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At least 829 records · Page 46

A multifidelity deep operator network approach to closure for multiscale systems

Projection-based reduced order models (PROMs) have shown promise in representing the behavior of multiscale systems using a small set of generalized (or latent) variables. Despite their success, PROMs can be susceptible to inaccuracies, even instabilities, due to the improper accounting of the interaction between the resolved and unresolved scales of the multiscale system (known as the closure problem). In the current work, we interpret closure as a multifidelity problem and use a multifidelity deep operator network (DeepONet) framework to address it. In addition, to enhance the stability and/or accuracy of the multifidelity-based closure, we employ the recently developed ``in-the-loop" training approach from the literature on coupling physics and machine learning models. The resulting approach is tested on shock advection for the one-dimensional viscous Burgers equation and vortex merging for the two-dimensional Navier-Stokes equations. Furthermore, the numerical experiments show significant improvement of the predictive ability of the closure-corrected PROM over the un-corrected one both in the interpolative and the extrapolative regimes.

42 ENGINEERING↗

Quasi-one-dimensional hydrogen bonding in nanoconfined ice

Abstract The Bernal-Fowler ice rules stipulate that each water molecule in an ice crystal should form four hydrogen bonds. However, in extreme or constrained conditions, the arrangement of water molecules deviates from conventional ice rules, resulting in properties significantly different from bulk water. In this study, we employ machine learning-driven first-principles simulations to identify a new stabilization mechanism in nanoconfined ice phases. Instead of forming four hydrogen bonds, nanoconfined crystalline ice can form a quasi-one-dimensional hydrogen-bonded structure that exhibits only two hydrogen bonds per water molecule. These structures consist of strongly hydrogen-bonded linear chains of water molecules that zig-zag along one dimension, stabilized by van der Waals interactions that stack these chains along the other dimension. The unusual interplay of hydrogen bonding and van der Waals interactions in nanoconfined ice results in atypical proton behavior such as potential ferroelectric behavior, low dielectric response, and long-range proton dynamics.

Science & Technology - Other Topics↗

Weighted Composition Operators for Learning Nonlinear Dynamics

Operator theoretic methods in dynamical system have been dominated by the use of Koopman operators and their continuous time counterparts, such as Koopman Generators and Liouville Operators. The advantage gained from their use primarily stems from the ability to extract subspaces and eigenfunctions within a space of observables that are invariant with respect to the Koopman operator over that space. When this occurs, a dynamic mode decomposition of the systems state provides a linear model for the dynamical system. Not all Koopman operators have eigenfunctions that may be exploited in this manner. However, the framework can still be leveraged for approximations using other operators. In this setting, we present a different operator for the study of dynamical systems, the weighted composition operator. These operators are compact for a wide range of dynamics and spaces, and through their interactions with occupation kernels and vector valued kernels, they admit an estimation of the underlying dynamics. Here, this manuscript presents a new algorithm for the data driven study of dynamical systems from data, and also provides two numerical experiments where convergence is achieved as a proof of concept.

97 MATHEMATICS AND COMPUTING↗

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

Real-time dynamics of the Schwinger model as an open quantum system with Neural Density Operators

Ab-initio simulations of multiple heavy quarks propagating in a Quark-Gluon Plasma are computationally difficult to perform due to the large dimension of the space of density matrices. This work develops machine learning algorithms to overcome this difficulty by approximating exact quantum states with neural network parametrisations, specifically Neural Density Operators. As a proof of principle demonstration in a QCD-like theory, the approach is applied to solve the Lindblad master equation in the 1 + 1d lattice Schwinger Model as an open quantum system. Neural Density Operators enable the study of in-medium dynamics on large lattice volumes, where multiple-string interactions and their effects on string-breaking and recombination phenomena can be studied. Thermal properties of the system at equilibrium can also be probed with these methods by variationally constructing the steady state of the Lindblad master equation. Scaling of this approach with system size is studied, and numerical demonstrations on up to 32 spatial lattice sites and with up to 3 interacting strings are performed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The Role of Chemistry in Fracture Pattern Development and Opportunities to Advance Interpretations of Geological Materials

Abstract Fracture pattern development has been a challenging area of research in the Earth sciences for more than 100 years. Much has been learned about the spatial and temporal complexity inherent to these systems, but severe challenges remain. Future advances will require new approaches. Chemical processes play a larger role in opening‐mode fracture pattern development than has hitherto been appreciated. This review examines relationships between mechanical and geochemical processes that influence the fracture patterns recorded in natural settings. For fractures formed in diagenetic settings (~50 to 200 °C), we review evidence of chemical reactions in fractures and show how a chemical perspective helps solve problems in fracture analysis. We also outline impediments to subsurface pattern measurement and interpretation, assess implications of discoveries in fracture history reconstruction for process‐based models, review models of fracture cementation and chemically assisted fracture growth, and discuss promising paths for future work. To accurately predict the mechanical and fluid flow properties of fracture systems, a processes‐based approach is needed. Progress is possible using observational, experimental, and modeling approaches that view fracture patterns and properties as the result of coupled mechanical and chemical processes. A critical area is reconstructing patterns through time. Such data sets are essential for developing and testing predictive models. Other topics that need work include models of crystal growth and dissolution rates under geological conditions, cement mechanical effects, and subcritical crack propagation. Advances in machine learning and 3‐D imaging present opportunities for a mechanistic understanding of fracture formation and development, enabling prediction of spatial and temporal complexity over geologic timescales. Geophysical research with a chemical perspective is needed to correctly identify and interpret fractures from geophysical measurements during site characterization and monitoring of subsurface engineering activities.

58 GEOSCIENCES↗

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗

CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling

Large-scale simulations with complex electron interactions remain one of the greatest challenges for atomistic modelling. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study technologically relevant phenomena. Here we present the Crystal Hamiltonian Graph Neural Network (CHGNet), a graph neural network-based machine-learning interatomic potential (MLIP) that models the universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory calculations of more than 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li x MnO 2 , the finite temperature phase diagram for Li x FePO 4 and Li diffusion in garnet conductors. We highlight the significance of charge information for capturing appropriate chemistry and provide insights into ionic systems with additional electronic degrees of freedom that cannot be observed by previous MLIPs.

36 MATERIALS SCIENCE↗

My Virtual Cancer

Since each cancer has its own unique characteristics, each one can respond differently to the same treatments. Therefore, the creation of a digital twin (DT) of cancer can assist us in predicting the evolution of an individual's cancer through modeling each tumor's characteristics and response to treatment. Hence, we propose to take advantage of new advances in computational approaches and combine mechanistic, machine learning, and stochastic modeling approaches to create “My Virtual Cancer", a DT platform. To establish a personalized DT, we use patient-specific data for parameter estimations, sensitivity analysis, and uncertainty quantification. For each patient, we will estimate the values of parameters of their QSP model using the patient's data. We perform a multi-dimensional sensitivity analysis and uncertainty quantification on the mechanistic model to find a set of critical interactions and predict the intervals of confidence. Since this QSP model includes the data-driven mechanistic model of cells and molecules' interaction networks, one of the ultimate results of this DT would be the prediction of evolution of tumors.

60 APPLIED LIFE SCIENCES↗

Control simulations of many-body quantum systems by a synergism of discrete real-time learning and optimal control theory

We present a self-consistent algorithm for optimal control simulations of many-body quantum systems. The algorithm features a two-step synergism that combines discrete real-time machine learning (DRTL) with Quantum Optimal Control Theory (QOCT) using the time-dependent Schrödinger equation. Specifically, in step (1), DRTL is employed to identify a compact working space (i.e., the important portion of the Hilbert space) for the time evolution of the many-body quantum system in the presence of a control field (i.e., the initial or previously updated field), and in step (2), QOCT utilizes the DRTL-determined working space to find a newly updated control field for a chosen objective. Steps 1 and 2 are iterated until a self-consistent control objective value is reached such that the resulting optimal control field yields the same targeted objective value when the corresponding working space is systematically enlarged. Furthermore, to demonstrate this two-step self-consistent DRTL-QOCT synergistic algorithm, we perform optimal control simulations of strongly interacting 1D as well as 2D Heisenberg spin systems. In both scenarios, only a single spin (at the left end site for 1D and the upper left corner site for 2D) is driven by the time-dependent control fields to create an excitation at the opposite site as the target. It is found that, starting from all spin-down zero excitation states, the synergistic method is able to identify working spaces and convergence of the desired controlled dynamics with just a few iterations of the overall algorithm. In the cases studied, the dimensionality of the working space scales only quasi-linearly with the number of spins.

Artificial neural networks↗

MOOSE ProbML: Parallelized probabilistic machine learning and uncertainty quantification for computational energy applications

Here, this paper presents the development and demonstration of massively parallel probabilistic machine learning (ML) and uncertainty quantification (UQ) capabilities within the Multiphysics Object-Oriented Simulation Environment (MOOSE), an open-source computational platform for parallel finite element and finite volume analyses. In addressing the computational expense and uncertainties inherent in complex multiphysics simulations, this paper integrates Gaussian process (GP) variants, active learning, Bayesian inverse UQ, adaptive forward UQ, Bayesian optimization, evolutionary optimization, and Markov chain Monte Carlo (MCMC) within MOOSE. It also elaborates on the interaction among key MOOSE systems — Sampler, MultiApp, Reporter, and Surrogate — in enabling these capabilities. The modularity offered by these systems enables development of a multitude of probabilistic ML and UQ algorithms in MOOSE. Example code demonstrations include parallel active learning and parallel Bayesian inference via active learning. The impact of these developments is illustrated through five applications relevant to computational energy applications: UQ of nuclear fuel fission product release, using parallel active learning Bayesian inference; very rare events analysis in nuclear microreactors using active learning; advanced manufacturing process modeling using multi-output GPs (MOGPs) and dimensionality reduction; fluid flow using deep GPs (DGPs); and tritium transport model parameter optimization for fusion energy, using batch Bayesian optimization. These capabilities are part of the MOOSE framework.

97 - MATHEMATICS AND COMPUTING↗

Controlling extrapolations of nuclear properties with feature selection

Predictions of nuclear properties far from measured data are inherently inaccurate because of uncertainties in our knowledge of nuclear forces and in our treatment of quantum many-body effects in strongly-interacting systems. While the model bias can be directly calculated when experimental data is available, only an estimate can be made in the absence of such measurements. Current approaches to compute the estimated bias quickly lose predictive power when their input variables are taken far from the training region, resulting in uncontrolled uncertainties in applications such as nucleosynthesis simulations. In this letter, we present a novel technique to identify the input variables of machine learning algorithms that can provide robust estimates of model bias. Our process is based on selecting input variables, or features, based on their probability distribution functions across the entire nuclear chart. We illustrate our approach on the problem of quantifying the model bias in nuclear binding energies calculated with Density Functional Theory (DFT). We prove that building model biases with only Z and N as features leads to highly unreliable extrapolations. Conversely, we show that proper feature selection can systematically improve theoretical predictions without increasing uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability

Snow plays a critical role in carbon cycling, vegetation dynamics, and permafrost hydrology at high latitudes by influencing surface energy exchange. Predicting snow distribution patterns is essential for understanding the evolution of Arctic ecosystems, yet scaling process-level knowledge to landscape predictions remains challenging. Here, we analyze snow depth (2019 and 2022), terrain elevation, and vegetation height from a watershed on the Seward Peninsula, Alaska, to examine how topography and shrubs shape snow redistribution across spatial scales. We find that snow depth is strongly coupled to terrain at scales below ∼60 m but becomes increasingly decoupled at larger scales. The topographic model of snow depth variation, which transforms terrain data to align with these scale-dependent snow patterns, is well correlated with local snow depth variations (linear fit R 2 > 0.5 for 85% of 100-m patches). A machine learning reconstruction of shrub canopy snow trapping reveals a simple exponential relationship between canopy structure and snow accumulation ( R 2 = 0.59), highlighting the combined influence of topography and vegetation on snow distribution. Together, these empirical relationships capture much of the observed snow variability in the watershed ( R 2 = 0.49, root mean square error (RMSE) = 30 cm), though systematic limitations persist in areas of strong scour and at coarser scales where wind-terrain interactions are more complex. These findings provide a framework for more efficient snow depth prediction and offer insights to improve snow-vegetation feedback representation in Earth System Models.

54 ENVIRONMENTAL SCIENCES↗

Structure of chalcogen overlayers on Au(111): Density functional theory and lattice-gas modeling

Ordering of different chalcogens, S, Se, and Te, on Au(111) exhibit broad similarities but also some distinct features, which must reflect subtle differences in relative values of the long-range pair and many-body lateral interactions between adatoms. We develop lattice-gas (LG) models within a cluster expansion framework, which includes about 50 interaction parameters. These LG models are developed based on density functional theory (DFT) analysis of the energetics of key adlayer configurations in combination with the Monte Carlo (MC) simulation of the LG models to identify statistically relevant adlayer motifs, i.e., model development is based entirely on theoretical considerations. The MC simulation guides additional DFT analysis and iterative model refinement. Given their complexity, development of optimal models is also aided by strategies from supervised machine learning. The model for S successfully captures ordering motifs over a broader range of coverage than achieved by previous models, and models for Se and Te capture the features of ordering, which are distinct from those for S. More specifically, the modeling for all three chalcogens successfully explains the linear adatom rows (also subtle differences between them) observed at low coverages of ~0.1 monolayer. The model for S also leads to a new possible explanation for the experimentally observed phase with a (5 × 5)-type low energy electron diffraction (LEED) pattern at 0.28 ML and to predictions for LEED patterns that would be observed with Se and Te at this coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

matsim-agents v1.0

matsim-agents is a multi-agent AI framework for atomistic materials simulation and discovery. It orchestrates large language models (LLMs), machine-learned interatomic potentials (MLIPs), and DFT codes into a single agentic loop running on laptops and DOE leadership-class supercomputers. MULTI-AGENT ORCHESTRATION A LangGraph state machine with three nodes: a Planner that converts a natural-language research objective into structured tasks; an Executor that dispatches atomistic tools and loops until the queue is empty; and an Analyst that summarizes results into a human-readable report. State is checkpointed after every step and human-in-the-loop gates can be inserted at any edge. HYPOTHESIS-DRIVEN DISCOVERY CHAT An interactive REPL (matsim-agents chat) that couples LLM dialogue with atomistic simulation. Chemical formulas are automatically detected in conversation turns and trigger a full crystal-phase exploration: structure generation → relaxation → stability scoring → result injection back into the conversation, creating a closed hypothesis-refinement loop. CRYSTAL PHASE ENUMERATION Given a composition, the phase explorer enumerates prototypes by stoichiometry: elemental (fcc/bcc/hcp/sc/diamond), binary 1:1 (rocksalt/CsCl/zincblende/ wurtzite/fluorite/rutile), ternary 1:1:3 (cubic perovskite), ternary 1:2:4 (perovskite + spinel), quaternary 1:1:2:6 (Fm-3m double perovskite). 2-D prototypes (graphene, h-BN, MoS2 2H/1T) and multilayer stacking are also supported via --include-2d and --num-layers. SUPERCELL GENERATION AND SITE DECORATION Auto-tiling to a minimum atom count (--min-atoms), explicit NxNxN tiling (--supercell), symmetry-distinct site decorations (--n-orderings), and isotropic lattice-scale sweeps (--lattice-scales) for volume bracketing. MLFF RELAXATION AND STABILITY SCORING HydraGNN (multi-headed GNN) drives structure relaxation via ASE with FIRE, BFGS, or BFGSLineSearch. Stability output: delta-E/atom ranking across phases and a max-residual-force dynamical-stability proxy. Other MLIPs (MACE, NequIP, Orb) can be plugged in through the same interface. DFT BACKENDS Quantum ESPRESSO pw.x and VASP 6.6 are first-class labellers. Both have validated GPU builds and SLURM/PBS launchers for three DOE platforms: Frontier (AMD MI250X, ROCm), Aurora (Intel PVC, oneAPI), Perlmutter (NVIDIA A100, CUDA). QE produces ~100 binaries (pw.x, ph.x, epw.x, ...). VASP supports scf, relax, vc-relax, and vc-relax-shape run types. ACTIVE-LEARNING LOOP matsim-agents al run CONFIG.yaml drives an iterative HydraGNN-DFT loop: MD generates candidates → ensemble/MC-dropout uncertainty selects the most informative → DFT labels them in parallel inside one allocation → dataset grows → HydraGNN retrains → repeat. DFT backend is a single YAML toggle (dft.backend: vasp | qe). LLM-generated seed structures are supported (no curated POSCAR library needed). Config uses ${VAR}, ${VAR:-default}, ${VAR:?msg} shell-style substitution for cross-user/cross-site portability. LLM BACKENDS Ollama (local, default), vLLM (HPC multi-GPU serving), OpenAI, Anthropic, HuggingFace Transformers+Accelerate. Selected at runtime via flag or env var with no code changes. HPC PORTABILITY Same Python entry points run on Frontier (ROCm 7.2), Aurora (oneAPI), and Perlmutter (CUDA 12). DFT and ML stacks are never co-loaded in the same shell; they couple through the scheduler and filesystem. Advanced multi-node launchers (serve, discovery-chat, single-relaxation, active-learning, QE warm-start) are provided for all three platforms. CODABENCH COMPETITION BUNDLE A self-contained benchmark: 159 atomistic test structures across 11 material classes, 5 tasks (formation energy, forces, ML relaxation, AI-DFT relaxation, phase stability ranking), public/private leaderboard split (30/70), and four ready-to-run baselines: MACE-MP-0, HydraGNN, UMA, AllScAIP.

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗

Accelerating laser ray tracing in high fidelity physics simulations of laser melting using squeeze U-net

Laser melting is a core component of the ongoing industrial revolution, dubbed Industry 4.0, as lasers facilitate fast and precise melting and fusion in advanced manufacturing. There is a strong need to optimize the laser process using simulations. However, this has proven challenging as high fidelity simulations are needed for predictive modeling and this is currently prohibitively expensive even when run on hundreds of processors on high performance computers. The challenge is capturing complex physics of laser material interaction, fluid dynamics, thermal physics and material phase transformations at various length and time scales. To close this technological gap, we modified a squeeze U-net to accelerate the laser ray tracing component of such high fidelity models by ~4x–40x while preserving the core physics principle of conservation of energy with 97% accuracy. This approach enables the accurate modeling of global laser energy absorption as a function of local surface temperatures and complex surface topologies, which govern the reflection directions and energy losses of laser rays upon interacting with the material surface.

Computer science↗

Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant–microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.

59 BASIC BIOLOGICAL SCIENCES↗

Enabling robust offline active learning for machine learning potentials using simple physics-based priors

Abstract Machine learning surrogate models for quantum mechanical simulations have enabled the field to efficiently and accurately study material and molecular systems. Developed models typically rely on a substantial amount of data to make reliable predictions of the potential energy landscape or careful active learning (AL) and uncertainty estimates. When starting with small datasets, convergence of AL approaches is a major outstanding challenge which has limited most demonstrations to online AL. In this work we demonstrate a Δ-machine learning (ML) approach that enables stable convergence in offline AL strategies by avoiding unphysical configurations with initial datasets as little as a single data point. We demonstrate our framework’s capabilities on a structural relaxation, transition state calculation, and molecular dynamics simulation, with the number of first principle calculations being cut down anywhere from 70%–90%. The approach is incorporated and developed alongside AMP torch , an open-source ML potential package, along with interactive Google Colab notebook examples.

Shuaibi, Muhammed↗