Zatom v1.0.0
Zatom is an AI foundation model for 3D molecules and materials.
Morehead, Alex [Lawrence Berkeley National Laborat↗
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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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AdditiveFOAM: A Continuum Multiphysics Code for Additive Manufacturing
AdditiveFOAM is a computational framework that simulates transport phenomena in Additive Manufacturing (AM) processes. It is built on OpenFOAM (Weller et al., 1998), the leading free, open-source software package for computational fluid dynamics (CFD). OpenFOAM offers an extensible platform for solving complex multiphysics problems using state-of-the-art finite volume methods. AdditiveFOAM leverages these capabilities to develop specialized tools aimed at addressing challenges in AM processing. Metal additive manufacturing, also known as metal 3D printing, is an advanced manufacturing technique that creates physical parts from a three-dimensional (3D) digital model by melting metal powder or wire feedstock. A significant area of research in metal AM focuses on process planning to mitigate anomalous features during printing that are deleterious to part performance (e.g., porosity and cracking), as well as controlling localized microstructure and material properties. Given the high costs and substantial time requirements associated with experimental methods for qualifying new materials and processes, there is a compelling incentive for researchers to utilize advanced computational simulations. In this context, AdditiveFOAM offers a simulation framework to better understand undesirable features in printing, thereby enhancing process planning and reducing the reliance on labor-intensive experimental campaigns.
Coleman, John [Oak Ridge National Laboratory (ORNL↗
Integrated Multiscale Model for Design of Robust 3D Solid-state Lithium Batteries
Abstract not provided.
25 ENERGY STORAGE↗
Progress towards a fully 3D, thermodynamically-consistent, constitutive model for volume changes during crystallization and melting of semicrystalline polymers
A thermodynamically-consistent constitutive model for semicrystalline polymers has been developed that is capable of representing volume strains from crystallization and melting. The new model is targeted at representing the thermal strain behavior of polymeric photo-voltaic module polymer encapsulation which may undergo crystallization and melting in their service environments. In the model, a homogenized material point is represented by a Gibbs free energy incorporating contributions from the crystalline phase, the amorphous phase, and mixing terms.
36 MATERIALS SCIENCE↗
COMSOL Simulation of Optical Whispering Gallery Mode (WGM) Resonator
We simulate whispering-gallery mode coupling in a Si$_3$N$_4$--LiNbO$_3$ waveguide--resonator system using 2D and 3D COMSOL models. Results show that the TM$_{00}$ mode couples far more efficiently than TE$_{00}$ due to weaker confinement and stronger evanescent overlap, with critical coupling reached near a 0.20~µm gap. The study highlights polarization dependence, geometric sensitivity, and birefringence as key factors shaping resonant behavior.
42 ENGINEERING↗
COMSOL Simulation of Optical Whispering Gallery Mode (WGM) Resonator
We simulate whispering-gallery mode coupling in a Si$_3$N$_4$--LiNbO$_3$ waveguide--resonator system using 2D and 3D COMSOL models. Results show that the TM$_{00}$ mode couples far more efficiently than TE$_{00}$ due to weaker confinement and stronger evanescent overlap, with critical coupling reached near a 0.20~µm gap. The study highlights polarization dependence, geometric sensitivity, and birefringence as key factors shaping resonant behavior.
Xiaoyu, Chen [Fermilab]↗
0D, 1D, 2D, and 3D simulations of an idealized coaxial impedance-matched Marx generator
We have conducted 0D, 1D, 2D, and 3D simulations of an idealized coaxial impedance-matched Marx generator (IMG) []. The 0D calculations were conducted with a four-element circuit model; the 1D, 2D, and 3D calculations were conducted with highly resolved, fully electromagnetic representations. The IMG consists of 30 stages distributed axially and connected electrically in series. Each stage is powered by two bricks separated by 180° and connected electrically in parallel. Each brick comprises two opposite-polarity capacitors in series with a single switch. The bricks drive an internal impedance-matched coaxial transmission line terminated by a resistive load. The simulations neglect effects due to the switch-triggering circuit, the capacitor-charging circuit, external conducting boundaries, and reactive components of the load. We find dimensionality does not significantly affect the electrical power delivered by the IMG to its load: peak load powers estimated by the 0D, 1D, 2D, and 3D simulations agree to within 1%. The 3D calculations demonstrate that electromagnetic power radiated by the bricks, and axial gaps between stages, reduces the peak load power by less than ∼ 1 % . Each simulation assumes the load impedance is 34% above that at which the load power is maximized. Operating an IMG with such an overmatched load offers several advantages while decreasing the peak load power by only 2%. The 0D, 1D, 2D, and 3D models outlined herein could be adapted to assess computationally competing IMG designs, and conduct a variety of numerical IMG experiments, an IMG is constructed. Published by the American Physical Society 2024
43 PARTICLE ACCELERATORS↗
Geometry-complete diffusion for 3D molecule generation and optimization
Abstract Generative deep learning methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a denoising diffusion framework. However, such methods are unable to learn important geometric properties of 3D molecules, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which notably hinders their ability to generate valid large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset and the larger GEOM-Drugs dataset, respectively. Importantly, we demonstrate that GCDM’s generative denoising process enables the model to generate a significant proportion of valid and energetically-stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that extensions of GCDM can not only effectively design 3D molecules for specific protein pockets but can be repurposed to consistently optimize the geometry and chemical composition of existing 3D molecules for molecular stability and property specificity, demonstrating new versatility of molecular diffusion models. Code and data are freely available on GitHub .
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Remote sensing images, DEM, and point clouds associated with “Accuracy evaluation of cost-effective 3D reconstruction approaches for hydrobiogeochemical processes in non-perennial stream riverbeds”
This data package is associated with the publication “Accuracy evaluation of cost-effective 3D reconstruction approaches for hydrobiogeochemical processes in non-perennial stream riverbeds” published in Frontiers in Environmental Science, Environmental Informatics and Remote Sensing (Bao et al., 2026; doi: 10.3389/fenvs.2026.1725258). This data package includes the drone photos for a section of Umtanum Creek in Washington, Unted States. The photos were used to reconstruct the 3-dimensional (3D) digital elevation model (DEM) of the riverbed for the investigated stream section. The reconstruction results from four approaches are provided: (1) unoccupied aerial vehicle (UAV, colloquially known as drone) imagery-based Structure-from-Motion (SfM), (2) a machine learning-based 3D reconstruction model, Visual Geometry Grounded Deep Structure from Motion (VGGSfM), (3) Visual Geometry Grounded Transformer for long sequence of images (VGGT-Long), and (4) handheld smartphone LiDAR scanning. The ground truth measurements by tripod-mounted optical level kit and ground control points GPS locations for evaluating the accuracy of the four reconstruction approaches are also provided in this data package. A preliminary version of this data package was published in October 2025 at the time of manuscript submission. It was updated in March 2026, at the time of manuscript acceptance, to include additional metadata (this readme, data dictionary, and file level metadata). The data did not change. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) 8 folders; (2) the detailed flight configuration html files; (3) field metadata; (4) a readme; (5) a data dictionary; and (6) file-level metadata. The folders “2024_10_18_d01” and “2024_10_18_d02” contain the original drone photos for the two drone flights (d01 and d02) on October 18, 2024. The reconstruction results from each of the approaches are in the folders called “ODM_SfM”, “VGGSfM”, “VGGTLong”, and “LiDAR”. The ground truth measurements are in the folder called “optical_level_kit”. Lastly, results comparing the different approaches are in the folder called “comparisons”. All files are .csv, .html, .jpg, .obj, .txt, and .npy. For information on using the .obj and .npy files, see the readme files within the same folder as the files.
54 ENVIRONMENTAL SCIENCES↗
Cellular response of keratinocytes to the entry and accumulation of nanoplastic particles
Plastic accumulation in the environment is rapidly increasing, and nanoplastics (NP), byproducts of environmental weathering of bulk plastic waste, pose a significant public health risk. Particles may enter the human body through many possible routes such as ingestion, inhalation, and skin absorption. However, studies on NP penetration and accumulation in human skin are limited. Loss or reduction of the keratinized skin barrier may enhance the skin penetration of NPs. The present study investigated the entry of NPs into a human skin system modeling skin with compromised barrier functions and cellular responses to the intracellular accumulations of NPs. Two in vitro models were employed to simulate human skin lacking keratinized barriers. The first model was an ex vivo human skin culture with the keratinized dermal layer (stratum corneum) removed. The second model was a 3D keratinocyte/dermal fibroblast cell co-culture model with stratified keratinocytes on the top and a monolayer of skin fibroblast cells co-cultured at the bottom. The penetration and accumulation of the NPs in different cell types were observed using fluorescent microscopy, confocal microscopy, and cryogenic electron microscopy (cryo-EM). The cellular responses of keratinocytes and dermal fibroblast cells to stress induced by NPs stress were measured. The genetic regulatory pathway of keratinocytes to the intracellular NPs was identified using transcript analyses and KEGG pathway analysis. The cellular uptake of NPs by skin cells was confirmed by imaging analyses. Transepidermal transport and penetration of NPs through the skin epidermis were observed. According to the gene expression and pathway analyses, an IL-17 signaling pathway was identified as the trigger for cellular responses to internal NP accumulation in the keratinocytes. The transepidermal NPs were also found in co-cultured dermal fibroblast cells and resulted in a large-scale transition from fibroblast cells to myofibroblast cells with enhanced production of α-smooth muscle actin and pro-Collagen Ia. The upregulation of inflammatory factors and cell activation may result in skin inflammation and ultimately trigger immune responses.
36 MATERIALS SCIENCE↗
Energy Conversion and Electron Acceleration and Transport in 3D Simulations of Solar Flares
Recent observations and simulations indicate that solar flares undergo extremely complex 3D evolution, making 3D particle transport models essential for understanding electron acceleration and interpreting flare emissions. In this study, we investigate this problem by solving Parker’s transport equation with 3D MHD simulations of solar flares. By examining energy conversion in the 3D system, we evaluate the roles of different acceleration mechanisms, including reconnection current sheet (CS), termination shock (TS), and supra-arcade downflows (SADs). We find that large-amplitude turbulent fluctuations are generated and sustained in the 3D system. The model results demonstrate that a significant number of electrons are accelerated to hundreds of keV and even a few MeV, forming power-law energy spectra. These energetic particles are widely distributed, with concentrations at the TS and in the flare looptop region, consistent with results derived from recent hard X-ray (HXR) and microwave (MW) observations. By selectively turning particle acceleration on or off in specific regions, we find that the CS and SADs effectively accelerate electrons to several hundred keV, while the TS enables further acceleration to MeV. However, no single mechanism can independently account for the significant number of energetic electrons observed. Instead, the mechanisms work synergistically to produce a large population of accelerated electrons. Our model provides spatially and temporally resolved electron distributions in the whole flare region and at the flare footpoints, enabling synthetic HXR and MW emission modeling for comparison with observations. These results offer important insights into electron acceleration and transport in 3D solar flare regions.
79 ASTRONOMY AND ASTROPHYSICS↗
Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system
The soft corals (Cnidaria, Octocorallia), a diverse group of colonial marine invertebrates, can reversibly tune their body stiffness in response to external stimuli. This capability is attributed to their dynamic skeletal systems, which consist of thousands of mineralized skeletal elements, called sclerites, embedded within a gel-like matrix that swells/deswells and unjams/jams the sclerites, thus modulating skeletal stiffness. While sclerite morphology is widely used for species identification, its role in the mechanical performance of a soft coral’s skeletal system is largely unknown. Here, we investigated structure-jamming relationships in sclerite-based skeletal architectures using the red gorgonian octocoral Leptogorgia chilensis as a model system. The sclerites of L. chilensis exhibit a shaft-like geometry with two axial branches and two sets of triradiate side branches, which are aligned with the crystallographic symmetry of the constituent magnesium-containing calcite. By combining multiscale three-dimensional (3D) structural characterization, parametric geometrical modeling, 3D printing, mechanical testing, and discrete element simulations, we demonstrate how sclerite geometry achieves a balanced jamming performance in terms of stiffness, weight, strength, and fracture resistance in comparison to alternative geometries parametrically modified from the native sclerites (e.g., changes in the length and number of side branches). Here, we also found that these performance metrics are achieved through the effective interlocking among side and axial branches, which is further enhanced by the fractal-like microscopic spikes on the branch tips. The findings in this natural jamming system offer insights for designing synthetic mechanotunable material architectures for a wide range of applications, from soft robotics to mechanical dampeners.
36 MATERIALS SCIENCE↗
Multiscale Modeling Framework for Lithium Nucleation in 3D Porous Carbon Anodes
Porous carbon scaffolds offer a promising route for mitigating non-uniform lithium (Li) plating to enhance the safety and longevity of Li metal batteries. However, the influence of microstructural morphology on Li nucleation is not well understood. Here, we present a multiscale modeling framework to investigate how the porous microstructure of carbon materials affects Li nucleation behavior. Ab initio molecular dynamics simulations quantify the nucleation energy barriers of Li on graphene as a function of Li content, surface curvature, and applied potential, providing key parameters for a classical nucleation theory (CNT) model. From macroscale half-cell simulations, we obtained Li concentration and electrical potential profiles to define boundary conditions for mesoscopic simulations. At the mesoscale, three distinct synthetic 3D microstructures with different porosities and characteristic feature sizes are generated to resolve local distributions of Li flux, current density, and mechanical stress. These outputs are integrated into the CNT model to map spatial variation in nucleation rates. Our findings reveal trade-offs between suppressing nucleation rates and achieving spatial uniformity, offering design guidelines for optimizing porous carbon anodes to balance nucleation control and mechanical integrity.
Materials science↗
A machine-learning approach to measure 3D sample properties from 2D Transmission Electron Microscopy images
Transmission Electron Microscopy (TEM) is a powerful tool for the characterization of materials at the nanoscale; however, its inherent two-dimensional (2D) nature poses significant challenges to accurately measure three-dimensional (3D) properties. We introduce a supervised machine-learning model that predicts 3D structural information, such as sample thickness and curvature, from a series of conventional 2D TEM images. The model, a U-Net convolutional neural network, is trained on a large synthetic dataset generated from dynamical diffraction simulations that model TEM’s complex, nonlinear image formation, accounting for sample thickness and curvature. This physically realistic framework enables exploration of a broad parameter space impractical to sample experimentally. We demonstrate that the trained model has accurate predictions for experimental single-crystal silicon samples, achieving performance comparable to established measurement techniques. This work highlights the critical role of robust, simulation-based training in overcoming the limitations of real-world imaging artifacts and inconsistent sample geometries. By integrating machine learning with numerical simulations, we offer an efficient and scalable framework for quantitative TEM analysis, paving the way for more sophisticated 3D characterization of complex materials.
Dynamical diffraction↗
Clumping index estimation with 30°-tilted cameras in row crops: Evaluation of methods and segment size effects
The clumping index (CI) quantifies the spatial distribution of foliage elements and is essential for accurately estimating the plant area index (PAI), canopy radiative transfer, and photosynthesis. Traditionally, the finite-length averaging method (LX), the gap size distribution method (CC), and a combined approach of CC and LX (CLX) have been applied to instruments like TRAC and digital hemispherical photography to estimate CI. However, a comprehensive evaluation of these methods in row crops remains limited, especially regarding the influence of segment size on CI. Meanwhile, digital cameras offer a cost-effective and user-friendly solution for canopy measurements in row crops, yet their application in this context remains underexplored. In this study, we employed a new approach using a 30°-tilted digital camera to estimate CI in corn and soybean fields, applying the LX, CC, and CLX methods. We systematically assessed the performance of these three methods by combining field measurements in real-world fields with simulations using the LESS 3D radiative transfer model. Our results showed that CLX applied to the whole image and 45° segment offered accurate estimation of CI (bias within ±0.1, RMSE < 0.2) and PAI (bias within ±0.4, RMSE < 1) in real-world fields and LESS simulations. The accuracy of the LX method was highly sensitive to segment size, with the best performance observed at the 15° segment (PAI bias within ±0.4). In contrast, the CC method remained stable across different segment sizes, and its performance was generally comparable to that of LX, except at the 15° segment. Across view zenith angles, CI derived from CC generally showed a continuous increase, while those from LX and CLX followed a rising trend at small zenith angles but began to decline at 68°, likely due to an increasing proportion of no-gap segments. Seasonally, LX tended to show decreasing CI during early growth stages but increased as the canopy matured, whereas CC and CLX showed gradually increasing CI before plateauing at peak PAI. The 30°-tilted camera effectively captured CI variations across different angles and growth stages, making it a practical and robust instrument for row crop canopy structure analysis. Furthermore, applying these CI methods to digital cameras offers a low-cost and accessible CI estimation alternative, improving canopy structure monitoring accuracy in row crops.
30°-tilted camera↗
STILGAR End-of-Project Report
The Subsurface Tunnel Imaging LeveraGed by Analysis of Rayleigh wave ellipticity (STILGAR) project demonstrated an integrated geophysical approach for detecting, locating, and characterizing underground structural changes using dense seismic arrays and advanced inversion techniques. Field campaigns were conducted at two operational mines—the Redmond salt mine (Utah) and Graymont Pleasant Gap limestone mine (Pennsylvania)—providing real-world testbeds for monitoring anthropogenic subsurface activity. At the Redmond salt mine, seismic interferometry combined with back-projection inversion successfully identified continuous, low-amplitude signals from mining operations. The approach differentiated stationary from migrating anthropogenic sources, captured daily operational cycles, and validated the potential of passive seismic monitoring for remote detection of underground activity. At the Graymont Pleasant Gap mine, two dense seismic deployments in the spring and fall of 2023 generated over 4 TB of high-resolution data. Key outcomes included the relocation of 199 underground and 8 surface explosions with accuracies within tens of meters and the development of a 3D P-wave velocity model using the triple-difference tomography algorithm (tomoTD) that resolved major structural features such as the mine entrance, low-velocity tunnels, and roof-collapse areas. Ambient noise cross-correlation and back-projection analyses revealed persistent sources linked to ongoing mining activity, whereas horizontal-to-vertical spectral ratio (HVSR) and ellipticity studies confirmed stable site responses across seasons and identified soil thickness trends consistent with regional erosional and depositional processes. Checkerboard and sensitivity tests further validated the robustness of the tomographic results. Overall, the findings emphasize that although significant progress has been made in subsurface imaging, further work is needed to enhance the detection and localization of underground structures. Accurate imaging requires higher frequencies, yet anthropogenic sources tend to dominate the seismic record at those frequencies, and high-frequency surface waves are affected by higher modes that complicate interpretation. The improved detection and localization of human-induced signals enabled detailed temporal and spatial mapping of daily mine operations, demonstrating the feasibility of continuous anthropogenic source monitoring. Sensitivity to signals from nontraditional sources, such as fan operations, highlights the broader applicability of this approach to other industrial environments in which continuous and impulsive signals are present. The field campaigns produced a substantial volume of high-quality seismic data, supporting the development and testing of new methods for seismic source characterization and subsurface imaging. Future deployments should include sensors capable of recording lower frequencies to probe deeper structures, increase bandwidth to enhance resolution and sensitivity to both shallow and deep targets, and collect additional large-scale datasets to refine imaging and source characterization techniques. Moreover, conducting 3D modeling studies of seismic wavefields at higher frequencies will provide a better understanding of wave scattering and cavity–wavefield interactions in complex underground environments. In conclusion, the STILGAR project demonstrated that integrated seismic monitoring can effectively characterize underground operations, capturing both natural and anthropogenic signals. The approaches developed provide a foundation for improved detection, localization, and imaging of subsurface structures and are directly transferable to broader industrial monitoring applications.
58 GEOSCIENCES↗
Public Data Set: Modeling of Injected Current Stream-Induced 3D Perturbations in Local Helicity Injection Plasmas
This public dataset contains openly-documented, machine readable digital research data corresponding to figures published in C.E. Schaefer et al., “Modeling of Injected Current Stream-Induced 3D Perturbations in Local Helicity Injection Plasmas,” accepted for publication in Physics of Plasmas.
Schaefer, Carolyn E [University of Wisconsin-Madis↗
Automated 3D cytoplasm segmentation in soft X-ray tomography
Cells’ structure is key to understanding cellular function, diagnostics, and therapy development. Soft X-ray tomography (SXT) is a unique tool to image cellular structure without fixation or labeling at high spatial resolution and throughput. Fast acquisition times increase demand for accelerated image analysis, like segmentation. Currently, segmenting cellular structures is done manually and is a major bottleneck in the SXT data analysis. This paper introduces ACSeg, an automated 3D cytoplasm segmentation model. ACSeg is generated using semi-automated labels and 3D U-Net and is trained on 43 SXT tomograms of immune T cells, rapidly converging to high-accuracy segmentation, therefore reducing time and labor. Furthermore, adding only 6 SXT tomograms of other cell types diversifies the model, showing potential for optimal experimental design. ACSeg successfully segmented unseen tomograms and is published on Biomedisa, enabling high-throughput analysis of cell volume and structure of cytoplasm in diverse cell types.
59 BASIC BIOLOGICAL SCIENCES↗