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Jurgis Ruza

Publications and source records attributed to Jurgis Ruza.

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Harnessing AtomisticSkills for Agentic Atomistic Research

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.

physics.chem-ph

Temperature-transferable coarse-graining of ionic liquids with dual graph convolutional neural networks

Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic and ensemble motion. Coarse-grained models are therefore used in place of costly atomistic simulations, allowing simulation of longer time scales and larger systems. Nevertheless, constructing the many-body potential of mean force that defines the structure and dynamics of a coarse-grained system can be complicated and computationally intensive. Machine learning shows great promise for the key coupled challenges of dimensionality reduction and learning the potential of mean force. To improve the coarse-graining of ILs, we present a neural network model trained on all-atom classical molecular dynamics simulations. The potential of mean force is expressed as two jointly-trained neural network interatomic potentials that learn the coupled short-range and the many-body long range molecular interactions. These interatomic potentials treat temperature as an explicit input variable to capture the temperature dependence of the potential of mean force. The model reproduces structural quantities with high fidelity, outperforms the temperature-independent baseline at capturing dynamics, generalizes to unseen temperatures, and incurs low simulation cost.

physics.comp-ph