Molecular Dynamics

Calculation of binding energies for protein-ligand molecular systems requires accurate treatment of the electronic structure, a quantum chemistry problem that scales exponentially on classical hardware, while current quantum hardware remains too noisy for the required circuit depths. This report presents a hybrid quantum-classical workflow performed on the Fujitsu FX700 ideal state-vector simulator using QARP that addresses two structural inefficiencies in quantum-sampling-based diagonalization workflows. First, we integrate the Linear Scaling CNOT UCCSD (LCNot-UCCSD) ansatz into the QSCI framework, replacing the $\mathcal{O}(N^6)$ CCSD parameter initialization of the competing LUCJ ansatz approach with $\mathcal{O}(N^4)$ MP2-amplitude initialization. Second, we introduce QSCI-RBM, a variant that replaces the configuration recovery of the SQD framework with a Restricted Boltzmann Machine (RBM) acting as a compact generative subspace expansion model. Both are evaluated on eight different molecules in STO-3G across 14 controlled artificial error levels with 100 independent runs each, validated on potential energy surface scans of the N$_2$ molecule in cc-pVDZ, and embedded within DMET to treat the FDA-approved antiviral Amantadine (C$_{10}$H$_{17}$N, 11 DMET fragments) and the active region of the SARS-CoV-2 main protease complexed with its covalent inhibitor Carmofur (PDB: 7BUY, C$_{15}$H$_{28}$N$_4$O$_5$S, 10 fragments). To our knowledge, this is the first deployment of LCNot-UCCSD within QSCI on a quantum computing simulator, and the first DMET-QSCI(LCNot-UCCSD)-RBM application to an industry-relevant protein-ligand system. By utilizing a fraction of the classical computing resources required by the current state-of-the-art work by Cleveland Clinic, RIKEN, and IBM Quantum, this approach enables more efficient and economical drug discovery simulations for the industry.

Atomistic machine learning datasets are increasingly used for training: large immutable snapshots are read repeatedly, shuffled across epochs, staged across clusters' storage systems, and republished as reusable scientific artifacts. This workload differs from interactive scientific curation, where mutable records and ad hoc inspection are often more important than random indexed throughput. We present Atompack, an append-oriented storage format and distribution layer designed around a simple workload: training pipelines usually consume complete molecular records, while the order of records is randomized by the learning algorithm. Atompack appends records efficiently during dataset construction, then commits an immutable index and serves records through a memory-mapped read path optimized for training. We compare Atompack with HDF5, LMDB, and ASE baselines representing array stores, key-value records, serialized records, and object-oriented databases. The benchmarks measure sequential reads, shuffled reads, shared-filesystem behavior, write throughput, and artifact size. On a representative 64-atom workload, Atompack is 96x faster than ASE LMDB on shuffled training-style reads while producing artifacts about 79% smaller. The results indicate that serving complete molecule records, rather than field chunks or reconstructed objects, improves shuffled training throughput while keeping artifacts compact enough for public distribution.

Earth system infrastructures relying on satellite-based technologies, such as Global Positioning System (GPS) communications, are affected by ionospheric Total Electron Content (TEC) gradients. Modeling these gradients under physical constraints remains challenging due to their dynamic and transient nature. While existing machine learning (ML) models can predict hourly TEC variations, it remains unclear whether their temporal resolution is sufficient to preserve small-scale TEC irregularities within predicted signals. To address this gap, we introduce an interpretable ML-based model, t-STEP, designed to predict TEC at a 30-second resolution and estimate irregularity signatures from the modeled signals. This high cadence enables the derivation of Rate of TEC changes (ROT) and the ROT Index (ROTI) as diagnostic indicators of ionospheric variability. The model is developed using GPS observations from solar cycle 24 at a station located at 5.49°S, 47.49°W. A multi-metric evaluation framework, including dynamic time warping, is used for robustness assessment, while SHAP (SHapley Additive exPlanations) provides insight into feature contributions. The 30-second TEC predictions achieve 91% accuracy with a mean absolute error (MAE) of 4.38 TECU during high solar activity (2015). Compared with the International Reference Ionosphere (IRI-2020), the hourly model improves accuracy by 35%, reduces absolute errors by 57%, and increases prediction skill by 54%. More importantly, the 30-second model captures TEC irregularity dynamics and morphologies during geomagnetic storms of different intensities, outperforming an attention-based Long Short-Term Memory model under the same experimental conditions. This study demonstrates the potential of a single TEC prediction framework for scalable irregularity monitoring without requiring separate models for individual transient events.

$\mathrm{Cl}(3,0)$ interatomic potentials, despite their algebraic elegance, predict force magnitudes accurately but force directions poorly. Across ten rMD17 molecules, every $L \leq 1$ baseline in our twelve-model study attains aggregate force-cosine similarity below $0.25$. The cause is structural. The geometric product of two vectors in $\mathbb{R}^3$ realises only the $L=0$ and $L=1$ components of its irreducible representation content, leaving the symmetric-traceless rank-2 component absent from the per-edge bilinear that drives each message-passing layer. We address this with CliffordSTF, which couples the Clifford multivector to closed-form symmetric-traceless tensor tracks at ranks two and three through bilinear cross-track contractions, using a single learned bilinear and no Clebsch--Gordan tables, Wigner-$D$ matrices, or e3nn calls. On rMD17, CliffordSTF raises aggregate force-cosine similarity from $0.055$ (base Clifford) to $0.551$, an order-of-magnitude relative directional gain, alongside improved magnitude accuracy (force MAE $15.8\%$ lower; energy MAE $10.9\%$ lower). It outperforms all CG-free or body-ordered baselines in our study (all $\leq 0.17$). On catalysis benchmarks, CliffordSTF achieves the best out-of-distribution S2EF energy MAE on OC22 in our experiments, and the best in-distribution energy MAE among $L \geq 2$ methods on OC22 IS2RE. An eleven-variant ablation shows the two tracks are complementary: neither alone matches the combined model.

Inverse design of metal-organic frameworks (MOFs) requires searching a combinatorially vast space where property labels are expensive and most machine-learning models reveal little about why a structure succeeds. We introduce LLM4MOF, a closed-loop framework in which language-model agents reason about chemistry, build candidate MOFs, and test them in simulation, refining hypotheses over ten autonomous iterations. One agent proposes interpretable design hypotheses over metal nodes, linkers, pore geometry, and functional chemistry, and a second translates them into constraints that select candidate MOFs, each made of a metal node, organic linker, and matching topology. Each hypothesis is tested through four diagnostic beams that apply different subsets of its constraints, so comparing them shows whether geometry, chemistry, or metal choice drives performance. Even when blind to the global property landscape of databases, LLM4MOF concentrates its search on top-performing structures across six adsorption, separation, and electronic-structure tasks within 400 property evaluations. The same loop also generates new MOFs de novo and validates them in live simulation, where it adapts the geometry to each requested condition, outperforming random search and a genetic algorithm at roughly $1 per campaign. LLM4MOF shows that language-model agents can run interpretable, simulation-grounded inverse design without training a model per objective.

Machine-learned (ML) operator models can be trained to predict density functional theory (DFT) Hamiltonian/density matrices at significantly reduced computational cost, thus extending electronic-structure calculations to previously unfeasible scales. Here, we introduce MALOQ (Massively Accelerated Learning of Operators for Quantum Transport), an application built to train on and predict electronic-structure matrices for systems made of few to 100k atoms, described by large basis sets, and covering a wide range of atomic elements. Based on a state-of-the-art, SO(2)-equivariant backbone architecture, MALOQ provides (i) custom data-processing kernels to handle high-rank Hamiltonian matrix data and (ii) a scalable edge-wise distribution of atomic graph(s). Trained on the largest molecular Hamiltonian datasets available today, it reduces time-per-epoch by over 30% compared to a molecule-wise-distributed framework, and enables inference on material graphs of arbitrary size. We demonstrate scalable training and inference for 3,000-12,000 atoms on the Alps supercomputer, up to 192 GPUs and 256 GPUs, respectively.

Closed-loop materials discovery iterates between proposing candidate structures and evaluating their properties, and property evaluation dominates the cost. In the generative variant, a learned prior proposes candidate crystals and a property oracle scores them; we ask whether a cheap probabilistic surrogate can triage the generator's output, and what such a surrogate must do well. Across three architecturally distinct pretrained diffusion priors (MatterGen, CrystalFlow, ADiT) and two targets (room-temperature heat capacity and bulk modulus), we insert a Gaussian process acquisition gate between structure generation and the oracle in an RL-steered generative workflow. The gate matches or exceeds ungated fine-tuning of the generative model while capping oracle calls at a fixed per-cycle budget. Budget-matched ablations isolate the mechanism. At an identical four-call budget, ranking-based selection outperforms arbitrary selection, confirming that the gain comes from the surrogate's choice; the gate comes within $\sim$9% of exhaustive oracle spending at roughly one-fifth of the calls. A density-functional-theory check of the bulk-modulus discoveries confirms the learned oracle to within 2.5% on average and the surrogate's ranking of the generated structures at Spearman $ρ= 0.94$. A cross-factorial benchmark of surrogate performance spanning mechanical, electronic, and vibrational properties identifies pretrained ORB embeddings with a Gaussian process as the most reliable combination, which we adopt as the building blocks of the proposed workflow. The complete pipeline is released as open-source software.

Variational Monte Carlo (VMC) is a central algorithm in electronic structure theory and has gained renewed importance through modern neural-network ansätze such as FermiNet. At its core, VMC seeks ground states by minimizing the Rayleigh quotient by stochastic optimization. In this work, we show that the resulting stochastic optimization problem is intrinsically governed by the nodal geometry of the underlying wave function. More precisely, we establish that properties of the nodal set determine the integrability of the local energy and gradient estimators that drive VMC. For broad and practically relevant ansatz classes, including Slater-Jastrow wave functions with variable-exponent Slater-type orbitals, we prove that these estimators are generically heavy-tailed and fail to admit higher moments. At the same time, for general analytic ansätze, we prove weak moment bounds for the relevant estimators and identify precise low-moment regimes, showing how generic and degenerate nodal structures lead to different integrability thresholds. Building on this analysis, we introduce a new robust variant of VMC $\unicode{x2013}$ coined PS-Clip-VMC $\unicode{x2013}$ which is based on clipping both the local energy and the gradient random variable. We prove that PS-Clip-VMC converges both in expectation and with high probability in the weak moment regime of VMC. Preliminary experiments for training FermiNet on Atoms with up to 18 electrons suggest that PS-Clip-VMC is significantly more robust than standard methods.

Offline reinforcement-learning losses (RFT, RIFT, DFT, Offline GRPO, DPO) are widely used to distill reasoning from large teachers into smaller students, and are typically compared on downstream accuracy alone. We ask whether they are mechanistically distinct or converge to a similar weight update. Training six methods (SFT, RFT, DFT, RIFT, Offline GRPO, DPO) on identical math rollouts from a single base model (Qwen3-4B) with attention-only LoRA, we analyze the resulting deltas via cosine similarity, principal-angle subspace analysis, linear mode connectivity, and CKA. We observe: (i) SFT, RFT, and RIFT have nearly colinear weight deltas (cosine >= 0.97, top-1 principal angle ~7 deg median over 144 modules) and comparable GSM8K accuracy (87-88%, n=1319; pairwise McNemar p >= 0.15); (ii) DFT diverges further in direction than any reward-weighted method despite using the same data; (iii) Offline GRPO adds a substantial component orthogonal to the SFT direction (~67% globally, up to ~86% in late layers) while staying in the SFT loss basin; (iv) DPO sits in a near-orthogonal subspace, shows a mode-connectivity barrier, and collapses late-layer CKA to ~0.46. DPO also reaches the highest accuracy in our protocol on both GSM8K (93.5%, McNemar p < 10^-9 vs. each other method) and AIME26 (30.0% vs. 3.3-10.0%); its training uses a 10x smaller learning rate than the others (the standard convention), so the update-norm and accuracy gaps reflect loss-function and optimizer choices jointly, and a learning-rate-matched DPO comparison is left for future work.

Machine-learned interatomic potentials now enable efficient atomistic evaluation for interactive materials discovery, yet closed-loop crystal search methods remain fragmented across bespoke pipelines for editing, relaxation, scoring, constraints, and bookkeeping. We introduce SciVerseGym, a Gymnasium-compatible environment for sequential crystal discovery that frames crystal design as a Markov decision process. Agents observe an atomistic structure, apply chemically meaningful edits, and receive feedback from a configurable evaluator. SciVerseGym supports local and global actions, including elemental substitution, lattice perturbation, atomic displacement, vacancy creation, and atom insertion, along with configurable chemical spaces, structure pools, atomistic and graph-based observations, custom rewards, optional relaxation, and stability or phonon-related diagnostics. Each step applies an edit, evaluates the candidate using a machine-learned interatomic potential or any ASE-compatible calculator, and returns the standard (obs, reward, terminated, truncated, info) tuple. By decoupling agent logic from materials infrastructure, SciVerseGym provides an open, reproducible, and extensible testbed for reinforcement learning, Bayesian optimization, evolutionary search, and language-agent workflows in closed-loop crystal discovery. Code is available at: https://github.com/Bin-Cao/SciVerseGym.

Atomistic structure and natural language have long been modeled separately, with language models either calling atomistic models as tools or being fine-tuned on lossy textual encodings that discard atomistic information. We introduce Atomistic Language Models (ALMs) to pursue native multimodality, in which a single language backbone understands atomistic structures, generates materials from natural language, and optimizes crystal structures as instructed by text. By unifying a pretrained atomistic encoder, large language model, and denoising diffusion model through purely continuous projectors and staged training, ALMs achieve state-of-the-art results on crystal structure prediction and de novo generation. ALMs are enabled by a continuous bridge that maps language model embeddings directly into the steering space of atomistic diffusion, and are assisted by Text-to-Crystal Feynman-Kac (T2C-FK), a particle-based sampler that scores partial denoising trajectories to enforce stoichiometric targets at inference time. To evaluate the ability of ALMs to optimize and generate materials from natural-language prompts and 3D atom-coordinate inputs, we introduce ALM Bench, the first benchmark for text-conditioned crystal generation and optimization. Code, training data, and model weights will be released soon.

Quantum chemistry simulations underpin modern materials discovery, yet their impact is limited by steep computational cost and dependence on fixed approximation schemes. Foundation models, such as machine-learned interatomic potentials, have accelerated parts of this workflow, but their reliance on large-scale pretraining restricts adaptability at the frontier of chemical space, where methodological innovation and sparse data are the norm. Agentic AI systems can automate existing simulation pipelines, yet they remain constrained by the predefined tools and algorithms they orchestrate. In response, we introduce LADeQ, an LLM-guided workflow that discovers, implements, and benchmarks candidate approximation algorithms at test-time within existing quantum chemistry codes. Rather than selecting from a predefined repertoire, LADeQ constructs candidate approximation schemes on demand, drawing on techniques from disciplines such as spatial statistics, circuit simulation, and kernel methods that have had little prior presence in electronic-structure theory. Because it builds on an out-of-the-box language model, LADeQ requires no task-specific pretraining or curated data, and the resulting implementations are transparent and inspectable, with explicitly traceable approximation errors that enable principled control of accuracy--efficiency trade-offs. We show that LADeQ accelerates coupled cluster singles and doubles (CCSD) and configuration interaction singles and doubles (CISD) calculations while keeping correlation-energy errors within user-specified tolerances, demonstrating autonomous, objective-driven discovery of approximation algorithms inside existing electronic-structure solvers.

Pre-trained materials foundation models, or machine learning interatomic potentials, leverage general physicochemical knowledge to effectively approximate potential energy surfaces. However, they often require domain-specific calibration due to physicochemical diversity as well as mismatches between practical computational settings and those used in constructing the pre-training data. To address this, we propose a sparsity-promoting fine-tuning method that selectively updates model parameters by exploiting the structural properties of E(3)-equivariant materials foundation models. On energy and force prediction tasks across molecular and crystalline benchmarks, our method matches or surpasses full fine-tuning and equivariant low-rank adaptation while updating only $\sim$3~% of parameters, and in some cases as little as $\sim$0.5~%. Beyond energy and force calibration, we further demonstrate task generalizability by applying our method to magnetic moment prediction and magnetism-aware total energy modeling. Finally, analysis of sparsity patterns reveals physically interpretable signatures, such as enhanced $d$-orbital contributions in transition metal systems. Overall, our results establish sparsity-promoting fine-tuning as a flexible and interpretable method for domain specialization of equivariant materials foundation models.

Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis. Accurate forecast of the outcomes of a MD simulation is not only an attractive scientific challenge but also has substantial practical value. In this work, we developed a data-driven framework, termed ASTEROID (Advanced Spatiotemporal TransformER fOr Inferring Dynamics), that can directly predict multi-step atomic coordinates, avoiding conventional iterative integration. For this purpose, our ASTEROID reformulates MD trajectories as high-dimensional spatiotemporal sequences and integrates the Spatiotemporal Information (STI) Transformation equation into a Transformer architecture. The core innovation of ASTEROID lies in its ability to model multiscale spatiotemporal dependencies. In particular, for spatial dependencies, a local-global self-attention mechanism captures both short- and long-range interactions. For temporal dependencies, an encoder-decoder structure integrates global context with autoregressive forecasting. ASTEROID was evaluated on several quantum-mechanics derived molecular datasets. Our results indicate that ASTEROID achieved not only a higher level of accuracy in multi-step prediction than existing methods on various benchmarks, but also significantly reduced computational cost of conventional MD simulation. Moreover, the model supports iterative multi-step forecasting over an extended time scale. This work establishes a robust and generalizable data-driven paradigm for accelerating MD simulations.

Policy gradient algorithms for language models optimize the same objective $J(θ) = \mathbb{E}*{τ\sim p*θ(τ)}[R(τ)]$, which has exactly two factors: the trajectory probability $p_θ(τ)$ and the reward $R(τ)$. Every method from REINFORCE to PPO to GRPO and their descendants modifies one or both factors to address a specific failure in the preceding formulation. Existing surveys organize these methods by domain or chronology, which obscures the rationale behind each design choice and the precise location of its intervention within the gradient estimator. This survey revisits the landscape of LLM policy optimization from $J(θ)$ on first principles and uses the trajectory side, induced by $p_θ(τ)$, and the reward side, induced by $R(τ)$, as the two axes along which methods are located. It covers the path from REINFORCE and PPO to GRPO, as well as post-GRPO variants, Agentic RL, and GRPO-OPD. The resulting framework is unified, diagnostic, and extensible: it analyzes methods from a shared objective, identifies which side each method modifies and why, and applies the same trajectory and reward axes across these settings. Across these settings, the framework also exposes compound failures that no single-side fix resolves and that therefore require joint design of the trajectory side and the reward side. The boundary cases and coupled failures identified by this map mark where existing solutions run out and provide a principled starting point for designing the next generation of LLM policy optimization algorithms.

In this work, we develop two main Machine Learning based approaches to predict the runtime parameters of highly scalable parallel chemistry computations.These approaches employ active and generative learning together with the empirically determined gradient boosted regression tree models chosen among a rich suite of machine learning models. When evaluated on Coupled-Cluster with Singles and Doubles computations, our models achieve a mean absolute error percentage (MAPE) as low as 0.023 and a coefficient of determination as high as 99.9%. Furthermore, when combined with active learning to mitigate the lack of large amounts of training data, our models score a MAPE about 0.2 with 20-25% of the original dataset.

Inverse materials design starts from target functionality and searches for structures that can realize it. Its value in closed-loop discovery depends not only on prediction performance, but also on whether expensive first-principles results are independently validated, provenance-recorded, and admitted as feedback only when evidence is sufficient. This is especially important for composite properties such as carrier mobility, where a final scalar value hides intermediate quantities, fit quality, convergence history, and workflow assumptions. Here we present InvDesMobility, a reliability-gated first-principles feedback framework that integrates multi-agent automated DFT, evidence stratification, generative structure proposal, acquisition ranking, and auditable release. Using 516 2DMatPedia-derived candidates, the workflow produced 280 QC-passed materials and 573 retained carrier-direction seed channels after channel-level reliability gating. These records were split into two feedback objects: relaxed structures updated the generative model, while retained mobility channels trained the acquisition model and set validation priority. Over multiple iterations, InvDesMobility screened 2.4 x 10^6 structures, submitted 102 candidates for DFT validation, and retained 86 reliability-gated generated channels across 41 formulas. Overall, the main contribution is not a fixed list of high-mobility materials, but a transferable feedback contract that makes closed-loop inverse design both useful and auditable when learning from expensive calculated properties. All source data, retained feedback records, and workflows are available at https://github.com/DreamLufei/invDesMobility, with an accompanying evidence website at https://dreamlufei.github.io/invDesMobility/.

Accurate interatomic potentials enable molecular dynamics of materials, molecules, and interfaces beyond density-functional-theory length and time scales. Equivariant neural network potentials have improved the representation of local geometry. However, their deployable energy surfaces ultimately manifest through invariant scalar channels, whose aggregation and spectral resolution remain comparatively underexamined. Here we use Physics-Aware Neighborhood (PAN) pooling and Physics-Guided Spectral (PGS) mixers as controlled scalar-pathway probes: lightweight, symmetry-preserving modifications that act only on $\ell=0$ channels while leaving the equivariant tensor backbone unchanged. Using MACE as a high-body-order mechanistic scaffold, PAN adds coordination-sensitive amplitude modulation, whereas PGS augments edge and readout scalar features with radial and tapered spectral bases. Across metallic Ag, covalent Si, a short-range ionic LiF/Li--F subset, and MD17/rMD17 molecules, this scalar-pathway correction reduces MACE force errors by 22--27% and energy errors by 19--22%; on systems with stress labels, stress errors decrease by 27--28%, at approximately 5% additional inference-FLOPs cost. Directionally consistent gains in Allegro and NequIP further indicate that the correction is portable across distinct short-range equivariant backbones, although effect sizes remain architecture-dependent. These results identify scalar-pathway fidelity as a practical design dimension for short-range equivariant interatomic potentials.

Foundation machine learning interatomic potentials (MLIPs) have enabled atomistic simulations across broad regions of chemical and materials space, but many remain computationally expensive and lack explicit electrostatics, limiting their use for systems governed by long-range interactions and electrical response. Previously, we introduced Latent Ewald Summation (LES), which learns latent atomic charges and long-range electrostatics from density functional theory (DFT) energy and force labels alone. Here, we use LES to extract electrostatics that are latent in foundation models: energies and forces predicted by a teacher model are used to train a lightweight LES-augmented student MLIP, with optional fine-tuning on additional DFT data. The resulting models reduce computational cost while providing access to Born effective charge tensors, and infrared spectra. We benchmark student models distilled from a broad set of foundation MLIPs, including UMA, MACE, Orb, eSEN, GemNet-OC, PET, and EquiformerV2-based models, against experimental infrared spectra for liquid water, concentrated hydrochloric acid, and the anatase TiO2(101)-water interface. Across these systems, electrostatic response can be extracted from most foundation MLIPs. The benchmark further shows that the underlying DFT level and dataset used to train the teacher model play a larger role than architecture in determining electrostatic and spectroscopic accuracy. For the TiO2-water interface, fine-tuning with a modest amount of higher-level DFT data improves structural and infrared predictions. LES-based distillation therefore provides a practical route for converting foundation MLIPs into efficient, electrically responsive models, while also testing the physical fidelity encoded in foundation models.

Predicting the Kohn-Sham Hamiltonian with machine learning can accelerate density functional theory while retaining access to molecular orbitals, energy levels, and electronic-structure observables that energy-only surrogates cannot resolve. Yet element-wise agreement with the converged Hamiltonian, an implicit fixed point of the self-consistent field iteration, does not determine the occupied subspace that governs orbital energies and densities. Here we present HamEvo, a neural operator that learns the single-step self-consistent update and returns the converged Hamiltonian as its fixed point. HamEvo is pre-trained on intermediate self-consistent trajectories and calibrated at equilibrium with density-matrix supervision. Across benchmarks from MD17 to drug-like QMugs, HamEvo lowers Hamiltonian errors by 35-49% over direct-regression and deep-equilibrium baselines, and predicts QMugs HOMO and LUMO energies with mean absolute errors of 0.036 and 0.053 eV, near the 1 kcal/mol chemical-accuracy scale. Few-shot fine-tuning with only 20 reference conformations extends HamEvo to molecules of up to 122 atoms, well beyond the size range covered by pre-training. With thermal molecular-dynamics sampling, HamEvo captures temperature-dependent HOMO-LUMO gap renormalization beyond the harmonic approximation. Inference is up to 242 times faster than conventional DFT.

The design of high performing quantum circuits remains largely dependent on human expertise. We introduce an autonomous agentic framework that employs large language models (LLMs) to conduct iterative quantum circuit designs under explicit design constraints. Our system integrates seven components: Exploration, Generation, Discussion, Validation, Storage, Evaluation, and Review. These components form a closed-loop workflow that combines web-based knowledge acquisition, literature-grounded critique, executable code generation, and experimental feedback. We evaluate the framework on two tasks: quantum feature map construction for quantum machine learning and ansatz generation for variational quantum eigensolver applications in quantum chemistry. In image classification benchmarks, the best generated feature map outperforms representative quantum feature maps and, when scaled to larger qubit counts, surpasses the classical radial basis function kernel. In molecular ground state estimation across seven molecules, the generated ansatz attains competitive accuracy with widely used chemically inspired and hardware-efficient constructions while satisfying the imposed scaling constraints. These results establish LLM driven agentic system as a viable paradigm for automated quantum circuit design and illustrate how AI systems can participate in iterative scientific optimization workflows across scientific domains.

Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent's behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host-guest binding free-energy benchmarks, MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder. Our data and code are available at https://github.com/Zehong-Wang/MDForge.

In many materials and product design problems, desirable candidates exhibit properties that fall within an acceptable range rather than achieve a single optimum. Recovering multiple, distinct solutions that satisfy such specifications is also practically valuable, as some candidates may be preferred for reasons of cost, processability, or robustness that are difficult to encode directly in an objective function. Here, we develop a range-aware Bayesian optimization (BO) framework in which the acquisition function directly scores the posterior probability that a candidate satisfies a target range. The framework naturally extends to parallel pursuit of multiple distinct specifications over a shared candidate space. Across benchmark tasks, range-aware acquisition consistently recovers larger and more diverse sets of valid designs than standard BO baselines and recent goal-seeking methods. Its utility is further demonstrated in two practically motivated design case studies involving optimizing reaction conditions for polymer synthesis and sequence-defined oligomer discovery for prescribed optical absorption bands, supported by quantum chemical calculations. These results suggest that range-aware BO can provide a practical and sample-efficient foundation for specification-driven design, particularly when design flexibility and solution diversity are important considerations.

Molecular systems involve interactions across multiple spatial scales, from local coordination and short-range perturbations to long-range electrostatic and solvent-mediated effects. However, most molecular representation learning methods rely on manually predefined scales, and the task-optimal modeling scale may not coincide with these fixed levels. This study introduces a loss-guided adaptive scale refinement framework for molecular force prediction, treating predefined scales as initial anchors and discovering task-effective resolutions through interpolation, routing, differentiable scale updates, and scale pool refinement. Using a NaCl aqueous ionic system as a minimal testbed, this study constructs short-scale and long-range force prediction branches and analyzes their complementarity. Oracle hard routing reduces the overall force MAE from 399.65 to 382.67, while continuous oracle interpolation further reduces it to 380.96. In close-contact regimes with nearest-ion distance below 0.6 nm, the close-contact MAE decreases from 327.22 to 260.51. A minimal scale pool update experiment shows that starting from endpoint anchors {0,1}, loss-guided updates automatically generate intermediate scales and recover most of the continuous oracle performance. The final updated scale pool {0,0.125,0.25,0.375,0.5,0.75,1} achieves an overall MAE of 381.23. These results support adaptive scale refinement as a promising direction for molecular representation learning, especially when fixed-scale modeling is insufficient.

In science and engineering, Lagrangian simulation methods such as Smooth Particle Hydrodynamics (SPH) or Material Point Method (MPM) are often employed to study the behavior of dynamic systems. However, these methods can be prohibitively computationally expensive, particularly when simulating multi-scale spatial or temporal phenomena, e.g., void growth and coalescence within macro-scale geometries, structural failure of spacecraft components resulting from hypervelocity impact of space debris particles, etc. In contrast to graph-based methods, where the state of the system is understood as a discrete set of particles, we propose a learning framework for scalable representation and dynamics modeling of massive particle systems by treating the system state as a function and its evolution as a trajectory in Hilbert space. Rather than representing the state as a discrete set of particles or embedding it in a nonlinear latent manifold, we approximate the state space with a linear subspace spanned by learned neural basis functions. This parameterization enables direct projection to obtain latent coefficients and explicit access to the basis functions, avoiding optimization over a nonlinear latent space. The resulting representation admits a natural interpretation: latent variables correspond to coefficients in Hilbert space, and basis functions correspond to spatial modes, analogous to Proper Orthogonal Decomposition. The framework thus unifies classical projection-based reduced-order modeling with modern deep learning, while remaining invariant to the number of discretization points. Experiments on large-scale SPH simulations with over one million particles, including dynamic events with extreme deformation and fragmentation, demonstrate that the proposed method accurately reconstructs and predicts dynamics, achieving an R$^2$ score above $0.99$ with as few as $32$ basis functions.

We study data-driven real-time economic optimization of a multi-product chemical reactor when no reliable first-principles model is available beyond a steady-state energy balance. Instead of learning the economic objective directly as a black-box function, we use a composite formulation in which Gaussian process (GP) models predict physically meaningful outputs, including product concentrations and reactor temperature, while profit is computed analytically from these predictions together with raw-material, product, and utility prices. This preserves the structure of the economic objective, makes it parametric in changing prices without needing retraining, and allows candidate operating points to be checked against the available energy balance through a physics residual. The GPs also provide predictive uncertainty, which is exploited in a Bayesian optimization (BO) framework both for data-efficient exploration and for conservative enforcement of the reactor temperature constraint through an upper confidence bound. The acquisition function additionally penalizes large energy-balance mismatch obtained by substituting the GP-predicted outputs and candidate inputs into the available steady-state energy balance. The approach is demonstrated on a benchmark simulation of a non-isothermal multi-product reactor. Relative to a trust-region safe BO implementation, the proposed method achieves better simulated economic performance within the available iteration budget. Relative to a purely data-driven BO approach that does not use the available physics information, it avoids reactor temperature constraint violations.

Interatomic potentials (IPs) enable large-scale atomistic simulations beyond the reach of first-principles methods, but their predictive reliability depends critically on the selection of training data, quantified uncertainty, and model expressiveness. Active learning (AL) provides a principled framework for constructing efficient and accurate IPs, yet most strategies reduce parameter uncertainty without explicitly accounting for the specific material properties being predicted. The information-matching (IM) approach addresses this limitation by requiring that the selected training data provide at least as much parameter space information as needed to achieve prescribed uncertainty targets for selected quantities of interest (QoIs). Here, we apply IM to develop bespoke IPs specifically tailored for predicting plastic strength in metals. Due to the high computational cost of simulating plastic strength, we employ an indirect IM strategy that targets inexpensive intermediate QoIs that correlate with strength. The IM method enables precise parameter constraints with minimal training data, yielding precise predictions for both the intermediate QoIs and plastic strength. Yet, model error remains a key limitation, and a post hoc uncertainty inflation correction provides a viable means to mitigate this limitation. These findings illustrate both the promise and limits of uncertainty-aware AL for predicting complex material properties.

Single-step retrosynthesis needs both accurate first-ranked suggestions and candidate lists that are rich enough for downstream selection. We study this as a proposal-selection decomposition. Our system, RETROSPECT, combines a single Transformer proposal model, which we call the ChemAlign Transformer, with a LambdaMART reranker over structural, reaction-template, upstream-score, and optional DFT-derived descriptors. The generator is trained with hybrid root-aligned and random SMILES augmentation, Pre-LayerNorm, tied embeddings, exponential moving average weights, and a differentiable atom-balance auxiliary loss. On the full USPTO-50K test set of 5,007 reactions, the generator reaches 55.00% top-1 and 86.18% top-10 exact-match accuracy with 99.86% top-1 validity. On the merged candidate-pool benchmark used for reranking, which contains 5,007 test products and about 111 candidates per product, a LambdaMART model trained on the structural feature set reaches 59.4% top-1 with 0.7171 mean reciprocal rank. Feature ablations show that upstream proposal score and template-frequency statistics provide most of the reranking signal, while DFT and reaction-center DFT features provide smaller and less consistent gains. These results support a modular view of retrosynthesis: stronger single-model proposal and learned candidate selection are complementary, and the proposal model can serve as a drop-in component for ensemble systems such as RetroChimera (Maziarz et al., 2024)

Solubility prediction is a standard benchmark in computational chemistry, yet multi-solvent models which reportedly approach the experimental-noise ceiling (i.e. the aleatoric limit) are not yet reliable enough to be deployed. We argue that this gap is partly artefactual: published benchmarks differ in curation policies, evaluate on count-weighted RMSE that hides failure on tail-heavy solvent distributions, and treat the widely cited 0.6-0.8 log S inter-laboratory figure as the aleatoric ceiling even though it reflects worst-case, not expected, disagreement. We introduce SC3, a multi-solvent solubility benchmark built on BigSolDB v2.1 with three contributions: (i) a reproducible curation pipeline yielding 101,535 measurements over 1,327 solutes and 206 solvents, with a recalibrated aleatoric floor of 0.106 log S-roughly 6 times tighter than the conventional figure; (ii) nested Gold/Silver/Bronze consensus tiers with per-point standard deviation, three leakage-checked splits, and a multi-solvent metric suite (PS-RMSE, Z-RMSE); and (iii) a 31-model benchmark across six families, whose best Bronze PS-RMSE sits at 5 times the aleatoric limit, and we observe this is a gap unclosed by any deep alternative tested. We perform three follow-on analyses: data scaling, transfer from quantum-chemistry solvation energies, and feature-level attribution, which demonstrates that calibrated per-point uncertainty is a reusable infrastructure for diagnosis beyond point prediction.

Machine-learned (ML) exchange-correlation (XC) functionals aim to replace human-designed density functional approximations by learning directly from reference data, but they still do not consistently outperform traditional $\mathcal{O}(N^4)$-scaling hybrid functionals. We study a hybrid-distillation setting in which $\mathcal{O}(N^3)$-scaling ML-XC functionals are trained to reproduce B3LYP/def2-SVP targets. We introduce Derivative Informed XC-Loss (DI-Loss), a loss that incorporates additional information from the reference hybrid functional by supervising first and second derivatives of the energy on the Grassmannian of admissible density matrices. Rather than only matching the self-consistent fixed point, DI-Loss aligns the local first- and second-order response of the learned functional with that of the target functional. Across four evaluated architectures, DI-Loss consistently improves the main energy metrics. Averaged uniformly across architectures, the total-energy MAE decreases by 66% relative to energy and density supervision alone. The density-sensitive mean-field energy metric $E_ρ$ improves from $1.2$ to $0.8$ mEh on average, while dipole and $\mathcal{L}_2$ density errors do not improve uniformly. We further show that densities from the distilled functionals reduce hybrid-functional SCF iterations by up to 50%. In downstream TDDFT calculations, Hessian supervision improves excited-state predictions, with XCdiff reducing the mean excitation-energy MAE by 19 - 35%.

Machine learning interatomic potentials (MLIPs) enable efficient and accurate atomistic simulations but depend critically on the quality and diversity of the training data. We introduce Stein kernelized molecular dynamics (SKMD), an enhanced sampling method that uses interacting particle dynamics to acquire informative training configurations for the active learning and fine-tuning of MLIPs. SKMD corresponds to a stochastic variant of Stein variational gradient descent that is adapted for molecular dynamics by incorporating asynchronous particle updates and a kernel of global atomic descriptors, which provides a symmetry-aware measure of configurational similarity. Unlike other enhanced samplers used in molecular dynamics, SKMD preserves the Boltzmann distribution as the asymptotic distribution of the dynamics. This property enforces a balance between the exploration of diverse configurations and attraction toward high-probability regions of the energy landscape. We further propose an approach to efficient online data acquisition using an adaptive stopping criterion that selects non-redundant training data over the course of simulation. We demonstrate SKMD for the active learning of a neural network model of the Müller-Brown potential and the fine-tuning of a MACE interatomic potential for alanine dipeptide. Compared to active learning baselines, our method achieves higher model accuracy in fewer training iterations with the same number of acquired training samples.

Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings. Designing descriptors that are both expressive and broadly applicable, however, remains challenging. We study persistent homology (PH) as a general-purpose representation for MD and introduce the masked Flood complex, a protein-tailored modification of a recently introduced simplicial complex construction that emphasizes inter-residue structure at low computational cost. Vectorized persistence diagrams then provide information-rich, geometry-aware summaries of protein conformations, which we evaluate on protein class prediction, frame-level observable regression, and Markov state model (MSM) estimation from learned low-dimensional coordinates in a single shared representation space. Results on the mdCATH dataset show that PH-based descriptors are competitive across tasks, with masked Flood PH yielding the most consistent overall performance. Further, when using topologically-informed MSMs as a drop-in replacement within the recent MarS-FM framework for generative modeling of protein conformations, we obtain consistently better ensemble statistics than MSMs based on physical observables. Finally, we explore the transferability of the generative model to qualitatively different, fast folding, proteins.

Graph Neural Networks (GNNs) have revolutionized Neural Force Fields for atomistic simulations, achieving near-quantum accuracy at reduced cost, yet adapting these models to new chemical systems requires expensive retraining of foundation models. Inspired by model merging in vision and language processing, we introduce GFFMERGE, the first principled framework for closed-form model merging in GNNs. We exploit the linear structure of message-passing layers and formulate merging as a convex embedding-alignment problem with an analytical solution. Through the first systematic benchmarking of model merging for GNNs, we show that existing methods designed for vision and language catastrophically fail on force field regression, while GFFMERGE recovers performance approaching gold standard joint training. Across molecular (MD17, MD22), solid-state (LiPS20), and large-scale graph benchmarks, GFFMERGE and GNNMERGE (its generic GNN counterpart) achieve 5-27$\times$ speedups while enabling modular composition of specialized models. Remarkably, our closed-form solution alone outperforms all baseline methods before fine-tuning and provides superior initialization for faster, data-efficient convergence.

Molecular dynamics (MD) is a key tool for simulating the dynamical behavior of atomic systems. However, MD is inherently serial, which makes it difficult to increase single-system throughput with concurrent compute. To address this, we introduce Langevin Speculative Dynamics (LSD), a distributed and model-agnostic speculative sampler for accelerating MD without adding relative error. Inspired by speculative methods in language and diffusion modeling, LSD uses a draft model to propose fast simulation steps and verifies them in parallel with a slower target model, applying a transport map from the draft to the target distribution. We extend speculative sampling to second-order Langevin dynamics, derive the achievable speedup as a function of physical parameters, show that LSD generalizes across different systems and draft-target combinations with a 3-9x speedup, and confirm theoretically and empirically that LSD samples trajectories from its target model distribution.

Machine learning has accelerated quantum chemistry but is hindered by the prohibitive cost of generating high fidelity training data. Multifidelity machine learning (MFML) mitigates this overhead by systematically combining abundant low fidelity data with sparse high fidelity data. In spite of its success, standard MFML schemes rely on pre-defined scaling factors to determine sparse data ratio across fidelities, often generating redundant multifidelity data resulting in a loss of efficiency. Here, we introduce an adaptive on-the-fly multifidelity framework for machine learning that autonomously determines training dataset composition. By dynamically querying training samples at each fidelity, the algorithm saturates model accuracy at lower fidelities before moving up to more expensive reference calculations. We benchmark the novel adaptive-MFML across diverse chemical properties including the computational chemistry gold standard coupled cluster energies, and the more chemically challenging excitation energies. In our numerical experiments we show that our adaptive algorithm reduces data generation costs by up to a factor of 30 compared to single fidelity methods and improves upon standard MFML by up to a factor of 5. The mitigation of data redundancy establishes a high-accuracy low-cost pathway for sustainable cost-aware machine learning in quantum chemistry.

Modern neural audio models run on accelerators whose peak throughput comes from dense matrix multiplication, increasingly at the edge and in datacenters. The conventional acoustic frontend, however -- a Short-Time Fourier Transform (STFT) followed by sparse Mel aggregation -- remains a multi-stage pipeline centered on the Fast Fourier Transform (FFT), with execution overheads unlike the dense linear algebra dominating the inference stack. This work introduces MelT, a portable single-stage Mel frontend that precomputes Mel-spaced Non-Uniform Discrete Fourier Transform (NDFT) bases and applies them to time-domain frames through General Matrix Multiplication (GEMM). The contribution is a computational design principle: decoupling Mel feature extraction from vendor-specific FFT primitives and lowering it onto the matrix-multiplication substrate accelerators already optimize. It is not a new spectral operator. MelT's direct projection performs more arithmetic than the FFT pipeline. Yet in the compact-resolution regime of neural audio frontends, it achieves a 1.64-times to 3.29-times latency reduction and up to a 3.03-times reduction in measured active energy, from the Apple A18 Pro to the NVIDIA H100. All gains are within-platform comparisons, accompanied by task-level validation. Word error rate stays statistically equivalent to the native frontend's on frozen Whisper models of medium size and larger; speaker-attribute classification on VoxCeleb1 is non-inferior. The cepstral extension MFCCT preserves utility on a clinical respiratory-insufficiency classification task (SPIRA) while improving on the MFCC baseline. These results indicate that, in practical regimes on the accelerators evaluated here, hardware alignment rather than arithmetic count can govern the realized cost of feature extraction.

Merging first-principles calculations with machine learning (ML), we aim to accelerate the exploration of catalytic behaviour in novel materials. We focus on two-dimensional (2D) Ti$_2$CT$_y$ MXenes, whose versatile surface chemistry makes them particularly compelling candidates for catalysis. Resolving their composition and structure under realistic conditions exceeds the reach of standard density functional theory (DFT) due to computational cost. To address this challenge, we generate a comprehensive dataset of 50,000 DFT calculations for training and 10,000 for testing, encompassing both Ti$_2$CT$_y$ MXene configurations and molecular systems, along with an additional test dataset with 1000 genuinely new, larger systems to investigate how well models generalise. We train and validate widely used and competitive machine learning interatomic potential (MLIP) models, including EquiformerV2, MACE, MatRIS, and UPET, that accurately predict atomic forces and formation energies -- quantities that DFT must repeatedly compute for structural and catalytic investigations -- for these 2D materials. This combined DFT-ML framework achieves computational acceleration on the order of approximately $1-4 \cdot 10^3$ (on a CPU) while maintaining desired-level accuracy (approximately +/- $10$ meV/A for forces and approximately +/- $1$ meV for per-atom energies), paving the way for more efficient investigations of MXene catalytic behaviour. Moreover, we perform an extensive qualitative evaluation of the trained models, showcasing the importance of comprehensive simulation-based comparison beyond benchmark metrics. The dataset and the trained models with the code are available at https://huggingface.co/datasets/CatalystAnonymous/catalyst_mxenes.

Simulating large molecular systems comprising thousands of atoms requires highly scalable methodologies. While modern Density Functional Theory (DFT) codes exhibit linear scaling, solving the associated large, sparse generalized eigenproblems remains a critical computational bottleneck on exascale architectures. In the context of the LimitX project, we propose a data-driven framework to accelerate these calculations. By shifting the machine learning target from discrete eigenvalues to the coefficients of an interpolating Chebyshev polynomial, and by comparing both all-atom and fragment-based structural representations, we successfully overcome the dimensionality constraints of large-scale spectral prediction. We investigate three machine learning models (Kernel Ridge Regression, Graph Neural Networks, and Random Forests) trained on a novel 2 TB dataset of protein dimers. The predicted spectra provide initial guesses that effectively bypass early Self-Consistent Field (SCF) iterations in BigDFT. Ultimately, these spectral predictors will be deployed to dynamically optimize upcoming rational filter-based eigensolvers, such as FrASE, which is currently in initial development.

A long standing challenge in computational chemistry and biophysics is efficiently sampling the Boltzmann distribution of molecules. Advances in generative modeling have been proposed to address the limitations of conventional sampling techniques by eliminating the computational cost of simulation. A promising direction is iteratively finetuning diffusion models along a temperature ladder whereby training data is generated via importance sampling during inference-time annealing. Unfortunately, these methods require computing a divergence over the score field to estimate importance weights, rendering them intractable for larger systems. Here we present scalable inference-time annealing (SITA), which retrains flow-based models to generate samples at progressively lower temperatures using an energy-based model to facilitate fast surrogate likelihoods. We demonstrate state-of-the-art performance on both Alanine Dipeptide and Alanine Tripeptide while avoiding costly divergence terms. Our code is available at https://github.com/countrsignal/sita.git

Constructing production-quality machine-learned interatomic potentials (MLIPs) requires balancing accuracy, dynamical stability, and computational throughput under constraints that are not captured by a single training loss. We introduce MLIPilot, an auto-research framework in which tool-calling large language models propose hypotheses, edit MLIP training code, launch HPC jobs, and accept or revert changes using a fixed, physically constrained scorecard. We evaluate MLIPilot on MACE potential optimization using both commercial and open-weight LLM agents, including GPT-5.5, GPT-4.1, Mistral-24B, and Qwen3-32B. The benchmarks span molecular and periodic settings: a QM7-derived dataset for which we generated B3LYP/6-31G(d) energies and forces, and a Cu EMT dataset with periodic copper supercells labeled by ASE's Effective Medium Theory calculator. Across these benchmarks, the strongest agents move initially constraint-violating baselines to accepted models by discovering useful training strategies, including output normalization, loss-function changes, progressive training schedules, and model-capacity adjustments. These results suggest that LLM agents can serve as autonomous operators for scientific machine-learning workflows when their search is constrained by domain-specific validation criteria, shifting part of MLIP development from manual trial-and-error toward auditable, automated experimentation.

Accurately modeling the macroscopic dynamics of high-dimensional microscopic systems is of broad interest across the sciences. Many data-driven approaches learn a low-dimensional latent state through an autoencoder trained for pointwise input reconstruction. These methods typically assume a fixed ordering of microscopic degrees of freedom in the input. However, in many settings, such as particle systems, the microscopic state is inherently unordered. This motivates an autoencoder framework that learns permutation-invariant latent representations. To this end, we adopt a permutation-invariant encoder and design the decoder to reconstruct the mass distribution centered at the observed points rather than per-sample reconstruction. We then jointly learn the macroscopic dynamics of the observables together with the latent states. We demonstrate the effectiveness and robustness of the proposed method across a range of microscopic settings, including learning the energy dynamics in interacting particle systems, predicting mixing dynamics in Lennard-Jones fluids, and modeling the stretching dynamics from video data of polymers moving in an elongational force field.

Coupled-cluster (CC) theory is often considered the gold standard of quantum chemistry, but its high computational cost limits routine access to accurate energies, forces and response properties. While the right-hand $T$-amplitudes determine the correlated wavefunction, many practically important observables additionally require the left-hand $Λ$-amplitudes. We introduce MōLe-$Λ$, an extension of Molecular Orbital Learning (MōLe) that predicts the full ground-state coupled-cluster singles and doubles (CCSD) response state by jointly learning right-hand amplitudes $(T_1,T_2)$ and left-hand amplitudes $(Λ_1,Λ_2)$ from localized Hartree--Fock molecular orbitals. Architecturally, MōLe-$Λ$ extends MōLe with $Λ_1$ and $Λ_2$ readouts that mirror the symmetry constraints of the $T_1$ and $T_2$ heads, while preserving the original equivariant orbital encoder, odd sign-equivariant decoding, locality and size-extensivity. The resulting model yields accurate CC-quality energies and forces, while simultaneously recovering dipoles, quadrupoles, polarizabilities, the electron density, and 2-electron observables such as the pair density. We show that MōLe-$Λ$ further extends the speed advantage of MōLe over full CCSD while substantially expanding the accessible properties, providing a route to wavefunction-level surrogate models for correlated quantum chemistry.

While large language models (LLMs) excel at static scientific reasoning, they struggle to model the temporal structure of dynamic physical processes. We present EvoMD-LLM (Evolutionary Molecular Dynamics Large Language Model), a framework that reformulates species-level molecular dynamics as a symbolic temporal language modeling problem. Reactive MD trajectories are discretized into sequences of molecular events, where each token represents a chemical species augmented with its persistence duration, enabling standard autoregressive LLMs to learn compositional evolution over time through efficient fine-tuning. A key component of EvoMD-LLM is temporal scaffolding, which treats event duration as an explicit linguistic token and serves as a structured inductive bias, significantly reducing invalid or hallucinated molecular outputs compared to conventional sequence modeling approaches. We evaluate EvoMD-LLM on multiple temporal prediction tasks, achieving up to 66.14% accuracy and consistently outperforming sequential neural networks and language-based baselines. Beyond quantitative improvements, we qualitatively observe that the model is capable of generating interpretations for its own predictions by incorporating relevant chemical knowledge, even though it was not explicitly supervised with paired trajectory-explanation data. These results demonstrate that symbolic temporal language modeling provides an effective framework for grounding LLMs in dynamic physical simulations.

Realistic physical systems are characterised by emergent interactions across multiple length and time scales, posing a significant challenge for predictive machine learning (ML) models. Most scientific ML models focus on a narrow range of interactions. While machine learning force fields (MLFFs) offer near-quantum accuracy, the ubiquitous message-passing layers miss long-range many-body effects. Here we introduce the Multiscale Structural Ensemble (MuSE), a hierarchical model that uses Soft Coarse-Graining Pooling to construct coarse representations from smooth fractional assignments of atoms to coarse nodes, enabling MLFF modules to operate across multiple scales. MuSE is architecture-agnostic and coupled with SO3krates, MACE, and PaiNN MLFFs for both molecules and materials. We demonstrate the power of MuSE through Hessian-based benchmarks, folding trajectories for biomolecules, and energy profiles in molecule-graphene nanostructures, where MuSE accurately captures quantum-mechanical interactions at relevant scales -- unlike other recent long-range ML models.

Density functional theory (DFT) serves as the basis for computational discovery in materials science and chemistry, yet each calculation demands extensive human effort: adjusting algorithms when convergence stalls, revising plans when unexpected physics emerges, and inserting steps as intermediate results reshape the problem. Existing LLM-based agents automate only the initial planning stage, producing a full execution plan upfront and leaving all subsequent adaptation to hand-crafted rules. As a result, these workflows remain fragile, do not generalize well beyond pre-planned scenarios, and often require expert intervention when failures or unexpected intermediate results require changes to the calculation path. Here, we introduce AutoDFT, a closed-loop multi-agent framework that embeds LLM reasoning into every stage of the DFT lifecycle, where a strategic planner produces a skeletal plan of step objectives; a step planner generates numerical parameters just in time from preceding results; and a monitor-recover-reflect cycle diagnoses failures, repairs them, and revises the plan when the evidence justifies it. We demonstrate both breadth and depth: breadth on VASPBench, a purpose-built benchmark spanning 34 tasks and 9 DFT calculation types, where AutoDFT achieves 94.1% task-level success with GPT-5.2; and depth on established materials databases, where AutoDFT produces quantitatively reliable property predictions across electronic, magnetic, and energetic properties. By closing the loop between planning and execution, AutoDFT enables experimentalists without deep computational expertise to obtain reliable first-principles results.

Machine learning interatomic potentials (MLIPs) require generating computationally expensive, large-scale training datasets to accurately simulate materials and molecules. Incorporating electronic structure information using multitask learning improves sample efficiency, however, training on full Hamiltonian matrices, which scale quadratically with the number of atoms, is intractable for large datasets. In this work, we show that multitask learning utilizing orbitally resolved semiempirical charges significantly improves sample efficiency and accuracy in MLIPs. To efficiently predict orbital charges, we implement a specialized equivariant model, reducing charge prediction error compared to an invariant baseline. By augmenting training with computationally inexpensive GFN1-xTB orbital charges, which scale linearly with the number of atoms, our model achieves a 46% reduction in energy mean absolute error and requires five times less data to match the performance of energy-only models. Furthermore, our approach outperforms models trained on expensive density functional theory (DFT) atomic charges, capturing orbitally resolved electronic complexity and forcing the network to learn a physically accurate latent space that spontaneously clusters metals by shared chemical properties. Because orbital charges are only required during training, this approach preserves inference efficiency, providing a scalable recipe for developing accurate, data-efficient foundation models for complex chemical systems.

Sampling from discrete distributions with multiple modes and energy barriers is fundamental to machine learning and computational physics. Recent discrete neural samplers like MDNS suffer from mode collapse and fail to sample high-energy barrier regions between modes, which is critical for free energy estimation and understanding phase transitions. We propose Metadynamics Discrete Neural Sampler (MetaDNS), a general framework integrating well-tempered metadynamics into discrete diffusion or autoregressive samplers. By maintaining an adaptive, history-dependent bias potential along selected low-dimensional coordinates, MetaDNS forces exploration of previously inaccessible regions, enabling free energy reconstruction infeasible with standard neural samplers due to a lack of high-energy samples. On challenging low-temperature benchmarks including Ising, Potts, and the copper-gold binary alloy, MetaDNS reproduces the thermodynamic distribution. Compared to MCMC-based metadynamics, MetaDNS also achieves comparable exploration requiring fewer bias deposition steps.

Physics-informed diffusion models typically enforce PDE constraints only on final outputs, leaving intermediate representations unconstrained and prone to shortcut learning under shifted boundary conditions. We introduce REPA-P, a teacher-free, architecture-agnostic framework that aligns intermediate features with physical states using first-principles residuals. REPA-P attaches lightweight $1{\times}1$ projection heads to selected layers, decodes hidden activations into physical quantities, and applies PDE residual losses during training. These heads are discarded at inference, introducing zero overhead. Across four PDE tasks, including Darcy flow, topology optimization, electrostatic potential, and turbulent channel flow, REPA-P accelerates convergence by up to $2{\times}$, reduces physics residuals by up to $66.4\%$, and improves out-of-distribution robustness by up to $49.3\%$, with consistent gains on both U-Net and Diffusion Transformer backbones. Ablations show that supervising a small set of intermediate layers captures most benefits and complements output-level physics losses. Code is available at https://github.com/Hxxxz0/REPA-P.

Machine learning interatomic potentials (MLIPs) achieve excellent accuracy when trained on large Density Functional Theory (DFT) data. To be useful in practice, they must often be adapted to target chemistries using small and expensive task-specific datasets. However, MLIPs transfer inconsistently across domains, with representations that often loose accessible composition and structure information. To address this, we present TriForces, a model-agnostic three-stream framework that separates composition and structure information, combined with self-supervised learning to preserve transferable representations. TriForces improves performance on MatBench and QM9 over baselines without needing DFT labels and enables efficient similar structure retrieval through its learned latent space. On OMat24, in limited-data training regime, TriForces reduces energy MAE by 57% at 20K samples only and improves force MAE across sample sizes. We release pretrained TriForces variants across multiple MLIP architectures with code at https://github.com/Ramlaoui/triforces.

Computational materials science and chemistry span vast knowledge domains and fractured software ecosystems. Although large language models (LLMs) have demonstrated research capabilities, scaling monolithic agents to manage the rigor and complexity of atomistic research remains a challenge. Here, we introduce AtomisticSkills, an open-source harness framework that empowers general-purpose AI coding agents to conduct atomistic research across materials science, chemistry, and drug discovery. By hierarchically decomposing scientific workflows into agent skills and tools, AtomisticSkills provides agents with modular, extensible, and plug-and-play research capabilities. The framework integrates more than 100 human-curated multidisciplinary skills, including database access, thermodynamics and kinetics modeling, and diverse simulation engines employing machine learning interatomic potentials (MLIPs) and density functional theory (DFT). We validate its functional coverage against scientific literature and demonstrate robust orchestration capabilities across diverse scientific campaigns: generative design of Li-ion solid-state electrolytes, high-throughput screening of metal-organic frameworks for CO2 capture, autonomous MLIP benchmarking and fine-tuning, multi-stage structure-based virtual screening for drug design, multimodal X-ray diffraction pattern analysis, and screening of Fe-oxide catalysts for oxygen evolution reaction. AtomisticSkills provides a critical agent infrastructure towards building fully autonomous AI scientists.

Chemical disorder, originating from the mixed occupation of crystallographic sites by multiple elements, is widespread in alloys, ceramics, and compositionally complex materials, where short- and long-range orderings can strongly influence properties. A central obstacle is the representation gap between experiments and simulations: experiments often report disorder as partial occupancies and ensemble-averaged behaviors, whereas atomistic simulations and AI workflows usually require fully specified configurations. Tackling this gap requires computational methods that convert averaged disorder descriptions into representative configurational ensembles while balancing cost, bias, and fidelity. This challenge has become more urgent in AI-driven computational discovery, where ignoring disorder may cause AI workflows to misrank stability, misjudge novelty, and misdirect experiments with too-idealized representations. This Review highlights how classical and AI-driven methods can bridge this representation gap. We assess the strengths and limitations of approaches spanning mean-field theories, cluster expansion, quasi-random approximations, Monte Carlo, and emerging schemes powered by universal interatomic potentials and generative models. We further highlight how AI can accelerate classical computational schemes by lowering the cost of microstate evaluation, configurational exploration, and atomistic-to-thermodynamic closure. We also emphasize how AI can enable disorder-native capabilities, including workflow triage, ordering-sensitive and alchemical representations, generative models of disordered structures and distributions, and kinetics-aware disorder prediction. Together, this framework outlines a practical roadmap toward disorder-native AI, which can transform chemical disorder from a representational obstacle into a controllable variable for realistic AI-accelerated materials discovery.

Virtually all aspects of many-body atomic physics are challenging: experiments are technically demanding, datasets have become enormous, and the memory and CPU requirements for classical simulation of generic quantum systems often scale exponentially with system size. Machine learning (ML) methods are already assisting in each of these areas and are poised to become transformative. Here, we focus on two specific applications of ML to cold-atom-based quantum simulators. These devices generally generate data in the form of images; we first showcase denoising of raw images and then identify solitonic waves in Bose-Einstein condensates. In both of these examples, we comment on the interplay between performance, model complexity, and interpretability.

Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force (PMF), with density functional theory (DFT) accuracy is computationally expensive. Universal machine learning interatomic potentials (MLIPs) drastically reduce this cost, but their accuracy is strongly determined by their training data and hence can be uncertain for a given system. In this work, we present a systematic and scalable framework for reweighting PMFs, initially sampled with a single 'source' MLIP, across a representative suite of target MLIPs. Because traditional direct exponential reweighting fails for large system sizes due to low phase-space overlap between potentials, we deploy robust analytical corrections. Applying this to a complex 601-atom system of Li$^+$ transport in a nanoconfined electrolyte, we demonstrate that a mean energy-gap approximation effectively bypasses statistical collapse, producing a highly stable PMF matching the target PMF. Using this approach, we recover high-fidelity target thermodynamics across multiple DFT reference levels (PBE+D3, PBE-sol, r$^2$SCAN,r$^2$SCAN-D4) at a fraction of the computational cost of full simulations. Furthermore, thermodynamic analysis reveals that the studied MLIPs partition into two distinct clusters driven by their training data. Our reweighting framework successfully recovers target thermodynamic properties--specifically, reaction and activation free energies--even when the phase-space overlap between potentials is critically low. Ultimately, this approach establishes a vital diagnostic protocol to achieve affordable cross-model consensus on materials chemistry properties without redundant, resource-intensive simulations.

A unified simulator that can model diverse physical phenomena without solver-specific redesign is a long-standing goal across simulation science. We present a learning-based particle simulator built on a single transformer architecture to model cloth, elastic solds, Newtonian and non-Newtonian fluids, granular materials, and molecular dynamics. Our model follows a prediction-correction design on a shared Lagrangian particle representation. An explicit predictor first advances particles under the known external forces, producing an intermediate state that captures externally driven motion but not inter-particle interactions. A learned corrector then predicts the residual position and velocity updates through three stages: a particle tokenizer that encodes local particle-particle, particle-boundary, and topology-guided interactions; a super-token encoder that hierarchically merges particle tokens into a compact set of super tokens via alternating self-attention and token merging; and a super-token decoder that lifts these super tokens back to particle resolution through cross-attention to predict per-particle position and velocity corrections. Progressive token merging reduces the attention cost at successive encoder layers by halving the token count at each level, and the decoder communicates through the compact super-token set rather than full particle-to-particle attention. Across the six dynamics categories, the same architecture generalizes to unseen materials, boundary configurations, initial conditions, and external forces. We further demonstrate downstream interactive control, inverse design, and learning from real-world manipulation data, reducing the need for per-phenomenon solver engineering.

PyCSP$^3$ provides a productive way to build constraint models for solving combinatorial constrained problems and export them to XCSP$^3$, preserving a complete separation between modeling and solving. However, it lacks native support for scheduling abstractions such as interval variables, sequence variables, and resource functions. As a result, scheduling models must be encoded with low-level integer variables and manual channeling constraints, even though PyCSP$^3$ already provides global constraints like NoOverlap and Cumulative on integer arrays. We present PyCSP$^3$ Scheduling, a library that adds scheduling abstractions to PyCSP$^3$ through 53 dedicated constraints and 27 expressions, and compiles them down to standard PyCSP$^3$/XCSP$^3$ constraints, maintaining the modeling/solving separation that underpins the PyCSP$^3$ ecosystem. On 261 paired instances across 17 model families (5 runs each), both formulations produce identical objectives on all 72 doubly-proved optimal pairs and nearly half of the families (8/17) remain structurally unchanged after compilation; however, runtime performance diverges across families, with clear gains on some (up to 5.8x) and regressions on others due to the overhead of compilation decompositions. Code and benchmarks are available at: https://github.com/sohaibafifi/pycsp3-scheduling

Developing machine learning interatomic potentials (MLIPs) for complex materials systems remains challenging because it requires expertise in atomistic simulations, machine learning, and workflow design, as well as iterative active learning procedures. Existing automated pipelines typically assume a fixed sequence of stages or depend on domain experts, which limits their adaptability to heterogeneous materials systems where the optimal curriculum is not known in advance. To lower the barrier to developing MLIPs for non-experts, we propose Lang2MLIP, a multi-agent framework that takes natural-language input and formulates end-to-end MLIP development as a sequential decision-making problem solved by large language models (LLMs). At each step, a decision-making agent observes the current dataset, model, evaluation results, and execution log, and then automatically selects an appropriate action to improve the model. This removes the need for a predefined pipeline and enables the agent to self-correct by revisiting earlier subsystems when new failures arise. We evaluate this approach on a solid electrolyte interphase (SEI) system with multiple components and interfaces. These results suggest that LLM-based multi-agent systems are a promising direction for automating MLIP development and making it more accessible to non-experts.

Active learning for machine-learning interatomic potentials (MLIPs) must address several challenges to be practical: scaling to large candidate pools, leveraging energy-force supervision, and maintaining robustness when candidate pools are biased relative to the target distribution. In this work, we jointly address these challenges. We first introduce a linearly scaling acquisition framework based on chunked feature-space posterior-variance shortlisting. By avoiding materialisation of the candidate and train set kernels, this approach enables screening of ~200k structures within hours and applies broadly to acquisition strategies that score candidates based on molecular similarity metrics. We then extend the Neural Tangent Kernel (NTK) to a force-aware setting via mixed parameter-coordinate derivatives, yielding a force NTK and a joint energy-force NTK that provide natural similarity metrics for vector-field prediction. We demonstrate the effectiveness of the joint energy-force NTK on the OC20 dataset, where force-aware acquisition is crucial: it achieves the lowest energy and force MAE and RMSE across all metrics and distribution splits. Across T1x, PMechDB, and RGD benchmarks, our force NTK methods remain competitive with established baselines while being significantly more efficient than committee-based approaches. Under a controlled candidate-pool shift case study on T1x, acquisition based on pretrained MLIP embeddings and NTKs remains robust, whereas committee-based methods exhibit higher variance. Overall, these results show that a single pretrained MLIP can enable scalable, force-aware, and distribution-robust active learning for foundation-model fine-tuning.

Periodic crystals repeatedly instantiate similar local coordination motifs across translated cells and chemically related structures, but current equivariant atomistic models usually encode these patterns only implicitly in dense edge features. We introduce PaMM, a periodic motif memory that augments the UMA eSCN-MD edge encoder with explicit pair and triplet lookup features. Pair motifs are keyed by $(Z_j, Z_i, b_r)$ and triplet motifs by $(Z_j, Z_i, Z_k, b_θ)$, hashed into fixed-size tables and fused with the baseline edge representation through lightweight gate-only and affine-equipped variants. We evaluate PaMM in a matched UMA-S OMAT setting and focus on a narrow question: whether explicit motif memory helps at a fixed intermediate training budget. At the 10k-step checkpoint, both PaMM variants improve over the plain baseline; gate-only gives the best energy MAE, while the affine-equipped variant gives the best force MAE. A matched 20k follow-up keeps the same operating-point picture. Aligned controls show that the gain weakens for pair-only, triplet-only, random-bucket, and parameter-matched MLP alternatives, suggesting that the benefit is tied to structured pair/triplet organization rather than generic added capacity. A within-OMAT24 source-family evaluation also shows small but consistent gains across held-out generation families. We therefore make a focused claim: in the studied UMA-S + OMAT regime, explicit pair/ triplet motif memory is a useful inductive bias for periodic atomistic modeling. We do not claim broad cross-dataset transfer, a uniquely preferred fusion variant, or strong scientific interpretability beyond a more inspectable local-structure interface.

Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of the free-energy surface, leaving its curvature unconstrained. We introduce a framework that augments force matching with stochastic Hessian-vector product (HVP) matching, instilling second-order curvature information into CG potentials without constructing the full Hessian. We derive a decomposition of the target CG Hessian into a model-independent projected AA Hessian, precomputed once before training, and a model-dependent covariance correction computed online at negligible cost. We construct an unbiased stochastic estimator of the Hessian-matching objective by using random probe vectors. We evaluate our method by comparing against force matching on a benchmark of nine fast-folding proteins unseen during training. HVP matching outperforms plain force matching on 8 of 9 proteins on slow-mode metrics, with reductions of up to 85% in the Kullback--Leibler divergence between the CG and reference distributions along the slowest collective mode of the largest protein. Our results demonstrate that higher-order physical supervision is a practical path to more accurate and transferable CG potentials for biomolecular simulation.

Cold-chain storage limits access to insulin for hundreds of millions of people; a thermally protective patch polymer could help, but the design space is too large for exhaustive experiment. Starting from that problem, we narrow to an agentic workflow: a large language model (LLM) calls physics-based tools through the Model Context Protocol (MCP), searching the discrete PSMILES space under a budget of OpenMM Packmol-matrix evaluations. The LLM acts as an implicit acquisition function conditioned on a persistent "discovery world": hypotheses, literature claims, and simulation outcomes updated each iteration. Under matched oracle budgets, the best autonomous campaign reaches an insulin-polymer interaction energy of -2263 kJ/mol, outperforming reinforcement-learning baselines by 68% and Bayesian optimization by 19%. Three independent campaigns converge on one structural motif (dense hydrogen-bond donors and acceptors per repeat unit) while physics checks reject infeasible packings and name-structure mismatches before they steer the next step. The science stage is CPU-bound and runs on commodity hardware. More broadly, the same architecture and workflow designed here applies to other protein-stabilization tasks whenever a tractable screening oracle is available.