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At least 91 records · Page 5

AQuaRef: machine learning accelerated quantum refinement of protein structures

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.

Zubatyuk, Roman [Carnegie Mellon University, Pitts↗

Inverse design of cellular structures with the targeted nonlinear mechanical response

Advanced additive manufacturing capabilities have enabled a transformational ability to create sophisticated cellular structures using diverse materials. By altering the topology of the unit cell, the mechanical behavior, such as the stress-strain response during compression, can be modulated. Nevertheless, identifying a printable topology within an enormous design space that would precisely deliver the targeted nonlinear material response is challenging. We propose a data-driven generative framework based on a conditional variational autoencoder (cVAE) architecture that can inverse design the cellular structure based on the intended nonlinear stress-strain response. Trained on a dataset of structure-property pairs, the cVAE learns a compact and expressive latent space that enables efficient mapping from targets to feasible geometries. Two inference modes are explored: (1) decoder-only generation, which enables the exploration of diverse designs conditioned solely on the desired mechanical response, and (2) encoder-decoder generation, which further allows for the incorporation of desired topologies, ensuring the generated structure conforms to both mechanical properties and to desired-topology constraints. The results demonstrate that the model can generate structurally plausible and mechanically accurate designs, with the predicted stress-strain curves closely matching the targets. Even under joint conditioning, the model effectively balances geometric fidelity and functional performance.

36 MATERIALS SCIENCE↗

Deep transfer operator learning for partial differential equations under conditional shift

Transfer learning enables the transfer of knowledge gained while learning to perform one task (source) to a related but different task (target), hence addressing the expense of data acquisition and labelling, potential computational power limitations and dataset distribution mismatches. Here, we propose a new transfer learning framework for task-specific learning (functional regression in partial differential equations) under conditional shift based on the deep operator network (DeepONet). Task-specific operator learning is accomplished by fine-tuning task-specific layers of the target DeepONet using a hybrid loss function that allows for the matching of individual target samples while also preserving the global properties of the conditional distribution of the target data. Inspired by conditional embedding operator theory, we minimize the statistical distance between labelled target data and the surrogate prediction on unlabelled target data by embedding conditional distributions onto a reproducing kernel Hilbert space. We demonstrate the advantages of our approach for various transfer learning scenarios involving nonlinear partial differential equations under diverse conditions due to shifts in the geometric domain and model dynamics. Our transfer learning framework enables fast and efficient learning of heterogeneous tasks despite considerable differences between the source and target domains.

42 ENGINEERING↗

Controlling inversion disorder in a stoichiometric spinel magnet

In the study of frustrated quantum magnets, it is essential to be able to control the nature and degree of site disorder during the growth process, as many measurement techniques are incapable of distinguishing between site disorder and frustration-induced spin disorder. Pyrochlore-structured spinel oxides can serve as model systems of geometrically frustrated three-dimensional quantum magnets; however, the nature of the magnetism in one well-studied spinel, ZnFe 2 O 4 , remains unclear. Here, we demonstrate simultaneous control of both stoichiometry and inversion disorder in the growth of ZnFe 2 O 4 single crystals, directly yielding a revised understanding of both the collective spin behavior and lattice symmetry. Crystals grown in the stoichiometric limit with minimal site inversion disorder contravene all the previously suggested exotic spin phases in ZnFe 2 O 4 . Furthermore, the structure is confirmed on the F$\bar{4}$3m space group with broken inversion symmetry that induces antiferroelectricity. The effective tuning of magnetic behavior by site disorder in the presence of robust antiferroelectricity makes ZnFe 2 O 4 of special interest to multiferroic devices.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

VorLap

SAND2025-10210O VorLap is a vortex-induced vibration overlap prediction tool for static structures, such as parked wind turbines and marine turbines encountering fluid flow (water or air movement around them) that may induce vortex-induced vibration. This tool uses precomputed frequency domain data for specific cross-sectional shapes or a generalized shedding model, along with geometric data and structural natural frequency data, to identify areas and conditions where vortex-induced vibration may occur. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Moore, Kevin [Sandia National Lab. (SNL-CA), Liver↗

Information transfer with a twist

Holographic duals for CFTs compactified on a Riemann surface Σ with a twist are cast in the language of wedge holography. Σ starts as part of the field theory geometry in the UV and becomes part of the internal space in the IR. This allows to associate entanglement entropies with splits of the internal space in the IR geometry. Decomposing the internal space in the IR and geometrizing the corresponding subsystems separately leads to two interacting gravitational systems, similar to the intermediate holographic description in braneworld models. For Σ = T 2 the setups are used to model information transfer from a black hole to a gravitating bath. This leads to Page curves with a phase structure which precisely mirrors that in braneworld models. The transition from geometric to non-geometric entropies is also discussed for Σ = S 2 as a model for more general internal spaces in AdS/CFT.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dispersion Loss Counteracts Embedding Condensation and Improves Generalization in Small Language Models

Large language models (LLMs) achieve remarkable performance through ever-increasing parameter counts, but scaling incurs steep computational costs. To better understand LLM scaling, we study representational differences between LLMs and their smaller counterparts, with the goal of replicating the representational qualities of larger models in smaller models. We observe a geometric phenomenon which we term embedding condensation, where token embeddings collapse into a narrow cone-like subspace in some language models. Through systematic analyses across multiple Transformer families, we show that small models such as GPT2 and Qwen3-0.6B exhibit severe condensation, whereas larger models such as GPT2-x1 and Qwen3-32B are more resistant to this phenomenon. Additional observations show that embedding condensation is not reliably mitigated by knowledge distillation from larger models. To fight against it, we formulate a dispersion loss that explicitly encourages embedding dispersion during training. Experiments demonstrate that it mitigates condensation, recovers dispersion patterns seen in larger models, and yields performance gains across 10 benchmarks. We believe this work offers a principled path toward improving smaller Transformers without additional parameters.

Xiao, Xi [ORNL] (ORCID:0009000009316982)↗

Temporally continuous thermofluidic–thermomechanical modeling framework for metal additive manufacturing

Additive manufacturing (AM) is known to generate large magnitudes of residual stresses (RS) within builds due to steep and localized thermal gradients. In the current state of commercial AM technology, manufacturers generally perform heat treatments in effort to reduce the generated RS and its detrimental effects on part distortion and in-service failure. Computational models that effectively simulate the deposition process can provide valuable insights to improve RS distributions. Accordingly, it is common to employ Computational fluid dynamics (CFD) models or finite element (FE) models. While CFD can predict geometric and thermal-fluid behavior, it cannot predict the structural response (e.g., stress–strain) behavior. On the other hand, an FE model can predict mechanical behavior, but it lacks the ability to predict geometric and fluid behavior. Thus, an effectively integrated thermofluidic–thermomechanical modeling framework that exploits the benefits of both techniques while avoiding their respective limitations can offer valuable predictive capability for AM processes. In contrast to previously published efforts, the work herein describes a one-way coupled CFD-FEA framework that abandons major simplifying assumptions, such as geometric steady-state conditions, the absence of material plasticity, and the lack of detailed RS evolution/accumulation during deposition, as well as insufficient validation of results. Here, the presented framework is demonstrated for a directed energy deposition (DED) process, and experiments are performed to validate the predicted geometry and RS profile. Both single- and double-layer stainless steel 316L builds are considered. Geometric data is acquired via 3D optical surface scans and X-ray micro-computed tomography, and residual stress is measured using neutron diffraction (ND). Comparisons between the simulations and measurements reveal that the described CFD-FEA framework is effective in capturing the coupled thermomechanical and thermofluidic behaviors of the DED process. The methodology presented is extensible to other metal AM processes, including power bed fusion and wire-feed-based AM.

42 ENGINEERING↗

Microscale Mechanical‐Chemical Modeling of Granular Salt: Insights for Creep

Abstract Microscale numerical modeling is potentially an effective approach for understanding salt creep, but it is quite challenging because natural salt grain boundaries can have complex and evolving geometry, and because contacts between these deformable salt mineral grains are dynamic as a result of compaction, chemical reaction, fluid flow, and heat transfer. In this study, we have overcome these challenges and developed a new microscale mechanical‐chemical (MC) model to analyze creep of salt at the microscale, accounting for coupled deformation, dynamic contacts, and chemical reaction in granular systems with realistic geometric representations. The MC model was realized by linking a new microscale mechanical code based on the numerical manifold method (NMM) to a reactive transport code named Crunch. We simulated the processes of reorganization of the salt grains, microfracturing, and pressure solution that contribute to creep at larger scales. Based on this first quantitative microscale model, we found that sharp corners of mineral grains can dominate the contact dynamics, microfracturing, and pressure solution when salt is compacted, thus governing the structural changes and porosity loss of the system. We found that pressure solution, which preferentially dissolves sharp corners and edges, can lead to relatively high porosity loss in the system, thus playing an important role in the creep of salt. Our analysis shows that the dynamic changes of salt granular systems involving grain relocation and pressure solution can occur repeatedly and continuously, thus contributing to longer‐term creep of salt at larger scales.

58 GEOSCIENCES↗

A Machine Learning Framework for Predicting Microphysical Properties of Ice Crystals From Cloud Particle Imagery

The microphysical properties of ice crystals are important because they significantly alter the radiative properties and spatiotemporal distributions of clouds, which in turn strongly affect Earth's climate. However, it is challenging to measure key properties of ice crystals, such as mass or morphological features. Here, we present a proof-of-concept framework for predicting three-dimensional (3D) microphysical properties of ice crystals from in situ two-dimensional (2D) imagery. First, we computationally generated synthetic ice crystals using 3D modeling software along with geometric parameters estimated from the 2021 Ice Cryo-Encapsulation Balloon (ICEBall) field campaign. Then, we used synthetic crystals to train machine learning (ML) models to predict effective density ($ρ_e$), effective surface area ($A_e$), and number of bullets ($N_b$) from synthetic rosette imagery. On unseen synthetic images, our ML models accurately predicted ice crystal properties. ResNet-18 performed best, achieving $R^2$ values of 0.99 and 0.98 for $ρ_e$ and $A_e$, respectively, and MAE of 0.10 for mathematical equation in single view tasks. Stereo view ResNet-18 further reduced RMSE by 40% for $ρ_e$ and $A_e$ and reduced MAE by 0.08 for $N_b$. This work provides a novel ML-driven framework for estimating ice microphysical properties from in situ imagery, which will allow for downstream constraints on microphysical parameterizations, such as the mass-size relationship.

Ko, J. [Columbia Univ., New York, NY (United State↗

A Bayesian Multi-fidelity Neural Network to Predict Nonlinear Frequency Backbone Curves

The use of structural mechanics models during the design process often leads to the development of models of varying fidelity. Often low-fidelity models are efficient to simulate but lack accuracy, while the high-fidelity counterparts are accurate with less efficiency. Here, this paper presents a multi-fidelity surrogate modeling approach that combines the accuracy of a high-fidelity finite element model with the efficiency of a low-fidelity model to train an even faster surrogate model that parameterizes the design space of interest. The objective of these models is to predict the nonlinear frequency backbone curves of the Tribomechadynamics Research Challenge benchmark structure which exhibits simultaneous nonlinearities from frictional contact and geometric nonlinearity. The surrogate model consists of an ensemble of neural networks that learn the mapping between low and high-fidelity data through nonlinear transformations. Bayesian neural networks are used to assess the surrogate model's uncertainty. Once trained, the multi-fidelity neural network is used to perform sensitivity analysis to assess the influence of the design parameters on the predicted backbone curves. Additionally, Bayesian calibration is performed to update the input parameter distributions to correlate the model parameters to the collection of experimentally measured backbone curves.

42 ENGINEERING↗

Modular Hydronic Room Conditioning System (CRADA NFE-24-10120 Final Report)

This project presents the development and validation of high-fidelity numerical models for fin-tube heat exchangers to enable accurate performance prediction and informed design optimization. The modeling framework integrates detailed geometric specifications, thermophysical property data, and system-level constraints to simulate the heat exchanger’s behavior under a range of operating conditions. The model is calibrated using real-world product specifications and validated against experimental data collected from controlled cooling and heating tests. In cooling mode, the model captures the overall trends in capacity and outlet air temperature but tends to underpredict latent effects, especially at lower air flow rates. In heating mode, the simulation consistently overestimates both the thermal capacity and outlet air temperature, indicating the need for refinement in air-side heat transfer assumptions. Despite these deviations, the model provides a solid foundation for optimization, allowing key design variables to be tuned within physical and performance-based constraints. This research advances the ability to simulate, validate, and optimize fin-tube heat exchanger designs with greater confidence and efficiency.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Modular Hydronic Room Conditioning System

This project presents the development and validation of high-fidelity numerical models for fin-tube heat exchangers to enable accurate performance prediction and informed design optimization. The modeling framework integrates detailed geometric specifications, thermophysical property data, and system-level constraints to simulate the heat exchanger’s behavior under a range of operating conditions. The model is calibrated using real-world product specifications and validated against experimental data collected from controlled cooling and heating tests. In cooling mode, the model captures the overall trends in capacity and outlet air temperature but tends to underpredict latent effects, especially at lower air flow rates. In heating mode, the simulation consistently overestimates both the thermal capacity and outlet air temperature, indicating the need for refinement in air-side heat transfer assumptions. Despite these deviations, the model provides a solid foundation for optimization, allowing key design variables to be tuned within physical and performance-based constraints. This research advances the ability to simulate, validate, and optimize fin tube heat exchanger designs with greater confidence and efficiency.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A reaction–diffusion model for grayscale digital light processing 3D printing

We report that digital light processing (DLP) 3D printing is an additive manufacturing process that utilizes light patterns to photopolymerize a liquid resin into a solid. Due to the accuracy of modern digital micromirror devices (DMD) and recent advances in resin chemistry, it is now possible to create functionally graded structures using different light intensity values, also known as grayscale DLP (g-DLP). Different intensities of light lead to differences in the polymer crosslinking density after curing, which ultimately produces a part with gradients of material properties. However, g-DLP is a complicated process. First, the DLP printing is a highly coupled chemical and physical process that involves light propagation, chemical reactions, species diffusion, heat transfer, volume shrinkage, and changes in mechanical behaviors of the curing resin. Second, in g-DLP, light gradients create strong in plane gradients of chemical species concentrations in the curing liquid resin due to the strong dependence of light intensity on the rate of monomer crosslinking. Furthermore, light gradients through the depth create concentration gradients due to the degree of cure dependent light absorption and the use of photoabsorbers. These complex physical features of the printing process must be understood in order to properly control printing parameters such as light exposure time, printing speed, and grayscale variations to achieve accurate mechanical properties. In this paper, a photopolymerization reaction–diffusion model is developed and used in conjunction with experiments to investigate the coupled effects of light propagation, chemical reaction rates, and species diffusion during g-DLP 3D printing. The model is implemented numerically utilizing the finite difference method and simulation results are compared to experimental findings of simple printed structures. The agreement between experimental and model predictions of simple quantities of interest, such as geometric feature sizes, shows that the model can capture the overcure due to free-radical and other species diffusion during printing when grayscale patterns are employed. This model lays the groundwork for future extensions that can incorporate more complex coupled physics such as heat transfer, volume shrinkage, and material property evolution, which are critically important in utilizing g-DLP 3D printing for the fabrication of high-performance parts which excellent geometric and material property tolerances.

36 MATERIALS SCIENCE↗

Site-decorated model for unconventional frustrated magnets: Ultranarrow phase crossover and two-dimensional spin reversal transition

Here, the site-decorated Ising model is introduced to advance the understanding and experimental realization of the recently discovered one-dimensional (1D) finite-temperature ultranarrow phase crossover in an external magnetic field, while mitigating the geometric complexities of traditional bond-decorated models. The unconventional frustration and physics are clarified by exactly mapping the 1D site-decorated Ising model in a magnetic field onto a zero-field bond-decorated 𝐽 1 −𝐽 2 Ising model with conventional geometrical frustration. Furthermore, although higher-dimensional Ising models in an external field remain unsolved exactly, an exact solution for a spin-reversal transition—driven by an exotic, hidden half-ice, half-fire state induced by site decoration—is derived. This transition, triggered by a slight variation in temperature or magnetic field—without changing its direction—even in the weak-field limit, offers a promising route toward energy-efficient applications such as data storage and processing. The results suggest that site decoration offers an avenue for materials and device design, particularly in systems such as mixed 𝑑−𝑓 compounds, optical lattices, and neural networks, calling for further studies with site-decorated Heisenberg models. In addition, the site-decorated model offers a rigorous test ground for artificial intelligence (AI) in science, as the analytic derivation of the present results was not only validated but also improved by a general-purpose large language model, inspiring the use of AI as scientific discoverer.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Geometric remapping of particle distributions in the Discrete Element Model for Sea Ice (DEMSI v0.0)

Abstract. A new sea ice dynamical core, the Discrete Element Model for Sea Ice (DEMSI), is under development for use in coupled Earth system models. DEMSI is based on the discrete element method, which models collections of ice floes as interacting Lagrangian particles. In basin-scale sea ice simulations the Lagrangian motion results in significant convergence and ridging, which requires periodic remapping of sea ice variables from a deformed particle configuration back to an undeformed initial distribution. At the resolution required for Earth system models we cannot resolve individual sea ice floes, so we adopt the sub-grid-scale thickness distribution used in continuum sea ice models. This choice leads to a series of hierarchical tracers depending on ice fractional area or concentration that must be remapped consistently. The circular discrete elements employed in DEMSI help improve the computational efficiency at the cost of increased complexity in the effective element area definitions for sea ice cover that are required for the accurate enforcement of conservation. An additional challenge is the accurate remapping of element values along the ice edge, the location of which varies due to the Lagrangian motion of the particles. In this paper we describe a particle-to-particle remapping approach based on well-established geometric remapping ideas that enforces conservation, bounds preservation, and compatibility between associated tracer quantities, while also robustly managing remapping at the ice edge. One element of the remapping algorithm is a novel optimization-based flux correction that enforces concentration bounds in the case of nonuniform motion. We demonstrate the accuracy and utility of the algorithm in a series of numerical test cases.

58 GEOSCIENCES↗