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532 records · Page 30

Phase Equilibria and Thermochemistry of Advanced Fuels: Modeling Burnup Behavior (Final Report)

Achieving the goal of developing advanced fuel concepts that meet the DOE objectives of being robust, demonstrating high performance, and are more tolerant of accident conditions than current fuel systems will require a thorough understanding of the thermophysical and thermochemical properties of the constituent materials. Non-oxide fuel systems are being explored under the Advanced Fuels Program that hold significant promise for improved performance and accident tolerance, including the uranium silicide-based system considered in the current work. Prospective cladding materials currently considered that contribute to improved accident tolerance include silicon carbide composites and ferritic alloys (Fe-Cr-Al base compositions). Thus, the effort developed thermochemical models and values, supported with targeted experiments, to evaluate the ferritic alloy and silicon carbide composite cladding systems in contrast to current zirconium alloy cladding. The developed detailed understanding will serve to aid in relatively early screening of candidate systems to avoid wasted effort, guide development of new fuel forms, and to provide a basis for predicting and modeling fuel performance. Major deliverables for the project included: Thermochemical assessment and models of phases in the U-Si and U-Si-N systems; thermochemical evaluation supported by experimental measurements of fuel-cladding interactions of silicide fuel with baseline zirconium, ceramic composite, and ferritic alloy cladding; thermochemical assessment and models of phases supported by experimental measurements for silicide fuel with key fission products provided in a dataset and reported in refereed publications. Within the project a significantly refined U-Si phase diagram was developed and reported that now includes homogeneity ranges for key phases, such at the U 3 Si 2 proposed fuel phase, and settles issues with regard to uncertainty in the stability of some phases. Computational efforts together with key experiments has determined phase formation in interactions between U 3 Si 2 and Zircaloy-4 cladding material, a ferritic FeCrAlY alloy of interest as an advanced cladding material, and silicon carbide, also of interest as a fiber-reinforced composite cladding. As expected, very significant reactions occur between U3Si2 and Zircaloy-4, with much less interaction at higher temperatures for the ferritic alloy, and finally interactions with SiC only in the region of contact. A potentially major issue is the stability of U 3 Si 2 fuel that has undergone significant burnup. The result is the loss of the uranium metal, liberating silicon, and the formation of concomitant fission product elements that either dissolve in the U 3 Si 2 phase or form independent, and possibly silicide phases. A combination of experimental determinations of phase formation of U 3 Si 2 reacted with representative fission products yttrium, gadolinium, cerium, zirconium, and molybdenum and first principles calculations has helped understand the fuel chemistry. The behavior of the U 3 Si 2 phase and the partitioning of silicon to possible fission product phases with burnup was thus determined, with significant dissolution in U 3 Si 2 of cerium, gadolinium, zirconium, and plutonium predicted along with independent phase formation of a U-Mo-Si ternary phase, yttrium silicide, and elemental selenium. It can be concluded that at significant burnup there will be a very minor amount of the U 3 Si 2 fuel phase that will decompose to a lower silicide or a uranium alloy as silicon preferentially forms a secondary phase.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Observation-constrained kinetic modeling of isoprene SOA formation in the atmosphere

Isoprene has the largest global non-methane hydrocarbon emission, and the oxidation of isoprene plays a crucial role in the formation of secondary organic aerosol (SOA). Two primary processes are known to contribute to SOA formation from isoprene oxidation: (1) the reactive uptake of isoprene-derived epoxides on acidic or aqueous particle surfaces and (2) the absorptive gas–particle partitioning of low-volatility oxidation products. In this study, we developed a new multiphase condensed isoprene oxidation mechanism that includes these processes with key molecular intermediates and products. The new mechanism was applied to simulate isoprene gas-phase oxidation products and SOA formation from previously published chamber experiments under a variety of conditions and atmospheric observations during the Southern Oxidant and Aerosol Studies (SOAS) field campaign. Our results show that SOA formation from most of the chamber experiments is reasonably reproduced using our mechanism, except when the concentration ratios of initial nitric oxide to isoprene exceed ~ 2, the formed SOA is significantly underpredicted. The SOAS simulations also reasonably agree with the measurements regarding the diurnal pattern and concentrations of different product categories, while the total isoprene SOA remains underestimated. The molecular compositions of the modeled SOA indicate that multifunctional low-volatility products contribute to isoprene SOA more significantly than previously thought, with a median mass contribution of ~ 57 % to the total modeled isoprene SOA. However, this contribution is intricately intertwined with IEPOX-derived SOA (IEPOX: isoprene-derived epoxydiols), posing challenges for their differentiation using bulk aerosol composition analysis (e.g., the aerosol mass spectrometer with positive matrix factorization). Furthermore, the SOA from these pathways may vary greatly, mainly dependent on the volatility estimation and treatment of particle-phase processes (i.e., photolysis and hydrolysis). Our findings emphasize that the various pathways to produce these low-volatility species should be considered in models to more accurately predict isoprene SOA formation. The new condensed isoprene chemical mechanism can be further incorporated into regional-scale air quality models, such as the Community Multiscale Air Quality Modelling System (CMAQ), to assess isoprene SOA formation on a larger scale.

54 ENVIRONMENTAL SCIENCES↗

Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor

Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a molecularly informed biogeochemical framework for reactive transport modeling of subsurface carbon inventories, transformations and fluxes (Final Report)

The overall objective of the project was to combine new molecular-level characterization strategies with soil carbon flux measurements to develop and evaluate model representations of subsurface carbon cycling. We expanded on existing studies in the East River watershed, Colorado, in collaboration with the Berkeley Lab Watershed Function Scientific Focus Area (SFA), SLAC Groundwater Quality SFA, and Rocky Mountain Biological Laboratory (RMBL) to develop an elevation and vegetation gradient that is now the subject of long-term monitoring by the USGS. To achieve the overall objective, we combined field studies of soil respiration with laboratory analyses, ranging from spectroscopy to incubation studies. This combination of techniques enabled us to develop a new understanding of the drivers of high-elevation soil respiration. In the process, we developed three new modeling approaches that improve our ability to conceptualize and ultimately to represent soil respiration in numerical models. The first approach is a plot-scale transient inverse model that can be used to determine in situ CO 2 production rates from measured concentration profiles and surface fluxes. Application of this method revealed the importance of plant phenology and deep CO 2 production in moderating CO 2 fluxes to the atmosphere. The second modeling approach is a molecular-scale tool that enables spectroscopic and elemental data for carbon speciation to be transformed into functional group abundances, or the ‘SOC-fga model’. This method uniquely enables carbon speciation to be tracked within a reactive transport framework to partition carbon among different pathways and storage zones within the soil. The third modeling tool builds strongly on the previous approaches and captures the microbial processes driving heterotrophic respiration. This ‘dormancy model’ allows the native soil microbial population to respond transiently to the presence or absence of water in order to catalyze carbon respiration. This approach was also compared to the simpler and more widely used first-order model using two experimental datasets with different temporal and spatial resolutions. Our results illustrate that the simpler first order model provides a robust and efficient representation of deep (>1 meter) soil respiration, but that shallow soils, where most respiration occurs, require explicit representation of moisture-dependent activation and dormancy rates. By assessing soil organic carbon turnover at multiple scales, we see a complex array of controls emerge. Atte scale of a hillslope, spatial heterogeneity in soil respiration rates dominates and is uncorrelated with instantaneous soil moisture and plant community. At the profile scale, the balance between plant inputs and water availability is the dominant control. At the microbial to molecular scale, physiological processes associated with carbon use and carbon speciation are important controls. These scale-dependent controls emphasize the need for new modeling approaches that examine their interactions and hierarchies.

54 ENVIRONMENTAL SCIENCES↗

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗

Higher-Order VLP-Based Protein Macromolecular Framework Structures Assembled via Coiled-Coil Interactions

Hierarchical organization is one of the fundamental features observed in biological systems that allows for efficient and effective functioning. Virus-like particles (VLPs) are elegant examples of a hierarchically organized supramolecular structure, where many subunits are self-assembled to generate the functional cage-like architecture. Utilizing VLPs as building blocks to construct two- and three-dimensional (3D) higher-order structures is an emerging research area in developing functional biomimetic materials. VLPs derived from P22 bacteriophages can be repurposed as nanoreactors by encapsulating enzymes and modular units to build higher-order catalytic materials via several techniques. In this study, we have used coiled-coil peptide interactions to mediate the P22 interparticle assembly into a highly stable, amorphous protein macromolecular framework (PMF) material, where the assembly does not depend on the VLP morphology, a limitation observed in previously reported P22 PMF assemblies. Many encapsulated enzymes lose their optimum functionalities under the harsh conditions that are required for the P22 VLP morphology transitions. Therefore, the coiled-coil-based PMF provides a fitting and versatile platform for constructing functional higher-order catalytic materials compatible with sensitive enzymes. Finally, we have characterized the material properties of the PMF and utilized the disordered PMF to construct a biocatalytic 3D material performing single- and multistep catalysis.

59 BASIC BIOLOGICAL SCIENCES↗

Replica symmetry breaking for the integrable two-site Sachdev–Ye–Kitaev model

We analyze a two-body non-Hermitian two-site Sachdev–Ye–Kitaev (SYK) model with the couplings of one site complex conjugated to the other site. This model, with no explicit coupling between the sites, shows an infinite number of second-order phase transitions, which is a consequence of the factorization of the partition function into a product over Matsubara frequencies. We calculate the quenched free energy in two different ways: first in terms of the single-particle energies and second by solving the Schwinger–Dyson equations of the two-site model. The first calculation can be done entirely in terms of a one-site model. The conjugate replica enters due to non-analyticities when Matsubara frequencies enter the spectral support of the coupling matrix. The second calculation is based on the replica trick of the two-site partition function. Both methods give the same result. The free-fermion partition function can also be rephrased as a matrix model for the coupling matrix. Up to minor details, this model is the random matrix model that describes the chiral phase transition of QCD, and the order parameter of the two-body model corresponds to the chiral condensate of QCD. Comparing to the corresponding four-body model, we are able to determine which features of the free energy are due to the chaotic nature of the four-body model. The high-temperature phase of both models is entropy dominated, and in both cases, the free energy is determined by the spectral density. The chaotic four-body SYK model has a low-temperature phase whose free energy is almost temperature-independent, signaling an effective gap of the theory even though the actual spectrum does not exhibit a gap. On the other hand, the low-temperature free energy of the two-body SYK model is not flat; in fact, it oscillates to arbitrarily low temperature. This indicates a less desirable feature that the entropy of the two-body model is not always positive in the low-temperature phase, which most likely is a consequence of the non-hermiticity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Attributing differences of solar-induced chlorophyll fluorescence (SIF)-gross primary production (GPP) relationships between two C4 crops: corn and miscanthus

There remains limited information to characterize the solar-induced chlorophyll fluorescence (SIF)-gross primary production (GPP) relationship in C4 cropping systems. The annual C4 crop corn and perennial C4 crop miscanthus differ in phenology, canopy structure and leaf physiology. Investigating the SIF-GPP relationships in these species could deepen our understanding of SIF-GPP relationships within C4 crops. Using in situ canopy SIF and GPP measurements for both species along with leaf-level measurements, we found considerable differences in the SIF-GPP relationships between corn and miscanthus, with a stronger SIF-GPP relationship and higher slope of SIF-GPP observed in corn compared to miscanthus. These differences were mainly caused by leaf physiology. For miscanthus, high non-photochemical quenching (NPQ) under high light, temperature and water vapor deficit (VPD) conditions caused a large decline of fluorescence yield (Φ F ), which further led to a SIF midday depression and weakened the SIF-GPP relationship. The larger slope in corn than miscanthus was mainly due to its higher GPP in mid-summer, largely attributed to the higher leaf photosynthesis and less NPQ. Furthermore, our results demonstrated variation of the SIF-GPP relationship within C4 crops and highlighted the importance of leaf physiology in determining canopy SIF behaviors and SIF-GPP relationships.

54 ENVIRONMENTAL SCIENCES↗

2D reactive transport model of shale chemical weathering and biogeochemical fluxes along a mountainous hillslope, East River Watershed, Colorado: Input files and simulation results

This data package contains input files and simulation results for a two-dimensional (2D) reactive transport model used to quantitatively analyze the coupled hydrological and biogeochemical processes governing shale weathering and associated biogeochemical fluxes under realistic environmental conditions in the high-elevation East River Watershed. These data support the conclusions presented in Stolze et al. (Water Resources Research, under review), "Model-based interpretation of solute exports and carbon partitioning during shale weathering in a mountainous hillslope". The model simulates atmospheric-subsurface gas exchange, subsurface water flow, and shale weathering processes under dynamic, year-scale conditions along a shale-underlain hillslope located in the East River watershed. The simulations were performed using the PFLOTRAN flow and reactive transport code and executed on the Perlmutter supercomputer to leverage its large-scale parallel computing capabilities. The data package contains two zipped folders, "model_input_files" and "simulation_results", and one readme.txt file. "model_input_files" contains the necessary input files to run the calibrated base-base model presented in Stolze et al. (Water Resources Research, under review). "simulation_results" contains a single hdf5 file ("Output_2D_hillslope_model.h5") which includes the results of simulation performed using the base-case model. This file can be opened with HDFView 3.1.4, Python, or MATLAB. "readme.txt" contains relevant information about the base-case model and provides guidelines on how to run the associated input files provided in the folder "model_input_files". Furthermore, readme.txt provides information regarding the model results provided in "Output_2D_hillslope_model.h5" such as matrix dimensionality and output units. Field datasets used to evaluate model performance were collected at three monitoring wells located along a hillslope transect (PLM1, PLM2, and PLM3). Dissolved ion concentration data were collected from November 2016 to October 2021 for Ca, Mg, DIC, Na, K, SO4 (Dong et al., 2025 - dic_npoc_data_2014_2024.zip - DOI:10.15485/1660459; Williams et al., 2025 - anion_data_2014_2024.zip - DOI:10.15485/1668054; Dong et al., 2025 - cation_data_2014_2024.zip - DOI:10.15485/1668055). Note that we used the files named er_PLM1_xx_yy, er_PLM2_xx_yy, and er_PLM3_xx_yy where xx stands for the name of the aqueous species and yy stands for the depth where the measurements were performed. Soil water content ([0 - 1] m) and water table depth were collected from November 2016 to October 2021 (Wan et al., 2024 - Dynamic_water_table__depthsFig2b.csv and Soil_water_content_Fig4e.csv - DOI:10.15485/2322567). Gaseous CO2 concentration were collected from October 2020 to December 2021(Wan et al., 2024 - Soil_CO2_concentrations_Fig4h.csv - DOI:10.15485/2322567) Gaseous CO2 flux from the subsurface to the atmosphere were collected in the vicinity of PLM2 from October 2019 to May 2022 (Wu et al., 2025). Soil microbial biomass concentration was measured from August 2016 to June 2017 (Sorensen et al., 2019 - 2017_East_River_Pumphouse_Microbial_Biomass__1_.csv - DOI:10.15485/1577267) All field data are published as CSV files compatible with Microsoft Excel, MATLAB, and Python, or as text files. The coordinates of the monitoring wells and the CO2(g) flux sensor in the coordinate system WGS84 are: -PLM1: [38.9197710 ; -106.9492750] -PLM2: [38.9201580 ; -106.9487170] -PLM3: [38.9207843 ; -106.9483668] -PLM4: 38.9210060 ; -106.9479528] -CO2(g) flux sensor: [38.9199180 ; -106.9489906] ------------------------------------------------------------------------------------------- This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility using NERSC award BER-ERCAP 23980, BER-ERCAP 28550, and BER-ERCAP 33789.

54 ENVIRONMENTAL SCIENCES↗

Retaining Geochemical Signatures during Aragonite-Calcite Transformation at Hydrothermal Conditions

Transformation of aragonite, a mineral phase metastable at Earth’s surface, to calcite widely occurs in both sedimentary and metamorphic systems with the presence of an aqueous phase. The transformation process can affect geochemical signatures of aragonite (a protolith). This study focused on quantification of the retention of Mg/Ca and Sr/Ca ratios, and δ18O during the transformation process as well as evaluation of the transformation rate. To investigate the effect of transformation from aragonite to calcite on elemental and stable isotope ratios, we conducted a series of experiments in NaCl solutions at temperatures between 120 and 184 °C. Two additional experiments at 250 °C were conducted to estimate the transformation rate of aragonite to calcite. Protolith materials consist of (1) synthetic (Mg; Sr-bearing or non-Mg; Sr bearing) needle-shaped microcrystals of aragonite (<5 µm in size) and (2) larger chips (>100 µm in size) of natural aragonite. X-ray diffraction (XRD) showed that microcrystals successfully transformed to calcite within 30 h and scanning electron microscopy (SEM) yielded a change in the crystal size to >10 µm in rhombohedral shape. Electron backscatter diffraction (EBSD) of the larger aragonite chips showed that transformation to randomly oriented calcite occurred at the rims and along the cracks while the core retained an aragonite crystal structure. Isotope-ratio mass spectrometry (IRMS) analyses showed that calcite δ18O was controlled by temperature and δ18O of the solution. The obtained calibration curve of isotope fractionation factor versus temperature is consistent with other studies. Inductively coupled plasma optical emission spectroscopy (ICP-OES) analyses showed that calcite partially or completely retained Mg/Ca and Sr/Ca ratios through the transformation.

58 GEOSCIENCES↗