Molecular Dynamics

Machine-learned interatomic potentials (MLIPs) for solid-liquid interfaces in advanced materials applications, e.g., electrochemistry, catalysis and corrosion, require training data that samples both liquid environments, the solid and the interface itself. We present SoLiD26, a curated solid-liquid interface dataset, containing 15.4 million first-principles atomic structures with up to 576 atoms and 15 chemical elements for training and evaluating MLIPs. The structures were compiled from density functional theory (DFT) calculations performed in studies of solid-liquid interfaces, with most configurations originating from ab initio molecular dynamics (AIMD) simulations. Each record contains atomic species, positions, simulation cell, periodic boundary conditions, potential energy and atomic forces. SoLiD26 includes aqueous coinage metal interfaces, electrode-electrolyte systems, and selected bulk reference structures, calculated with VASP using the PBE functional and D3 dispersion corrections. We describe the data ingestion and preparation pipeline used to construct the dataset. The application of SoLiD26 for training and evaluating MLIPs is demonstrated with a suite of MACE models on a simple training, validation and test split. The dataset enables development and benchmarking of MLIPs for structurally and chemically heterogeneous solid-liquid interfaces.

Machine learning interatomic potentials (MLIPs) learn the mapping from atomic positions to potential energy. The forces, the negative gradient of this energy, drive molecular dynamics and are readily obtained using automatic differentiation. Higher-order derivatives, most notably the Hessian, describe collective motion and allow the direct prediction of experimental observables, but are considered computationally inaccessible for large systems. We suggest a solution: in physical systems, interactions decay with distance, and most MLIPs build on this locality through message passing up to a finite receptive field. This implies both sparsity of higher-order derivatives and their decay with distance. This structure can be exploited using automatic sparse differentiation (ASD). We explain how to compute the sparsity pattern for MLIP derivatives and demonstrate that, for multiple foundation MLIPs, ASD computes full Hessians of large porous materials exactly, but with modest speedups at best. The larger gains come from truncated ASD: discarding small, but nonzero, Hessian entries between distant atoms yields order-of-magnitude speedups with negligible impact on predicted observables.

Studying the dynamical behavior of a system often depends on characterizing how it transitions between long-lived states. Because such transitions are rare, observing them usually requires specialized enhanced sampling techniques. Transition Path Sampling (TPS) is a well-established method for generating reactive trajectories, which is simple to implement and does not require the definition of a preconceived reaction coordinate. However, its efficiency is limited by its sequential nature and the resulting correlations between sampled paths. Previous work addressed this limitation by combining TPS with a sampling scheme based on conditioned Boltzmann Generators, a generative machine learning model capable of sampling a given target probability distribution. This approach produces uncorrelated transition paths but relies on an accurate reaction coordinate, which is rarely known in advance. Building on recent advances in committor learning, specifically on the Artificial Intelligence for Molecular Mechanism Discovery (AIMMD) method, in this work we introduce GenAIMMD, an iterative algorithm that actively and self-consistently learns the ideal reaction coordinate (the committor) and trains a conditioned Boltzmann Generator to sample from arbitrary bias windows along it. GenAIMMD thereby provides a correlation-free and fully parallelizable path sampling scheme that does not require prior knowledge of the system's transition mechanism. We apply GenAIMMD to a two-dimensional toy model and a higher-dimensional polymer system. In both cases, GenAIMMD succeeds in training the Boltzmann Generator and learning the committor. Benchmark results show a substantial increase in performance compared to standard TPS.

Many proteins function through transitions between conformational states, yet rare states are rarely sampled by diffusion models trained on an equilibrium ensemble, demanding better sampling methods. We introduce METALICA, which implements Metadynamics on a pretrained diffusion model via Replica Exchange. It accumulates a bias potential along a Collective Variable, repels new samples from previous ones through biased sampling, and reweights samples onto the unbiased distribution. METALICA holds one replica per diffusion level, forming a Markov Chain that evolves through inter-replica communication and is refined in place as the bias grows. METALICA is the dual of sequential control, in which Sequential Monte Carlo parallelizes the sampler over a batch of particles. Parallelism over the levels of the diffusion-time schedule instead allows METALICA to generate samples from long chains, essential for the discovery of rare events, with accuracy set by run length rather than by the memory available. We validate on a bimodal target with known free energies, then apply METALICA to the unfolding of a protein. At a budget for which sequential control yields no unfolded structure, METALICA populates the basin and resolves a second free energy minimum.

Most molecular transitions occur on timescales far beyond direct molecular dynamics simulations. The committor, the probability that a configuration reaches a product state before a reactant state, is a central kinetic statistic, providing a mechanism-independent reaction coordinate and a foundation for transition path theory and the calculation of rates. This review surveys modern approaches for estimating the committor and related kinetic statistics from molecular simulations, with an emphasis on self-supervised methods that learn solutions of their defining dynamical equations rather than relying on labeled shooting data. We develop a common operator viewpoint connecting generator-based partial differential equations, variational principles, Markov state models, dynamical Galerkin approximation, and neural networks. Empirical and theoretical evidence points to the efficiency of these methods. We provide theoretical and practical guidance for realizing their full potential in applications, including strategies for treating non-Markovian effects and for sampling. We conclude by identifying opportunities for further research, including connections to reinforcement learning and generative modeling.

The Hohenberg-Kohn theorem establishes that, in principle, the ground state (GS) charge density contains all GS information of a many-electron system, such that all GS observables can be expressed as functionals of the GS charge density. Conventional Kohn-Sham density functional theory requires iterative solution of the self-consistent-field equations at substantial computational cost, motivating the development of deep learning surrogates for electronic structure calculations and, in turn, accelerating computer-aided materials design. Here, we propose \textbf{AIDEN}, an \underline{A}tomic-\underline{I}nteraction \underline{D}ensity \underline{E}quivariant \underline{N}etwork for solving real-space charge density. AIDEN separates the element-dependent one-center density from environment-induced density redistribution and represents the latter through complementary atom- and edge-centered tensor correlations. A continuous low-rank Gaussian decoder then reconstructs the density at arbitrary spatial coordinates while reusing atomic encodings independently of the evaluation grid. AIDEN achieves state-of-the-art accuracy on periodic crystal benchmarks while remaining competitive for molecular systems, and further demonstrates zero-shot transferability across several structurally distinct out-of-distribution case studies. Furthermore, AIDEN provides substantially faster inference than both baseline models and full SCF calculations, enabling efficient charge density reconstruction for large-scale electronic structure calculations.

High-throughput calculations using density-functional theory (DFT) are commonly used to explore point defects for applications in power electronics and quantum technologies. There is currently a major shift away from these traditional simulation techniques towards machine learning (ML) methods. We explore a class of physics-guided ML models for predicting defect formation energies and zero-phonon lines (ZPL) to identify point defects for quantum applications. The models are specifically targeted for use in a prescreening step for accelerated high-throughput workflows, and are therefore designed to avoid the costly relaxation step typically present with ML interatomic potentials (MLIPs). We compare performance for single and double point defect systems in 4H-SiC with ridge, kernel ridge, and multilayer perceptron (MLP) models using three different descriptors representing the defect systems. For vacancies and substitutions, the optimized models give mean absolute errors (MAEs) of 0.437 eV for the formation energy and 0.202 eV for ZPLs, which is just above the level at which such predictions can be useful even beyond the targeted prescreening, i.e., in some applications they may completely replace the need for costly DFT calculations. For interstitials the MAEs are larger, 1.101 eV for the formation energy and 0.230 eV for the ZPL, which, while still useful for prescreening, will not generally be useful for more detailed characterization. Hence, while the results may be further improved by model design and optimization, the models presented in this work are already useful for prescreening in high-throughput characterization of point defects.

Foundational machine-learning interatomic potentials (MLIPs) are transforming atomistic simulations by achieving near-ab initio accuracy across large chemical spaces at a fraction of the computational cost. A central challenge in using these tools for high-throughput property calculations is translating high-level scientific intent into adaptive simulation campaigns without compromising workflow rigour. We introduce El Agente Potente, an agentic system that combines typed execution graphs with a complementary coding mode for MLIPs-driven atomistic simulations. Typed execution graphs provide structured and provenance-aware execution for standardized workflows, with large language models (LLMs) restricted to planning and routing while deterministic Python components perform scientific computation and validation. Complementing this structured execution, a coding agent constructs customized workflows for tasks requiring greater procedural flexibility while invoking existing Potente functions for supported calculations. We demonstrate El Agente Potente across computational materials discovery, molecular energy-landscape exploration, adsorption, and catalytic reaction workflows, together with systematic benchmarks of reproducibility and LLM token cost. These results establish typed execution graphs and code-based workflow construction as complementary mechanisms for agentic scientific computing, combining controlled, auditable execution with the flexibility required for customized atomistic simulations

Unraveling reaction mechanisms is central to modern chemistry, yet automating these investigations remains challenging because computational workflows still rely heavily on expert intervention. Here we introduce ARCHE, an autonomous agentic system that integrates a general-purpose reasoning model, a domain-specialized computational chemistry model, and a structured tool registry to transform mechanistic inquiry into a scalable, self-validating process. ARCHE interprets scientific questions, generates and prioritizes mechanistic hypotheses, orchestrates computational workflows, and iteratively refines conclusions based on computed evidence within a closed loop. We validate its capabilities across three increasingly demanding scenarios: reconstructing stereocontrolling transition states and validating the corresponding reaction mechanism in a previously reported asymmetric catalytic reaction; proposing and validating a plausible radical pathway through iterative hypothesis refinement for a recently discovered but unpublished $\alpha$-iodoboronate C-I cleavage reaction; and identifying a chemically interpretable descriptor that governs selectivity in nickel-catalysed migratory cross-coupling reactions. By coupling agentic reasoning with rigorous computational validation, ARCHE advances autonomous mechanistic discovery and establishes a foundation for broader machine-assisted chemical research. The code for ARCHE is publicly available at https://github.com/JetAstra/Arche-Harness.

Universal machine-learning interatomic potentials (u-MLIPs) aim to generalize across diverse configurations. Benchmarks enable reproducible evaluation but may not expose failures outside their predefined scope. Here, we show that physics-informed search can complement benchmark-based evaluation by uncovering hidden failure modes. We introduce MLIP Detective, an agentic framework for active failure mode discovery. Starting from benchmark evidence, MLIP Detective generates falsifiable, physics-informed failure hypotheses, screens them with inexpensive simulations, and escalates only the most suspicious cases to human experts together with proposed verification protocols. Without issue-specific prompting, MLIP Detective identified and characterized a systematic anomaly in MACE-MPA-0: the model predicted some relaxed adsorbate-surface systems involving O- or F-containing adsorbates to be higher in energy than their corresponding separated fragments. Using cross-model comparisons, MLIP Detective further inferred a likely training-data origin for the anomaly, consistent with recent reports.

Equivariant networks are commonly trained with Adam, yet recent work reports that matrix-structured optimizers such as Muon can perform better on these architectures without explaining why. We identify one source of this difference inside equivariant linear layers. Each irrep block learns a channel-mixing matrix $W_l$ shared across its $2l+1$ components, giving the expanded map $W_l \otimes I_{2l+1}$. For a single application of the layer, the gradient of $W_l$ sums $2l+1$ outer product contributions and has rank at most $2l+1$. Adam rescales stored weights individually without using the irrep boundaries, so one learning rate can produce different spectral step sizes across blocks within a layer. We address this mismatch by normalizing each block update separately, without introducing a new hyperparameter. This changes only the scale of the update, leaving Adam's moment estimates and its direction within each block unchanged. We evaluate the mechanism in a controlled $\mathrm{SO}(3)$-equivariant model with a matched dense control and in an e3nn interatomic potential model trained on rMD17 and MD22. The toy setup isolates a mismatch that grows with width while the dense control shows no corresponding growth. In the interatomic potential model, block normalization and tuning Adam's momentum coefficients independently improve performance, but neither alone matches Muon. Combined, they make Adam competitive with Muon on all datasets, indicating that blockwise step control and momentum accumulation account for much of Muon's advantage.

While machine-learning interatomic potentials (MLIPs) have successfully learned potential energy surfaces (PES) and atomic forces, many practical applications, such as vibrational analysis and transition state search, rely heavily on the PES Hessian. Yet standard MLIPs are trained on energy and forces alone, and existing methods that incorporate the Hessian into training objectives require architectural modifications and incur significant computational and memory overheads from higher-order backpropagation. To address these limitations, we propose two Hessian-derived data augmentation schemes: isotropic Gaussian displacement (\textbf{UniAug}) and normal mode-weighted displacement (\textbf{ModeAug}). Both methods utilize simple Taylor expansions, achieving effective augmentation without altering training objectives or extending the autograd graph. This allows seamless, plug-and-play integration with existing architectures and training pipelines. Comprehensive evaluations across non-equilibrium and equilibrium datasets demonstrate that our approach enhances model accuracy where reference forces are large while providing practical, task-specific guidelines.

Nested sampling (NS) resolves the thermodynamics of an atomistic system from a single simulation, but its practical reach is limited by the Markov-chain updates needed to decorrelate walkers within each likelihood-constrained ensemble. Flow-based NS has removed this bottleneck for gravitational-wave (GW) inference, yet its transfer to atomistic systems is not merely a change of application. Comparing a GW150914-like binary-black-hole likelihood with an eight-particle two-dimensional Lennard-Jones (LJ) system of comparable dimensionality, we show that the two landscapes differ fundamentally: atomistic multimodality is discrete and combinatorial, generated by particle permutations separated by hard collision walls, and its coordinate coupling is dense and collective, whereas the GW posterior exhibits smooth degeneracies and localized parameter coupling. Guided by this diagnosis, we introduce NS-Flows: a single conditional normalizing flow, conditioned on the NS energy bound and trained on a sliding window of recent live sets, that replaces MCMC by direct parallel draws corrected by importance-weighted rejection resampling. Live sets supply data self-consistently, allowing flow training without structured priors or a pre-existing dataset. For LJ disks in PBC, the algorithm reduces energy evaluations by over two orders of magnitude and wall-clock time by roughly one third, an advantage that becomes increasingly favorable as the cost of the potential grows. The flow's generation efficiency further acts as a physical diagnostic: it varies non-monotonically along the annealing trajectory, is lowest in the dense disordered regime, and is quantitatively captured by the constrained ensemble's internal mode complexity together with target drift across the training window, identifying liquid-like ensembles, rather than prior-target separation, as the hard case for current flow architectures.

Learned graph simulators provide an efficient alternative to high-fidelity solvers for granular dynamics. However, granular motion depends strongly on inter-granular contact history, which is difficult to preserve when particle contacts form, break, and rearrange. Existing simulators mainly store temporal information in node features or node-level memory. Here we introduce TRACE, a graph-network simulator that stores interaction history directly on contact edges. Each edge maintains a persistent memory updated by attention-based message passing and a gated recurrent unit, while an edge-identity dictionary preserves this memory as the contact graph changes. A physics-structured decoder predicts inter-granular normal and tangential contact forces, enforces the Coulomb friction limit, and applies equal-and-opposite internal forces. The model is trained with single-step pretraining followed by autoregressive rollout fine-tuning. We evaluate TRACE on 2D and 3D granular column-collapse benchmarks. In both cases, TRACE produces stable, physically consistent long-horizon rollouts, closely reproducing the final deposit geometry and the kinetic energy released during collapse. Compared with graph network simulator (GNS) and node-memory graph neural simulator (NMGNS), TRACE reduces long-rollout position error by 31-62% and final-deposit error by 58-89% across the two benchmarks, while using fewer parameters and maintaining near-zero particle interpenetration. TRACE also achieves 12.2$\times$ and 8.9$\times$ speedups over the material point method (MPM) reference solver in 2D and 3D, respectively. Our code is available at https://github.com/Data-Driven-Computational-Geotechnics/TRACE.

High-fidelity TCAD simulation of drift-diffusion transport remains the workhorse of emerging FinFET device design, but it is computationally expensive, especially for 3D structures where runtime escalates steeply with mesh complexity. This sharply limits multi-objective design space exploration. Existing machine-learning surrogates map a fixed set of design parameters to a few scalar device metrics, discarding the underlying physics and losing transferability across device geometries and families. A physics-informed graph attention network (GAT) surrogate is proposed. It operates directly on the tetrahedral TCAD mesh and predicts, at every mesh node, the electrostatic potential together with the electron and hole quasi-Fermi levels, the fundamental unknowns of the drift-diffusion system. Training combines a data loss with finite-volume current-continuity residuals, embedding carrier-transport physics into the objective. Operating on the mesh as a graph, the surrogate inherits size generalization: a model trained on few-fin meshes applies unchanged to substantially larger arrays, bounded at inference only by GPU memory. Per-node uncertainty from a deep ensemble drives an active-learning loop that screens large candidate pools in seconds and forwards only the most informative designs for full simulation. Benchmarked against Sentaurus Device on multi-fin tri-gate FinFETs, the surrogate reproduces the three drift-diffusion fields with sub-volt per-field RMSE and reaches a per-design throughput orders of magnitude higher than the full simulator. The advantage grows with device size: on large multi-fin arrays that are prohibitively slow to simulate directly, inference still completes in under a second per device, enabling Pareto-front exploration across device scales infeasible for direct TCAD sweeps.

Physics-informed neural networks (PINNs) offer a promising framework for modeling semiconductor devices, yet standard architectures struggle with severe numerical stiffness and multiscale spatial discrepancies inherent to oxide heterostructures. Here, we demonstrate a cascaded PINN architecture coupled with a custom second-order Chebyshev second kind polynomial spectral optimizer (DSO V2 Hybrid) to model ion-electronic drift-diffusion transport in Pt/SrTiO$_3$/Si memristive heterostructures across a 20 nm STO film on a 380 $μ$m Si substrate. By isolating potential, carrier density, and vacancy transport into four sequentially trained sub-neural-networks, our model circumvents condition numbers exceeding $10^{16}$ without operator splitting. The trained surrogate reproduces experimental conductive-AFM current-voltage hysteresis ($R^2 > 0.96$) while ensuring strict Poisson consistency across continuous space. Compared to conventional finite-element solvers (e.g., COMSOL), the PINN surrogate enables differentiable inverse parameter estimation and linear time inference.

Predicting the thermodynamic properties of an alloy requires sampling its configurations across many chemical conditions and recovering free energies on a common absolute scale. Markov chain Monte Carlo (MCMC) is the standard tool, but it requires separate simulations at different conditions, and auxiliary free-energy methods such as thermodynamic integration are used to place results on a common absolute scale. Modern discrete neural samplers typically use reverse KL divergence as the objective and can be mode-seeking or biased. We present Free energy Offering Generative Sampler (FrOGS), a hybrid discrete neural sampler that couples an autoregressive model to a continuous-time Markov chain (CTMC) to be trained jointly under a single shared loss. FrOGS draws i.i.d. configurations, returns an unbiased estimate of the partition function, and gives consistent estimates of thermodynamic observables. We train a single model across a wide range of chemical conditions to produce estimates on a common absolute free-energy scale. FrOGS matches exact finite-size results on the 2D Ising model and reference phase diagrams for AgPd and CuAu, without mode collapse. We additionally compare to SEGAL, a published autoregressive baseline, and find that only FrOGS recovers the stability range of the CuAu$_3$ phase.

We describe a neural network architecture and training procedure designed to model electronic ground and excited states of arbitrary molecular systems. By indirectly learning a latent, implicit basis representation of the electronic-state Hamiltonian, the model offers a unified treatment of multiple electronic states, conical intersections, and non-adiabatic couplings. The formalism can be further extended to learn consistent latent representations of additional operators such as transition dipole moments, for example. To demonstrate the general capabilities of our architecture, we train and evaluate networks on two realistic photochemical systems, thymine and azobenzene. The resulting models accurately reproduce energies and oscillator strengths for the ground- and low-lying excited states relevant to the photochemistry of these systems. We highlight the performance of the trained networks by studying critical molecular geometries, including conical intersections and excited state minima. By construction, the proposed framework also recovers the emergence of Berry phase accumulation around conical intersections. By pairing key mathematical structure from quantum chemistry with the representation learning power of transformers, the presented architecture offers a qualitatively new path toward fast and accurate ground- and excited-state simulations.

Computational materials science has traditionally delegated algorithmic tasks to computers while leaving scientific judgments to humans. We argue that recent LLM-based agent harnesses enable an emerging form of scientific software, agentic programs, that combine deterministic algorithms with bounded LLM-based judgment, task-specific verification, episodic maturation, and complete delegation in production. We illustrate this concept with DeMARS, an agentic program for constructing atomistic models from experimentally measured disordered crystal structures.

We prove that the Hypergraph Neural Network, an invariant architecture with 3-body message passing, is a universal approximator for potential energy surfaces. Our main contribution is a multi-layer completeness theory. We show that $L$ layers of message passing on sparse, cutoff-based graphs achieve the same representational power as having access to the full $L$-hop neighborhood, provided the configurations are generic, satisfy an overlap condition and a connectivity condition. This provides the first rigorous justification for the common practice of using multi-layer message passing with a per-layer cutoff smaller than the physical interaction range, the setting used by virtually all practical graph neural network based machine-learned interatomic potentials. As immediate consequences, we show that both DPA3 and CHGNet architectures inherit universal approximation.

Machine learning interatomic potentials bridge the gap between quantum chemical precision and classical computational speed, enabling molecular dynamics simulations with first-principles accuracy. Their reliability is often improved through active learning, which iteratively expands the training set by identifying uncertain, out-of-distribution configurations. Existing uncertainty-quantification methods often involve a trade-off between computational cost and reliability, and generally cannot account for redundancy as an acquisition batch is assembled. Here, we introduce AdaptNTK, a single-model framework that measures uncertainty as a regularized Mahalanobis distance in empirical neural tangent kernel (NTK) feature space. With the NTK features fixed during acquisition, the uncertainty depends on the acquired configurations but not their reference labels. This allows the uncertainty to be updated recursively after each selection without retraining, reducing redundancy within an acquisition batch. On held-out rMD17 data, AdaptNTK achieves the highest mean correlations with force errors (Spearman 0.68, Pearson 0.71) and matches a three-member ensemble in error retention. In active learning experiments, AdaptNTK achieves the lowest force errors across rMD17 and Transition-1X, with particularly strong performance on transition-state configurations in Transition-1X. AdaptNTK provides a 2.6-fold speedup per Transition-1X cycle relative to the ensemble, providing efficient single-model uncertainty estimation with sequential updates for data-efficient active learning.

Muon motivates designing optimizer geometry around the function of each parameter block and uses the spectral norm for hidden linear layers. For the language-model head, the spectral norm is not a faithful measure of functional change. Softmax removes shared logit shifts, whereas the spectral norm can assign arbitrarily large size to updates that change no output probability. We therefore treat the LM head and softmax as one module and derive an update geometry for their composition. Hilbert's projective distance respects this invariance as it measures the largest change in pairwise log odds. For an update $S$ with token rows $s_i^\top$, we show that the largest Hilbert distance over $\left\lVert h\right\rVert_2\leq H$ is exactly $H D(S)$, where $D(S)=\max_{i<j}\left\lVert s_i - s_j\right\rVert_2$ is the Euclidean row diameter. This diameter replaces the spectral norm in the resulting Muon-style steepest descent problem. An exact solution is possible, but its direct formulation contains one $d$-dimensional vector variable for every token pair. For a vocabulary size of approximately $50$k, this means more than one billion token pairs, making the calculation impractical at every training step. We instead impose a stronger common-ball constraint and derive projected RowNorm as an $O(Vd)$ solution. For the exact RowNorm oracle, we prove that its first-order decrease is at least $1/\sqrt{2}$ of the exact diameter-constrained optimum. With Muon on the backbone, experiments across three seeds at 190M, 380M, and 640M parameters show that RowNorm reduces mean final step diameters and empirical Hilbert RMS perturbations by factors of $45$--$60$ and $12$--$15$, respectively, with only a $0.0057$--$0.0153$ increase in mean final validation loss.

Liquids exhibit collective behavior that depends sensitively on thermodynamic conditions, interfaces and confinement, yet predicting each new state commonly requires a separate atomistic simulation. Classical density functional theory offers a reusable variational description, but its central excess free-energy functional is generally unknown, and learned approximations have largely remained restricted to planar or lower-dimensional settings. Here we show that this functional can be learned directly from fully three-dimensional equilibrium density fields while preserving spatial symmetry and variational consistency, without free-energy or chemical-potential labels. A single learned functional transfers across temperatures, system sizes and statistical ensembles, and recovers structure factors, the equation of state, liquid--vapor coexistence and interfacial broadening, none of which are used as training targets. Applied to complex three-dimensional geometries, it predicts the non-monotonic force associated with formation and rupture of a solvent-depleted bridge between colloids and adsorption in an interconnected gyroid pore. These results demonstrate that equilibrium density data can be converted into a transferable thermodynamic generator connecting microscopic liquid structure to response, phase behavior and collective phenomena.

Modernizing legacy Fortran is a problem of volume: the transformations are individually routine, but the codebases can be enormous, and across much of computational science the work simply goes undone. We propose an agentic workflow that takes this work on at production scale, and we set out to measure how far such delegation can reach. In this work, three prompt-specialized agent roles operate under a version-controlled specification that the agents themselves authored and revised, while humans hold a small number of gates. The arrangement is kept safe by an exact verification oracle inherited from the domain, and the boundary of safe delegation lies exactly where that oracle stops seeing. We apply the proposed workflow in a case study, converting the two-electron-integral routines of GAMESS (General Atomic and Molecular Electronic Structure System), a mature quantum-chemistry package with a 48-year development history, from fixed-form Fortran 77 to free-form Fortran 2008. The scope of this work was twelve source files, 56,448 lines, and 225 subroutines for computing electron repulsion integrals. The agents ran as three Claude Code roles in isolated worktrees, and the work spanned four Claude model generations. Because the GAMESS group ships a standard test suite whose printed energies its user community treats as canonical, we could adopt bit-for-bit reproduction of those energies as the merge criterion, where a deviation in the twelfth decimal place counts as a failure rather than drift. All twelve source files pass a 51-test validation battery comprising the 49 standard GAMESS tests and two additional calculations, and across 612 test runs the number of chemistry-relevant differences is zero, and every file also passes the Jenkins tests that are used for continuous integration.

Diffusion models have been widely explored in protein backbone generation due to their powerful generation capabilities.However, in today's AI-driven biological research, predicting the structure of unknown multi-chain protein aggregates (called "complexes" in biology) remains an unsolved challenge.This is because existing static or dynamic protein datasets focus solely on static snapshots or single-entity trajectories, neglecting the dynamic process of multiple monomers forming complexes.To alleviate this dilemma, we present DynaPPI, a dynamic protein dataset comprising molecular dynamics (MD) trajectories of protein complex formation from dissociated chains to the bound state, as a pivotal resource to bridge the gap between static structural biology and the inherently temporal nature of dynamic molecular interactions.Benefiting from this dataset, diffusion models can explicitly learn the dynamic binding trajectories of known complexes and accurately predict the structures of unknown complexes based on their diverse generative properties, thereby further catalyzing AI-driven structural biology and protein interactomics.

Long-running molecular simulation campaigns require repeated continuation from saved states, provenance-aware progression, adaptive assessment, and occasional interpretation of workflow conditions that cannot be resolved safely by fixed rules. Here, we present Agent-MD, a framework that places large language model (LLM) reasoning selectively at campaign construction and event-triggered review, while routine simulation, analysis, continuation, archiving, and state progression are handled by a persistent rule-based campaign agent using approved policies and explicit state records. Agent-MD was demonstrated in a grand canonical Monte Carlo-molecular dynamics (GCMC-MD) water-vapor desorption campaign comprising five montmorillonite systems and three sequential relative-humidity states (RH = 0.9-0.3-0.1). Across 15 system-RH states, the workflow completed 120 segmented simulation cycles with state-specific sampling lengths and provenance-aware restart inheritance. Routine production required no live reasoning-agent invocation, while one state reached a review boundary; two preserved incidents were subsequently evaluated through blinded reasoning-agent replay, which identified the underlying workflow problems and recommended appropriate follow-up actions. The simulations also revealed distinct composition-dependent low-RH responses, with Ca-bearing montmorillonite retaining more interlayer water and maintaining a larger basal spacing than the Na- and K-bearing systems, while the highest-charge Na system retained more residual water under dry conditions. These results demonstrate that long-running scientific workflows need not place every operation inside an LLM reasoning loop: selective reasoning can instead be combined with deterministic execution, structured evidence, and validated control handoffs to provide reproducible and auditable agent-assisted molecular simulation.

Coarse-grained (CG) molecular dynamics extends polymer simulation beyond the scales accessible to all-atom (AA) methods, but bottom-up CG modeling is laborious. The CG resolution is a design choice, so a transferable parameter set is generally not available and the potentials are derived anew for each polymer mapping. Here we present CGMas, a multi-agent framework that automates topology construction, equilibration, mapping, potential derivation, and validation from a natural-language specification of the polymer and target resolution. A large-language-model (LLM) reasoning agent infers the AA topology from polymer name, while layered self-correction resolves physical errors common to unsaturated, heteroatom-containing, and polar polymers. Downstream agents equilibrate the system, map it onto CG representation, derive potentials through Boltzmann inversion, and benchmark the model against its atomistic reference. CGMas completed all 27 homopolymer and copolymer tasks, matched the AA density to within 5% in 22, and reduced simulation from 38-88 min to 1 min, establishing agentic LLMs as a route to automated polymer coarse-graining.

Nonadiabatic dynamics needs an excited-state gradient and an interstate nonadiabatic coupling matrix element (NACME) at every nuclear geometry, and a double-hybrid functional's accuracy has been unavailable for the coupling. We report the first analytic derivative NACME for a double-hybrid excited state---deferred in the original hh-TDA method and supplied for hybrids only by Yu \emph{et al.}---derived, with the hole-hole and particle-particle Tamm--Dancoff (\hhTDA/\ppTDA) gradients and NACMEs, as a single reverse-mode transpose of one contraction graph closed under a non-symmetric atomic-orbital-direct $J/K$ kernel. Its double-hybrid excitation energy lowers the vertical-excitation mean absolute deviation from bare-\hhTDA\ $0.86$ to $0.47$~eV and removes the $+0.53\!\rightarrow\!+0.05$eV over-excitation bias, improving seven of ten states while over-correcting the ionic $ππ^*$ states---the expected perturbative-doubles failure, reported not trimmed. Every coupling is validated to $\sim\!10^{-4}$ against an independent \emph{literal many-electron wavefunction-overlap} oracle that shares no code path with the method, and is physically meaningful at the ammonia $n\!\rightarrow\!σ^*$ \emph{covalent} conical intersection, where the \hhTDA/\ppTDA manifolds recover the $F\!-\!2$ seam and adiabatic linear-response TDDFT gives $τ\!\equiv\!0$ by construction. Gradients, NACMEs, and the double-hybrid coupling all run device-resident and AO-direct through one shared Cholesky-decomposed $J/K$ engine within the 8,GB of a consumer RTX4060 (a profile-guided $\sim\!10^2\times$ launch collapse preserving double-precision bit-identity)---placing on a commodity desktop card a correlated excited-state derivative capability that has until now required datacenter hardware.

Design campaigns in chemistry, materials science, and machine learning share a bottleneck: determining how good a candidate truly is requires an expensive evaluation - an experiment, a first-principles simulation, or a full training run. Machine-learning surrogates that predict these outcomes are increasingly used not only to propose candidates but to grade them, and even to feed their own predictions back into the search as though they were measurements. Through mathematical analysis validated on three exhaustively ground-truthed design tasks, we establish when this practice is safe, what any certificate of safety must cost, and when the substitution provably pays. Predictive accuracy cannot anchor trust: near-perfect R^2 is compatible with worst-possible selections, and screening N candidates inflates the over-prediction at the selected candidate by a quantifiable "selection tax" with matching upper and lower bounds. Safety follows instead from an architectural rule - predictions may propose and train without restriction, but every certified conclusion must rest on true evaluations - which is sufficient with no assumptions on the surrogate, and necessary, since admitting predictions into certification with the standing of measurements opens a deterministic self-confirmation failure mode. We derive the minimal criterion under which a model may act as an oracle (rank preservation, not accuracy), show that trust must be purchased through selection-aware audits that are optimal in query complexity, and prove a dichotomy fixing when audited surrogates cut certified evaluation cost. Across 432 surrogate fits over six task-regime conditions, the audit statistic tracks deployed search performance at Spearman rank correlation 0.80-0.99, while the rank correlation of R^2 with deployed regret falls as low as 0.33; audited screening reduces certified oracle cost by a measured factor of 25.

Spatial atomic layer deposition (SALD) is a leading atmospheric-pressure, high-throughput route to industrial ALD, but design and control are limited by the cost of predicting surface coverage: high-fidelity CFD is far too slow for operating-window scans, while analytic models miss transport modulation such as the gas curtain. We present a physics-chemistry-informed neural network (PCINN), a hybrid surrogate with CFD-level accuracy at real-time speed: a query returns coverage in about 7 ms, roughly 5x10^4 times faster than a CFD solve, reaching a test R^2_log = 0.998 (leave-one-out R^2_raw = 0.974) from only 30 training cases spanning four orders of magnitude in coverage. The architecture is not a black box: a small network learns only the operating-condition to near-wall concentration closure, while the known surface kinetics is a hard-coded, trainable chemistry layer integrated along the substrate trajectory. This single-scalar bottleneck keeps it accurate under sparse data, interpretable and invertible. We add a full identifiability analysis (Fisher information, profile likelihood). The adsorption energy E_ads and desorption rate k_des are robustly identifiable; k_ads is not separately identifiable at a single temperature (only k_ads*c_wall is). Across four temperatures the prefactor nu and E_ads bind along a weakly identifiable degeneracy valley of slope 0.065 eV/decade, derived analytically as k_B T_eff ln(10) and turned into a reliability diagnostic: a seven-chemistry mismatch matrix shows it is invariant under any single-Arrhenius mismatch and shifts only when a second thermally activated process appears, so a slope departure flags unmodelled site heterogeneity. Data come from simulation with known ground truth inverted by the same kinetic form, so the study verifies pipeline self-consistency and the identifiability boundary, not real parameters.

High-entropy perovskite oxides (HEPOs) represent a chemically complex class of materials with promising functional properties, yet their vast compositional space and, chemical/structural disorder pose significant challenge for accurate property prediction. Graph neural networks (GNNs) enable rapid exploration of materials space but are often limited by the availability of representative training data. Here, we investigate ordered-to-disordered transfer learning using GNNs for formation-energy and HOMO-LUMO gap prediction in HEPOs by transferring knowledge learned from chemically ordered perovskites. Four representative GNN models, including CGCNN, GATGNN, ALIGNN and M3GNet are evaluated to understand the role of structural representations, spanning pairwise two-body and angular three-body interactions in transfer performance. We find strong property-dependent transfer behavior: formation-energy prediction transfers effectively to disordered HEPOs, whereas HOMO-LUMO gap prediction shows limited transferability due to its sensitivity to local chemical environments. Incorporating a small HEPO-specific training dataset substantially improves HOMO-LUMO gap prediction. Representation-level analysis using UMAP further highlights the importance of encoding three-body geometric information such as in ALIGNN for capturing complex structure-property relationships and improving transferability.

Reinforcement-learning-based quantum architecture search (RL-QAS) repeatedly optimizes a variational quantum eigensolver (VQE) after extending a circuit, although circuit construction and action legality are deterministic and known. We introduce DreamQAS, a model-based RL framework that preserves these exact circuit dynamics and learns only the expensive post-VQE feedback. A recurrent randomized-prior ensemble predicts an oracle-free score relative to an empirical energy frontier and supports multi-step imagined policy learning over explicit legal circuits. Ranking-based activation, uncertainty-aware pessimism and truncation, and selective real-VQE verification form a reliability-controlled learning loop. Under a common 15,000-episode budget and frozen evaluation for the RL methods, DreamQAS has the lowest mean frozen-policy energy error on four of five molecular tasks and the second-lowest on one. At fine-error targets reached by all seeds of both methods, it uses 1.6x to 2.0x fewer real VQE calls on four tasks and 10.6x fewer on BeH2-8q. Counterfactual action-ranking utility increases across all five tasks, with a mean increase of 0.346 and a 95 percent confidence interval of [0.185, 0.507], while direct greedy and beam use of the same model does not recover the gains of imagined policy learning. Ensemble disagreement also improves risk-coverage over random rejection on all three probed tasks. These results establish a world-model design for QAS whose value lies in decision-useful feedback rather than exact energy prediction.

Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within this broader effort. Coding agents promise to automate significant portions of this workflow, yet their reliability on realistic molecular dynamics (MD) tasks remains poorly characterized. To address this issue, we introduce MDArena, a benchmark of 50 containerized tasks drawn from active biomolecular simulation projects, spanning 29 molecular systems and 14 broad research protocols, including trajectory analysis, complex system preparation, free-energy protocols, and enhanced sampling. We evaluate six model/harness configurations spanning Codex and OpenCode. Among the evaluated configurations, Codex GPT-5.5 at extra-high reasoning effort performs best, reaching 24/50 Strict-Pass@1 successes (48%), followed by Codex GPT-5.5 Medium with 21/50, and OpenCode Gemini Flash 3.5 with 20/50. Average correctness and process rewards are substantially higher than strict success rates across all configurations, indicating that agents frequently make meaningful partial progress but fail on the fine-grained details required for reproducible scientific workflows. Hard tasks remain largely unsolved, particularly membrane-protein system preparation and alchemical free-energy setup, both unsolved or near-unsolved by every evaluated configuration. MDArena thus exposes a substantial gap between the usefulness of coding agents as supervised assistants and their reliability as autonomous MD researchers, while providing a reproducible and extensible platform for tracking progress toward closing it.

We introduce implicit machine learning force fields (I-MLFFs), which replace explicit stacks of neural network layers with self-consistent fixed-point equations. In molecular simulations, this formulation enables intermediate representations to be reused across successive timesteps, thereby warm-starting force evaluation. The resulting models effectively combine the computational footprint of a shallow, single-layer MLFF with the representational capacity and accuracy of a deep neural network. Our approach unlocks architecture-agnostic efficiency gains that are inaccessible when force prediction and trajectory integration are considered separately. We demonstrate this across three major classes of graph neural networks: invariant, equivariant Cartesian tensor, and SO(3)-equivariant spherical-tensor architectures. Each yields a two- to five-fold reduction in compute and memory footprint. Crucially, these gains are achieved while retaining full atomistic resolution and the original integration timestep, avoiding spatial or temporal coarse graining. Our contribution therefore advances the scaling frontier of quantum-mechanically faithful molecular simulation, enabling longer trajectories and larger atomistic systems within fixed GPU memory and compute budgets, and thereby opening access to new insights across biomolecular and material systems.

Generative machine learning is increasingly used for inorganic crystal structure generation. Most models and the corresponding evaluation approaches rely on simple forms of crystal structure representation. In this paper, we showcase the power of atom-averaged features from pretrained Machine-Learning Interatomic Potentials (MLIPs), such as MACE, for such tasks. We first introduce a distance measure that assesses the output of material generative models by capturing both quality and novelty in a single distribution-based evaluation framework. In particular, we introduce the Coarse-Fine Transport Distance (CFTD) using two different featurizers, where the quality component is based on coarse MACE features. We showcase CFTD's versatility in capturing crystal-structure quality while also detecting memorization, and compare it with the recently introduced continuous SUN metrics. We further show that coarse MACE features can be used as guidance for a material generative model.

Chemical property prediction plays a critical role in accelerating scientific discovery in chemistry, materials science, and drug development. However, existing benchmarks often suffer from limited task diversity, fragmented datasets, and inconsistent evaluation protocols, making it challenging to systematically assess the reliability and generalization of AI models. In this work, we introduce Chem World, a comprehensive benchmark for chemical property prediction that integrates 17 diverse chemical datasets with over 800,000 molecular samples, covering various properties including density, electrical conductivity, solubility, and other molecular characteristics. Chem World provides a unified platform for evaluating AI models across multiple property prediction tasks. Furthermore, we propose Mixture-PINN, a physics-informed neural network based prediction framework that incorporates chemical prior knowledge into data-driven learning, improving the accuracy, robustness, and reliability of chemical property prediction. Extensive experiments on Chem World demonstrate the effectiveness of our approach compared with existing methods. By combining large-scale standardized evaluation with physics-informed learning, Chem World establishes a foundation for developing trustworthy AI systems for computational chemistry and advancing AI-driven scientific discovery.

Mapping an atomic structure to a compact set of geometric descriptors is an essential step in any machine-learning application to atomic-scale modeling. A powerful and widely-used approach can be understood as a discretization of the histogram of pair distances, triangles, etc., that results in a hierarchy of symmetry-invariant atom-centered descriptors. Unfortunately, the lower rungs on this hierarchy (two, three, four-neighbor clusters) were found to be incomplete, with symmetry-unrelated pairs of structures having exactly the same descriptors. However, all the ``descriptor degeneracies'' reported so far are resolved by considering larger clusters of neighbors to build the descriptors. We report examples of 3D structures that are indistinguishable even if one considers clusters of up to seven neighbors, and to arbitrary order when considering a practical level of discretization of the descriptors, discovered with the assistance of large language models. The key ingredients in their construction can be traced to results that have been known for decades in different communities; the model was able to find the references and recognize their significance for the problem at hand. We believe this experiment exposes an extremely fruitful usage pattern for AI in science: translating results between different communities and application domains, accelerating the process by which serendipitous discoveries in a field become paradigm-shifting breakthroughs in another.

Transformer-based surrogate models are increasingly used to replace expensive first-principles simulation in engineering design. But conventional transformer architectures are often over parameterized for the small, low-dimensional datasets typical of engineering design spaces, where large simulation data is expensive to generate. Under these conditions, excess parameter capacity leads to overfitting rather than improved accuracy, while also incurring unnecessary memory and compute overhead. This motivates a shift towards architectures that focus on additional compute rather than additional learnable parameters. This paper presents a hardware-aware evaluation of three recursive transformer paradigms for surrogate thermo-mechanical analysis of advanced packages: a)Tiny Recursive Model, b) our proposed Depth Recursive transformer, c) and a simple recursive transformer. We systematically compare their predictive performance (Recall, Mean Reciprocal Rank), parameter count, computational complexity (FLOPs), providing practical design guidelines for selecting recursive transformer architectures under resource-constrained scenarios. We validate this principle on two low-dimensional engineering prediction tasks: 1) thermo-mechanical reliability analysis of advanced semiconductor packages, where stress and warpage from thermal cycling must be evaluated repeatedly across a design-of-experiments sweep under costly finite element analysis (FEA). 2) Laplace PDE iterative numerical solver for capacitance field. Overall, recursive weight-sharing transformers provide an effective and generalizable trade-off between prediction accuracy, parameter efficiency, and computational cost for small data engineering surrogate modeling.

Structure-prediction networks built on co-evolutionary statistics have transformed protein-based drug discovery, yet their accuracy does not extend to peptide therapeutics--an increasingly important modality defined by non-canonical residues, macrocyclization, and complex topologies. We introduce Vilya-2, a diffusion transformer that extends the all-atom representation of Vilya-1 from modeling individual molecules to modeling their interactions with protein targets. This all-atom representation enables transfer learning between different molecular types, and delivers highly accurate structural modeling of peptides across sizes, classes, and compositions bound to therapeutically relevant targets. By generating diverse structural ensembles and ranking them with calibrated confidence, Vilya-2 recovers 59.1% of peptide interfaces to sub-2 Å backbone RMSD, far exceeding the performance of a representative co-folding model even when that model is given the bound receptor as a template. In addition, Vilya-2 is state-of-the-art at small-molecule docking, and generalizes to novel protein-small molecule complexes unlike those seen in training. It also generalizes to modeling molecular conformations of diverse macrocycles and disulfide-stapled miniproteins several-fold larger than any molecule seen in training. Finally, Vilya-2 can be used as a foundation model, and fine-tuned to enrich for active compounds in hit-to-lead campaigns. By unifying predictive accuracy with broad generalizability across chemical space, Vilya-2 is the structure-prediction oracle that de novo peptide design pipelines require--establishing the all-atom approach as a general foundation for the design and evaluation of de novo peptide therapeutics.

Machine learning interatomic potentials (MLIPs) approximate quantum-mechanical energies and forces---conventionally computed by density functional theory (DFT) or wave-function methods---at a fraction of the cost. The field encompasses a growing ecosystem of algorithms, training datasets, hyperparameters, and target materials, yet the metadata needed to systematically compare, reproduce, and build upon MLIP studies remains scattered across papers, scripts, and ad-hoc file formats. We present the MLIPs ontology, an OWL 2 DL ontology that captures the concepts needed to describe MLIP methods, their hyperparameters, training datasets with DFT provenance, and published benchmarks. The ontology is organized into three modules---Method, Training Data, and Benchmark---and connects existing ontologies in materials science (MDO, CMSO/ASMO) and machine learning (ML-Schema), complementing dataset-side schemas such as Croissant. It declares 27 formal axioms enforcing data completeness and consistency, including property chains that link trained models to their methods and training data. We demonstrate the ontology through a running example based on Moment Tensor Potentials and evaluate it through competency-question execution on a 20-paper seeded knowledge graph, OWL reasoning, and comparison with existing ontologies.

Quantum state preparation is a key component of many quantum algorithms. Performing this step efficiently is essential for realizing practical quantum advantage in quantum chemistry applications. Iterative algorithms like ADAPT-VQE can produce shallow ground-state preparation circuits, but become computationally prohibitive for the larger molecules relevant to materials science and pharmaceutical development. Here, we introduce ADAPT-GQE, a generative AI framework that learns to synthesize ground-state preparation circuits for electronic structure calculations. We first use ADAPT-VQE to generate high-quality reference circuits, which are then used as targets for training models for circuit generation. Once trained, the model can efficiently propose and score circuits, enabling reinforcement learning (RL) to drive circuit generation accuracy beyond the accuracy of the ADAPT-VQE training data. This pipeline achieves order-of-magnitude reductions in circuit generation time relative to ADAPT-VQE while maintaining comparable or improved state-preparation accuracy. We demonstrate ADAPT-GQE on imipramine, a well-established tricyclic antidepressant that serves as a representative, challenging target for computational modelling in drug stability protocols. We execute generated circuits on Quantinuum Helios-1, representing a milestone for AI-generated quantum chemistry circuits on state-of-the-art quantum hardware. These results establish a pathway toward automated quantum circuit synthesis for utility-scale quantum computational chemistry.

Accurate ab initio molecular dynamics (AIMD) simulations of complex, fluxional chemical systems are severely limited by the high computational scaling of correlated electronic structure methods. To overcome this bottleneck, we present a robust, graph-theoretic molecular fragmentation framework integrated with machine learning to directly model post-Hartree-Fock nuclear forces at coupled cluster accuracy. Bypassing the limitations of automatic differentiation on learned energy surfaces that may struggle with link-atom Jacobians, our approach directly predicts nuclear force vectors. By projecting these vectors onto fragment-fixed principal axes of inertia, we establish co-variant descriptors that naturally preserve rotational, translational, and permutational invariance. The methodology achieves exceptional high parameter efficiency through a vector-valued training protocol that reduces trainable parameters by over an order of magnitude, while an unsupervised mini-batch k-means space tessellation algorithm constructs highly representative training databases using only 10% to 20% of reference configurations. We rigorously validated this framework on the highly fluxional solvated Zundel cation H_{13}O_6^+ ). Our fully machine-learning-predicted AIMD trajectories successfully reproduced complex dynamical signatures and key structural characteristics, including radial distribution functions and the velocity autocorrelation power spectrum. Ultimately, this scalable, systematically improvable framework bridges the gap between high-level correlated wavefunction theories and long-timescale reactive sampling, laying the foundation for advanced, LLM-inspired transfer learning in modern chemical dynamics simulations.

Sample-based Quantum Diagonalization (SQD), an extension of Quantum Selected Configuration Interaction (QSCI), has emerged as a promising hybrid quantum-classical paradigm for computing molecular ground state energies. By leveraging quantum sampling instead of variational optimization, QSCI avoids barren plateaus and enables direct reconstruction of correlated electronic wavefunctions. However, existing configuration recovery techniques primarily enforce symmetry constraints without guaranteeing optimal selection of the most physically relevant configurations, often leading to unnecessarily large subspaces and increased classical diagonalization costs. In this work, we introduce a machine-learned compact subspace generation protocol based on Restricted Boltzmann Machines (RBMs), termed QSCI-RBM, and integrate it within the Density Matrix Embedding Theory (DMET) framework. The RBM is trained on quantum-sampled configurations to learn the underlying probability distribution of dominant determinants, enabling the targeted generation of high-probability configurations. We apply this framework to the simulation of a protein-ligand complex involving the inhibitor Carmofur bound to the SARS-CoV-2 main protease ($M^{\text{pro}}$). Our results demonstrate that DMET-QSCI-RBM achieves energies within the chemical accuracy threshold by accessing only approximately 4% of the configuration subspace. In contrast, standard DMET-SQD simulations failed to reach chemical accuracy while accessing up to 20% of the subspace, even as the chemical potential itself nearly converged. These findings highlight that RBM-assisted configuration generation produces significantly more compact subspaces while preserving physical accuracy, thereby reducing classical computational overhead and enabling the scalable quantum embedding simulation of complex biological systems.

Amorphous materials exhibit exceptional mechanical and functional properties, yet their rugged energy landscapes are notoriously difficult to sample. Below the glass-transition temperature, conventional molecular dynamics and Monte Carlo become inefficient because equilibration relies on rare barrier-crossing events, while data-driven generative models are constrained by scarce and biased reference ensembles. Here, we introduce ATLAS, an efficient sampler that learns a diffusion process to generate Boltzmann-distributed amorphous structures directly from a target energy function. Parameterized by an equivariant graph neural network, ATLAS generalizes across system size, temperature, and composition. By exploiting the time reversal of the diffusion process, it enables efficient estimation of thermodynamic quantities and steering toward target observables. In two-dimensional Kob-Andersen systems, ATLAS reproduces parallel tempering Markov chain Monte Carlo structural distributions, free energies and entropies, achieving below 0.2% free energy error in the low-temperature glass regime with over 500-fold fewer energy evaluations. In Cu-Zr and Cr-Co-Ni metallic glasses, ATLAS recovers experimentally observed short-range-order trends and steers structures toward prescribed order parameters and optimized bulk moduli. Moreover, composition-amortized pretraining outperforms composition-specific training from scratch, reduces inverse-design costs by several hundred-fold, and enables sampling with expensive universal machine learning interatomic potentials. Coupled to a large language model agent, ATLAS searches an eight-element space for high-entropy metallic glasses balancing stiffness and ductility, identifying a converged Pareto frontier within 480 oracle evaluations. Together, these results establish ATLAS as a foundation model for sampling, steering and designing amorphous materials.

Organic mixed ionic electronic conductors (OMIECs) are a promising class of polymer materials for applications spanning neuromorphic computation to energy efficient electronics and bioelectronics. Despite being highly tunable, the relationship between structural features and key performance properties such as charge carrier mobility is poorly understood. Scanning nanodiffraction in the transmission electron microscope (TEM) is a powerful probe for elucidating this structure-property relationship, but produces large, noisy datasets that are difficult to interpret because polymer reflections exhibit several distinct morphologies. To address the complexity, we trained a machine learning (ML) model to detect these polymer diffraction peaks and their intensities from synthetic data. Compared to correlative peak detection algorithms, the conventional method for analyzing nanobeam 4D scanning transmission electron microscopy (4DSTEM) data, we show that the ML model is significantly faster and outperforms correlative algorithms in almost all cases, opening up the possibility of near-live visualization of 4DSTEM experiments.

For low-data and resource-constrained regimes typical of quantum chemistry, parameter-efficient learning is a key objective. Here, we propose a topology-aligned inductive bias in which the model architecture mirrors the molecular bond graph: atoms map to a fixed register of computational units, and bonds determine which pairs interact through shared learnable parameters. This principle is instantiated in two architectures: a variational quantum circuit (Iso-QGNN), and a parameter-matched classical message-passing model (Iso-CGNN). The models are benchmarked on HOMO-LUMO and dipole moment binary classification tasks over the QM9 benchmark. With 64 trainable parameters, the implementations achieve test AUCs of approximately 0.88 (quantum) and 0.91 (classical) on the gap task, and close to 0.78 (both) on the dipole task. The models reach 90% of asymptotic performance within about 250 training molecules and gradient norms remain stable throughout training. These results indicate that the topology-aligned inductive bias is the active ingredient driving parameter efficiency at QM9 scale, with implications for matched-baseline benchmarking in quantum machine learning.

The experimental reconstruction of the 3D two-photon momentum density (TPMD) via angular correlation of electron-positron annihilation radiation (ACAR) is a particularly useful method for studying material Fermi surfaces. It does not rely on low temperatures, UHV conditions, or strong magnetic fields, and enables the study of the spin-resolved electronic structure of materials. Yet, it remains a challenging inverse problem. Typically, 10^8 positron annihilation events are measured for 3--6 projections of the TPMD at different angles. The standard reconstruction approach is an ACAR adaptation of Cormack's method (the MCM) that leverages the inherent symmetry in the crystal's structure. However, the poor signal-to-noise ratio means collecting data of sufficient quality for Fermi surface studies can take months per sample. We present DeepCormack, a family of data-driven model-based reconstruction algorithms that augments the MCM by integrating supervised deep-learning models (CNN, MLP, and UNet) at various stages. To overcome the lack of large experimental training sets, we propose a method which leverages singular value decomposition with dynamic mode decomposition to generate realistic synthetic TPMD volumes, requiring only a single reference momentum density computed via density functional theory. On test data, DeepCormack improves reconstruction quality over MCM by about 8.5 dB PSNR at 200M counts and remains stable at reduced counts, enabling significantly faster acquisition times. Generalisation to experimental data depends strongly on how well the training distribution from the reference momentum density matches the sample. We therefore recommend pairing DeepCormack with a DFT calculation of the target material to create sample-specific training data. Our proposed method offers either much higher quality reconstructions, or enables significantly faster ones, on the order of weeks.

Machine learning interatomic potentials (MLPs) have revolutionized atomistic modeling, offering the potential to replace traditional methods like Density Functional Theory (DFT). However, inference time of MLPs is orders of magnitude slower than that of classical force fields, hindering real-world applications for biomolecular systems that require timescales of microseconds and beyond. Implicit solvent MLPs can address this issue, but are faced with data challenges associated with coarse-grained modeling. Consequently, previous approaches relied on empirical force field data, thereby inherently limiting the MLP's accuracy. Here, we introduce the Transferable Water Implicit Network (TWIN), an implicit water MLP parametrized entirely by an Equivariant Graph Neural Network and trained solely on ab initio and experimental labels. We demonstrate TWIN's transferability across drug-like molecules, peptides, and proteins, achieving excellent results on ab initio and experimental crystallographic and NMR benchmarks, consistently outperforming previous machine-learning-based implicit solvent or coarse-grained models. Furthermore, TWIN closely matches DFT-based explicit solvent MLPs while providing a two-order-of-magnitude faster timestep evaluation, paving the way for efficient ab initio-level modeling of biomolecular systems in aqueous environments.

In this paper, we provide a systematic investigation of SO(2) theory to machine learning interatomic potentials (MLIPs) and identify the limitations of conventional SO(2) Linear architectures relative to SO(3) Clebsch-Gordan Tensor Products (CGTP). Building on these insights, we propose direct Cartesian construction and recursive Clebsch-Gordan construction of Wigner D-matrices and introduce two novel interaction building blocks. First, we propose the Edge Complex Product Basis based on Generalized Asymmetric Contraction, a new formulation for many-body expansion that directly constructs higher-order interactions on edges through complex-valued equivariant multiplications. Second, we introduce Radial Rotary Complex Attention(RRA), which enhances extrapolation performance and surpasses existing attention vector formulations. We also introduce several improvements to the Atomic Cluster Expansion module. Building on these advances, we train our models on OMat24, sAlex, and MPTrj, and introduce TECE-OAM-RRA-1.0, which achieve state-of-the-art (SOTA) performance on the Matbench Discovery.

Universal machine learning interatomic potentials (uMLIPs) bridge quantum-mechanical accuracy and large-scale molecular dynamics, but the cost of high-accuracy calculations such as r$^2$SCAN limits training to datasets that remain small relative to the open materials space. Strong average benchmark performance also does not guarantee reliable energy--force predictions for every structure. We propose Adaptive Multi-Teacher Routing (ATR), which reformulates high-fidelity data construction as a structure-wise decision problem under uncertainty. Using a small set of real r$^2$SCAN labels, ATR calibrates multiple pretrained uMLIP teachers and combines structural descriptors, teacher identity, and inter-teacher disagreement to estimate the reliability of each structure--teacher pair. It selects high-confidence predictions for pseudo-label generation and rejects structures for which no teacher is sufficiently reliable. With real r$^2$SCAN labels for only 0.2% of candidate structures, ATR distils 2.89 million traceable r$^2$SCAN-level pseudo-labels for pretraining. On held-out r$^2$SCAN structures and the MP-r$^2$SCAN benchmark, a lightweight CHGNet trained on the ATR-generated dataset consistently outperforms the baseline and non-routed controls. Finite-temperature molecular dynamics further shows that ATR improves dynamical robustness across multiple material systems, maintaining stable trajectories where baseline simulations undergo catastrophic structural collapse. These results establish active rejection as an effective mechanism for converting multiple pretrained uMLIPs into a scalable and reliable data-construction system for high-fidelity uMLIPs.

As part of a series on first-principles modeling of cognitive functions, this paper attempts to provide a mathematical formulation of thinking and perception. It formally derives slow thinking or more generally, active perception, and encompasses the design, training and inference of slow thinking large language models. Our starting point is the lifting and projection of probability distributions on the observable and latent spaces, with the objective of representing complex data distributions by simple function families such as neural networks. A theory called "active lifting" is proposed, based on the sampling of latent sequences and an intrinsic drive to reduce uncertainty with maximum rate. It derives a large design space, containing the slow thinking models in a subspace that we call the static theory. These models are positioned on the representation hierarchy and sampler hierarchy induced by the static theory, and can be upgraded by climbing the two hierarchies. Active lifting further derives an inference process with an internal time axis, and a training objective that resembles minimum-length coding as well as the invention of languages. Thus, it characterizes the agency of perception, including the emergence of the slow thinking formats. Technical by-products of this theory include a three-stage pathway for improving slow thinking models, a unified approach to constructing encoders and generative models for all data modalities, a priori formation of human-like visual representations, and a possible solution to policy collapse.

LLM systems for scientific discovery increasingly assist with ideation, literature synthesis, experiment planning, and report generation, but the first research question they propose can remain difficult to audit: it may sound plausible without exposing the mechanism, falsifier, or assumption that a scientist should inspect. We introduce FirstResearch, a first-principles research-question formation framework for scientific LLM agents whose core artifact is a structured Research Question Certificate. The certificate records primitive definitions, assumptions, a mechanism model, a tension or contradiction, a falsifiable hypothesis, a minimal decisive test, and a failure update rule, making the proposed question inspectable before downstream execution. On ten LLM-agent research topics, FirstResearch outperforms controlled prompt-level baselines inspired by AI co-scientist, Agent Laboratory, and AI Scientist-v2 under a primary DeepSeek-blind-judge protocol. A Gemini-2.5-Flash independent-judge rescore of the same 40 baseline packages preserves the system-level ranking, with FirstResearch scoring 4.86/5 versus 4.38/5 for the strongest baseline and Pearson agreement of 0.865 on average score. A one-repeat ablation checkpoint further suggests that the certificate-centered core is the strongest component: certificate-only scoring reaches 4.90/5 under DeepSeek and 4.88/5 under Gemini, while removing certificates drops below 1/5 under both judges. These results are preliminary and use LLM judges rather than human domain experts, but they support a narrow scientific-discovery claim: explicit derivation constraints are a promising mechanism for making LLM-generated scientific questions more auditable. Code, prompts, saved outputs, and reproduction scripts are available at https://github.com/louiswang524/FirstResearch.

Foundation machine learning force fields (MLFFs) such as MACE-MP-0 and UMA cover broad chemical space at near density functional theory (DFT) accuracy. However, they assume equilibrium ground-state physics and do not natively handle externally induced changes to the electronic state, such as charging, applied fields, or electronic excitation, which limits their use for driven processes such as photoexcitation and charge injection. We propose EquiFiLM, a lightweight extension that adds continuous external conditioning to any equivariant foundation MLFF via a per-layer Feature-wise Linear Modulation (FiLM) block, learning externally driven changes to the potential energy surface from minimal training data. The block modulates only scalar channels and preserves E(3)-equivariance exactly. We demonstrate the recipe on charged liquid water with the foundation model MACE-MatPES as the backbone, yielding E-MACE. On the four training charges, E-MACE delivers a $3.1\times$ reduction in force RMSE ($21.3$ to $6.96$ meV/$\mathring{A}$) and a $61\times$ reduction in per-atom energy RMSE ($6.1$ to $0.1$ meV/atom) over a baseline without EquiFiLM trained on the same data, at indistinguishable inference cost. Across seven held-out interpolation and extrapolation charges, force RMSE stays within $18-61$ meV/$\mathring{A}$ and energy RMSE within $0.7-5.4$ meV/atom. The model runs stable molecular dynamics across the full range tested and predicts the charge-dependent first-shell response of the reduced pair distribution function probed by ultrafast electron diffraction. Adding this conditioning axis to the foundation requires only a few thousand DFT-labeled frames, against the $\approx 10^8$ structures of a charge-aware foundation trained from scratch. The recipe is backbone- and conditioning-agnostic: it applies without architectural change to any equivariant MLFF with scalar interaction-layer channels.

Understanding the physics of many-body complex dynamical systems may be a non-trivial task. High-dimensional analysis approaches are often deemed necessary to prevent losing important information. Typically, these use order parameters or descriptors capturing information related to, e.g., relative positions, symmetries, etc., of the units in the studied system. However, in many cases, gaining information related to the relative positions of the constitutive units (or their velocities) alone may be insufficient, and to reach a more complete physical knowledge, one should ideally learn and correlate with each other both structure and dynamics. Here we demonstrate how to achieve such a goal efficiently by building and navigating high-dimensional Time-Derivatives (TiDe) spaces. A TiDe space can be generated for virtually any type of system/phenomenon from the time-series data collected along its observation over time. Each TiDe's dimension corresponds to a growing-order time-derivative of the extracted data, thus containing information related to different physical phenomena/events, which can be easily extracted via unsupervised approaches. We demonstrate how, by definition, TiDes can be directly analyzed without a need for prior dimensionality reduction, providing results that are intrinsically intuitive to interpret. We show the potential of the method by analyzing two prototypical example datasets extracted from molecular dynamics simulations or experimental tracking of different types of complex dynamical systems. Our results demonstrate how efficiently one can navigate and learn in information-rich TiDe spaces, which provide a robust general framework for data analysis and for studying complex dynamical systems from the data collected along their observation over time.

We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution at a fraction of the cost of molecular dynamics (MD). This is in contrast with existing generative models that remove degrees of freedom by operating on coarse-grained, vacuum, or implicit solvent systems. Operating at this resolution allows for post-processing through force field energy evaluations and MD simulations, and enables the prediction of relevant properties in a gray-box manner (as ensemble averages of potential energy evaluations over generated samples). We demonstrate the utility of this paradigm on absolute hydration free energy (AHFE), producing estimates 4-10x faster and with comparable accuracy to standard GPU-based MD. By generating uncorrelated samples from alchemical Boltzmann distributions, we create more accurate, interpretable, and refinable ensemble predictions with calibrated uncertainty estimates, unlike regression methods which are entirely black-box predictors. Our approach also yields predictable benefits from increasing train- and test-time compute, realized by scaling model size and generating more samples, respectively. We believe that this approach demonstrates the utility of high-resolution ensemble generation for free energy estimation, with future potential to replace MD in tasks such as the prediction of lipophilicity, membrane permeability, or absolute binding free energy (ABFE) -- whose grounding and interpretability may be critical for the development of new drugs and materials.

Machine learning interatomic potentials (MLIPs) have become a hallmark of AI for scientific simulation. While efforts on new architectures and datasets have led to increasingly accurate and general models, the choice of optimizer for training has largely remained unexplored, defaulting to Adam and its variants in the community. Here, we implement and systematically compare a class of recently proposed matrix-structured optimizers, including Muon, SOAP, and the hybrid SOAP-Muon, for training NequIP and Allegro MLIP models. We find that these optimizers can substantially outperform Adam in both convergence speed and final accuracy. SOAP and SOAP-Muon emerge as robust and consistently strong methods, while Muon only provides partial gains relative to Adam. The improvements are particularly pronounced under partial force supervision. Our results indicate that optimizer choice is an overlooked yet impactful design axis for MLIPs.

Molecular docking predicts how a small molecule binds to a protein and is a key bottleneck in drug discovery. Classical scoring functions sum empirical pairwise contacts, blind to quantum-mechanical effects like orbital charge transfer that govern binding specificity. We introduce Q-Score, encoding GNN-predicted orbital donor-acceptor energies into a weighted graph and scoring binding by solving a maximum-weight vertex clique problem via Digitized-Counterdiabatic QAOA. Each interaction anchor maps to one qubit and compatibility constraints become edges. Across 11 protein targets, DC-QAOA recovers the exact optimum on 8 at 10 qubits. On 1000 AI-generated molecules, Q-Score is orthogonal to classical scoring with Spearman rho of 0.05, driven by orbital quality with rho of 0.90, and free of molecular-weight bias, enriching for strong orbital interactions at twice the random rate. DC-QAOA achieves a mean approximation ratio of 0.94 with 52 percent exact. Execution of 1000 circuits on IBM Eagle confirms 6-qubit solvability on NISQ hardware.

$\mathrm{E}(3)$-equivariant networks are promising for 3D atomistic system modeling, yet their scalability is limited by the $O(L^6)$ complexity of the Clebsch-Gordan Tensor Product (CGTP). The recently proposed Gaunt Tensor Product (GTP) reduces the complexity but is unable to capture the antisymmetric paths, resulting in incomplete expressivity. In this work, we present SpinGTP, an approach to overcome the GTP incompleteness by generalizing from scalar functions to Spin-Weighted Spherical Harmonics (SWSH). By relying on the algebraic properties of SWSH, SpinGTP recovers the missing antisymmetric interactions while maintaining the asymptotic efficiency of GTP. It also allows for a more expressive equivariant basis that naturally accounts for the parity-odd components of tensor products. We evaluate SpinGTP across diverse benchmarks, including Tetris, 3BPA, SPICE-MACE-OFF, and OC20. Our results show that SpinGTP achieves accuracies comparable to full CGTP. Notably, by explicitly capturing antisymmetric paths, SpinGTP exhibits superior performance in tasks involving chiral materials and non-centrosymmetric geometries. This work provides a complete, scalable, and mathematically rigorous path toward high-order equivariance in large-scale 3D atomistic system simulations.

Modern deep neural networks often contain far more parameters than needed to fit their training data, yet they achieve impressive generalization. A common explanation for this success is the implicit bias of stochastic gradient descent (SGD). An alternative volume hypothesis posits that, within low training-loss regions, loss-landscape basins leading to strong generalization occupy much larger regions of weight space than basins that generalize poorly, and therefore SGD is simply more likely to land in the former. Recent experimental explorations of this idea present seemingly contradictory results. While in one set of experiments randomly sampling the network weights until achieving zero training error yielded poor generalization, molecular dynamics density estimates supported the volume hypothesis. We observe that these experiments were performed at different dataset size regimes, and explore an intermediate regime using the Replica Exchange Wang-Landau algorithm to estimate the joint density of states over training and test accuracies in binary networks. Across several architectures and datasets, we show that the generalization advantage of gradient learning over random sampling training generally diminishes as the training data size grows, suggesting a resolution of the paradox.

We introduce a novel technique for scalable sampling of spin-system states with continuous symmetries using diffusion models. By applying our approach to the XY model, a fundamental continuous-spin model in condensed matter physics, we show that our technique addresses the shortfalls of the Markov chain Monte Carlo (MCMC) in generalization to varying system sizes. More specifically, we show that training a temperature-conditioned diffusion model on smaller-size XY model lattices enables the generation of accurate samples in larger lattice sizes. By tracking physically important observables of the model, such as spin correlations, our experiments demonstrate that diffusion sampling followed by a few MCMC steps reduces the thermalization time by an order of magnitude relative to the standard MCMC with random initialization. Our study provides valuable insight as to how generative models can be used to study continuous-state condensed matter systems at scale.