Sathya Edamadaka

Bowen Deng, Bohan Li, Matthew Cox et al.

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.

Xiaochen Du, Juno Nam, Jaemoo Choi et al.

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.

Aritra Roy, Kevin Shen, Andrew MacBride et al.

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

Sathya Edamadaka, Soojung Yang, Ju Li et al.

Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of matter. Understanding their latent structure is essential for building scientific foundation models that generalize reliably beyond their training domains. Although representational convergence has been observed in language and vision, its counterpart in the sciences has not been systematically explored. Here, we show that representations learned by nearly sixty scientific models, spanning string-, graph-, 3D atomistic, and protein-based modalities, are highly aligned across a wide range of chemical systems. Models trained on different datasets have highly similar representations of small molecules, and machine learning interatomic potentials converge in representation space as they improve in performance, suggesting that foundation models learn a common underlying representation of physical reality. We then show two distinct regimes of scientific models: on inputs similar to those seen during training, high-performing models align closely and weak models diverge into local sub-optima in representation space; on vastly different structures from those seen during training, nearly all models collapse onto a low-information representation, indicating that today's models remain limited by training data and inductive bias and do not yet encode truly universal structure. Our findings establish representational alignment as a quantitative benchmark for foundation-level generality in scientific models. More broadly, our work can track the emergence of universal representations of matter as models scale, and for selecting and distilling models whose learned representations transfer best across modalities, domains of matter, and scientific tasks.