AtomMOF: All-Atom Flow Matching for MOF-Adsorbate Structure Prediction

Metal-organic frameworks (MOFs) are promising materials for applications such as direct air capture, where performance depends on how adsorbates bind within the framework. Accurately predicting MOF-adsorbate configurations is therefore important for screening candidate materials. However, traditional approaches are computationally expensive and require a known host structure, while existing generative models rely on rigid-body assumptions and do not explicitly model adsorbates. We introduce AtomMOF, a scalable all-atom flow-matching model that jointly predicts MOF-adsorbate structures from discrete building blocks and adsorbates. Built on a Diffusion Transformer with a building block-based pairwise attention bias, AtomMOF operates in an unconstrained all-atom space and exhibits clear scaling behavior. To improve the structural validity of flexible all-atom models, we also propose Feynman-Kac (FK) steering with machine-learned interatomic potentials (MLIPs). On the BW dataset, AtomMOF achieves a 58.17% relative increase in match rate and a 31.84% relative reduction in RMSD compared with prior work. MLIP-guided steering further improves validity by 28.7% and reduces formation energy error by 86.5%. On ODAC25, AtomMOF generates adsorption configurations faster than GCMC and, when combined with MLIP relaxation, identifies lower-energy configurations than those in the reference dataset.