Orchestrating Multi-Zone Shuttling in Trapped-Ion Quantum Computers

Trapped-ion quantum computers are a promising platform, offering high-quality qubits with long coherence times and high-fidelity gate operations. The Quantum Charge Coupled Device (QCCD) architecture provides a scalable blueprint by leveraging the ability to shuttle ions between distinct zones. However, realizing such architectures in practice requires software support to manage ion movement across multi-zone layouts. In this work, we propose a compilation strategy for QCCD architectures with multiple processing zones located outside a grid-type memory zone. Unlike previous approaches that treat processing zones as black-boxes, our method explicitly models their structural constraints, enabling optimized ion movement to and through them. It combines qubit partitioning with dependency-aware gate selection to reduce inter-zone shuttling while enabling simultaneous gate execution. We implemented the method in an open-source tool and empirically demonstrated its effectiveness across several QCCD layouts, laying a foundation for the compilation of multi-zone trapped-ion systems.