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DOE OSTI2022

Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay

Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Galaxy bispectrum in the spherical Fourier-Bessel basis

The bispectrum, the three-point correlation in Fourier space, is a crucial statistic for studying many effects targeted by the next-generation galaxy surveys, such as primordial non-Gaussianity (PNG) and general relativistic (GR) effects on large scales. In this work we develop a formalism for the bispectrum in the spherical Fourier-Bessel (SFB) basis—a natural basis for computing correlation functions on the curved sky, as it diagonalizes the Laplacian operator in spherical coordinates. Working in the SFB basis allows for line-of-sight effects such as redshift space distortions and GR to be accounted for exactly, i.e., without having to resort to perturbative expansions to go beyond the plane-parallel approximation. Only analytic results for the SFB bispectrum exist in the literature given the intensive computations needed. We numerically calculate the SFB bispectrum for the first time, enabled by a few techniques: We implement a template decomposition of the redshift-space kernel Z 2 into Legendre polynomials, and separately treat the PNG and velocity-divergence terms. We derive an identity to integrate a product of three spherical harmonics connected by a Dirac delta function as a simple sum and use it to investigate the limit of a homogeneous and isotropic Universe. Furthermore, we present a formalism for convolving the signal with separable window functions and use a toy spherically symmetric window to demonstrate the computation and give insights into the properties of the observed bispectrum signal. While our implementation remains computationally challenging, it is a step toward a feasible full extraction of information on large scales via a SFB bispectrum analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Light Regulation of Phytoplankton Growth in San Francisco Bay Studied Using a 3D Sediment Transport Model

In San Francisco Bay (SFB), light availability is largely determined by the concentration of suspended particulate matter (SPM) in the water column. SPM exhibits substantial variation with time, depth, and location. To study how SPM influences light and phytoplankton growth, we coupled a sediment transport model with a hydrodynamic model and a biogeochemical model. The coupled models were used to simulate conditions for the year of 2011 with a focus on northern SFB. For comparison, two simulations were conducted with ecosystem processes driven by SPM concentrations supplied by the sediment transport model and by applying a constant SPM concentration of 20 mg l –1 . The sediment transport model successfully reproduced the general pattern of SPM variation in northern SFB, which improved the chlorophyll-a simulation resulting from the biogeochemical model, with vertically integrated primary productivity varying greatly, from 40 g[C] m –2 year –1 over shoals to 160 g[C] m –2 year –1 in the deep channel. Primary productivity in northern SFB is influenced by euphotic zone depth ( Ze ). Our results show that Ze in shallow water regions (<2 m) is mainly determined by water depth, while Ze in deep water regions is controlled by SPM concentration. As a result, Ze has low (high) values in shallow (deep) water regions. Large (small) differences in primary productivity exist between the two simulations in deep (shallow) water regions. Furthermore, we defined a new parameter F light for “averaged light limitation” in the euphotic zone. The averaged chlorophyll-a concentration in the euphotic zone and F light share a similar distribution such that both have high (low) values in shallow (deep) water regions. Our study demonstrates that light is a critical factor in regulating the phytoplankton growth in northern SFB, and a sediment transport model improves simulation of light availability in the water column.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Linking spout fluidization hydrodynamics to pyrolytic carbon deposition characteristics in a fluidized bed chemical vapor deposition reactor

Spout fluidized bed chemical vapor deposition (SFB-CVD) is the dominant method for producing pyrolytic carbon (PyC) coatings on tristructural-isotropic (TRISO) fuel particles, yet the relationship between gas injector design, fluidization hydrodynamics, and resulting coating quality remains poorly quantified. Here, in this work, three spout fluidized bed (SFB) nozzle geometries were designed and fabricated to empirically investigate how injector-driven changes in particle circulation influence PyC deposition. The geometries were first evaluated in a room temperature fluidization apparatus using time-resolved particle image velocimetry, which highlighted distinct differences in particle velocity fields, circulation pathways, and overall fluidization quality. Graphite versions of each injector geometry were subsequently implemented in a laboratory-scale SFB-CVD reactor to deposit PyC onto surrogate fuel kernels under similar conditions. Post-deposition characterization included particle morphology, coating thickness, porosity distribution, optical anisotropy, and microindentation mechanical testing. Overall, the results show clear differences in coating microstructure as a function of changing injector geometry, despite mechanical testing indicating comparable elastic modulus values across all coatings. This study provides one of the first fully experimental, quantitative mappings between SFB nozzle geometry, fluidization hydrodynamics, and resulting PyC coating structure. The framework established here supports rational injector design and offers a pathway toward improved coating control in future pilot- and production-scale TRISO fuel fabrication systems.

Coated particle fuel↗

DOE OSTI2026

Development of a coupled experimental–computational approach for engineering optimization of spout-fluidized bed particle coating systems

The design of spout-fluidized bed (SFB) coating systems for nuclear particle fuels typically relies on trial-and-error processes, comprising iterative and time-consuming coating deposition experiments and post-deposition characterization. At an engineering scale, this approach to guided SFB system design is inefficient, highlighting the need for streamlined experimental methodologies which can correlate fluidization conditions to downstream coating outcomes. In this study, we combine time-resolved particle image velocimetry (PIV) with CFD–DEM simulations to benchmark hydrodynamic behavior in a 3D spout-fluidized bed. By exploiting easily accessible optical measurements of particle motion at the bed wall and within the spouting region, we obtain quantitative velocity fields that can be directly compared with model predictions of the occluded bed region, without resorting to complex imaging and characterization techniques such as X-ray or magnetic resonance tomography. Experimental benchmarking reveals strong agreement between CFD–DEM and PIV in the spout and annulus regions, while discrepancies near the wall highlight areas for future model development. Here, the proposed integrated experimental–numerical framework will enable a direct connection between measured variables and numerically predicted fluidization performance of dense, surrogate nuclear particle fuel feedstock such that experimental SFB component design can be rapidly evaluated, informing design decisions for nozzle geometry and operating conditions. Future work will extend this framework by correlating quantified fluidization metrics across nozzle geometries and operating conditions with the resulting coating morphology, microstructure, and uniformity. Establishing these correlations will enable predictive links between hydrodynamic performance and coating quality, providing a rational, scalable basis for optimizing SFB design prior to coating deposition.

CFD/DEM↗

DOE OSTI2021

Self-Assembly of Flexible Linear–Semiflexible Bottlebrush–Flexible Linear Triblock Copolymers

Block copolymer (BCP) self-assembly is a fundamental process in which incompatible blocks spontaneously form organized microstructures with broad practical applications. Classical understanding is that the domain spacing is limited by the contour length of the polymer backbone. Here, using a combination of molecular design, chemical synthesis, small-/wide-angle X-ray scattering, transmission electron microscopy, and electron tomography, we discover that this molecular picture does not hold for architecturally semiflexible BCPs. For strongly segregated linear–semiflexible bottlebrush–linear triblock copolymers, the size of the bottlebrush domain can be twice the bottlebrush backbone contour length. The mechanism of such anomalous self-assembly is likely that the interfacial repulsion between the incompatible blocks is large enough to pull a part of the linear end blocks into the bottlebrush domain. This effectively increases the bottlebrush domain size. Moreover, the semiflexible bottlebrush widens the regime for the cylinder morphology that is associated with the volume fraction of the end blocks fC SFB ∈ (0.10, >0.41). This window is much wider than that for flexible linear BCPs, fC F ∈ (0.14, 0.35), and that predicted by the recent self-consistent field theory for linear-bottlebrush BCPs of the same chemistry and molecular architecture. Finally, our experimental findings reveal previously unrecognized mechanisms for the self-assembly of architecturally complex BCPs.

36 MATERIALS SCIENCE↗

DOE OSTI2021

(Paper) TRIPWIRE: Multi-modal Distributed Sensing For Repository Verification

Underground geological repositories for storing used nuclear fuel are being planned and developed around the world. Research is being performed to understand technical aspects of sealing entombed materials and underground repositories to ensure the radiological and nuclear materials remain contained. To support safeguards verification for these facilities research at Idaho National Laboratory (INL) is underway to develop and demonstrate a multi-modal sensor system, TRIPWIRE, for containment verification in inaccessible radiological and nuclear waste repositories. The TRIPWIRE system will continuously monitor ionizing radiation and electromagnetic fields in the vicinity of emplaced nuclear materials buried in a repository, reporting on disturbances with a real-time alarm control station. The system will use long-length scintillating fiber bundles (SFBs) to perform area radiation monitoring; these will be coupled to kilometer-scale multimodal optical communication fibers – all light sensors and electronic components used with this system will be located above ground. Electromagnetic fields, and changes in local dielectric conditions caused by intrusion and soil movement, will be monitored using commercial grade, ported "leaky" coaxial cables (PCCs), with control electronics also located above ground. Tamper-indicating self-diagnostic assessments will be done using optical and electronic time domain reflectometry in the SFBs and PCCs, respectively. The result will be a long, kilometer-scale multi-modal SFB-PCC system. Simulation and modeling are being used to inform the work and a demonstration of the system's utility is planned at a nuclear storage facility in the future.

98 - NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL↗

DOE OSTI2022

Progress of Tripwire: Multi-Modal Distributed Sensing for Repository Verification

This project is developing and demonstrating a multi-modal sensor system, TRIPWIRE, for containment verification in inaccessible radiological and nuclear waste repositories. The TRIPWIRE system will continuously monitor ionizing radiation and electromagnetic fields in the vicinity of emplaced nuclear materials buried in a repository, reporting on disturbances with a real-time alarm control station. The system will use long-length scintillating fiber bundles (SFBs) to perform area radiation monitoring; these will be coupled to kilometer-scale multimodal optical communication fibers – all light sensors and electronic components used with this system will be located above ground. Electromagnetic fields, and changes in local dielectric conditions caused by intrusion and soil movement, will be monitored using commercial grade, ported "leaky" coaxial cables (PCCs), with control electronics also located above ground. This paper documents the results of the simulations and modeling efforts that have helped identify the optimal placement of the SFBs. Additionally, the paper includes the current progress on the multi-modal SFB-PCC system, including the fabrication of long-length (>3-m) fibers and their coupling to optical fibers.

98 - NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL↗

DOE OSTI2022

Progress of Tripwire: Multi-modal Distributed Sensing for Repository Verification

98 - NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL↗

DOE OSTI2019

Polymorphic Immune Mechanisms Regulate Commensal Repertoire

Environmental influences (infections and diet) strongly affect a host’s microbiota. However, host genetics may influence commensal communities, as suggested by the greater similarity between the microbiomes of identical twins compared to non-identical twins. Variability of human genomes and microbiomes complicates the understanding of polymorphic mechanisms regulating the commensal communities. Whereas animal studies allow genetic modifications, they are sensitive to influences known as “cage” or “legacy” effects. Here, we analyze ex-germ-free mice of various genetic backgrounds, including immunodeficient and major histocompatibility complex (MHC) congenic strains, receiving identical input microbiota. The host’s polymorphic mechanisms affect the gut microbiome, and both innate (anti-microbial peptides, complement, pentraxins, and enzymes affecting microbial survival) and adaptive (MHC-dependent and MHC-independent) pathways influence the microbiota. In our experiments, polymorphic mechanisms regulate only a limited number of microbial lineages (independently of their abundance). Our comparative analyses suggest that some microbes may benefit from the specific immune responses that they elicit.

59 BASIC BIOLOGICAL SCIENCES↗