Daily Papers

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.

The ability to quickly and accurately compute properties from atomic simulations is critical for advancing a large number of applications in chemistry and materials science including drug discovery, energy storage, and semiconductor manufacturing. To address this need, Meta FAIR presents a family of Universal Models for Atoms (UMA), designed to push the frontier of speed, accuracy, and generalization. UMA models are trained on half a billion unique 3D atomic structures (the largest training runs to date) by compiling data across multiple chemical domains, e.g. molecules, materials, and catalysts. We develop empirical scaling laws to help understand how to increase model capacity alongside dataset size to achieve the best accuracy. The UMA small and medium models utilize a novel architectural design we refer to as mixture of linear experts that enables increasing model capacity without sacrificing speed. For example, UMA-medium has 1.4B parameters but only ~50M active parameters per atomic structure. We evaluate UMA models on a diverse set of applications across multiple domains and find that, remarkably, a single model without any fine-tuning can perform similarly or better than specialized models. We are releasing the UMA code, weights, and associated data to accelerate computational workflows and enable the community to continue to build increasingly capable AI models.

We report on the trapping of single rubidium atoms in large arrays of optical tweezers comprising up to 2088 sites in a cryogenic environment at 6 K. Our approach relies on the use of microscope objectives that are in-vacuum but at room temperature, in combination with windowless thermal shields into which the objectives are protruding to ensure a cryogenic environment for the trapped atoms. To achieve enough optical power for efficient trapping, we combine two lasers at slightly different wavelengths. We discuss the performance and limitations of our design. Finally, we demonstrate atom-by-atom rearrangement of an 828-atom target array using moving optical tweezers controlled by a field-programmable gate array.

We introduce Orb-v3, the next generation of the Orb family of universal interatomic potentials. Models in this family expand the performance-speed-memory Pareto frontier, offering near SoTA performance across a range of evaluations with a >10x reduction in latency and > 8x reduction in memory. Our experiments systematically traverse this frontier, charting the trade-off induced by roto-equivariance, conservatism and graph sparsity. Contrary to recent literature, we find that non-equivariant, non-conservative architectures can accurately model physical properties, including those which require higher-order derivatives of the potential energy surface. This model release is guided by the principle that the most valuable foundation models for atomic simulation will excel on all fronts: accuracy, latency and system size scalability. The reward for doing so is a new era of computational chemistry driven by high-throughput and mesoscale all-atom simulations.

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems - such as molecules and materials - the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on QM9 and MP20 datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, exceeding state-of-the-art results from molecule and crystal-specific models. ADiT uses standard Transformers for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

Single-atom catalysts (SACs) have emerged as frontiers for catalyzing chemical reactions, yet the diverse combinations of active elements and support materials, the nature of coordination environments, elude traditional methodologies in searching optimal SAC systems with superior catalytic performance. Herein, by integrating multi-branch Convolutional Neural Network (CNN) analysis models to hybrid descriptor based activity volcano plot, 2D SAC system composed of diverse metallic single atoms anchored on six type of 2D supports, including graphitic carbon nitride, nitrogen-doped graphene, graphene with dual-vacancy, black phosphorous, boron nitride, and C2N, are screened for efficient CO2RR. Starting from establishing a correlation map between the adsorption energies of intermediates and diverse electronic and elementary descriptors, sole singular descriptor lost magic to predict catalytic activity. Deep learning method utilizing multi-branch CNN model therefore was employed, using 2D electronic density of states as input to predict adsorption energies. Hybrid-descriptor enveloping both C- and O-types of CO2RR intermediates was introduced to construct volcano plots and limiting potential periodic table, aiming for intuitive screening of catalyst candidates for efficient CO2 reduction to CH4. The eDOS occlusion experiments were performed to unravel individual orbital contribution to adsorption energy. To explore the electronic scale principle governing practical engineering catalytic CO2RR activity, orbitalwise eDOS shifting experiments based on CNN model were employed. The study involves examining the adsorption energy and, consequently, catalytic activities while varying supported single atoms. This work offers a tangible framework to inform both theoretical screening and experimental synthesis, thereby paving the way for systematically designing efficient SACs.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Networks of atom-centered coordination octahedra commonly occur in inorganic and hybrid solid-state materials. Characterizing their spatial arrangements and characteristics is crucial for relating structures to properties for many materials families. The traditional method using case-by-case inspection becomes prohibitive for discovering trends and similarities in large datasets. Here, we operationalize chemical intuition to automate the geometric parsing, quantification, and classification of coordination octahedral networks. We find axis-resolved tilting trends in ABO_{3} perovskite polymorphs, which assist in detecting oxidation state changes. Moreover, we develop a scale-invariant encoding scheme to represent these networks, which, combined with human-assisted unsupervised machine learning, allows us to taxonomize the inorganic framework polytypes in hybrid iodoplumbates (A_xPb_yI_z). Consequently, we uncover a violation of Pauling's third rule and the design principles underpinning their topological diversity. Our results offer a glimpse into the vast design space of atomic octahedral networks and inform high-throughput, targeted screening of specific structure types.

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.

Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution electron microscopy offers a potential source of structural data, converting these images into simulation-ready formats remains labor-intensive and error-prone, creating a bottleneck for model training and validation. We introduce AutoMat, an end-to-end, agent-assisted pipeline that automatically transforms scanning transmission electron microscopy (STEM) images into atomic crystal structures and predicts their physical properties. AutoMat combines pattern-adaptive denoising, physics-guided template retrieval, symmetry-aware atomic reconstruction, fast relaxation and property prediction via MatterSim, and coordinated orchestration across all stages. We propose the first dedicated STEM2Mat-Bench for this task and evaluate performance using lattice RMSD, formation energy MAE, and structure-matching success rate. By orchestrating external tool calls, AutoMat enables a text-only LLM to outperform vision-language models in this domain, achieving closed-loop reasoning throughout the pipeline. In large-scale experiments over 450 structure samples, AutoMat substantially outperforms existing multimodal large language models and tools. These results validate both AutoMat and STEM2Mat-Bench, marking a key step toward bridging microscopy and atomistic simulation in materials science.The code and dataset are publicly available at https://github.com/yyt-2378/AutoMat and https://huggingface.co/datasets/yaotianvector/STEM2Mat.

This work aims to develop a method based on a structurally reliable ice model and a statistically and physico-chemically robust approach for BE distribution inference, with the aim to be applicable to various relevant interstellar species. A multiscale computational approach is presented, with a Molecular Dynamics (MD) Heat & Quench protocol for the amorphous water ice model, and an ONIOM(B3LYP-D3(BJ)/6-311+G**:GFN2-xtb) scheme for the BE inference, with a prime emphasis onto the BE/real system size convergence. The sampling of the binding configurations is twofold, exploring both regularly spaced binding sites, as well as various adsorbate-to-substrate orientations on each locally distinct site. This second source of BE diversity accounts for the local roughness of the potential energy landscape of the substrate. Three different adsorbate test cases are considered, i.e. NH3, CO and CH4, owing to their significance in dust icy mantles, and their distinct binding behavior with water ices. The BE distributions for NH3, CO and CH4 have been inferred, with converged statistics. The distribution for NH3 is better represented by a double Gaussian component profile. Three starting adsorbate orientations per site are required to reach convergence for both Gaussian components of NH3, while 2 orientations are sufficient for CO, and one unique for CH4 (symmetric). Further geometrical and molecular surrounding insights have been provided. These results encompass previously reported results.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

Accurate and scalable machine-learned inter-atomic potentials (MLIPs) are essential for molecular simulations ranging from drug discovery to new material design. Current state-of-the-art models enforce roto-translational symmetries through equivariant neural network architectures, a hard-wired inductive bias that can often lead to reduced flexibility, computational efficiency, and scalability. In this work, we introduce TransIP: Transformer-based Inter-Atomic Potentials, a novel training paradigm for interatomic potentials achieving symmetry compliance without explicit architectural constraints. Our approach guides a generic non-equivariant Transformer-based model to learn SO(3)-equivariance by optimizing its representations in the embedding space. Trained on the recent Open Molecules (OMol25) collection, a large and diverse molecular dataset built specifically for MLIPs and covering different types of molecules (including small organics, biomolecular fragments, and electrolyte-like species), TransIP attains comparable performance in machine-learning force fields versus state-of-the-art equivariant baselines. Further, compared to a data augmentation baseline, TransIP achieves 40% to 60% improvement in performance across varying OMol25 dataset sizes. More broadly, our work shows that learned equivariance can be a powerful and efficient alternative to equivariant or augmentation-based MLIP models.

Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model -- and its qualitative and at times quantitative accuracy -- on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, and chemical reactions. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.

Modeling the time-dependent evolution of electron density is essential for understanding quantum mechanical behaviors of condensed matter and enabling predictive simulations in spectroscopy, photochemistry, and ultrafast science. Yet, while machine learning methods have advanced static density prediction, modeling its spatiotemporal dynamics remains largely unexplored. In this work, we introduce a generative framework that combines a 3D convolutional autoencoder with a latent diffusion model (LDM) to learn electron density trajectories from ab-initio molecular dynamics (AIMD) simulations. Our method encodes electron densities into a compact latent space and predicts their future states by sampling from the learned conditional distribution, enabling stable long-horizon rollouts without drift or collapse. To preserve statistical fidelity, we incorporate a scaled Jensen-Shannon divergence regularization that aligns generated and reference density distributions. On AIMD trajectories of liquid lithium at 800 K, our model accurately captures both the spatial correlations and the log-normal-like statistical structure of the density. The proposed framework has the potential to accelerate the simulation of quantum dynamics and overcome key challenges faced by current spatiotemporal machine learning methods as surrogates of quantum mechanical simulators.

We present a compact design of dual-beam Zeeman slower optimized for efficient production of cold atom applications. Traditional single-beam configurations face challenges from substantial residual atomic flux impacting downstream optical windows, resulting in increased system size, atomic deposition contamination, and a reduced operational lifetime. Our approach employs two oblique laser beams and a capillary-array collimation system to address these challenges while maintaining efficient deceleration. For rubidium (^{87}Rb), simulations demonstrate a significant increase in the fraction of atoms captured by a two-dimensional magneto-optical trap (2D-MOT) and nearly eliminate atom-induced contamination probability at optical windows, all within a compact Zeeman slower length of 44 cm. Experimental validation with Rb and Yb demonstrates highly efficient atomic loading within the same compact design. This advancement represents a substantial improvement for high-flux cold atom applications, providing reliable performance for high-precision metrology, quantum computation and simulation.

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

We present FreeBird, an extensible Julia-based platform for computational studies of phase equilibria at generic interfaces. The package supports a range of system configurations, from atomistic solid surfaces to coarse-grained lattice-gas models, with energies evaluated using classical interatomic potentials or lattice Hamiltonians. Both atomistic and lattice systems accommodate single- or multi-component mixtures with flexibly definable surface and lattice geometries. Implemented sampling algorithms include nested sampling, Wang-Landau sampling, Metropolis Monte Carlo, and, for tractable lattice systems, exact enumeration. Leveraging Julia's type hierarchies and multiple dispatch, FreeBird provides a modular interface that allows seamless integration of system definitions, energy evaluators, and sampling schemes. Designed for flexibility, extensibility, and performance, FreeBird offers a versatile framework for exploring the thermodynamics of interfacial phenomena.

The energy levels of hydrogen-like atoms are obtained from the phase-space quantization, one of the pillars of the old quantum theory, by three different methods - (i) direct integration, (ii) Sommerfeld's original method, and (iii) complex integration. The difficulties come from the imposition of elliptical orbits to the electron, resulting in a variable radial component of the linear momentum. Details of the calculation, which constitute a recurrent gap in textbooks that deal with phase-space quantization, are shown in depth in an accessible fashion for students of introductory quantum mechanics courses.

Recently, sophisticated deep learning-based approaches have been developed for generating efficient initial guesses to accelerate the convergence of density functional theory (DFT) calculations. While the actual initial guesses are often density matrices (DM), quantities that can convert into density matrices also qualify as alternative forms of initial guesses. Hence, existing works mostly rely on the prediction of the Hamiltonian matrix for obtaining high-quality initial guesses. However, the Hamiltonian matrix is both numerically difficult to predict and intrinsically non-transferable, hindering the application of such models in real scenarios. In light of this, we propose a method that constructs DFT initial guesses by predicting the electron density in a compact auxiliary basis representation using E(3)-equivariant neural networks. Trained on small molecules with up to 20 atoms, our model is able to achieve an average 33.3% self-consistent field (SCF) step reduction on systems up to 60 atoms, substantially outperforming Hamiltonian-centric and DM-centric models. Critically, this acceleration remains nearly constant with increasing system sizes and exhibits strong transferring behaviors across orbital basis sets and exchange-correlation (XC) functionals. To the best of our knowledge, this work represents the first and robust candidate for a universally transferable DFT acceleration method. We are also releasing the SCFbench dataset and its accompanying code to facilitate future research in this promising direction.

Quantum computers can be used to address molecular structure, materials science and condensed matter physics problems, which currently stretch the limits of existing high-performance computing resources. Finding exact numerical solutions to these interacting fermion problems has exponential cost, while Monte Carlo methods are plagued by the fermionic sign problem. These limitations of classical computational methods have made even few-atom molecular structures problems of practical interest for medium-sized quantum computers. Yet, thus far experimental implementations have been restricted to molecules involving only Period I elements. Here, we demonstrate the experimental optimization of up to six-qubit Hamiltonian problems with over a hundred Pauli terms, determining the ground state energy for molecules of increasing size, up to BeH2. This is enabled by a hardware-efficient variational quantum eigensolver with trial states specifically tailored to the available interactions in our quantum processor, combined with a compact encoding of fermionic Hamiltonians and a robust stochastic optimization routine. We further demonstrate the flexibility of our approach by applying the technique to a problem of quantum magnetism. Across all studied problems, we find agreement between experiment and numerical simulations with a noisy model of the device. These results help elucidate the requirements for scaling the method to larger systems, and aim at bridging the gap between problems at the forefront of high-performance computing and their implementation on quantum hardware.

We introduce featom, an open source code that implements a high-order finite element solver for the radial Schr\"odinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. To address the slow convergence of the kappa=pm1 states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10^{-8} Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schr\"odinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

Accurate potential energy surface (PES) descriptions are essential for atomistic simulations of materials. Universal machine learning interatomic potentials (UMLIPs)^{1-3} offer a computationally efficient alternative to density functional theory (DFT)^4 for PES modeling across the periodic table. However, their accuracy today is fundamentally constrained due to a reliance on DFT relaxation data.^{5,6} Here, we introduce MatPES, a foundational PES dataset comprising sim 400,000 structures carefully sampled from 281 million molecular dynamics snapshots that span 16 billion atomic environments. We demonstrate that UMLIPs trained on the modestly sized MatPES dataset can rival, or even outperform, prior models trained on much larger datasets across a broad range of equilibrium, near-equilibrium, and molecular dynamics property benchmarks. We also introduce the first high-fidelity PES dataset based on the revised regularized strongly constrained and appropriately normed (r^2SCAN) functional^7 with greatly improved descriptions of interatomic bonding. The open source MatPES initiative emphasizes the importance of data quality over quantity in materials science and enables broad community-driven advancements toward more reliable, generalizable, and efficient UMLIPs for large-scale materials discovery and design.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

Lack of rigorous reproducibility and validation are major hurdles for scientific development across many fields. Materials science in particular encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with both perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard

Scaling has been critical in improving model performance and generalization in machine learning. It involves how a model's performance changes with increases in model size or input data, as well as how efficiently computational resources are utilized to support this growth. Despite successes in other areas, the study of scaling in Neural Network Interatomic Potentials (NNIPs) remains limited. NNIPs act as surrogate models for ab initio quantum mechanical calculations. The dominant paradigm here is to incorporate many physical domain constraints into the model, such as rotational equivariance. We contend that these complex constraints inhibit the scaling ability of NNIPs, and are likely to lead to performance plateaus in the long run. In this work, we take an alternative approach and start by systematically studying NNIP scaling strategies. Our findings indicate that scaling the model through attention mechanisms is efficient and improves model expressivity. These insights motivate us to develop an NNIP architecture designed for scalability: the Efficiently Scaled Attention Interatomic Potential (EScAIP). EScAIP leverages a multi-head self-attention formulation within graph neural networks, applying attention at the neighbor-level representations. Implemented with highly-optimized attention GPU kernels, EScAIP achieves substantial gains in efficiency--at least 10x faster inference, 5x less memory usage--compared to existing NNIPs. EScAIP also achieves state-of-the-art performance on a wide range of datasets including catalysts (OC20 and OC22), molecules (SPICE), and materials (MPTrj). We emphasize that our approach should be thought of as a philosophy rather than a specific model, representing a proof-of-concept for developing general-purpose NNIPs that achieve better expressivity through scaling, and continue to scale efficiently with increased computational resources and training data.

Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.

Ultracold gases of highly magnetic lanthanide atoms have enabled the realisation of dipolar quantum droplets and supersolids. However, future studies could be limited by the achievable atom numbers and hindered by high three-body loss rates. Here we study density-dependent atom loss in an ultracold gas of {}^{166}Er for magnetic fields below 4 G, identifying six previously unreported, strongly temperature-dependent features. We find that their positions and widths show a linear temperature dependence up to at least 15,muK. In addition, we observe a weak, polarisation-dependent shift of the loss features with the intensity of the light used to optically trap the atoms. This detailed knowledge of the loss landscape allows us to optimise the production of dipolar BECs with more than 2 times 10^5 atoms and points towards optimal strategies for the study of large-atom-number dipolar gases in the droplet and supersolid regimes.

The groundbreaking advance in materials and chemical research has been driven by the development of atomistic simulations. However, the broader applicability of the atomistic simulations remains restricted, as they inherently depend on energy models that are either inaccurate or computationally prohibitive. Machine learning interatomic potentials (MLIPs) have recently emerged as a promising class of energy models, but their deployment remains challenging due to the lack of systematic protocols for generating diverse training data. Here we automate the construction of training datasets to enable the development of general-purpose MLIPs, by introducing GAIA, an end-to-end framework to build a wide range of atomic arrangements. By employing systematic evaluation of metadynamics for effective structural exploration, GAIA overcomes the heuristic nature of conventional dataset generation. Using GAIA, we constructed Titan25, a benchmark-scale dataset, and trained MLIPs that closely match both static and dynamic density functional theory results. The models further reproduce experimental observations across reactive regimes, including detonation, coalescence, and catalytic activity. GAIA narrows the gap between experiment and simulation, and paves the way for the development of universal MLIPs that can reliably describe a wide spectrum of materials and chemical processes.

Rydberg atom arrays have emerged as a powerful platform to simulate a number of exotic quantum ground states and phase transitions. To verify these capabilities numerically, we develop a versatile quantum Monte Carlo sampling technique which operates in the reduced Hilbert space generated by enforcing the constraint of a Rydberg blockade. We use the framework of stochastic series expansion and show that in the restricted space, the configuration space of operator strings can be understood as a hard rod gas in d+1 dimensions. We use this mapping to develop cluster algorithms which can be visualized as various non-local movements of rods. We study the efficiency of each of our updates individually and collectively. To elucidate the utility of the algorithm, we show that it can efficiently generate the phase diagram of a Rydberg atom array, to temperatures much smaller than all energy scales involved, on a Kagom\'e link lattice. This is of broad interest as the presence of a Z_2 spin liquid has been hypothesized recently.

We introduce Orb, a family of universal interatomic potentials for atomistic modelling of materials. Orb models are 3-6 times faster than existing universal potentials, stable under simulation for a range of out of distribution materials and, upon release, represented a 31% reduction in error over other methods on the Matbench Discovery benchmark. We explore several aspects of foundation model development for materials, with a focus on diffusion pretraining. We evaluate Orb as a model for geometry optimization, Monte Carlo and molecular dynamics simulations.

Optimization of atomic structures presents a challenging problem, due to their highly rough and non-convex energy landscape, with wide applications in the fields of drug design, materials discovery, and mechanics. Here, we present a graph reinforcement learning approach, StriderNET, that learns a policy to displace the atoms towards low energy configurations. We evaluate the performance of StriderNET on three complex atomic systems, namely, binary Lennard-Jones particles, calcium silicate hydrates gel, and disordered silicon. We show that StriderNET outperforms all classical optimization algorithms and enables the discovery of a lower energy minimum. In addition, StriderNET exhibits a higher rate of reaching minima with energies, as confirmed by the average over multiple realizations. Finally, we show that StriderNET exhibits inductivity to unseen system sizes that are an order of magnitude different from the training system.

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose Unified Variational Auto-Encoder for 3D Molecular Latent Diffusion Modeling (UAE-3D), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both de novo and conditional 3D molecule generation, achieving leading efficiency and quality.

Creating a single unified interatomic potential capable of attaining ab initio accuracy across all chemistry remains a long-standing challenge in computational chemistry and materials science. This work introduces a training protocol for foundation machine-learning interatomic potentials (MLIPs) that bridge molecular, surface, and materials chemistry through cross-domain learning. First, we introduce enhancements to the MACE architecture that improve its performance on chemically diverse databases by increasing weight sharing across chemical elements and introducing non-linear factors into the tensor decomposition of the product basis. Second, we develop a multi-head replay post-training methodology that enables efficient knowledge transfer across diverse chemical domains. By fine-tuning on datasets at different levels of electronic structure theory, including inorganic crystals, molecular systems, surface chemistry, and reactive organic chemistry, we demonstrate that a single unified model achieves state-of-the-art performance across several chemical domains. Comprehensive benchmarking reveals superior cross-domain transferability compared with existing specialised and multi-task models, with notable improvements in molecular and surface properties while maintaining state-of-the-art performance in materials-property prediction.

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of two-dimensional materials. The displacement cross sections of monolayer hBN are measured using aberration-corrected scanning transmission electron microscopy in near ultra-high vacuum at primary beam energies between 50 and 90 keV. Damage rates below 80 keV are up to three orders of magnitude lower than previously measured at edges under poorer residual vacuum conditions where chemical etching appears to have been dominant. Notably, is possible to create single vacancies in hBN using electron irradiation, with boron almost twice as likely as nitrogen to be ejected below 80 keV. Moreover, any damage at such low energies cannot be explained by elastic knock-on, even when accounting for vibrations of the atoms. A theoretical description is developed to account for lowering of the displacement threshold due to valence ionization resulting from inelastic scattering of probe electrons, modelled using charge-constrained density functional theory molecular dynamics. Although significant reductions are found depending on the constrained charge, quantitative predictions for realistic ionization states are currently not possible. Nonetheless, there is potential for defect-engineering of hBN at the level of single vacancies using electron irradiation.

Foundation models, or large atomistic models (LAMs), aim to universally represent the ground-state potential energy surface (PES) of atomistic systems as defined by density functional theory (DFT). The scaling law is pivotal in the development of large models, suggesting that their generalizability in downstream tasks consistently improves with increased model size, expanded training datasets, and larger computational budgets. In this study, we present DPA3, a multi-layer graph neural network founded on line graph series (LiGS), designed explicitly for the era of LAMs. We demonstrate that the generalization error of the DPA3 model adheres to the scaling law. The scalability in the number of model parameters is attained by stacking additional layers within DPA3. Additionally, the model employs a dataset encoding mechanism that decouples the scaling of training data size from the model size within its multi-task training framework. When trained as problem-oriented potential energy models, the DPA3 model exhibits superior accuracy in the majority of benchmark cases, encompassing systems with diverse features, including molecules, bulk materials, surface and cluster catalysts, two-dimensional materials, and battery materials. When trained as a LAM on the OpenLAM-v1 dataset, the DPA-3.1-3M model exhibits state-of-the-art performance in the LAMBench benchmark suite for LAMs, demonstrating lowest overall zero-shot generalization error across 17 downstream tasks from a broad spectrum of research domains. This performance suggests superior accuracy as an out-of-the-box potential model, requiring minimal fine-tuning data for downstream scientific applications.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

Complex chemical space and limited knowledge scope with biases holds immense challenge for human scientists, yet in automated materials discovery. Existing intelligent methods relies more on numerical computation, leading to inefficient exploration and results with hard-interpretability. To bridge this gap, we introduce a principles-guided material discovery system powered by language inferential multi-agent system (MAS), namely PriM. Our framework integrates automated hypothesis generation with experimental validation in a roundtable system of MAS, enabling systematic exploration while maintaining scientific rigor. Based on our framework, the case study of nano helix demonstrates higher materials exploration rate and property value while providing transparent reasoning pathways. This approach develops an automated-and-transparent paradigm for material discovery, with broad implications for rational design of functional materials. Code is publicly available at our https://github.com/amair-lab/PriM{GitHub}.

Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD by providing inexpensive predictions of the forces, but they remain constrained to minuscule time integration steps, which are required by the fast time scale of atomic motion. In this work, we propose FlashMD, a method to predict the evolution of positions and momenta over strides that are between one and two orders of magnitude longer than typical MD time steps. We incorporate considerations on the mathematical and physical properties of Hamiltonian dynamics in the architecture, generalize the approach to allow the simulation of any thermodynamic ensemble, and carefully assess the possible failure modes of such a long-stride MD approach. We validate FlashMD's accuracy in reproducing equilibrium and time-dependent properties, using both system-specific and general-purpose models, extending the ability of MD simulation to reach the long time scales needed to model microscopic processes of high scientific and technological relevance.

Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.

Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, as well as software ecosystems that are very well developed in their own merit, but do not share many commonalities. To address these issues and facilitate the adoption of ML in atomistic simulations, we introduce two dedicated software libraries. The first one, metatensor, provides multi-platform and multi-language storage and manipulation of arrays with many potentially sparse indices, designed from the ground up for atomistic ML applications. By combining the actual values with metadata that describes their nature and that facilitates the handling of geometric information and gradients with respect to the atomic positions, metatensor provides a common framework to enable data sharing between ML software -- typically written in Python -- and established atomistic modeling tools -- typically written in Fortran, C or C++. The second library, metatomic, provides an interface to store an atomistic ML model and metadata about this model in a portable way, facilitating the implementation, training and distribution of models, and their use across different simulation packages. We showcase a growing ecosystem of tools, from low-level libraries, training utilities, to interfaces with existing software packages that demonstrate the effectiveness of metatensor and metatomic in bridging the gap between traditional simulation software and modern ML frameworks.

The study of the long-time dynamics of quantum systems can be a real challenge, especially in systems like ultracold gases, where the required timescales may be longer than the lifetime of the system itself. In this work, we show that it is possible to access the long-time dynamics of a strongly repulsive atomic gas mixture in shorter times. The shortcut-to-dynamics protocol that we propose does not modify the fate of the observables, but effectively jumps ahead in time without changing the system's inherent evolution. Just like the next-chapter button in a movie player that allows to quickly reach the part of the movie one wants to watch, it is a leap into the future.

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the minimum binding energy - the adsorption energy - for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration, within a 0.1 eV threshold, 86.33% of the time, while achieving a 1331x speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1,000 diverse surfaces and 85,658 unique configurations.

High-pressure crystal structure prediction (CSP) underpins advances in condensed matter physics, planetary science, and materials discovery. Yet, most large atomistic models are trained on near-ambient, equilibrium data, leading to degraded stress accuracy at tens to hundreds of gigapascals and sparse coverage of pressure-stabilized stoichiometries and dense coordination motifs. Here, we introduce OpenCSP, a machine learning framework for CSP tasks spanning ambient to high-pressure conditions. This framework comprises an open-source pressure-resolved dataset alongside a suite of publicly available atomistic models that are jointly optimized for accuracy in energy, force, and stress predictions. The dataset is constructed via randomized high-pressure sampling and iteratively refined through an uncertainty-guided concurrent learning strategy, which enriches underrepresented compression regimes while suppressing redundant DFT labeling. Despite employing a training corpus one to two orders of magnitude smaller than those of leading large models, OpenCSP achieves comparable or superior performance in high-pressure enthalpy ranking and stability prediction. Across benchmark CSP tasks spanning a wide pressure window, our models match or surpass MACE-MPA-0, MatterSim v1 5M, and GRACE-2L-OAM, with the largest gains observed at elevated pressures. These results demonstrate that targeted, pressure-aware data acquisition coupled with scalable architectures enables data-efficient, high-fidelity CSP, paving the way for autonomous materials discovery under ambient and extreme conditions.

Although quantum simulation can give insight into elusive or intractable physical phenomena, many quantum simulators are unavoidably limited in the models they mimic. Such is also the case for atom arrays interacting via Rydberg states - a platform potentially capable of simulating any kind of spin exchange model, albeit with currently unattainable experimental capabilities. Here, we propose a new route towards simulating generic spin exchange Hamiltonians in atom arrays, using Floquet engineering with both global and local control. To demonstrate the versatility and applicability of our approach, we numerically investigate the generation of several spin exchange models which have yet to be realized in atom arrays, using only previously-demonstrated experimental capabilities. Our proposed scheme can be readily explored in many existing setups, providing a path to investigate a large class of exotic quantum spin models.

The simulation of large-scale systems with complex electron interactions remains one of the greatest challenges for the atomistic modeling of materials. 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 many technologically relevant phenomena, such as reactions, ion migrations, phase transformations, and degradation. In this work, we present the Crystal Hamiltonian Graph neural Network (CHGNet) as a novel machine-learning interatomic potential (MLIP), using a graph-neural-network-based force field to model a 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 static and relaxation trajectories of sim 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_xMnO_2, the finite temperature phase diagram for Li_xFePO_4 and Li diffusion in garnet conductors. We critically analyze the significance of including charge information for capturing appropriate chemistry, and we provide new insights into ionic systems with additional electronic degrees of freedom that can not be observed by previous MLIPs.

Despite the variety of available computational approaches, state-of-the-art methods for calculating excitation energies such as time-dependent density functional theory (TDDFT), are computationally demanding and thus limited to moderate system sizes. Here, we introduce a new variation of constrained DFT (CDFT), wherein the constraint corresponds to a particular transition (T), or combination of transitions, between occupied and virtual orbitals, rather than a region of the simulation space as in traditional CDFT. We compare T-CDFT with TDDFT and DeltaSCF results for the low lying excited states (S_{1} and T_{1}) of a set of gas phase acene molecules and OLED emitters, as well as with reference results from the literature. At the PBE level of theory, T-CDFT outperforms DeltaSCF for both classes of molecules, while also proving to be more robust. For the local excitations seen in the acenes, T-CDFT and TDDFT perform equally well. For the charge-transfer (CT)-like excitations seen in the OLED molecules, T-CDFT also performs well, in contrast to the severe energy underestimation seen with TDDFT. In other words, T-CDFT is equally applicable to both local excitations and CT states, providing more reliable excitation energies at a much lower computational cost than TDDFT. T-CDFT is designed for large systems and has been implemented in the linear scaling BigDFT code. It is therefore ideally suited for exploring the effects of explicit environments on excitation energies, paving the way for future simulations of excited states in complex realistic morphologies, such as those which occur in OLED materials.

The ability to discover new materials with desirable properties is critical for numerous applications from helping mitigate climate change to advances in next generation computing hardware. AI has the potential to accelerate materials discovery and design by more effectively exploring the chemical space compared to other computational methods or by trial-and-error. While substantial progress has been made on AI for materials data, benchmarks, and models, a barrier that has emerged is the lack of publicly available training data and open pre-trained models. To address this, we present a Meta FAIR release of the Open Materials 2024 (OMat24) large-scale open dataset and an accompanying set of pre-trained models. OMat24 contains over 110 million density functional theory (DFT) calculations focused on structural and compositional diversity. Our EquiformerV2 models achieve state-of-the-art performance on the Matbench Discovery leaderboard and are capable of predicting ground-state stability and formation energies to an F1 score above 0.9 and an accuracy of 20 meV/atom, respectively. We explore the impact of model size, auxiliary denoising objectives, and fine-tuning on performance across a range of datasets including OMat24, MPtraj, and Alexandria. The open release of the OMat24 dataset and models enables the research community to build upon our efforts and drive further advancements in AI-assisted materials science.

Simulating atomic-scale processes, such as protein dynamics and catalytic reactions, is crucial for advancements in biology, chemistry, and materials science. Machine learning force fields (MLFFs) have emerged as powerful tools that achieve near quantum mechanical accuracy, with promising generalization capabilities. However, their practical use is often limited by long inference times compared to classical force fields, especially when running extensive molecular dynamics (MD) simulations required for many biological applications. In this study, we introduce BoostMD, a surrogate model architecture designed to accelerate MD simulations. BoostMD leverages node features computed at previous time steps to predict energies and forces based on positional changes. This approach reduces the complexity of the learning task, allowing BoostMD to be both smaller and significantly faster than conventional MLFFs. During simulations, the computationally intensive reference MLFF is evaluated only every N steps, while the lightweight BoostMD model handles the intermediate steps at a fraction of the computational cost. Our experiments demonstrate that BoostMD achieves an eight-fold speedup compared to the reference model and generalizes to unseen dipeptides. Furthermore, we find that BoostMD accurately samples the ground-truth Boltzmann distribution when running molecular dynamics. By combining efficient feature reuse with a streamlined architecture, BoostMD offers a robust solution for conducting large-scale, long-timescale molecular simulations, making high-accuracy ML-driven modeling more accessible and practical.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

Identifying useful sorbent materials for direct air capture (DAC) from humid air remains a challenge. We present the Open DAC 2025 (ODAC25) dataset, a significant expansion and improvement upon ODAC23 (Sriram et al., ACS Central Science, 10 (2024) 923), comprising nearly 70 million DFT single-point calculations for CO_2, H_2O, N_2, and O_2 adsorption in 15,000 MOFs. ODAC25 introduces chemical and configurational diversity through functionalized MOFs, high-energy GCMC-derived placements, and synthetically generated frameworks. ODAC25 also significantly improves upon the accuracy of DFT calculations and the treatment of flexible MOFs in ODAC23. Along with the dataset, we release new state-of-the-art machine-learned interatomic potentials trained on ODAC25 and evaluate them on adsorption energy and Henry's law coefficient predictions.

Catalysis at solid-liquid interfaces plays a central role in the advancement of energy storage and sustainable chemical production technologies. By enabling accurate, long-time scale simulations, machine learning (ML) models have the potential to accelerate the discovery of (electro)catalysts. While prior Open Catalyst datasets (OC20 and OC22) have advanced the field by providing large-scale density functional theory (DFT) data of adsorbates on surfaces at solid-gas interfaces, they do not capture the critical role of solvent and electrolyte effects at solid-liquid interfaces. To bridge this gap, we introduce the Open Catalyst 2025 (OC25) dataset, consisting of 7,801,261 calculations across 1,511,270 unique explicit solvent environments. OC25 constitutes the largest and most diverse solid-liquid interface dataset that is currently available and provides configurational and elemental diversity: spanning 88 elements, commonly used solvents/ions, varying solvent layers, and off-equilibrium sampling. State-of-the-art models trained on the OC25 dataset exhibit energy, force, and solvation energy errors as low as 0.1 eV, 0.015 eV/A, and 0.04 eV, respectively; significantly lower than than the recently released Universal Models for Atoms (UMA-OC20). Additionally, we discuss the impact of the quality of DFT-calculated forces on model training and performance. The dataset and accompanying baseline models are made openly available for the community. We anticipate the dataset to facilitate large length-scale and long-timescale simulations of catalytic transformations at solid-liquid interfaces, advancing molecular-level insights into functional interfaces and enabling the discovery of next-generation energy storage and conversion technologies.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

Crystalline materials are a fundamental component in next-generation technologies, yet modeling their distribution presents unique computational challenges. Of the plausible arrangements of atoms in a periodic lattice only a vanishingly small percentage are thermodynamically stable, which is a key indicator of the materials that can be experimentally realized. Two fundamental tasks in this area are to (a) predict the stable crystal structure of a known composition of elements and (b) propose novel compositions along with their stable structures. We present FlowMM, a pair of generative models that achieve state-of-the-art performance on both tasks while being more efficient and more flexible than competing methods. We generalize Riemannian Flow Matching to suit the symmetries inherent to crystals: translation, rotation, permutation, and periodic boundary conditions. Our framework enables the freedom to choose the flow base distributions, drastically simplifying the problem of learning crystal structures compared with diffusion models. In addition to standard benchmarks, we validate FlowMM's generated structures with quantum chemistry calculations, demonstrating that it is about 3x more efficient, in terms of integration steps, at finding stable materials compared to previous open methods.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.

The direct collapse scenario, which predicts the formation of supermassive stars (SMSs) as precursors to supermassive black holes (SMBHs), has been explored primarily under the assumption of metal-free conditions. However, environments exposed to strong far-ultraviolet (FUV) radiation, which is another requirement for the direct collapse, are often chemically enriched to varying degrees. In this study, we perform radiation hydrodynamic simulations of star-cluster formation in clouds with finite metallicities, Z=10^{-6} to 10^{-2} Z_{odot}, incorporating detailed thermal and chemical processes and radiative feedback from forming stars. Extending the simulations to approximately two million years, we demonstrate that SMSs with masses exceeding 10^4~M_odot can form even in metal-enriched clouds with Z lesssim 10^{-3} Z_{odot}. The accretion process in these cases, driven by "super-competitive accretion," preferentially channels gas into central massive stars in spite of small (sub-pc) scale fragmentation. At Z simeq 10^{-2} Z_{odot}, however, enhanced cooling leads to intense fragmentation on larger scales, resulting in the formation of dense star clusters dominated by very massive stars with 10^3 M_{odot} rather than SMSs. These clusters resemble young massive or globular clusters observed in the distant and local universe, exhibiting compact morphologies and high stellar surface densities. Our findings suggest that SMS formation is viable below a metallicity threshold of approximately 10^{-3} Z_{odot}, significantly increasing the number density of massive seed black holes to levels sufficient to account for the ubiquitous SMBHs observed in the local universe. Moreover, above this metallicity, this scenario naturally explains the transition from SMS formation to dense stellar cluster formation.

Diffusion-based samplers learn to sample complex, high-dimensional distributions using energies or log densities alone, without training data. Yet, they remain impractical for molecular sampling because they are often slower than molecular dynamics and miss thermodynamically relevant modes. Inspired by enhanced sampling, we encourage exploration by introducing a sequential bias along bespoke, information-rich, low-dimensional projections of atomic coordinates known as collective variables (CVs). We introduce a repulsive potential centered on the CVs from recent samples, which pushes future samples towards novel CV regions and effectively increases the temperature in the projected space. Our resulting method improves efficiency, mode discovery, enables the estimation of free energy differences, and retains independent sampling from the approximate Boltzmann distribution via reweighting by the bias. On standard peptide conformational sampling benchmarks, the method recovers diverse conformational states and accurate free energy profiles. We are the first to demonstrate reactive sampling using a diffusion-based sampler, capturing bond breaking and formation with universal interatomic potentials at near-first-principles accuracy. The approach resolves reactive energy landscapes at a fraction of the wall-clock time of standard sampling methods, advancing diffusion-based sampling towards practical use in molecular sciences.

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

Machine learning interatomic potentials (MLIPs) have become increasingly effective at approximating quantum mechanical calculations at a fraction of the computational cost. However, lower errors on held out test sets do not always translate to improved results on downstream physical property prediction tasks. In this paper, we propose testing MLIPs on their practical ability to conserve energy during molecular dynamic simulations. If passed, improved correlations are found between test errors and their performance on physical property prediction tasks. We identify choices which may lead to models failing this test, and use these observations to improve upon highly-expressive models. The resulting model, eSEN, provides state-of-the-art results on a range of physical property prediction tasks, including materials stability prediction, thermal conductivity prediction, and phonon calculations.

Silicon nitride has emerged as a promising photonic platform for integrated single-photon sources, yet the microscopic origin of the recently observed bright quantum emissions remains unclear. Using hybrid density functional theory, we show that the negatively charged N_SiV_N center (NV^{-}) in the C_{1h} configuration exhibits a linearly polarized zero-phonon line (ZPL) at 2.46 eV, with a radiative lifetime of 9.01 ns and a high Debye-Waller (DW) factor of 33%. We further find that the C_{1h} configuration is prone to a pseudo-Jahn-Teller distortion, yielding two symmetrically equivalent defect structures that emit bright, linearly polarized ZPL at 1.80 eV with a lifetime of 10.17 ns and an increased DW factor of 41%. These nitrogen-vacancy-related defects explain the origins of visible quantum emissions, paving the way for deterministic and monolithically integrated silicon-nitride quantum photonics.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

A central challenge of the clean energy transition is the development of catalysts for low-emissions technologies. Recent advances in Machine Learning for quantum chemistry drastically accelerate the computation of catalytic activity descriptors such as adsorption energies. Here we introduce AdsorbRL, a Deep Reinforcement Learning agent aiming to identify potential catalysts given a multi-objective binding energy target, trained using offline learning on the Open Catalyst 2020 and Materials Project data sets. We experiment with Deep Q-Network agents to traverse the space of all ~160,000 possible unary, binary and ternary compounds of 55 chemical elements, with very sparse rewards based on adsorption energy known for only between 2,000 and 3,000 catalysts per adsorbate. To constrain the actions space, we introduce Random Edge Traversal and train a single-objective DQN agent on the known states subgraph, which we find strengthens target binding energy by an average of 4.1 eV. We extend this approach to multi-objective, goal-conditioned learning, and train a DQN agent to identify materials with the highest (respectively lowest) adsorption energies for multiple simultaneous target adsorbates. We experiment with Objective Sub-Sampling, a novel training scheme aimed at encouraging exploration in the multi-objective setup, and demonstrate simultaneous adsorption energy improvement across all target adsorbates, by an average of 0.8 eV. Overall, our results suggest strong potential for Deep Reinforcement Learning applied to the inverse catalysts design problem.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

A theoretical approach to describing transport of an entire ensemble of clusters with different sizes as a single species in gas has been developed. The major assumption is an existence of local partial chemical equilibrium between the clusters. It is shown that thermal diffusion emerges in the collective description as a significant factor even if it is negligible when transport of the original molecular species is considered. Analytical expressions for the effective diffusion and thermal diffusion coefficients at temperature, pressure, and chemical composition gradients have been derived. The theory has been applied to a technology of H2S conversion in a centrifugal plasma-chemical reactor and has made it possible to account for sulfur clusters in numerical process modeling.

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the observation of their conformational changes in real time. The innovative liquid-phase electron microscopy (liquid-phase EM) technique allows molecules to be placed in the native liquid environment, providing a unique opportunity to observe their dynamics. In this paper, we propose TEMPOR, a Temporal Electron MicroscoPy Object Reconstruction algorithm for liquid-phase EM that leverages an implicit neural representation (INR) and a dynamical variational auto-encoder (DVAE) to recover time series of molecular structures. We demonstrate its advantages in recovering different motion dynamics from two simulated datasets, 7bcq and Cas9. To our knowledge, our work is the first attempt to directly recover 3D structures of a temporally-varying particle from liquid-phase EM movies. It provides a promising new approach for studying molecules' 3D dynamics in structural biology.

Accurate prediction of bond dissociation energies (BDEs) underpins mechanistic insight and the rational design of molecules and materials. We present a systematic, reproducible benchmark comparing quantum and classical machine learning models for BDE prediction using a chemically curated feature set encompassing atomic properties (atomic numbers, hybridization), bond characteristics (bond order, type), and local environmental descriptors. Our quantum framework, implemented in Qiskit Aer on six qubits, employs ZZFeatureMap encodings with variational ansatz (RealAmplitudes) across multiple architectures Variational Quantum Regressors (VQR), Quantum Support Vector Regressors (QSVR), Quantum Neural Networks (QNN), Quantum Convolutional Neural Networks (QCNN), and Quantum Random Forests (QRF). These are rigorously benchmarked against strong classical baselines, including Support Vector Regression (SVR), Random Forests (RF), and Multi-Layer Perceptrons (MLP). Comprehensive evaluation spanning absolute and relative error metrics, threshold accuracies, and error distributions shows that top-performing quantum models (QCNN, QRF) match the predictive accuracy and robustness of classical ensembles and deep networks, particularly within the chemically prevalent mid-range BDE regime. These findings establish a transparent baseline for quantum-enhanced molecular property prediction and outline a practical foundation for advancing quantum computational chemistry toward near chemical accuracy.

Computational materials discovery is limited by the high cost of first-principles calculations. Machine learning (ML) potentials that predict energies from crystal structures are promising, but existing methods face computational bottlenecks. Steerable graph neural networks (GNNs) encode geometry with spherical harmonics, respecting atomic symmetries -- permutation, rotation, and translation -- for physically realistic predictions. Yet maintaining equivariance is difficult: activation functions must be modified, and each layer must handle multiple data types for different harmonic orders. We present Facet, a GNN architecture for efficient ML potentials, developed through systematic analysis of steerable GNNs. Our innovations include replacing expensive multi-layer perceptrons (MLPs) for interatomic distances with splines, which match performance while cutting computational and memory demands. We also introduce a general-purpose equivariant layer that mixes node information via spherical grid projection followed by standard MLPs -- faster than tensor products and more expressive than linear or gate layers. On the MPTrj dataset, Facet matches leading models with far fewer parameters and under 10% of their training compute. On a crystal relaxation task, it runs twice as fast as MACE models. We further show SevenNet-0's parameters can be reduced by over 25% with no accuracy loss. These techniques enable more than 10x faster training of large-scale foundation models for ML potentials, potentially reshaping computational materials discovery.

We report the measurement of the electric dipole moment of aluminum monochloride (AlCl) using a cryogenic buffer-gas beam source. Our measurements provide values for the dipole moments of the two lowest vibrational states of the X^1Sigma^+ and the A^1Pi electronic states. We also show that spin-orbit coupling with an extended number of spin states is essential in the ab initio calculation to correctly describe both the dipole moment and the Te energy of AlCl. We further lay out the implications of these results for astrophysical models of stellar and planetary evolution that have used a substitute value for the dipole moment of AlCl until now.

Machine learning interatomic potentials (MLIPs) have revolutionized molecular and materials modeling, but existing benchmarks suffer from data leakage, limited transferability, and an over-reliance on error-based metrics tied to specific density functional theory (DFT) references. We introduce MLIP Arena, a benchmark platform that evaluates force field performance based on physics awareness, chemical reactivity, stability under extreme conditions, and predictive capabilities for thermodynamic properties and physical phenomena. By moving beyond static DFT references and revealing the important failure modes of current foundation MLIPs in real-world settings, MLIP Arena provides a reproducible framework to guide the next-generation MLIP development toward improved predictive accuracy and runtime efficiency while maintaining physical consistency. The Python package and online leaderboard are available at https://github.com/atomind-ai/mlip-arena.

We present OrbNet Denali, a machine learning model for electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 million DFT calculations on molecules and geometries. This dataset covers the most common elements in bio- and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) as well as charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformers benchmark set, OrbNet Denali has a median correlation coefficient of R^2=0.90 compared to the reference DLPNO-CCSD(T) calculation, and R^2=0.97 compared to the method used to generate the training data (wB97X-D3/def2-TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for non-covalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of wB97X-D3/def2-TZVP with an average MAE of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

We review Bohr's atomic model and its extension by Sommerfeld from a mathematical perspective of wave mechanics. The derivation of quantization rules and energy levels is revisited using semiclassical methods. Sommerfeld-type integrals are evaluated by elementary techniques, and connections with the Schr\"{o}dinger and Dirac equations are established. Historical developments and key transitions from classical to quantum theory are discussed to clarify the structure and significance of the old quantum mechanics.

The history of science is punctuated by serendipitous discoveries, where unexpected observations, rather than targeted hypotheses, opened new fields of inquiry. While modern autonomous laboratories excel at accelerating hypothesis testing, their optimization for efficiency risks overlooking these crucial, unplanned findings. To address this gap, we introduce SciLink, an open-source, multi-agent artificial intelligence framework designed to operationalize serendipity in materials research by creating a direct, automated link between experimental observation, novelty assessment, and theoretical simulations. The framework employs a hybrid AI strategy where specialized machine learning models perform quantitative analysis of experimental data, while large language models handle higher-level reasoning. These agents autonomously convert raw data from materials characterization techniques into falsifiable scientific claims, which are then quantitatively scored for novelty against the published literature. We demonstrate the framework's versatility across diverse research scenarios, showcasing its application to atomic-resolution and hyperspectral data, its capacity to integrate real-time human expert guidance, and its ability to close the research loop by proposing targeted follow-up experiments. By systematically analyzing all observations and contextualizing them, SciLink provides a practical framework for AI-driven materials research that not only enhances efficiency but also actively cultivates an environment ripe for serendipitous discoveries, thereby bridging the gap between automated experimentation and open-ended scientific exploration.

Large language models have demonstrated remarkable reasoning capabilities across diverse natural language tasks. However, comparable breakthroughs in scientific discovery are more limited, because understanding complex physical phenomena demands multifaceted representations far beyond language alone. A compelling example is the design of functional materials such as MOFs-critical for a range of impactful applications like carbon capture and hydrogen storage. Navigating their vast and intricate design space in language-based representations interpretable by LLMs is challenging due to the numerous possible three-dimensional atomic arrangements and strict reticular rules of coordination geometry and topology. Despite promising early results in LLM-assisted discovery for simpler materials systems, MOF design remains heavily reliant on tacit human expertise rarely codified in textual information alone. To overcome this barrier, we introduce L2M3OF, the first multimodal LLM for MOFs. L2M3OF integrates crystal representation learning with language understanding to process structural, textual, and knowledge modalities jointly. L2M3OF employs a pre-trained crystal encoder with a lightweight projection layer to compress structural information into a token space, enabling efficient alignment with language instructions. To facilitate training and evaluation, we curate a structure-property-knowledge database of crystalline materials and benchmark L2M3OF against state-of-the-art closed-source LLMs such as GPT-5, Gemini-2.5-Pro and DeepSeek-R1. Experiments show that L2M3OF outperforms leading text-based closed-source LLMs in property prediction and knowledge generation tasks, despite using far fewer parameters. These results highlight the importance of multimodal approaches for porous material understanding and establish L2M3OF as a foundation for next-generation AI systems in materials discovery.

Machine learning (ML) models hold the promise of transforming atomic simulations by delivering quantum chemical accuracy at a fraction of the computational cost. Realization of this potential would enable high-throughout, high-accuracy molecular screening campaigns to explore vast regions of chemical space and facilitate ab initio simulations at sizes and time scales that were previously inaccessible. However, a fundamental challenge to creating ML models that perform well across molecular chemistry is the lack of comprehensive data for training. Despite substantial efforts in data generation, no large-scale molecular dataset exists that combines broad chemical diversity with a high level of accuracy. To address this gap, Meta FAIR introduces Open Molecules 2025 (OMol25), a large-scale dataset composed of more than 100 million density functional theory (DFT) calculations at the omegaB97M-V/def2-TZVPD level of theory, representing billions of CPU core-hours of compute. OMol25 uniquely blends elemental, chemical, and structural diversity including: 83 elements, a wide-range of intra- and intermolecular interactions, explicit solvation, variable charge/spin, conformers, and reactive structures. There are ~83M unique molecular systems in OMol25 covering small molecules, biomolecules, metal complexes, and electrolytes, including structures obtained from existing datasets. OMol25 also greatly expands on the size of systems typically included in DFT datasets, with systems of up to 350 atoms. In addition to the public release of the data, we provide baseline models and a comprehensive set of model evaluations to encourage community engagement in developing the next-generation ML models for molecular chemistry.

The decay of metastable 'false vacuum' states via bubble nucleation plays a crucial role in many cosmological scenarios. Cold-atom analog experiments will soon provide the first empirical probes of this process, with potentially far-reaching implications for early-Universe cosmology and high-energy physics. However, an inevitable difference between these analog systems and the early Universe is that the former have a boundary. We show, using a combination of Euclidean calculations and real-time lattice simulations, that these boundaries generically cause rapid bubble nucleation on the edge of the experiment, obscuring the bulk nucleation that is relevant for cosmology. We demonstrate that implementing a high-density 'trench' region at the boundary completely eliminates this problem, and recovers the desired cosmological behavior. Our findings are relevant for ongoing efforts to probe vacuum decay in the laboratory, providing a practical solution to a key experimental obstacle.

Accurate thermochemical data with sub-chemical accuracy (i.e., within pm1 kcal mol^{-1} from sufficiently accurate experimental or theoretical reference data) is essential for the development and improvement of computational chemistry methods. Challenging thermochemical properties such as heats of formation and total atomization energies (TAEs) are of particular interest because they rigorously test the ability of computational chemistry methods to accurately describe complex chemical transformations involving multiple bond rearrangements. Yet, existing thermochemical datasets that confidently reach this level of accuracy are limited in either size or scope. Datasets with highly accurate reference values include a small number of data points, and larger datasets provide less accurate data or only cover a narrow portion of the chemical space. The existing datasets are therefore insufficient for developing data-driven methods with predictive accuracy over a large chemical space. The Microsoft Research Accurate Chemistry Collection (MSR-ACC) will address this challenge. Here, it offers the MSR-ACC/TAE25 dataset of 76,879 total atomization energies obtained at the CCSD(T)/CBS level via the W1-F12 thermochemical protocol. The dataset is constructed to exhaustively cover chemical space for all elements up to argon by enumerating and sampling chemical graphs, thus avoiding bias towards any particular subspace of the chemical space (such as drug-like, organic, or experimentally observed molecules). With this first dataset in MSR-ACC, we enable data-driven approaches for developing predictive computational chemistry methods with unprecedented accuracy and scope.

As computational demands continue to rise, assessing the environmental footprint of AI requires moving beyond energy and water consumption to include the material demands of specialized hardware. This study quantifies the material footprint of AI training by linking computational workloads to physical hardware needs. The elemental composition of the Nvidia A100 SXM 40 GB graphics processing unit (GPU) was analyzed using inductively coupled plasma optical emission spectroscopy, which identified 32 elements. The results show that AI hardware consists of about 90% heavy metals and only trace amounts of precious metals. The elements copper, iron, tin, silicon, and nickel dominate the GPU composition by mass. In a multi-step methodology, we integrate these measurements with computational throughput per GPU across varying lifespans, accounting for the computational requirements of training specific AI models at different training efficiency regimes. Scenario-based analyses reveal that, depending on Model FLOPs Utilization (MFU) and hardware lifespan, training GPT-4 requires between 1,174 and 8,800 A100 GPUs, corresponding to the extraction and eventual disposal of up to 7 tons of toxic elements. Combined software and hardware optimization strategies can reduce material demands: increasing MFU from 20% to 60% lowers GPU requirements by 67%, while extending lifespan from 1 to 3 years yields comparable savings; implementing both measures together reduces GPU needs by up to 93%. Our findings highlight that incremental performance gains, such as those observed between GPT-3.5 and GPT-4, come at disproportionately high material costs. The study underscores the necessity of incorporating material resource considerations into discussions of AI scalability, emphasizing that future progress in AI must align with principles of resource efficiency and environmental responsibility.

We explore the integration of Kolmogorov Networks (KANs) into molecular dynamics (MD) simulations to improve interatomic potentials. We propose that widely used potentials, such as the Lennard-Jones (LJ) potential, the embedded atom model (EAM), and artificial neural network (ANN) potentials, can be interpreted within the KAN framework. Specifically, we demonstrate that the descriptors for ANN potentials, typically constructed using polynomials, can be redefined using KAN's non-linear functions. By employing linear or cubic spline interpolations for these KAN functions, we show that the computational cost of evaluating ANN potentials and their derivatives is reduced.

System design is often taught through domain-specific solutions specific to particular domains, such as databases, operating systems, or computer architecture, each with its own methods and vocabulary. While this diversity is a strength, it can obscure cross-cutting principles that recur across domains. This paper proposes a preliminary "periodic table" of system design principles distilled from several domains in computer systems. The goal is a shared, concise vocabulary that helps students, researchers, and practitioners reason about structure and trade-offs, compare designs across domains, and communicate choices more clearly. For supporting materials and updates, please refer to the repository at: https://github.com/jarulraj/periodic-table.

This paper will discuss the microphysical simulation of interactions in liquid xenon, the active detector medium in many leading rare-event searches for new physics, and describe experimental observables useful for understanding detector performance. The scintillation and ionization yield distributions for signal and background will be presented using the Noble Element Simulation Technique (NEST), which is a toolkit based on experimental data and simple, empirical formulae, which mimic previous microphysics modeling, but are guided by data. The NEST models for light and charge production as a function of the particle type, energy, and electric field will be reviewed, as well as models for energy resolution and final pulse areas. NEST will be compared to other models or sets of models, and vetted against real data, with several specific examples pulled from XENON, ZEPLIN, LUX, LZ, PandaX, and table-top experiments used for calibrations.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

HeH^+ was the first heteronuclear molecule to form in the metal-free Universe after the Big Bang. The molecule gained significant attention following its first circumstellar detection in the young and dense planetary nebula NGC 7027. We target some hydride ions associated with the noble gases (HeH^+, ArH^+, and NeH^+) to investigate their formation in harsh environments like the nova outburst region. We use a photoionization modeling (based on previously published best-fit physical parameters) of the moderately fast ONe type nova, QU Vulpeculae 1984, and the CO type novae, RS Ophiuchi and V1716 Scorpii. Our steady-state modeling reveals a convincing amount of HeH^+, especially in the dense clump of RS Ophiuchi and V1716 Scorpii. The calculated upper limit on the surface brightness of HeH^+ transitions suggests that the James Webb Space Telescope (JWST) could detect some of them, particularly in sources like RS Ophiuchi and V1716 Scorpii, which have similar physical and chemical conditions and evolution. It must be clearly noted that the sources studied are used as templates, and not as targets for observations. The detection of these lines could be useful for determining the physical conditions in similar types of systems and for validating our predictions based on new electron-impact ro-vibrational collisional data at temperatures of up to 20,000 K.

Cassiopeia A (Cas A) is the youngest known core-collapse supernova remnant (SNR) in the Galaxy and is perhaps the best-studied SNR in X-rays. Cas A has a line-rich spectrum dominated by thermal emission and given its high flux, it is an appealing target for high-resolution X-ray spectroscopy. Cas A was observed at two different locations during the Performance Verification phase of the XRISM mission, one location in the southeastern part (SE) of the remnant and one in the northwestern part (NW). This paper serves as an overview of these observations and discusses some of the issues relevant for the analysis of the data. We present maps of the so-called ``spatial-spectral mixing'' effect due to the fact that the XRISM point-spread function is larger than a pixel in the Resolve calorimeter array. We analyze spectra from two bright, on-axis regions such that the effects of spatial-spectral mixing are minimized. We find that it is critical to include redshifts/blueshifts and broadening of the emission lines in the two thermal components to achieve a reasonable fit given the high spectral resolution of the Resolve calorimeter. We fit the spectra with two versions of the AtomDB atomic database (3.0.9 and 3.1.0) and two versions of the SPEX (3.08.00 and 3.08.01*) spectral fitting software. Overall we find good agreement between AtomDB 3.1.0 and SPEX 3.08.01* for the spectral models considered in this paper. The most significant difference we found between AtomDB 3.0.9 and 3.1.0 and between AtomDB 3.1.0 and SPEX 3.08.01* is the Ni abundance, with the new atomic data favoring a considerably lower (up to a factor of 3) Ni abundance. Both regions exhibit significantly enhanced abundances compared to Solar values indicating that supernova ejecta dominate the emission in these regions. We find that the abundance ratios of Ti/Fe, Mn/Fe, \& Ni/Fe are significantly lower in the NW than the SE.

Solid-state quantum emitters have emerged as a leading quantum memory for quantum networking applications. However, standard optical characterization techniques are neither efficient nor repeatable at scale. In this work, we introduce and demonstrate spectroscopic techniques that enable large-scale, automated characterization of color centers. We first demonstrate the ability to track color centers by registering them to a fabricated machine-readable global coordinate system, enabling systematic comparison of the same color center sites over many experiments. We then implement resonant photoluminescence excitation in a widefield cryogenic microscope to parallelize resonant spectroscopy, achieving two orders of magnitude speed-up over confocal microscopy. Finally, we demonstrate automated chip-scale characterization of color centers and devices at room temperature, imaging thousands of microscope fields of view. These tools will enable accelerated identification of useful quantum emitters at chip-scale, enabling advances in scaling up color center platforms for quantum information applications, materials science, and device design and characterization.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the ``clean'' molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (i.e., diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. VoxMol achieves comparable results to state of the art on unconditional 3D molecule generation while being simpler to train and faster to generate molecules.

In recent years, diffusion-based models have demonstrated exceptional performance in searching for simultaneously stable, unique, and novel (S.U.N.) crystalline materials. However, most of these models don't have the ability to change the number of atoms in the crystal during the generation process, which limits the variability of model sampling trajectories. In this paper, we demonstrate the severity of this restriction and introduce a simple yet powerful technique, mirage infusion, which enables diffusion models to change the state of the atoms that make up the crystal from existent to non-existent (mirage) and vice versa. We show that this technique improves model quality by up to times2.5 compared to the same model without this modification. The resulting model, Mirage Atom Diffusion (MiAD), is an equivariant joint diffusion model for de novo crystal generation that is capable of altering the number of atoms during the generation process. MiAD achieves an 8.2% S.U.N. rate on the MP-20 dataset, which substantially exceeds existing state-of-the-art approaches. The source code can be found at https://github.com/andrey-okhotin/miad.git{github.com/andrey-okhotin/miad}.

Recent advances in diffusion models have shown remarkable potential in the conditional generation of novel molecules. These models can be guided in two ways: (i) explicitly, through additional features representing the condition, or (ii) implicitly, using a property predictor. However, training property predictors or conditional diffusion models requires an abundance of labeled data and is inherently challenging in real-world applications. We propose a novel approach that attenuates the limitations of acquiring large labeled datasets by leveraging domain knowledge from quantum chemistry as a non-differentiable oracle to guide an unconditional diffusion model. Instead of relying on neural networks, the oracle provides accurate guidance in the form of estimated gradients, allowing the diffusion process to sample from a conditional distribution specified by quantum chemistry. We show that this results in more precise conditional generation of novel and stable molecular structures. Our experiments demonstrate that our method: (1) significantly reduces atomic forces, enhancing the validity of generated molecules when used for stability optimization; (2) is compatible with both explicit and implicit guidance in diffusion models, enabling joint optimization of molecular properties and stability; and (3) generalizes effectively to molecular optimization tasks beyond stability optimization.

The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.

Self-supervised learning holds promise to revolutionize molecule property prediction - a central task to drug discovery and many more industries - by enabling data efficient learning from scarce experimental data. Despite significant progress, non-pretrained methods can be still competitive in certain settings. We reason that architecture might be a key bottleneck. In particular, enriching the backbone architecture with domain-specific inductive biases has been key for the success of self-supervised learning in other domains. In this spirit, we methodologically explore the design space of the self-attention mechanism tailored to molecular data. We identify a novel variant of self-attention adapted to processing molecules, inspired by the relative self-attention layer, which involves fusing embedded graph and distance relationships between atoms. Our main contribution is Relative Molecule Attention Transformer (R-MAT): a novel Transformer-based model based on the developed self-attention layer that achieves state-of-the-art or very competitive results across a~wide range of molecule property prediction tasks.

Recent advances in synthetic methods enable designing subunits that self-assemble into structures with well-defined sizes and architectures, but yields are frequently suppressed by the formation of off-target metastable structures. Increasing the complexity (number of distinct inter-subunit interaction types) can inhibit off-target structures, but leads to slower kinetics and higher synthesis costs. Here, we use icosahedral shells formed of programmable triangular subunits as a model system, and identify design principles that produce the highest target yield at the lowest complexity. We use a symmetry-based construction to create a range of design complexities, starting from the maximal symmetry Caspar-Klug assembly up to the fully addressable, zero-symmetry assembly. Kinetic Monte Carlo simulations reveal that the most prominent defects leading to off-target assemblies are a class of disclinations. We derive symmetry-based rules for identifying the optimal (lowest-complexity, highest-symmetry) design that inhibits these disclinations, leading to robust, high-fidelity assembly of targets with arbitrarily large sizes. Optimal complexity varies non-monotonically with target size, with `magic' sizes appearing for high-symmetry designs in which symmetry axes do not intersect vertices of the triangular net. The optimal designs at magic sizes require 12 times fewer inequivalent interaction-types than the (minimal symmetry) fully addressable construction.

The statistical mechanics of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. In this paper, we follow the path set out by Jaynes, including elements added subsequently to that original work, to explore the consequences of the purely statistical point of view. We show how standard methods in the equilibrium theory could have been derived simply from a description of the available problem information. In addition, our presentation leads to novel insights into questions associated with symmetry and non-equilibrium statistical mechanics. Two surprising consequences to be explored in further work are that (in)distinguishability factors are automatically predicted from the problem formulation and that a quantity related to the thermodynamic entropy production is found by considering information loss in non-equilibrium processes. Using the problem of ion channel thermodynamics as an example, we illustrate the idea of building up complexity by successively adding information to create progressively more complex descriptions of a physical system. Our result is that such statistical mechanical descriptions can be used to create transparent, computable, experimentally-relevant models that may be informed by more detailed atomistic simulations. We also derive a theory for the kinetic behavior of this system, identifying the nonequilibrium `process' free energy functional. The Gibbs relation for this functional is a fluctuation-dissipation theorem applicable arbitrarily far from equilibrium, that captures the effect of non-local and time-dependent behavior from transient driving forces. Based on this work, it is clear that statistical mechanics is a general tool for constructing the relationships between constraints on system information.

The prediction of material degradation is an important problem to solve in many industries. Environmental conditions, such as humidity and temperature, are important drivers of degradation processes, with corrosion being one of the most prominent ones. Quantum machine learning is a promising research field but suffers from well known deficits such as barren plateaus and measurement overheads. To address this problem, recent research has examined quantum reservoir computing to address time-series prediction tasks. Although a promising idea, developing circuits that are expressive enough while respecting the limited depths available on current devices is challenging. In classical reservoir computing, the onion echo state network model (ESN) [https://doi.org/10.1007/978-3-031-72359-9_9] was introduced to increase the interpretability of the representation structure of the embeddings. This onion ESN model utilizes a concatenation of smaller reservoirs that describe different time scales by covering different regions of the eigenvalue spectrum. Here, we use the same idea in the realm of quantum reservoir computing by simultaneously evolving smaller quantum reservoirs to better capture all the relevant time-scales while keeping the circuit depth small. We do this by modifying the rotation angles which we show alters the eigenvalues of the quantum evolution, but also note that modifying the number of mid-circuit measurements accomplishes the same goals of changing the long-term or short-term memory. This onion QRC outperforms a simple model and a single classical reservoir for predicting the degradation of aluminum alloys in different environmental conditions. By combining the onion QRC with an additional classical reservoir layer, the prediction accuracy is further improved.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

The intricate relationship between electrons and the crystal lattice is a linchpin in condensed matter, traditionally described by the Fr\"ohlich model encompassing the lowest-order lattice-electron coupling. Recently developed quantum acoustics, emphasizing the wave nature of lattice vibrations, has enabled the exploration of previously uncharted territories of electron-lattice interaction not accessible with conventional tools such as perturbation theory. In this context, our agenda here is two-fold. First, we showcase the application of machine learning methods to categorize various interaction regimes within the subtle interplay of electrons and the dynamical lattice landscape. Second, we shed light on a nebulous region of electron dynamics identified by the machine learning approach and then attribute it to transient localization, where strong lattice vibrations result in a momentary Anderson prison for electronic wavepackets, which are later released by the evolution of the lattice. Overall, our research illuminates the spectrum of dynamics within the Fr\"ohlich model, such as transient localization, which has been suggested as a pivotal factor contributing to the mysteries surrounding strange metals. Furthermore, this paves the way for utilizing time-dependent perspectives in machine learning techniques for designing materials with tailored electron-lattice properties.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

In molecular research, simulation \& design of molecules are key areas with significant implications for drug development, material science, and other fields. Current classical computational power falls inadequate to simulate any more than small molecules, let alone protein chains on hundreds of peptide. Therefore these experiment are done physically in wet-lab, but it takes a lot of time \& not possible to examine every molecule due to the size of the search area, tens of billions of dollars are spent every year in these research experiments. Molecule simulation \& design has lately advanced significantly by machine learning models, A fresh perspective on the issue of chemical synthesis is provided by deep generative models for graph-structured data. By optimising differentiable models that produce molecular graphs directly, it is feasible to avoid costly search techniques in the discrete and huge space of chemical structures. But these models also suffer from computational limitations when dimensions become huge and consume huge amount of resources. Quantum Generative machine learning in recent years have shown some empirical results promising significant advantages over classical counterparts.

Materials discovery and design are essential for advancing technology across various industries by enabling the development of application-specific materials. Recent research has leveraged Large Language Models (LLMs) to accelerate this process. We explore the potential of LLMs to generate viable hypotheses that, once validated, can expedite materials discovery. Collaborating with materials science experts, we curated a novel dataset from recent journal publications, featuring real-world goals, constraints, and methods for designing real-world applications. Using this dataset, we test LLM-based agents that generate hypotheses for achieving given goals under specific constraints. To assess the relevance and quality of these hypotheses, we propose a novel scalable evaluation metric that emulates the process a materials scientist would use to evaluate a hypothesis critically. Our curated dataset, proposed method, and evaluation framework aim to advance future research in accelerating materials discovery and design with LLMs.

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN.

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.

We present CrystalDiT, a diffusion transformer for crystal structure generation that achieves state-of-the-art performance by challenging the trend of architectural complexity. Instead of intricate, multi-stream designs, CrystalDiT employs a unified transformer that imposes a powerful inductive bias: treating lattice and atomic properties as a single, interdependent system. Combined with a periodic table-based atomic representation and a balanced training strategy, our approach achieves 9.62% SUN (Stable, Unique, Novel) rate on MP-20, substantially outperforming recent methods including FlowMM (4.38%) and MatterGen (3.42%). Notably, CrystalDiT generates 63.28% unique and novel structures while maintaining comparable stability rates, demonstrating that architectural simplicity can be more effective than complexity for materials discovery. Our results suggest that in data-limited scientific domains, carefully designed simple architectures outperform sophisticated alternatives that are prone to overfitting.

We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and the neural network potential is optimized to match the corresponding equilibrium potential at every intermediate time-step. Once the interpolating potentials and samples are well-aligned, the free-energy difference can be estimated using (neural) thermodynamic integration. To target molecular systems, we simultaneously couple Lennard-Jones and electrostatic interactions and model the rigid-body rotation of molecules. We report accurate results for several benchmark systems: a Lennard-Jones particle in a Lennard-Jones fluid, as well as the insertion of both water and methane solutes in a water solvent at atomistic resolution using a simple three-body neural-network potential.

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.