original license. The terms of the new license allow the Slab Creek Powerhouse to utilize the original required dam releases, while the new South Fork Powerhouse will use the new instream flow requirements above the original license requirement. The South Fork Powerhouse routes flows back to the South Fork of the American River via a new penstock that is tied into the White Rock Tunnel at Adit #3. This new penstock bifurcates at the Adit #3 portal with one leg going to the BFRF and the other to the new powerhouse. The South Fork Powerhouse is a single generating unit with a capacity of 2.98 kVA. The BFRF is valve house with an energy dissipation chamber for a 60” fixed cone valve capable of passing 1,300 cfs for meeting the recreational flow requirements of the license.

power tunnel↗
DOE OSTI2024

Building a framework to genetically characterize “feather spots” and understand demographic impacts of solar energy sites on migratory bird populations

The lack of data on the impact of utility-scale solar facilities on avian species and populations adds to the cost of siting and operation. As much as 32 percent of the avian biological material (feathers and carcasses) recovered from solar facilities remain unidentified, because they often take the form of “feather spots”. Feather spots are remains of impacted animals that can be separated into two broad categories: 1) those remains that may be visually identified to a species, or 2) those that cannot be visually identified to a species due to degradation from the environment and/or scavenger activity (listed as “unknown”). Even when feather spots can be identified to species, they cannot be visually assigned to particular breeding populations. In some cases, it is unknown whether multiple feather spots represent single or multiple individuals. This project’s objectives were to: 1. Use a developed, genetic-based technique to identify and determine the species, population of origin, and number of individuals found in feather spots recovered from solar facilities. 2. Implement collected data and resulting analyses to develop a publicly accessible web-based decision-making tool that can be used by the solar industry, regulators and other stakeholders to inform siting, mitigation, and conservation management efforts. 3. Establish a not-for-profit fee-for-service center at UCLA to ensure collection and identification of feather spots continue after the project period of performance. During the Project Period, we proposed to establish a pipeline for collecting, transporting, and storing of avian biological material collected at solar facilities and the collection and identification of feather spots to species and individual. We proposed the development of a genetic-based framework that would recover viable DNA from feather spots, amplify this DNA (i.e., make millions of copies of the original DNA), and use it to match the resulting sequences to a national database of known species of birds. The result would be the identification of feathers spots that were previously unidentified, and the incorporation of these samples into a larger database that included all samples recovered from solar facilities. The resulting report (below) details the result of this work and its alignment with proposed activities. We proposed the use of the data collected to assess the comparative risk to specific species or populations of species from solar facilities. For some species, we have already identified genomic markers of specific breeding populations and developed “genoscapes,” maps of unique genetic variation across the full breeding range of a species. We used these (previously and newly developed) genoscapes to probabilistically link a feather spot to the specific breeding populations from which it originated (assignment probabilities range from 75%-100% depending on species and population groups). For those species without genoscapes, we developed a vulnerability and susceptibility estimate that determines the relative local and regional risk to populations that are in geographic proximity to solar facilities, using citizen science data (Breeding Bird Survey (BBS) and eBird). These two feather spot processing pipelines (see Figure 1 below) provide quantitative estimates as to the numbers of individuals from a given population of origin that are affected by solar facilities, and ultimately can reduce costs to the consumer by reducing the industry costs associated with mitigation and siting strategies for future solar energy development.

14 SOLAR ENERGY↗
DOE OSTI2025

Data Qualification Report: SRNL Glass Composition-Properties (ComPro) Database

The Savannah River National Laboratory Glass Composition-Properties (ComPro) database is an extensive database containing pertinent composition and durability data to support the accelerated clean-up mission at the Defense Waste Processing Facility. The activities described in this data qualification report were performed to support the information contained in the database. There were two objectives of the original data qualification process. The first objective was to review supporting documentation to determine if DOE/RW-0333P Quality Assurance Requirements and Description had been implemented during the original work. If the DOE/RW-0333P Quality Assurance Requirements and Description had not been directly implemented during the original work, the second objective was to determine if the controls that were used were adequate to meet the intent of the DOE/RW-0333P Quality Assurance Requirements and Description. The results of these two objectives and the activities performed to support these decisions are described in this document. An assessment of each dataset was made to determine if the data were RW-0333P Compliant, RW-0333P Equivalent or Non-RW-0333P Compliant. The original data qualification was performed in accordance with E7, Conduct of Engineering Manual, Procedure 3.70, Revision 4, Qualification of Data. The specific method that was used was Equivalent Controls as described in E7, 3.70. Revision 2 of this document adds supporting information for the RW-0333P Compliant datasets added to Revision 3 of the database.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗
DOE OSTI2020

Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae)

Polyploidy is an important evolutionary mechanism and is prevalent among land plants. Most polyploid species examined have multiple origins, which provide genetic diversity and may enhance the success of polyploids. In some polyploids, recurrent origins can result from reciprocal crosses between the same diploid progenitors. Although great progress has been made in understanding the genetic consequences of polyploidy, the genetic implications of reciprocal polyploidization remain poorly understood, especially in natural polyploids. Tragopogon (Asteraceae) has become an evolutionary model system for studies of recent and recurrent polyploidy. Allotetraploid T. miscellus has formed reciprocally in nature with resultant distinctive floral and inflorescence morphologies (i.e., short- vs. long-liguled forms). In this study, we performed comparative inflorescence transcriptome analyses of reciprocally formed T. miscellus and its diploid parents, T. dubius and T. pratensis. In both forms of T. miscellus, homeolog expression of ~70% of the loci showed vertical transmission of the parental expression patterns (i.e., parental legacy), and ~20% of the loci showed biased homeolog expression, which was unbalanced toward T. pratensis. However, 17.9% of orthologous pairs showed different homeolog expression patterns between the two forms of T. miscellus. No clear effect of cytonuclear interaction on biased expression of the maternal homeolog was found. In terms of the total expression level of the homeologs studied, 22.6% and 16.2% of the loci displayed non-additive expression in short- and long-liguled T. miscellus, respectively. Unbalanced expression level dominance toward T. pratensis was observed in both forms of T. miscellus. Significantly, genes annotated as being involved in pectin catabolic processes were highly expressed in long-liguled T. miscellus relative to the short-liguled form, and the majority of these differentially expressed genes were transgressively down-regulated in short-liguled T. miscellus. Given the known role of these genes in cell expansion, they may play a role in the differing floral and inflorescence morphologies of the two forms. In summary, the overall inflorescence transcriptome profiles are highly similar between reciprocal origins of T. miscellus. However, the dynamic homeolog-specific expression and non-additive expression patterns observed in T. miscellus emphasize the importance of reciprocal origins in promoting the genetic diversity of polyploids.

54 ENVIRONMENTAL SCIENCES↗