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At least 937 records · Page 52

Multiplexed binary assembly and quantitative tracking of bacterial populations

Compositions and methods for tracking combinations of mutations in populations by coupling DNA assembly and paired-end sequencing technology with high-throughput sequencing. This allows for an unlimited number of mutation sites in a population of microorganisms to be identified, and allows sites to be sequenced across several replicates. Unique identifiers (DNA barcodes) can be used to measure fitness data by sequencing of the barcodes multiplexed with the mutation sites with high-throughput short sequencing read technology, allowing selections to be rapidly performed on populations of known combinatorial genotypes.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of Polyethylene and Blank Pulsed Sphere Experiments Using Deuteron Transport Feature in COG

From the late 1960s to about 1985, LLNL undertook a series of ‘pulsed sphere’ experiments for 31 materials involving 148 different experiments using 75 different spheres. The purpose was to measure the neutron leakage spectra for different materials from 14-MeV neutrons generated by 3 H(d,n) 4 He reactions induced by an incident D+ beam from the Insulated Core Transfer (ICT) accelerator at LLNL. This deuteron beam was focused to impinge upon tritium loaded onto a titanium substrate within a low mass target assembly placed within the center of a spherical shell constructed from the material of interest. COG is a three-dimensional, continuous energy, Monte Carlo code, developed by Lawrence Livermore National Laboratory (LLNL). Recent additions to COG include alpha and deuteron particle transport in order to directly calculate (α,n) and 3 H(d,n) 4 He reactions, and resulting neutron emission spectra. Results of the direct deuteron transport calculation for the 0.8 MFP (mean free path) polyethylene sphere with PILOT B detector was previously published. The purpose of this paper is to present expanded COG results showing the neutron peak from deuterium buildup ( 2 H(d,n) 3 He) due to tritium decay in the target. Cross section data libraries used are ENDF/B-VIII.0 for neutrons and ENDF/B-VII.1 for deuterons, respectively.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Conceptual design of the modular detector and readout system for the CMB-S4 survey experiment

We present the conceptual design of the modular detector and readout system for the Cosmic Microwave Background – Stage four (CMB-S4) ground-based survey experiment. CMB-S4 will map the cosmic microwave background (CMB) and the millimeter-wave sky to unprecedented sensitivity, using 500,000 superconducting detectors observing from Chile and Antarctica to map over 60% of the sky. The fundamental building block of the detector and readout system is a detector module package operated at 100 mK, which is connected to a readout and amplification chain that carries signals out to room temperature. It uses arrays of feedhorn-coupled orthomode transducers (OMT) that collect optical power from the sky onto dc-voltage-biased transition-edge sensor (TES) bolometers. The resulting current signal in the TESs is then amplified by a two-stage cryogenic Superconducting Quantum Interference Device (SQUID) system with a time-division multiplexer to reduce wire count, and matching room-temperature electronics to condition and transmit signals to the data acquisition system. Sensitivity and systematics requirements are being developed for the detector and readout system over wide range of observing bands (20 to 300 GHz) and optical powers to accomplish CMB-S4’s science goals. While the design incorporates the successes of previous generations of CMB instruments, CMB-S4 requires an order of magnitude more detectors than any prior experiment. This requires fabrication of complex superconducting circuits on over 10 m2 of silicon, as well as significant amounts of precision wiring, assembly and cryogenic testing

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (June 2018)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken June 2018 at two locations (OBJ1 and OBJ2) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 50 to 150 cm depth below surface at discrete depths every 20 cm for microbial analyses. A total of 12 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (GOLD) sequencing project: Gs0142591. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 1233 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (June to October 2019)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken at three time points from June 12, 2019 to October 23,2019 at a location (PTT1) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Sediment samples were collected from 60 to 180 cm below surface every 30cm for microbial analyses through metagenomic sequencing. 15 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0131241. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 780 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. A sample metadata file (samples.csv) that contains site information has also been included.

54 ENVIRONMENTAL SCIENCES↗

ROADRUNNER MiniFuel Experiment: Irradiation Target Design and Sample Characterization

High-density uranium nitride (UN) is a fuel candidate for several advanced nuclear reactor designs currently under development. Because there are limited UN performance data relative to fuel fabrication impurity and density variation, an irradiation campaign has been developed as part of a collaborative effort among the University of Texas at San Antonio (UTSA), Westinghouse Electric Company, Oak Ridge National Laboratory (ORNL), and Los Alamos National Laboratory (LANL) under the Nuclear Science User Facilities program. This project, entitled ROADRUNNER, or Research On ADvancing the peRformance of UraNium Nitrides in Extreme enviRonments, aimsto support UN fuel qualification for advanced reactors by investigating the impact of density and impurity variations on UN performance as a function of irradiation temperature and burnup. The MiniFuel experiment vehicle developed by ORNL, which leverages the High Flux Isotope Reactor, was selected to perform this accelerated separate-effects irradiation testing. The experiment test matrix consists of six MiniFuel targets containing miniature UN fuel disks, and targets three distinct burnup levels (37.5, 60, and 75 MWd/kg U) and three distinct temperatures (600, 900, and 1200°C). Neutronics and thermal analyses were performed to determine the experimental parameters needed to meet the desired irradiation conditions and to predict the experiment components temperatures. UN pellets were fabricated at LANL with tightly controlled parameters to produce specimens with three distinct densities and three levels of carbon content. The pellets were then thinned down by UTSA to the experiment-required thickness. The pre-characterization of the specimens includes density measurements, carbon and oxygen contents, microstructure analysis, and x-ray computed tomography. The selected specimens will be assembled into the MiniFuel experiment, and the first ROADRUNNER MiniFuel targets are intended for HFIR insertion during the Fall of 2024. After irradiation, the targets will be shipped to ORNL’s hot cell facility for disassembly. The post-irradiation examination on the fuel specimens includes fission gas release measurements, visual inspection, fuel swelling measurements, gamma spectroscopy, and microstructure analysis. The data collected post-irradiation will be used to develop fuel performance models.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair

Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC’s assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD’s DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC’s dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5' ssDNA, exposing XPA’s crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.

60 APPLIED LIFE SCIENCES↗

In situ chamber for studying battery failure using high-speed synchrotron radiography

The investigation of lithium-ion battery failures is a major challenge for personnel and equipment due to the associated hazards (thermal reaction, toxic gases and explosions). To perform such experiments safely, a battery abuse-test chamber has been developed and installed at the microtomography beamline ID19 of the European Synchrotron Radiation Facility (ESRF). The chamber provides the capability to robustly perform in situ abuse tests through the heat-resistant and gas-tight design for flexible battery geometries and configurations, including single-cell and multi-cell assemblies. High-speed X-ray imaging can be complemented by supplementary equipment, including additional probes (voltage, pressure and temperature) and thermal imaging. Together with the test chamber, a synchronization graphical user interface was developed, which allows an initial interpretation by time-synchronous visualization of the acquired data. Enabled by this setup, new meaningful insights can be gained into the internal processes of a thermal runaway of current and future energy-storage devices such as lithium-ion cells.

25 ENERGY STORAGE↗

FATES crown damage simulation outputs 2022

This dataset contains outputs from the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) and accompanies the paper "Needham, J.F., Arellano, A., Davies, S.J., Fisher, R.A., Hammer, V., Knox, R., Mitre, D., Muller-Landau, H.C., Zuleta, D., Koven, C.D. Tree crown damage and its effects on forest carbon cycling in a tropical forest, 2022, Global Change Biology". Data are unprocessed netcdf file outputs from simulations that were run to test the effect of a new crown damage module in FATES. Specifically, this data package contains a sensitivity analysis to the carbon cushion parameter damage_Ccushion_ensemble_e1b5bd9_bf013ef_2021-09-02.h0.ensemble.sofar.nc, a sensitivity analysis to the root nitrogen stoichiometry parameter damage_Nstoich_ensemble_e1b5bd9_bf013ef_2021-09-02.h0.ensemble.sofar.nc, a sensitivity analysis to parameters controlling crown damage and recovery damage_recovery_ensemble_e1b5bd9_354f0b0_2021-09-02.h0.ensemble.sofar.nc, and a sensitivity analysis to the number of crown damage bins elm_fates_bci_*_damagebins.Eac53ccb80b-F8f994c29.2022-04-19.elm.h0.fullrun.nc. This data package also contains a high root nitrogen configuration of FATES, including both a control, and a crown damage simulation high_root_N_control_e1b5bd9_354f0b0_2021-09-02.clm2.h0.fullrun.nc and high_root_N_damage_e1b5bd9_354f0b0_2021-09-02.clm2.h0.fullrun.nc. There is an analogous low root nitrogen configuration of FATES, including a control, low_root_N_control_e1b5bd9_bf013ef_2021-09-02.clm2.h0.fullrun.nc a damage only simulation low_root_N_damageonly_e1b5bd9_bf013ef_2021-09-02.clm2.h0.fullrun.nc, a damage plus mortality simulation low_root_N_damage_mort_e1b5bd9_bf013ef_2021-09-02.clm2.h0.fullrun.nc, and a mortality only simulation low_root_N_mort_only_e1b5bd9_ef845c8_2021-09-02.clm2.h0.fullrun.nc. Finally, there is a two PFT simulation in which we test the effect of recovery on competitive dynamics, low_root_N_damage_two_pfts_stoichastic_e1b5bd9_bf013ef_2021-09-10.clm2.h0.fullrun.nc. These simulations test the effect of representing crown damage in FATES, compared with simulations that have an equivalent increase in mortality. Jupyter notebooks to analyse these files can be found at https://github.com/JessicaNeedham/Needham_etal_GCB_2022_FATES_crown_damage.

54 ENVIRONMENTAL SCIENCES↗

Magnetic Field Vector Measurements Using Doppler-Free Saturation Spectroscopy

Experimentally measuring the magnetic-field vector topology in low-cost fusion-concept devices will provide critical information required to optimize and accelerate the development of those concepts for economical fusion energy. The magnetic-field measurement techniques most commonly used in modern tokamaks, i.e., beam-emission spectroscopy and optical emission spectroscopy, are not suitable below 5000 Gauss due to a lack of sensitivity. To diagnose magnetic field relevant to some of the ARPA-E-supported fusion concepts (50 to 1000 Gauss), a novel approach is required. Doppler-free saturation spectroscopy (DFSS) is a pump/probe laser-based technique and has been successfully demonstrated in the laboratory to provide a magnetic-field measurement accuracy of <10 Gauss. DFSS is implemented to obtain ultra-high-resolution spectra at a localized point in space. The spectral data is then fit to the Schrödinger equation for determination of the magnetic-field vector. To obtain the magnetic-field topology, the measurement spatial location is scanned over the desired region of space by steering the DFSS pump laser beam. The goal of this project is to assemble and commission a portable DFSS diagnostic capable of 2-D magnetic-field vector measurements utilizing the Hα spectral line profile.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Formatting and V&V of Consistent 238,240−24 2Pu $\overline{v}_p$ Evaluated Mean Values and Covariances

This report is in answer to the Nuclear Criticality Safety Program FY24 quarter 4 milestone that requires: “Format and V&V nu-bar means and covariances” for 238,240-242 Pu average prompt fission neutron multiplicities, $\overline{ν}$ p , that were obtained by a consistent evaluation leveraging the fission-event generator CGMF and a detailed uncertainty quantification of experimental data. It is described how nuclear data mean values and covariances were formatted using ENDFtk. Implementing the new 238,240-242 Pu $\overline{ν}$ p into the ENDF/B-VIII.1β 4 library leads to only small overall changes in criticality values of the Jezebel, Dirty Jezebel, Jupiter-001, Jupiter-002, EUCLID 3x2 and EUCLID 8x1 critical assemblies. Simulated k eff uncertainties due to $\overline{ν}$ p covariances change only little if cross-isotope covariances are considered or not for those assemblies with low percentage content of minor Pu isotopes. However, for the Dirty Jezebel critical assembly, that has a sizeable 240 Pu and non-negligible 241 Pu content, the simulated k eff uncertainties due to considering or neglecting cross-isotope $\overline{ν}$ p covariances is 443 versus 374 pcm.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Effect of stereochemistry on nanoscale assembly of ABA triblock copolymers with crystallizable blocks

We report on the nanoscale assembly of poly(lactic acid)-b-poly(ethylene oxide)-b-poly(lactic acid) (PLA-PEO-PLA) triblock copolymers in water, focusing on the effect of stereochemistry, where the PLA blocks are statistical copolymers of l-lactide and d-lactide with l/d ratios of 100/0, 95/5, 90/10, 85/15, 75/25, and 50/50. Small-angle neutron scattering (SANS) shows a nearly constant d-spacing as concentration varies in triblock systems with l/d ratios of 90/10 and 95/5, which we attribute to inhomogeneity in the structure of these gels, supported by previous USANS and confocal microscopy studies. The SANS data fit well to a core-shell ellipsoid form factor model with a hard-sphere structure factor. Polymeric micelles with l/d ratios from 75/25 to 85/15 displayed very high aggregation numbers, consistent with a strong interaction between PLA chains and the enhanced storage modulus observed in rheological studies of these systems. While the 90/10 and 95/5 samples showed lower aggregation numbers, their SANS profiles shows close spacing between micelles, which may promote a high fraction of intermicellar bridging chains, also consistent with a higher storage modulus. Overall, these results provide insight into the micellar assembly behavior of block copolymers with a crystallizable block, and indicate that tuning stereochemistry of PLA-based block copolymers is an effective means of modifying micellar properties for specific applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken September 2019 at one locations (OBJ1) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 50 to 150 cm depth below surface at discrete depths every 20 cm for microbial analyses. A total of 6 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (GOLD) sequencing project: Gs0142591. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 2562 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes. Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla. We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.

54 ENVIRONMENTAL SCIENCES↗

Proposed Updates to Pu Evaluation for ENDF/B-VIII.0β 2 [Slides]

This presentation shows current status of in ENDF/B-VIII.0 and ENDF/B-VIII.0β 1 Pu evaluations. With a focus on the Pu thermal solutions (PST) and sanity check on fast metal assemblies (PMF). Pu ENDFβ 1 file in the low-energy region included updates in RRR (up to 2.5 keV), TNC and PFNS. Discussed are improvements over ENDF/B-VIII.0 in the C/E benchmarks (PST 81 cases) with preliminary ν p and cross section covariance generation for the resolved resonance energy range up to 2.25 keV. Highlighted are proposed updates for ENDFβ 2 with an extension of the RRR evaluation up to 5 keV, inclusion of Mosby’s data including proper resolution function (thanks to Marian J.), and a particular focus on η energy dependence from thermal up to 10 eV with the impact of the capture-to-fission ratio at 0.29 eV. This presentation concludes with an updated ν p and cross section covariance generation for the resolved resonance energy range up to 5 keV. And additional validation to test performance at about 2 eV and in the keV region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The structure of the RCAN1:CN complex explains the inhibition of and substrate recruitment by calcineurin

Regulator of calcineurin 1 (RCAN1) is an endogenous inhibitor of the Ser/Thr phosphatase calcineurin (CN). It has been shown that excessive inhibition of CN is a critical factor for Down syndrome and Alzheimer’s disease. Here, we determined RCAN1’s mode of action. Using a combination of structural, biophysical, and biochemical studies, we show that RCAN1 inhibits CN via multiple routes: first, by blocking essential substrate recruitment sites and, second, by blocking the CN active site using two distinct mechanisms. We also show that phosphorylation either inhibits RCAN1-CN assembly or converts RCAN1 into a weak inhibitor, which can be reversed by CN via dephosphorylation. This highlights the interplay between posttranslational modifications in regulating CN activity. Last, this work advances our understanding of how active site inhibition of CN can be achieved in a highly specific manner. Together, these data provide the necessary road map for targeting multiple neurological disorders.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Performing k eff Validation of As-Loaded Criticality Safety Calculations Using UNF-ST&DARDS: Applicable Experiment Selection

The general method for performing validation of as loaded criticality safety calculations using UNF ST&DARDS is presented in a paper by Clarity, which includes a description of the UNF-ST&DARDS system. Proof-of-principle analyses were performed in the summer of 2019 for MPC-32 dual purpose canisters (DPCs) containing pressurized water reactor (PWR) fuel assemblies. Summaries of these results are presented in this and a companion paper for this conference. The current paper describes the TSUNAMI-IP calculations performed to select applicable experiments for validation of 11 MPC-32 DPCs. The companion paper discusses the TSUNAMI-3D calculations used to generate sensitivity data to support the experiment selections discussed here. Experiment selection is based on the sensitivity/uncertainty (S/U) methods used to validate criticality safety calculations of as-loaded DPCs containing pressurized water reactor (PWR) spent nuclear fuel (SNF). This process has been demonstrated and is summarized in this paper. The approach is similar to that used in NUREG/CR-7109, which provides an approach for validation of PWR burnup credit (BUC), including major and minor actinides and major fission products. The premise of S/U-based validation is that applicable experiments—those having a similar bias to a given application system—will have similar sensitivities for each isotope and reaction in the two systems. It is assumed that cross sections with larger uncertainties are more likely to contain data errors which contribute to the bias. The integral index c k thus propagates the system sensitivities with the nuclear covariance data to calculate a correlation coefficient representing the similarity of the two systems. In this work, a c k value of 0.8 or higher is interpreted as identifying an experiment with sufficient similarity for use in validation. This paper presents a brief summary of the characteristics of the 11 MPC-32 DPCs used in the proof of-principle analysis for as-loaded criticality safety calculation validation and an overview of the critical experiment suite with which each of these DPC models was compared. A summary and discussion of c k results is also presented, followed by conclusions and a discussion of future work to be performed for validation of UNF ST&DARDS as-loaded criticality safety calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗