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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Abstract The Escherichia coli genome‐scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision–recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene‐protein‐reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high‐throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dwarf AGNs from Optical Variability for the Origins of Seeds (DAVOS): insights from the dark energy survey deep fields

ABSTRACT We present a sample of 706, z < 1.5 active galactic nuclei (AGNs) selected from optical photometric variability in three of the Dark Energy Survey (DES) deep fields (E2, C3, and X3) over an area of 4.64 deg2. We construct light curves using difference imaging aperture photometry for resolved sources and non-difference imaging PSF photometry for unresolved sources, respectively, and characterize the variability significance. Our DES light curves have a mean cadence of 7 d, a 6-yr baseline, and a single-epoch imaging depth of up to g ∼ 24.5. Using spectral energy distribution (SED) fitting, we find 26 out of total 706 variable galaxies are consistent with dwarf galaxies with a reliable stellar mass estimate ($M_{\ast }\lt 10^{9.5}\, {\rm M}_\odot$; median photometric redshift of 0.9). We were able to constrain rapid characteristic variability time-scales (∼ weeks) using the DES light curves in 15 dwarf AGN candidates (a subset of our variable AGN candidates) at a median photometric redshift of 0.4. This rapid variability is consistent with their low black hole (BH) masses. We confirm the low-mass AGN nature of one source with a high S/N optical spectrum. We publish our catalogue, optical light curves, and supplementary data, such as X-ray properties and optical spectra, when available. We measure a variable AGN fraction versus stellar mass and compare to results from a forward model. This work demonstrates the feasibility of optical variability to identify AGNs with lower BH masses in deep fields, which may be more ‘pristine’ analogues of supermassive BH seeds.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The GMRT archive atomic gas survey – II. Mass modelling and dark matter halo properties across late-type spirals

Studying the kinematics and mass modelling of galaxies from H i 21 cm data provides valuable insights into the properties of both the baryonic components and the dark matter halo in nearby galaxies. Despite many observational studies, mass modelling of galaxies remains challenging due to different limitations. For example, most of the previous studies involving mass modelling are based on rotation curves derived from 2D velocity fields from H i or H α spectroscopic observation which are often affected by beam smearing and projection effect. However, kinematic modelling done by fitting the ‘Tilted ring model’ to 3D data cube is not affected by these issues. In this study, we present and compare 3D kinematic modelling of a pilot sample of 11 galaxies from the GMRT archive atomic gas survey (GARCIA) using two different publicly available pipelines. We model the observed H i rotation curve using 3.6-μm infrared data and SDSS r-band data for stellar contribution, H i surface density profile for gas, and Navarro–Frenk–White profile for dark matter halo; and employ the Markov chain Monte Carlo optimization method for parameter estimation. Further, to validate our analysis, we revisit important scaling relations, e.g. the M gas –M star relation, M star –M halo relation, M gas –M halo relation and Baryonic Tully–Fisher relation. Here, the scaling relations from our analysis are broadly consistent with that reported in the literature. A larger sample of galaxies from GARCIA in the near future will allow studying these scaling relations in greater details.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Shock-induced melting of [100] lithium fluoride: Sound speed and Hugoniot measurements to 230 GPa

Although [100] lithium flouride (LiF) is the most widely used optical window material in dynamic compression experiments, its high stress (>100 GPa) shock compression response, including melting, is not well understood. To address this need, we measured wave profiles in plate impact experiments to determine the Hugoniot states and longitudinal sound speeds in [100] LiF crystals shock compressed to 231 GPa. The measured peak states are fitted well by a linear shock velocity-particle velocity relation, providing an accurate determination of the LiF Hugoniot curve to significantly higher stresses than previous experiments. The longitudinal sound speeds show a near linear increase with density compression to 182 GPa. Between 182 GPa and 195 GPa, the sound speed and the longitudinal modulus decrease abruptly, due to shock-induced melting. The increasing sound speeds and moduli at higher stresses suggest that shock compressed LiF is fully liquid at 195 GPa and above, allowing determination of the Gruneisen parameter for liquid LiF. Here, the melt stress determined here differs from that predicted by current multiphase equations of state for LiF. Our results provide important insight into the high stress solid and liquid states of shock compressed LiF and point to the need for an improved multiphase equation of state at high pressures and high temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Sliding dynamics for bubble phases on periodic modulated substrates

We analyze a bubble-forming system composed of particles with competing long-range repulsive and short-range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a function of substrate strength and drive amplitude. When the substrate is weak, a pinned bubble phase appears that depins elastically into a sliding bubble lattice. For stronger substrates, we find anisotropic bubbles, disordered bubbles, and stripe phases. Plastic depinning occurs via the hopping of individual particles from one bubble to the next in a pinned bubble lattice, and as the drive increases, there is a transition to a state where all of the bubbles are moving but are continuously shedding and absorbing individual particles. This is followed at high drives by a moving bubble lattice in which the particles can no longer escape their individual bubbles. The transition between the plastic and elastic sliding phases can be detected via signatures in the velocity-force curves, differential conductivity, and noise. When the bubbles shrink due to an increase in the attractive interaction term, they fit better inside the pinning troughs and become more strongly pinned, leading to a reentrant pinning phase. For weaker attractive terms, the size of the bubbles becomes greater than the width of the pinning troughs and the depinning becomes elastic with a reduced depinning threshold. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Wide-field probing of silica laser-induced damage precursors by photoluminescence photochemical quenching

Here, we describe a wide-field approach to probe transient changes in photoluminescence (PL) of defects on silica surfaces. This technique allows simultaneous capture of spatially resolved PL with spontaneous quenching behavior. We attribute the quenching of PL intensity to photochemical reactions of surface defects and/or subsurface fractures with ambient molecules. Such quenching curves can be accurately reproduced by our theoretical model using two quenchable defect populations with different reaction rates. The fitting parameters of our model are spatially correlated to fractures in silica where point defects and mechanical stresses are known to be present, potentially indicating regions prone to laser-induced damage growth. We believe that our approach allows rapid spatial resolved identification of damage prone morphology, providing a new pathway to fast, non-destructive predictions of laser-induced damage growth.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Sliding Dynamics for Bubble Phases on Periodic Modulated Substrates

We analyze a bubble-forming system composed of particles with competing long-range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a function of substrate strength and drive amplitude. When the substrate is weak, a pinned bubble phase appears that depins elastically into a sliding bubble lattice. For stronger substrates, we find anisotropic bubbles, disordered bubbles, and stripe phases. Plastic depinning occurs via the hopping of individual particles from one bubble to the next in a pinned bubble lattice, and as the drive increases, there is a transition to a state where all of the bubbles are moving but are continuously shedding and absorbing individual particles. This is followed at high drives by a moving bubble lattice in which the particles can no longer escape their individual bubbles. The transition between the plastic and elastic sliding phases can be detected via signatures in the velocity-force curves, differential conductivity, and noise. When the bubbles shrink due to an increase in the attractive interaction term, they fit better inside the pinning troughs and become more strongly pinned, leading to a reentrant pinning phase. For weaker attractive terms, the size of the bubbles becomes greater than the width of the pinning troughs and the depinning becomes elastic with a reduced depinning threshold.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A generalized and adaptable tensor-contraction-based cluster expansion formalism for multicomponent solids

Density functional theory (DFT)-based simulations of materials have first-principles accuracy, but are very computationally expensive. For simulating various properties of multi-component alloys, the cluster expansion (CE) technique has served as the standard workaround to improve computational efficiency. However, the standard CE technique is difficult to extend to exotic and/or low-symmetry lattices, often implemented via iteration over particular cluster types, which must be enumerated per lattice structure. In this work, we introduce the tensor cluster expansion (TCE), implemented in the open-source code tce-lib, which maps correlation functions to mixed tensor contractions, eliminating the need to iterate over cluster types and additionally making the calculation of correlation functions well-suited for massively parallel architectures like GPUs. We show that local interaction energies are an immediate consequence of the TCE formalism, yielding nearly $\mathcal{O}$(1) energy difference calculations. We then use this formalism to fit CE models for the TaW and CoNiCrFeMn systems, and use these models to respectively compute the enthalpy of mixing curve and Cowley short-range order parameters, showing excellent agreement with ground truth data.

Cluster expansion↗
DOE OSTI2025

Probing signals of self-interacting dark matter core collapse in H I -rich galaxies

Here, we analyze rotation curves of five Hi-rich galaxies recently discovered with MeerKAT. These galaxies exhibit sharply rising rotation curves, while their baryonic components are not dynamically dominant, suggesting that their dark matter halos have high inner densities. When fitting the standard Navarro–Frenk–White (NFW) halo model, four galaxies require extremely high halo concentrations, exceeding the cosmological median by 5σ. In contrast, self-interacting dark matter (SIDM) halos in the core-collapse phase naturally account for the high densities in these galaxies. For halos with masses around 10 11 M ⊙ , those in cosmic filaments exhibit concentrations consistent with the cosmological average, while halos in cosmic nodes show relatively higher concentrations that align with the SIDM fits but remain insufficient for the NFW fits. Our analysis indicates that these Hi-rich galaxies may have formed in cosmic nodes of dark matter with significant self-interactions.

dark matter↗
DOE OSTI2020

Preserving Symmetry and Degeneracy in the Localized Orbital Scaling Correction Approach

Symmetry is a fundamental concept that plays a critical role in many chemical and physical phenomena and processes, which highlights the importance of theoretical methods to correctly handle symmetry. The recently developed localized orbital scaling correction (LOSC1) shows great improvement on the description of band gaps, photoemission spectra, and dissociation limits of cationic species. However, issues remain with LOSC1 in dealing with the symmetry and degeneracy of electronic states, which are also relevant to other methods using localization. In this work, we utilize a new method that deals with the physical-space and the energy-space localization on an equal footing. The resulting localized orbitals, i.e., orbitalets, are able to maintain more symmetry and the desired state degeneracy, which is important in calculating the electronic structure of both molecules and periodic bulk systems. Furthermore, the curvature matrix is redefined to improve potential energy curves for systems with stretched bonds, while retaining the correct dissociation limits. This new approach, termed LOSC2, includes only two fitting parameters. It maintains accuracy similar to that of LOSC1 over many properties, while overcoming LOSC1’s deficiencies in symmetry and degeneracy. Our tests have shown that LOSC2 orbitalets possess the full- or subgroup of molecular symmetry if allowed, which preserves the state degeneracy. Tests on differently sized planar annulenes, odd-numbered allenes, and triphenylene again verify that LOSC2 is able to maintain the state degeneracy, while LOSC1 cannot. Finally, all the tests demonstrate the advantage of LOSC2 in the calculation of molecular systems and its potential for application to periodic bulk systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Snodgrass Mountain in East River Watershed, Colorado 2020-2025

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors at Snodgrass Mountain. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format SG-X-Y, where SG refers to Snodgrass Mountain, X is the location identifier, and Y is the depth identifier at the same X (shallow Y=1). Specifically, SG-EHS is associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and SG-ERTn (upslope n=1) are points along the Snodgrass electrical resistivity tomography transect not associated with the existing site names in the directory. The sample and location information can be found in metadata.csv. Sampling and Measurements Each sample falls into one of the three sampling methods – (1) intact cores, (2) repacked samples, or (3) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. Both intact cores and repacked samples were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores and in-situ soil sensors could be prioritized because these sampling methods are less destructive. While the repacked samples were packed to the target bulk density (estimated post-sampling, when sample volume was known), these samples had altered pore structures. Nevertheless, intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method also has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. 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.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Trail Creek in Taylor River Watershed, Colorado 2024-2025

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors near Trail Creek. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format TR-X-Y, where TR refers to Trail Creek, X is the treatment block identifier, and Y is the location identifier. Specifically, TR-ASCC1 is the control treatment block under the Adaptive Silviculture for Climate Change (ASCC) project, and TR-ASCC2 is the clear-cut treatment block. TR-ASCC-EHSn is associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and TR-ASCC-ERTn (upslope n=1) are ecohydrology sites along the electrical resistivity tomography transects. The sample and location information can be found in metadata.csv, and the data from the soil sensors will be included in a future data version when the observation period becomes sufficiently long for data analysis. Sampling and Measurements Each sample falls into one of the two sampling methods – (1) intact cores or (2) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. The intact cores were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. 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.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2024

The black hole interior from non-isometric codes and complexity

Quantum error correction has given us a natural language for the emergence of spacetime, but the black hole interior poses a challenge for this framework: at late times the apparent number of interior degrees of freedom in effective field theory can vastly exceed the true number of fundamental degrees of freedom, so there can be no isometric (i.e. inner-product preserving) encoding of the former into the latter. In this paper we explain how quantum error correction nonetheless can be used to explain the emergence of the black hole interior, via the idea of “non-isometric codes protected by computational complexity”. We show that many previous ideas, such as the existence of a large number of “null states”, a breakdown of effective field theory for operations of exponential complexity, the quantum extremal surface calculation of the Page curve, post-selection, “state-dependent/state-specific” operator reconstruction, and the “simple entropy” approach to complexity coarse-graining, all fit naturally into this framework, and we illustrate all of these phenomena simultaneously in a soluble model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Modeling of Radiolytic Hydrogen Generation of Irradiated Surrogate Aluminum Plates

The hydrogen generation from oxyhydroxide layers under irradiation is an important effect to understand for the long-term storage of aluminum-clad spent nuclear fuel. The original chemical model shows steady production of hydrogen from aluminum oxyhydroxide layers, with no roll-over effect in the curves of the hydrogen concentration until significant pressure has built up within the canister. This study uses a variety of kinetic fits to adjust the old chemical model to have roll-over effects that are consistent with new high-dose experiments. The data from aluminum 6061 coupon tests at high doses were used to fit several kinetic models. The 6061 aluminum samples are representative of the aluminum-clad fuel from the ATR. The fitted kinetic models were then used in a model of a mini-canister with much higher packing density to determine which kinetic rates would fit both sets of experimental tests. The rate constants for the kinetic mechanisms that were close were then tweaked such that the chemical models fit both the experimental data from the capsule tests and the data from the mini-canister tests. The kinetic models which fit the best are either inhibition by hydrogen, or a back reaction wherein H radical is reabsorbed onto the oxyhydroxide layer. The H back reaction rolls over quicker and may fit future collected data.

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

Quantification of the REE 3+ aqua ions and chloride species in aqueous fluids by in situ Raman spectroscopy using perturbations of the water band

Acidic NaCl-rich aqueous fluids play a crucial role in forming hydrothermal rare earth elements (REE) mineral deposits. Aqueous REE mobility is mostly controlled by the stabilities of REE 3+ and REE chloride species. Our current knowledge of REE speciation is based on solubility data, thermodynamic models and in situ spectroscopic measurements, sometimes coupled with molecular simulations. Here, in this study, we investigate Nd and Yb speciation in pH2 Cl-bearing solutions at 25 °C and 0.1 MPa with variable Cl/REE ratios using Raman Spectroscopy in solutions with 0.1 to 0.6 mol/kg NdCl 3 or YbCl 3 and 0.2 to 3.2 mol/kg NaCl. Due to the challenges in resolving the REE-Cl band, we developed a new method using the water vibrational mode and multivariate curve resolution (MCR) analysis. The Raman spectra for the vibrational band of water (2700 to 3900 cm –1 ) were collected at 25 °C and fitted by three Gaussian sub-peaks, then quantified using MCR analysis to de-convolute the water band into bulk H 2 O and the perturbations caused by of Cl – , REE 3+ , and REE chloride species. REE speciation based on the perturbations of the water band indicates that REE 3+ aqua ions dominate acidic solutions at 25 °C, but up to ~20 mol% YbCl 2+ forms at high YbCl 3 concentrations. The new method is promising for quantifying in situ speciation of the REE 3+ aqua ions and REE chloride species in aqueous fluids while providing information on the hydration of ions. This method improves our molecular level understanding of REE aqueous species stability and their role in REE mobilization during fluid-rock interaction.

58 GEOSCIENCES↗
DOE OSTI2021

Heterogeneous multiphase flow properties of volcanic rocks and implications for noble gas transport from underground nuclear explosions

Of interest to the Underground Nuclear Explosion Signatures Experiment are patterns and timing of explosion-generated noble gases that reach the land surface. The impact of potentially simultaneous flow of water and gas on noble gas transport in heterogeneous fractured rock is a current scientific knowledge gap. This article presents field and laboratory data to constrain and justify a triple continua conceptual model with multimodal multiphase fluid flow constitutive equations that represents host rock matrix, natural fractures, and induced fractures from past underground nuclear explosions (UNEs) at Aqueduct and Pahute Mesas, Nevada National Security Site, Nevada, USA. Capillary pressure from mercury intrusion and direct air–water measurements on volcanic tuff core samples exhibit extreme spatial heterogeneity (i.e., variation over multiple orders of magnitude). Petrographic observations indicate that heterogeneity derives from multimodal pore structures in ash-flow tuff components and post-depositional alteration processes. Comparisons of pre- and post-UNE samples reveal different pore size distributions that are due in part to microfractures. Capillary pressure relationships require a multimodal van Genuchten (VG) constitutive model to best fit the data. Relative permeability estimations based on unimodal VG fits to capillary pressure can be different from those based on bimodal VG fits, implying the choice of unimodal vs. bimodal fits may greatly affect flow and transport predictions of noble gas signatures. The range in measured capillary pressure and predicted relative permeability curves for a given lithology and between lithologies highlights the need for future modeling to consider spatially distributed properties.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2022

A Double-Wiebe Function for Reactivity Controlled Compression Ignition Combustion Using Reformate Diesel

Abstract Reactivity controlled compression ignition (RCCI) combustion has previously been proposed as a method to achieve high fuel conversion efficiency and reduce engine emissions. A single-fuel RCCI combustion strategy can have decreased fuel system complexity by using a reformate fuel for port fuel injection and the parent fuel (diesel) for direct injection. This paper presents a one-dimensional computational model of a compression ignition engine with single-fuel RCCI. A Wiebe function is used to predict the combustion process by representing the mass fraction burned (MFB) on a crank angle resolved basis. One single-Wiebe function (SWF) and two double-Wiebe functions(DWFs) were fitted to experimentally derive MFB data using the least-square method. The fitted results were compared with MFBs calculated from experimental data to verify the accuracy. The SWF did not fully capture the MFB curve with high fidelity while the detailed DWF captured the MFB curve within a root mean square error of 1.4%. The reduced double-Wiebe function (RDWF) also resulted in a predicted combustion profile with similar accuracy. Hence, the RDWF was used in a GT-power thermodynamic study to understand the effects of the low-temperature heat release (LTHR) fraction and combustion phasing on combustion characteristics. At optimum phasing of 5–10 crank angle degree after the top dead center, increasing the LTHR fraction from 20% to 60% resulted in the fuel conversion efficiency increasing from 39.5% to 41.1%, thus suggesting that the reformate fuel-based RCCI strategy is viable to unlock improved combustion performance.

Energy & Fuels↗
DOE OSTI2022

Considerations for Optimizing the Photometric Classification of Supernovae from the Rubin Observatory

The Vera C. Rubin Observatory will increase the number of observed supernovae (SNe) by an order of magnitude; however, it is impossible to spectroscopically confirm the class for all SNe discovered. Thus, photometric classification is crucial, but its accuracy depends on the not-yet-finalized observing strategy of Rubin Observatory's Legacy Survey of Space and Time (LSST). We quantitatively analyze the impact of the LSST observing strategy on SNe classification using simulated multiband light curves from the Photometric LSST Astronomical Time-Series Classification Challenge (PLAsTiCC). First, we augment the simulated training set to be representative of the photometric redshift distribution per SNe class, the cadence of observations, and the flux uncertainty distribution of the test set. Then we build a classifier using the photometric transient classification library snmachine, based on wavelet features obtained from Gaussian process fits, yielding a similar performance to the winning PLAsTiCC entry. We study the classification performance for SNe with different properties within a single simulated observing strategy. We find that season length is important, with light curves of 150 days yielding the highest performance. Cadence also has an important impact on SNe classification; events with median inter-night gap <3.5 days yield higher classification performance. Interestingly, we find that large gaps (>10 days) in light-curve observations do not impact performance if sufficient observations are available on either side, due to the effectiveness of the Gaussian process interpolation. This analysis is the first exploration of the impact of observing strategy on photometric SN classification with LSST.

79 ASTRONOMY AND ASTROPHYSICS↗