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Data and scripts associated with a manuscript analyzing ELM-FATES parameter sensitivity under pre-fire and postfire scenarios using machine learning

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript “Fire Severity-Dependent Shifts in Vegetation Parameter Sensitivity: A Pre- and Post-Fire Analysis Using ELM-FATES and Explainable AI” submitted to Journal of Advances in Modeling Earth Systems (Zahura et al. 2026). The study examines vegetation physiological parameters controlling pre-fire and post-fire vegetation dynamics. To support this analysis, 73 vegetation parameters in Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (Fisher et al., 2018) , which is coupled with E3SM (Energy Exascale Earth System Model) land model (ELM, ELM-FATES), were perturbed using a Sobol sequence to generate 1,024 ensemble members for two plant functional types: needleleaf evergreen extratropical trees (NEET) and C3 grass. Simulations were conducted for the pre-fire period (2016) and post-fire period (2018–2023). Burn severity was represented by modifying the Nesterov index in FATES to 75,000, 150,000, and 300,000 for low, moderate, and high severity, respectively. A no-fire scenario was also included. Simulations were performed for 16 grid cells in the American River Watershed across different burn severities and plant functional types. XGBoost (eXtreme Gradient Boosting) models were trained using the parameter ensembles and ELM-FATES-simulated outputs, including leaf area index (LAI), gross primary productivity (GPP), aboveground biomass, vegetation evaporation, transpiration, and soil evaporation. Models were trained separately for each year and burn severity, followed by SHAP (SHapley Additive exPlanations) analysis to identify changes in dominant parameters after fire disturbance. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. The data package contains the ELM-FATES simulation data. The scripts and data related to the analysis will be added later. The inputs and outputs from ELM-FATES are inside the “FATES” folder. “FATES_domain_surface” contains the domain and surface netcdfs that were used to run ELM-FATES in the study area. “FATES_parameters” contains the 1024 ensembles that were generated using Sobol sequence. “FATES_outputs” folder contains ELM-FATES simulated variables. All files are .csv and .nc (NetCDF).

Aboveground biomass↗

Thermodynamic Modeling of Calcium and Magnesium Partitioning Between Sulfide and Silicate and Implications for Mercury’s Differentiation

Mercury is the least oxidized terrestrial planet of the solar system and is enriched in sulfur, which may be saturated in its mantle, possibly forming Ca- and Mg-rich sulfides. Using literature experimental data, we developed a thermodynamic model for calcium and magnesium partitioning between sulfide and silicate melts to enhance our understanding of the chemical equilibria involved in Mercury’s mantle-crust differentiation. Our models show that temperature and carbon abundance in sulfide have a positive effect on Ca partitioning into sulfides, while pressure decreases it. In addition, carbon abundance and sulfur concentration in the silicate melt are the primary controls on Mg partitioning, both favoring Mg partitioning into sulfides. Our results will be used to better understand the abundance as well as presence of calcium and magnesium sulfides within Mercury’s mantle and crust.

Taylor McCombs↗

Technical report series on global modeling and data assimilation. Volume 3: An efficient thermal infrared radiation parameterization for use in general circulation models

A detailed description of a parameterization for thermal infrared radiative transfer designed specifically for use in global climate models is presented. The parameterization includes the effects of the main absorbers of terrestrial radiation: water vapor, carbon dioxide, and ozone. While being computationally efficient, the schemes compute very accurately the clear-sky fluxes and cooling rates from the Earth's surface to 0.01 mb. This combination of accuracy and speed makes the parameterization suitable for both tropospheric and middle atmospheric modeling applications. Since no transmittances are precomputed the atmospheric layers and the vertical distribution of the absorbers may be freely specified. The scheme can also account for any vertical distribution of fractional cloudiness with arbitrary optical thickness. These features make the parameterization very flexible and extremely well suited for use in climate modeling studies. In addition, the numerics and the FORTRAN implementation have been carefully designed to conserve both memory and computer time. This code should be particularly attractive to those contemplating long-term climate simulations, wishing to model the middle atmosphere, or planning to use a large number of levels in the vertical.

Suarex, Max J.↗

Mantle rare gas relative abundances in a steady-state mass transport model

A model for He and Xe was presented previously which incorporates mass transfer of rare gases from an undegassed lower mantle (P) and the atmosphere into a degassed upper mantle (D). We extend the model to include Ne and Ar. Model constraints on rare gas relative abundances within P are derived. Discussions of terrestrial volatile acquisition have focused on the rare gas abundance pattern of the atmosphere relative to meteoritic components, and the pattern of rare gases still trapped in the Ear,th is important in identifying volatile capture and loss processes operating during Earth formation. The assumptions and principles of the model are discussed in Wasserburg and Porcelli (this volume). For P, the concentrations in P of the decay/nuclear products 4 He, 21 Ne, 40 Ar, and 136 Xe can be calculated from the concentrations of the parent elements U, Th, K, and Pu. The total concentration of the daughter element in P is proportional to the isotopic shifts in P. For Ar, ((40)Ar/(36)Ar)p - ((40)Ar/(36)Ar)o =Delta (exp 40) p= 40 Cp/(exp 36)C where(i)C(sub j) the concentration of isotope i in j. In D, isotope compositions are the result of mixing rare gases from P, decay/nuclear products generated in the upper mantle, and subducted rare gases (for Ar and Xe).

Porcelli, D.↗

The Analysis of Using Satellite Soil Moisture Observations for Flood Detection, Evaluating Over the Thailand’s Great Flood of 2011

A flood monitoring and warning system provides critical information that can protect property and save lives. A basin-scale flood monitoring system requires an effective observation platform that offers extensive ground coverage of flood conditions, low latency, and high spatiotemporal resolution. While satellite imagery offers substantial spatial flood extent in detail due to its high spatial resolution, the coarse temporal resolution and cloud obstruction limit its near real-time application. Daily soil moisture data derived from satellite sensors at a scale of a few km can be used to monitor extreme wet surface conditions arising in flood occurrences. This study analyses the flood detection capabilities of several sources of soil moisture information, including the Soil Moisture and Ocean Salinity mission (SMOS), the Advanced Microwave Scanning Radiometer on EOS (AMSR-E), the Advanced SCATterometer (ASCAT) on MetOp, the Global Land Data Assimilation System (GLDAS), and the WaterGAP Global Hydrology Model (WGHM). In addition to soil moisture, the analysis includes measurements of surface reflectance from the Moderate Resolution Imaging Spectroradiometer (MODIS), precipitation measurements from the Tropical Rainfall Measuring Mission (TRMM), and terrestrial water storage estimates from the Gravity Recovery And Climate Experiment (GRACE) as proxies for flood inundations. The analysis was conducted over the Chao Phraya River Basin (CPB) in Thailand, where the Great Flood of 2011 led to one of the most significant economic losses in the country's history. Satellite-derived soil moisture exhibits a stronger correlation with the flood inundations than the precipitation, model-derived soil moisture, and terrestrial water storage data. SMOS soil moisture observation agrees best with the MODIS-derived flood extent/occurrence, both in terms of spatial distribution and timing, and providing approximated flood lead-time of one week or longer. A neural network constructed from SMOS and MODIS data is used to predict flood intensity/occurrence (given soil moisture input) with a predicted time window from eight days to thirty-two days. The short-term prediction (e.g., eight days) achieves the highest accuracy with an averaged recovery rate of approximately 60% (correlation coefficient). This study's results suggest a potential application of satellite soil moisture data in assisting flood monitoring and warning systems.

Satellite soil moisture↗

Type II Seesaw leptogenesis

The Type II Seesaw Mechanism provides a minimal framework to explain the neutrino masses involving the introduction of a single triplet Higgs to the Standard Model. However, this simple extension was believed to be unable to successfully explain the observed baryon asymmetry of the universe through Leptogenesis. In our previous work (Phys. Rev. Lett. 128 (2022) 141801), we demonstrated that the triplet Higgs of the Type II Seesaw Mechanism alone can simultaneously generate the observed baryon asymmetry of the universe and the neutrino masses while playing a role in setting up Inflation. This is achievable with a triplet Higgs mass as low as 1 TeV, and predicts that the neutral component obtains a small vacuum expectation value $v_Δ$ < 10 keV. We find that our model has very rich phenomenology and can be tested by various terrestrial experiments as well as by astronomical observations. Particularly, we show that the successful parameter region may be probed at a future 100 TeV collider, upcoming lepton flavor violation experiments such as Mu3e, and neutrinoless double beta decay experiments. Additionally, the tensor-to-scalar ratio from the inflationary scenario will be probed by the LiteBIRD telescope, and observable isocurvature perturbations may be produced for some parameter choices. In this article, we present all the technical details of our calculations and further discussion of its phenomenological implications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Formation of the giant planets

The observed properties of giant planets, models of their evolution and observations of protoplanetary disks provide constraints on the formation of gas giant planets. The four largest planets in our Solar System contain considerable quantities of hydrogen and helium, which could not have condensed into solid planetesimals within the protoplanetary disk. All three (transiting) extrasolar giant planets with well determined masses and radii also must contain substantial amounts of these light gases. Jupiter and Saturn are mostly hydrogen and helium, but have larger abundances of heavier elements than does the Sun. Neptune and Uranus are primarily composed of heavier elements. HD 149026 b, which is slightly more massive than is Saturn, appears to have comparable quantities of light gases and heavy elements. HD 209458 b and TrES-1 are primarily hydrogen and helium, but may contain supersolar abundances of heavy elements. Spacecraft flybys and observations of satellite orbits provide estimates of the gravitational moments of the giant planets in our Solar System, which in turn provide information on the internal distribution of matter within Jupiter, Saturn, Uranus and Neptune. Atmospheric thermal structure and heat flow measurements constrain the interior temperatures of planets. Internal processes may cause giant planets to become more compositionally differentiated or alternatively more homogeneous; high-pressure laboratory .experiments provide data useful for modeling these processes. The preponderance of evidence supports the core nucleated gas accretion model. According to this model, giant planets begin their growth by the accumulation of small solid bodies, as do terrestrial planets. However, unlike terrestrial planets, the growing giant planet cores become massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates. The primary questions regarding the core nucleated growth model is under what conditions planets with small cores/total heavy element abundances can accrete gaseous envelopes within the lifetimes of gaseous protoplanetary disks.

Lissauer, Jack J.↗

Terrestrial Planet Formation in Binary Star Systems

Most stars reside in multiple star systems; however, virtually all models of planetary growth have assumed an isolated single star. Numerical simulations of the collapse of molecular cloud cores to form binary stars suggest that disks will form within such systems. Observations indirectly suggest disk material around one or both components within young binary star systems. If planets form at the right places within such circumstellar disks, they can remain in stable orbits within the binary star systems for eons. We are simulating the late stages of growth of terrestrial planets within binary star systems, using a new, ultrafast, symplectic integrator that we have developed for this purpose. We show that the late stages of terrestrial planet formation can indeed take place in a wide variety of binary systems and we have begun to delineate the range of parameter space for which this statement is true. Results of our initial simulations of planetary growth around each star in the alpha Centauri system and other 'wide' binary systems, as well as around both stars in very close binary systems, will be presented.

Lissauer, Jack J.↗

Terrestrial Planet Formation Around Close Binary Stars

Most stars reside in multiple star systems; however, virtually all models of planetary growth have assumed an isolated single star. Numerical simulations of the collapse of molecular cloud cores to form binary stars suggest that disks will form within such systems. Observations indirectly suggest disk material around one or both components within young binary star systems. If planets form at the right places within such circumstellar disks, they can remain in stable orbits within the binary star systems for eons. We are simulating the late stages of growth of terrestrial planets around close binary stars, using a new, ultrafast, symplectic integrator that we have developed for this purpose. The sum of the masses of the two stars is one solar mass, and the initial disk of planetary embryos is the same as that used for simulating the late stages of terrestrial planet growth within our Solar System and in the Alpha Centauri wide binary star system. Giant planets &are included in the simulations, as they are in most simulations of the late stages of terrestrial planet accumulation in our Solar System. When the stars travel on a circular orbit with semimajor axis of up to 0.1 AU about their mutual center of mass, the planetary embryos grow into a system of terrestrial planets that is statistically identical to those formed about single stars, but a larger semimajor axis and/or a significantly eccentric binary orbit can lead to significantly more dynamically hot terrestrial planet systems.

Lissauer, Jack J.↗

Historically inconsistent productivity and respiration fluxes in the global terrestrial carbon cycle

The terrestrial carbon cycle is a major source of uncertainty in climate projections. Its dominant fluxes, gross primary productivity (GPP), and respiration (in particular soil respiration, RS), are typically estimated from independent satellite-driven models and upscaled in situ measurements, respectively. We combine carbon-cycle flux estimates and partitioning coefficients to show that historical estimates of global GPP and RS are irreconcilable. When we estimate GPP based on RS measurements and some assumptions about RS:GPP ratios, we found the resulted global GPP values (bootstrap mean 149^(+29)_(−23) Pg C/yr) are significantly higher than most GPP estimates reported in the literature (113^(+18)_(−18) Pg C/yr). Similarly, historical GPP estimates imply a soil respiration flux (Rs(_GPP), bootstrap mean of 68^(+10)_(−8) Pg C/yr) statistically inconsistent with most published RS values (87^(+9)_(−8) Pg C/yr), although recent, higher, GPP estimates are narrowing this gap. Furthermore, global R_(S):GPP ratios are inconsistent with spatial averages of this ratio calculated from individual sites as well as CMIP6 model results. This discrepancy has implications for our understanding of carbon turnover times and the terrestrial sensitivity to climate change. Future efforts should reconcile the discrepancies associated with calculations for GPP and Rs to improve estimates of the global carbon budget.

Jinshi Jian↗

Comparing different generations of idealized solar geoengineering simulations in the Geoengineering Model Intercomparison Project (GeoMIP)

Abstract. Solar geoengineering has been receiving increased attention in recent years as a potential temporary solution to offset global warming. One method of approximating global-scale solar geoengineering in climate models is via solar reduction experiments. Two generations of models in the Geoengineering Model Intercomparison Project (GeoMIP) have now simulated offsetting a quadrupling of the CO2 concentration with solar reduction. This simulation is idealized and designed to elicit large responses in the models. Here, we show that energetics, temperature, and hydrological cycle changes in this experiment are statistically indistinguishable between the two ensembles. Of the variables analyzed here, the only major differences involve highly parameterized and uncertain processes, such as cloud forcing or terrestrial net primary productivity. We conclude that despite numerous structural differences and uncertainties in models over the past two generations of models, including an increase in climate sensitivity in the latest generation of models, the models are consistent in their aggregate climate response to global solar dimming.

54 ENVIRONMENTAL SCIENCES↗

SWOT Applications for WRF-Hydro Modeling in Alaska

The Surface Water Ocean Topography (SWOT) mission, launching next year, will provide high-spatial resolution measurements of terrestrial surface water, including global rivers with widths greater than 50-100 m. SWOT measurements are naturally suited for stream hydrology, and many previous studies have worked to quantify the impact of SWOT observations on the modeling of channel flow. This work highlights the application of SWOT for WRF-Hydro modeling in Alaska for data assimilation and model calibration to support ongoing National Oceanic and Atmospheric Administration (NOAA) National Water Model development. Results demonstrate the effectiveness of using SWOT discharge estimates to calibrate WRF-Hydro in ungauged basins, and quantifies the impact of SWOT data assimilation on WRF-Hydro performance.

Nicholas Elmer↗

Nitrification, denitrification, and competition for soil N : Evaluation of two Earth System Models against observations

Abstract Earth System Models (ESMs) have implemented nitrogen (N) cycles to account for N limitation on terrestrial carbon uptake. However, representing inputs, losses, and recycling of N in ESMs is challenging. Here, we use global rates and ratios of key soil N fluxes, including nitrification, denitrification, mineralization, leaching, immobilization, and plant uptake (both NH 4 + and NO 3 − ), from the literature to evaluate the N cycles in the land model components of two ESMs. The two land models evaluated here, E3SM Land Model version 1 (ELMv1)‐ECA and CLM5.0, originated from a common model but have diverged in their representation of plant–microbe competition for soil N. The models predict similar global rates of gross primary productivity (GPP) but have approximately two‐fold to three‐fold differences in their underlying global mineralization, immobilization, plant N uptake, nitrification, and denitrification fluxes. Both models dramatically underestimate the immobilization of NO 3 − by soil bacteria compared with literature values and predict dominance of plant uptake by a single form of mineral nitrogen (NO 3 − for ELM, with regional exceptions, and NH 4 + for CLM5.0). CLM5.0 strongly underestimates the global ratio of gross nitrification:gross mineralization and both models are likely to substantially underestimate the ratio of nitrification:denitrification. Few experimental data exist to evaluate this last ratio, in part because nitrification and denitrification are quantified using different techniques and because denitrification fluxes are difficult to measure at all. More observational constraints on soil nitrogen fluxes such as nitrification and denitrification, as well as greater scrutiny of the functional impact of introducing separate NH 4 + and NO 3 − pools into ESMs, could help to improve confidence in present and future simulations of N limitation on the carbon cycle.

Nevison, Cynthia↗

Variations in lithospheric thickness on Venus

Recent analyses of Magellan data have indicated many regions exhibiting topograhic flexure. On Venus, flexure is associated predominantly with coronae and the chasmata with Aphrodite Terra. Modeling of these flexural signatures allows the elastic and mechanical thickness of the lithosphere to be estimated. In areas where the lithosphere is flexed beyond its elastic limit the saturation moment provides information on the strength of the lithosphere. Modeling of 12 flexural features on Venus has indicated lithospheric thicknesses comparable with terrestrial values. This has important implications for the venusian heat budget. Flexure of a thin elastic plate due simultaneously to a line load on a continuous plate and a bending moment applied to the end of a broken plate is considered. The mean radius and regional topographic gradient are also included in the model. Features with a large radius of curvature were selected so that a two-dimensional approximation could be used. Comparisons with an axisymmetric model were made for some features to check the validity of the two-dimensional assumption. The best-fit elastic thickness was found for each profile crossing a given flexural feature. In addition, the surface stress and bending moment at the first zero crossing of each profile were also calculated. Flexural amplitudes and elastic thicknesses obtained for 12 features vary significantly. Three examples of the model fitting procedures are discussed.

Johnson, C. L.↗

Wind enhanced planetary escape: Collisional modifications

The problem of thermal escape is considered in which both the effects of thermospheric winds at the exobase and collisions below the exobase are included in a Monte Carlo calculation. The collisions are included by means of a collisional relaxation layer of a background gas which models the transition region between the exosphere and the thermosphere. The wind effects are considered in the limiting cases of vertical and horizontal flows. Two species are considered: terrestrial hydrogen and terrestrial helium. In the cases of terrestrial hydrogen the escape fluxes were found to be strongly filtered or throttled by collisions at high exospheric temperatures. The model is applied to molecular hydrogen diffusing through a methane relaxation layer under conditions possible on Titan. The results are similar to the case of terrestrial hydrogen with wind enhanced escape being strongly suppressed by collisions. It is concluded that wind enhanced escape is not an important process on Titan.

Curtis, S. A.↗

Possible wave amplitudes in shocks in the solar corona - Predictions for Solar Probe

Terrestrial shock measurements are scaled to coronal parameters to demonstrate the need for improvements for the Solar Probe instrumentation. A model of coronal shock is presented to estimate corresponding shock parameters, and a comparison is made with ISEE 3 crossings to examine terrestrial bow shock and wave activity downstream. The turbulence in the magnetosheath is scaled to predict the specific range of amplitudes and frequencies of wave regions that the Solar Probe can encounter. The high velocity of the spacecraft at perihelion constrains the potential application of present instrumentation. In order to properly characterize the coronal shocks the Solar Probe requires instrumentation that can detect shock-generated Alfven waves Doppler-shifted to frequencies of a few kHz.

Moses, S. L.↗

Selected contribution: a three-dimensional model for assessment of in vitro toxicity in balaena mysticetus renal tissue

This study established two- and three-dimensional renal proximal tubular cell cultures of the endangered species bowhead whale (Balaena mysticetus), developed SV40-transfected cultures, and cloned the 61-amino acid open reading frame for the metallothionein protein, the primary binding site for heavy metal contamination in mammals. Microgravity research, modulations in mechanical culture conditions (modeled microgravity), and shear stress have spawned innovative approaches to understanding the dynamics of cellular interactions, gene expression, and differentiation in several cellular systems. These investigations have led to the creation of ex vivo tissue models capable of serving as physiological research analogs for three-dimensional cellular interactions. These models are enabling studies in immune function, tissue modeling for basic research, and neoplasia. Three-dimensional cellular models emulate aspects of in vivo cellular architecture and physiology and may facilitate environmental toxicological studies aimed at elucidating biological functions and responses at the cellular level. Marine mammals occupy a significant ecological niche (72% of the Earth's surface is water) in terms of the potential for information on bioaccumulation and transport of terrestrial and marine environmental toxins in high-order vertebrates. Few ex vivo models of marine mammal physiology exist in vitro to accomplish the aforementioned studies. Techniques developed in this investigation, based on previous tissue modeling successes, may serve to facilitate similar research in other marine mammals.

Whales/genetics/physiology↗

Cellular Responses to Mechanical Stress Selected Contribution: A Three-Dimensional Model for Assessment of in Vitro Toxicity in Balaena Mysticetus Renal Tissue

This study established two- and three-dimensional renal proximal tubular cell cultures of the endangered species bowhead whale (Balaena mysticetus), developed SV40-transfected cultures, and cloned the 61-amino acid open reading frame for the metallothionein protein, the primary binding site for heavy metal contamination in mammals. Microgravity research, modulations in mechanical culture conditions (modeled microgravity), and shear stress have spawned innovative approaches to understanding the dynamics of cellular interactions, gene expression, and differentiation in several cellular systems. These investigations have led to the creation of ex vivo tissue models capable of serving as physiological research analogs for three-dimensional cellular interactions. These models are enabling studies in immune function, tissue modeling for basic research, and neoplasia. Three-dimensional cellular models emulate aspects of in vivo cellular architecture and physiology and may facilitate environmental toxicological studies aimed at elucidating biological functions and responses at the cellular level. Marine mammals occupy a significant ecological niche (72% of the Earth's surface is water) in terms of the potential for information on bioaccumulation and transport of terrestrial and marine environmental toxins in high-order vertebrates. Few ex vivo models of marine mammal physiology exist in vitro to accomplish the aforementioned studies. Techniques developed in this investigation, based on previous tissue modeling successes, may serve to facilitate similar research in other marine mammals.

Goodwin, T. J.↗