Efficient and Safe Molecular Assembly via Reinforcement Learning and Constraint Solving

Scanning tunneling microscopy (STM) enables precise manipulation of individual atoms and molecules, offering a pathway to constructing nanoscale assemblies with rich quantum mechanical behavior. Despite its potential, STM-based fabrication remains limited by the inherent complexity of manipulation procedures and the extensive manual effort required. In this work, we take a substantial step toward autonomous manufacturing with STMs by introducing a novel AI-based planning framework for molecular assembly and a high-fidelity simulation environment. Our framework computes collision-free assembly plans that minimize the total distance traveled by molecules. Given an assignment of molecules to target positions, satisfiability solving is used to compute execution schedules in which each molecule has an empty corridor available when it is scheduled to move. Reinforcement learning (RL) agents then execute sequences of STM actions to manipulate molecules to their targets. We further introduce NanoAssemblyGym, a high-fidelity simulation environment for molecular manipulation built on the Gymnasium API, allowing seamless integration with existing RL libraries and workflows. Using NanoAssemblyGym, we demonstrate autonomous assembly of structures containing up to 420 molecules.