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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

"Source Term Modeling for Advanced Gas Micro-Reactors"

Maintaining the safety of the public, environment, and operating personnel is the most important factor in designing, operating, maintaining, and decommissioning nuclear reactors. In recent years, there has been a growing interest in the development of micro-reactors employing TRi-structural ISOtropic (TRISO)-coated particle fuel. In gas reactors, TRISO fuel plays an important role in the safety case for high temperature reactors because of the fission product retention properties of the fuel. This ability enables the use of a functional containment strategy for the reactor where multiple barriers are used to prevent fission product release to the environment. Part of the safety analysis of these advanced reactors is the assessment of radionuclide releases under normal and accident conditions through the multiple credited safety barriers. Using conservative assumptions, a mechanistic analysis can be performed to quantify these releases that combines the probabilistic assessment of failure with analytic solutions to radionuclide transport equations. Source term modeling for TRISO fuel has been performed for previous reactor designs; however, these models are outdated, in many cases proprietary, and need updates to be applied to the current state of TRISO fuel technology and alternative gas reactor core configurations [1]. Currently, the only publicly available source term assessment for gas reactors is an expert-based Monte Carlo simulation based on the effectiveness of the fuel kernel, coating layers, and graphite block in a modular high temperature gas reactor [2]. Thus, there is a need to develop a simple, versatile, and mechanistic model of fission product release and transport in gas reactor cores that could be applied to a variety of reactors through user inputs and reactor-specific radionuclide inventories. The release is calculated by the diffusion of the key safety important fission products through the kernel, silicon carbide (SiC), graphite for both intact and defective TRISO particles based on fuel and graphite temperatures in the reactor under normal operation. These releases from the fuel enter the coolant where they can plate-out on cooler surfaces. A clean-up model is included for designs with a coolant purification system to remove fission gases. This initial distribution of fission products in the reactor serves as an initial condition for potential releases under postulated accident conditions. The model then can calculate the fission product release for any transient temperature profile and fission product releases can then be used to assess radiological dose to the workers and the public using conventional dose tools. Data on the diffusion of fission products is based on historic German TRISO experiments and the more current Department of Energy (DOE) Advanced Gas Reactor (AGR) TRISO fuel development program. The model is coded in python with inputs and outputs in excel spreadsheets, as well as python plotting utilities to aid in the interpretation of the results. References: [1] INL, NGNP Mechanistic Source Term White Paper, INL-10-17997, July 2010. [2] David A. Petti, Richard R. Hobbins, Peter Lowry, Hans Gougar, “Representative Source Terms and The Influence of Reactor Attributes on Functional Containment in Modular High Temperature Gas-cooled Reactors,” Nuclear Technology, Vol. 184, p. 181-197, Nov. 2013.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2025

Mechanistic Insights into Molecular Copper Hydride Catalysis: the Kinetic Stability of CuH Monomers toward Aggregation is a Critical Parameter for Catalyst Performance

The activity of molecular copper hydride (CuH) complexes towards the selective insertion of unsaturated hydrocarbons under mild conditions has contributed significantly to versatile methodologies for upgrading these feedstocks. However, these catalysts are particularly susceptible to deleterious aggregation, leading to the depletion of active CuH species. Little is known about the mechanisms of CuH aggregation, how it influences overall catalyst performance, and how it can be controlled. We address these challenges with mechanistic studies on a model reaction of unactivated alkene hydroboration catalyzed by (IPr*CPh 3 )CuH (LCuH). Here, we report a comprehensive mechanistic investigation of this system, identifying an aggregation pathway that continuously depletes catalytically active LCuH to form inactive CuH clusters during turnover. Deactivation of LCuH is controlled primarily by the competition between the kinetics of the initial LCuH dimerization step and that of alkene insertion. We therefore propose that a more comprehensive understanding of CuH catalyst performance must account for the kinetics of the initial LCuH dimerization step, revising a previously explored thermodynamic understanding of CuH aggregation, where the concentration of active species is controlled by equilibria established between CuH dimers and monomers. With a series of (NHC)CuH congeners (NHC = N-heterocyclic carbene), we demonstrate that ostensibly minor structural modifications to the ligand peripheries can drastically affect the LCuH dimerization kinetics, while maintaining reactivity towards on–cycle alkene insertion. We employed a computational approach based on molecular dynamics simulations to provide an in-depth understanding of how specific structural ligand modifications can substantially increase the kinetic stability of monomeric CuH catalysts. Our combined experimental and computational studies suggest strategies for rational ligand design that can be broadly applied to molecular catalyst systems that are susceptible to deactivation via aggregation pathways.

Ryan, David E. [Pacific Northwest National Laborat↗
DOE OSTI2026

A Statistician’s Overview of Physics-Informed Neural Networks for Spatio-Temporal Data

The recent success of deep neural network models with physical constraints (so-called, Physics-Informed Neural Networks, PINNs) has led to renewed interest in the incorporation of mechanistic information in predictive models. Statisticians and others have long been interested in this problem, which has led to several practical and innovative solutions dating back decades. In this overview, we focus on the problem of data-driven prediction and inference of dynamic spatio-temporal processes that include mechanistic information, such as would be available from partial differential equations, with a strong focus on the quantification of uncertainty associated with data, process, and parameters. Here, we give a brief review of several paradigms and focus our attention on Bayesian implementations given they naturally accommodate uncertainty quantification. We then show that it is straight-forward to include the Bayesian PINN (B-PINN) within the Bayesian hierarchical model (BHM) framework that has long been considered for modeling dynamic spatio-temporal processes. Such a BHM-PINN is illustrated via a simulation study in which a latent nonlinear Burgers’ equation PDE governs the dynamics of Poisson distributed spatio-temporal data. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Bayesian↗
DOE OSTI2025

From tides to seasons: How cyclic tidal drivers and plant physiology interact to affect carbon cycling at the terrestrial-estuarine boundary (Final technical report)

Coastal ecosystems are among the most biologically and biogeochemically active and diverse systems on Earth. Because they act as important linkages between terrestrial ecosystems and the open ocean, their incorporation in Earth system models (ESMs) is critical to predict coastal and global responses to environmental changes. However, they vary greatly in the magnitude of tides and the volume and timing of freshwater input from land, making it challenging to model the major biogeochemical reactions that control productivity and greenhouse gas emissions across coastal terrestrial aquatic interfaces (TAIs). Our overall objective was to improve mechanistic process understanding and modeling of tidal wetland hydro-biogeochemistry in coastal TAIs. We established a new flux tower site (Ameriflux US-PLo) in the oligohaline part of the Parker River to continuously monitor ecosystem-scale carbon fluxes under temporally varying salinity conditions. The site is co-located with long-term monitoring plots of the Plum Island Ecosystems LTER project. We installed wells and redox sensors in the marsh interior and creek bank, established biomass monitoring plots and deployed novel optode sensors in both locations. We used this data to parameterize plant-mediated transport in PFLOTRAN and tested the impact of soil heterogeneity on porewater constituents and gas fluxes. We collected observations of root oxygen release with a novel planar optode system in the field. Flux data collected during the measurement period encompasses a large variation in salinity ranging from drought to record precipitation years. We developed a method to extract functional relationships from the flux data using artificial neural networks, identifying salinity thresholds for CH 4 fluxes. Finally, we are using the coupled ELM-PFLOTRAN model to test the impact of antecedent hydrological conditions on the salinity-CH 4 flux relationship. This grant contributed to the professional development of one postdoc, three research assistants and one graduate student. The sensor data has been shared with external collaborators.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

Artificial Intelligence/Machine Learning (AI/ML)↗
DOE OSTI2025

Enhancing carbon storage through proactively managing fire-prone coniferous mountain forests

Mountain ecosystems typically serve as carbon (C) sinks. However, studies also suggest that they could be C sources due to climate warming, drought and insect-related mortality, wildfires, and management actions. We applied the Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS), a process-based dynamic vegetation-ecosystem model, to investigate the role of ecosystem management in C storage under Mediterranean climate over the 21 st century. We modified LPJ-GUESS to include implementing mechanical thinning by vegetation size classes, components, and types along with a new mechanistic fire-occurrence model that accounts for wind speed and lightning ignition. Simulations show that mechanical thinning or prescribed fire performed 5-20 years in advance of a high-severity wildfire reduced direct wildfire C emissions by 38-66 %. Our results also show that long-term management actions repeated every 5-20 years, including thinning relatively small trees (diameters up to 7 inches or ∼178 mm), can maintain stable C levels in the forest and lower dead-fuel amounts. We found that, although prescribed fire mitigated wildfire severity, ecosystem C storage from reduced wildfire emissions can be outweighed by the added emissions from the prescribed fire themselves. Thinning plus removing and sequestering the thinned biomass can ensure that forests act as net C sinks through the end of the 21 st century. However, addition of prescribed fire is needed to reduce understory and lower the projected extent of high-severity wildfire. Achieving the competing goals of reducing wildfire and making the Sierra Nevada long-term C sink can be advanced through carefully coordinated thinning, sequestration of thinned biomass, and prescribed fire.

Climate solutions↗
DOE OSTI2025

Attractive Noncovalent Interactions versus Steric Confinement in Asymmetric Supramolecular Catalysis

The remarkable catalytic performance of enzymes stems from their ability to engage in precise noncovalent interactions (NCIs) within a sterically confined space. Supramolecular catalysis seeks to emulate and understand these strategies through the rational design of simple and controlled catalyst microenvironments. While both steric confinement and attractive interactions have been invoked as key to host activity, their relative contribution to rate enhancement and selectivity, as well as potential trade-offs, remains an outstanding question. Here, we address this question by systematically comparing two metal–organic supramolecular catalysts, which differ in the strength of their attractive noncovalent interactions and in their cavity volume. Our findings reveal that the catalyst with the larger cavity, and with stronger available NCIs, exhibits both significant rate acceleration (100-fold) and enhanced enantioselectivity (84% vs 14% ee) in a model ketone reduction compared to its smaller analogue. Mechanistic analysis, binding competition experiments, and computational modeling indicate that these differences predominantly stem from stabilizing noncovalent interactions in the larger catalyst, a result that challenges existing steric-based models of supramolecular stereoinduction. Understanding the governing factors of asymmetric induction and rate acceleration in supramolecular hosts will undoubtedly inform future catalyst design.

Catalysts↗
DOE OSTI2026

Mechanistic mass transfer in hollow fiber membrane solvent extraction for bio-based isobutanol

Membrane solvent extraction (MSE) has emerged as a promising method for selectively recovering bioproducts from complex aqueous streams. Bio-isobutanol, a next-generation feedstock for biofuel, remains challenging to recover because of its low concentration and the presence of inhibitory substances. This study explores the potential of hollow fiber (HF) MSE for bio-isobutanol recovery and systematically examines the coupled effects of fiber packing, shell-side flow dynamics, and aqueous chemistry on performance. A resistance-in-series model is applied to understand mass transfer in the HF MSE modules, quantify local resistances, and validate overall performance. The results show that increasing the fiber packing provides a larger interfacial area but induces poor flow distribution and channeling, hindering effective isobutanol transport. Meanwhile, increasing the shell-side velocity improves isobutanol recovery due to reductions in the boundary layer thickness. The presence of salts, added to mimic fermentation broth, increases the partition coefficient through salting-out effects, further improving isobutanol flux. A modified correlation for the shell-side mass transfer coefficient (k s,ϕ+v ), integrating geometric and hydrodynamic effects, was developed and validated. The proposed model achieves highly predictive accuracy (r 2 = 0.9808) across a wide range of conditions, outperforming previous models. The findings provide mechanistic insight into the interaction of geometric packing, hydrodynamics, and chemistry in governing mass transfer in HF MSE. Overall, this work demonstrates the potential of HF MSE for efficient bio-isobutanol recovery and also provides practical guidelines on critical factors (packing fraction, partition coefficient, and shell-side velocity), aiding in the design and scaling of MSE systems for resource recovery.

Aqueous chemistry↗
DOE OSTI2026

Controlled Acidity Gradients Enable CO 2 Reduction to Formic Acid (Not Formate) by Molecular Electrocatalysts

Neutral or basic conditions are commonly required for the selective electrochemical reduction of CO 2 , leading to the accumulation of carbonate salts and the generation of formate rather than formic acid. A generalizable strategy for obtaining formic acid (not formate) in the electroreduction of CO 2 with molecular catalysts is introduced, based on controlling acidity gradients using a dual-electrolyte cell with a proton-exchange membrane. This approach uses anodic water oxidation as the source of protons and electrons for CO 2 reduction to formic acid, while mitigating H 2 evolution near the cathode and avoiding carbonate formation. Mechanistic studies, including systems modeling, provide insight into the origin of the formic acid selectivity and guide the broader implementation of this strategy in molecular electrocatalysis for CO 2 utilization.

Alcohols↗
DOE OSTI2025

Bulky Phosphine Ligands Promote Palladium-Catalyzed Protodeboronation

The Suzuki-Miyaura cross-coupling reaction is plagued by protodeboronation, an undesirable side reaction with water that consumes the boronic acid derivatives required for the cross-coupling reaction. Meticulous mechanistic studies have previously established protodeboronation to be highly sensitive to the nature of the boronic reagent and reaction conditions. Particularly, the presence of bases, which are essential for the Suzuki-Miyaura coupling, is known to catalyze protodeboronation. However, protodeboronation catalyzed by palladium-phosphine complexes, the benchmark catalyst system for Suzuki-Miyaura cross-coupling, has been understudied compared to its base-catalyzed counterpart. Here, we demonstrate, using automated high-throughput experimentation, comprehensive computational mechanistic analyses and kinetic modeling, that protodeboronation is accelerated by palladium(II) complexes bound to bulky phosphine ligands. While sterically hindered ligands are typically used to facilitate difficult cross-couplings, these ligands can instead paradoxically impede cross-coupling product formation, requiring careful and judicious consideration when choosing ligands for Suzuki-Miyaura cross-couplings.

Ser, Cher Tian [University of Toronto, ON (Canada)↗
DOE OSTI2024

Preserving isohydricity: vertical environmental variability explains Amazon forest water-use strategies

Abstract Increases in hydrological extremes, including drought, are expected for Amazon forests. A fundamental challenge for predicting forest responses lies in identifying ecological strategies which underlie such responses. Characterization of species-specific hydraulic strategies for regulating water-use, thought to be arrayed along an ‘isohydric–anisohydric’ spectrum, is a widely used approach. However, recent studies have questioned the usefulness of this classification scheme, because its metrics are strongly influenced by environments, and hence can lead to divergent classifications even within the same species. Here, we propose an alternative approach positing that individual hydraulic regulation strategies emerge from the interaction of environments with traits. Specifically, we hypothesize that the vertical forest profile represents a key gradient in drought-related environments (atmospheric vapor pressure deficit, soil water availability) that drives divergent tree water-use strategies for coordinated regulation of stomatal conductance (gs) and leaf water potentials (ΨL) with tree rooting depth, a proxy for water availability. Testing this hypothesis in a seasonal eastern Amazon forest in Brazil, we found that hydraulic strategies indeed depend on height-associated environments. Upper canopy trees, experiencing high vapor pressure deficit (VPD), but stable soil water access through deep rooting, exhibited isohydric strategies, defined by little seasonal change in the diurnal pattern of gs and steady seasonal minimum ΨL. In contrast, understory trees, exposed to less variable VPD but highly variable soil water availability, exhibited anisohydric strategies, with fluctuations in diurnal gs that increased in the dry season along with increasing variation in ΨL. Our finding that canopy height structures the coordination between drought-related environmental stressors and hydraulic traits provides a basis for preserving the applicability of the isohydric-to-anisohydric spectrum, which we show here may consistently emerge from environmental context. Our work highlights the importance of understanding how environmental heterogeneity structures forest responses to climate change, providing a mechanistic basis for improving models of tropical ecosystems.

Forestry↗
DOE OSTI2026

Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.

comparative genomics↗
DOE OSTI2021

Tradeoffs and Synergies in Tropical Forest Root Traits and Dynamics for Nutrient and Water Acquisition: Field and Modeling Advances

Vegetation processes are fundamentally limited by nutrient and water availability, the uptake of which is mediated by plant roots in terrestrial ecosystems. While tropical forests play a central role in global water, carbon, and nutrient cycling, we know very little about tradeoffs and synergies in root traits that respond to resource scarcity. Tropical trees face a unique set of resource limitations, with rock-derived nutrients and moisture seasonality governing many ecosystem functions, and nutrient versus water availability often separated spatially and temporally. Root traits that characterize biomass, depth distributions, production and phenology, morphology, physiology, chemistry, and symbiotic relationships can be predictive of plants’ capacities to access and acquire nutrients and water, with links to aboveground processes like transpiration, wood productivity, and leaf phenology. In this review, we identify an emerging trend in the literature that tropical fine root biomass and production in surface soils are greatest in infertile or sufficiently moist soils. We also identify interesting paradoxes in tropical forest root responses to changing resources that merit further exploration. For example, specific root length, which typically increases under resource scarcity to expand the volume of soil explored, instead can increase with greater base cation availability, both across natural tropical forest gradients and in fertilization experiments. Also, nutrient additions, rather than reducing mycorrhizal colonization of fine roots as might be expected, increased colonization rates under scenarios of water scarcity in some forests. Efforts to include fine root traits and functions in vegetation models have grown more sophisticated over time, yet there is a disconnect between the emphasis in models characterizing nutrient and water uptake rates and carbon costs versus the emphasis in field experiments on measuring root biomass, production, and morphology in response to changes in resource availability. Closer integration of field and modeling efforts could connect mechanistic investigation of fine-root dynamics to ecosystem-scale understanding of nutrient and water cycling, allowing us to better predict tropical forest-climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Evaluation of UKESM aerosol size and composition using ATom measurements indicates missing marine aerosol formation mechanisms

Atmospheric aerosols influence climate through their interactions with radiation and clouds, yet large uncertainties remain in their simulation by global models. This study evaluates the United Kingdom Earth System Model version 1.1 (UKESM1.1) using global-scale aircraft observations from the Atmospheric Tomography (ATom) mission, focusing on aerosol lifecycle processes in the remote marine atmosphere. We assess model performance in simulating aerosol precursor vapours, number size distributions, chemical composition, and environmental conditions. Several process improvements are tested, including sulfuric acid-ammonia nucleation, ammonium nitrate scheme, methanesulfonic acid condensation, and low-temperature isoprene-derived secondary organic aerosol formation. Model biases differ significantly between the upper troposphere (UT) and the marine boundary layer (MBL). In the UT, UKESM1.1 overestimates nucleation and Aitken mode particles while underestimating accumulation mode, indicating insufficient growth. In the MBL, the model overestimates primary aerosols (e.g. seasalt) and precursor gases but underestimates nucleation and Aitken mode particles, even after incorporating updated nucleation and ammonium nitrate scheme. The persistence of low aerosol number concentrations, despite overestimated precursors, suggests missing formation pathways likely involving other species such as iodine, amines, and organic vapours. These limitations result in an unbalanced cloud condensation nuclei budget that over-relies on primary emissions. Sensitivity tests reveal that model outputs are strongly influenced by dimethyl sulfide emissions and vapour condensation schemes. Our results highlight the need for future model development to prioritise mechanistic representation of currently missing aerosol sources, rather than relying on empirical tuning, to improve aerosol-climate interaction estimates.

He, Xu-Cheng [Univ. of Cambridge (United Kingdom);↗
DOE OSTI2025

Toward a Unified Kinetic Model of Nitrogenase Catalysis

The microbial enzyme nitrogenase catalyzes the MgATP-dependent reduction of N 2 to 2NH 3 , a transformation central to the global nitrogen cycle. While the canonical Thorneley−Lowe (TL) kinetic model has long served as a mechanistic framework, it does not incorporate several recent insights. Here, we present an updated kinetic model for Monitrogenase that incorporates these new findings. A significant insight is that electron transfer (ET) from the reduced Fe protein to the FeMo-cofactor is gated by MgATP-dependent conformational transitions and can be described as a probabilistic event that is dependent on the ligand bound to the active-site metallocofactor. The updated kinetic model quantitatively reproduces steady-state product formation rates across a broad range of experimental conditions, yielding revised estimates for key rate constants. It is demonstrated that under N 2 turnover, the probability of productive ET to the active site decreases by ∼60%, resulting in a significant fraction of Fe protein cycles that are unproductive for electron delivery. This mechanistic feature explains the observed rate limitation in N 2 reduction and implies a revised minimum energetic cost of approximately 25 MgATP per N 2 reduced. Integrating these new features into the revised kinetic model provides a more complete and usable foundation for understanding nitrogenase catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

RSPECT: A PROSPECT-based model incorporating the real structure of rice leaves

Radiative transfer models (RTMs) describe how light is absorbed, scattered, and transmitted within leaves by simulating mechanistic light propagation processes. The PROSPECT model is based on measurable parameters (the leaf biochemical content) and a non-measurable parameter (the leaf anatomical structure represented by the leaf structure parameter (N)). The effect of N on the optical properties of leaves has been investigated through a number of local and global sensitivity analyses. Other studies have directly evaluated the effect of the leaf anatomical structure on spectral reflectance, particularly in the near infrared region. However, the relationship between N and the anatomical structure is unclear. Here, in this study, we leveraged eLeaf, a ray tracing-based 3D rice leaf simulator, to establish relationships between leaf anatomical features and spectral properties, enabling us to replace N in the PROSPECT-4 model with measurable leaf anatomical parameters and develop the RSPECT model. The leaf thickness at minor vein, leaf thickness at bulliform cells, mesophyll thickness at minor vein, and distance between two minor veins could be used to predict N effectively. The RSPECT model achieved spectral simulation accuracy comparable to PROSPECT-4 and was more suitable for parameter inversion of the physical and chemical properties of rice leaves, with relative root mean square errors of 7.4% for chlorophyll content, 5.6% for equivalent water thickness, and 7.5% for dry matter content. In conclusion, RSPECT improves radiative transfer modeling by integrating measurable anatomical features and provides a framework for extending this approach to other vegetation types.

hyperspectral↗
DOE OSTI2025

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 562 times compared to single-core CPM code execution on CPU. Over short timescales of up to 3 recursive evaluations, or 300 MCS, our model captures the emergent behaviors demonstrated by the original Cellular-Potts model such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as a step toward efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM simulations of biological processes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

A Parallel Kinetic Model for Surface and Bulk Charge Storage in ε -MnO 2 Pseudocapacitors

Pseudocapacitive materials such as manganese dioxide (MnO 2 ) are attractive for energy storage applications due to their ability to combine the fast kinetics of capacitors with the higher energy density of battery-type systems. However, the electrochemical behavior of MnO 2 remains difficult to interpret mechanistically, in part because existing models often fail to distinguish between surface-based redox processes and bulk intercalation mechanisms. In this work, we develop a physics-based model that represents MnO 2 pseudocapacitance as a linear combination of two independent, parallel electrochemical processes: (i) the surface or near-surface redox storage and (ii) lithium ion intercalation into the bulk material. These two processes are treated with distinct kinetic and thermodynamic parameters and are assumed to proceed independently. The total measured current is assumed to be the sum of these two partial currents. We validate the model using rate-dependent cyclic voltammetry experiments, demonstrating that it captures key trends and provides physically interpretable parameters reflecting the relative contributions of surface and bulk processes. By enabling a clear separation between these mechanisms, the model offers a useful framework for analyzing pseudocapacitive materials and can guide the rational design of high-performance energy storage electrodes.

Energy - Storage↗