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Neutral atom arrays have become a promising platform for quantum computing,especially the \textit{field programmable qubit array} (FPQA) endowed with theunique capability of atom movement. This feature allows dynamic alterations inqubit connectivity during runtime, which can reduce the cost of executinglong-range gates and improve parallelism. However, this added flexibilityintroduces new challenges in circuit compilation. Inspired by the placement androuting strategies for FPGAs, we propose to map all data qubits to fixed atomswhile utilizing movable atoms to route for 2-qubit gates between data qubits.Coined \textit{flying ancillas}, these mobile atoms function as ancilla qubits,dynamically generated and recycled during execution. We present Q-Pilot, ascalable compiler for FPQA employing flying ancillas to maximize circuitparallelism. For two important quantum applications, quantum simulation and theQuantum Approximate Optimization Algorithm (QAOA), we devise domain-specificrouting strategies. In comparison to alternative technologies such assuperconducting devices or fixed atom arrays, Q-Pilot effectively harnesses theflexibility of FPQA, achieving reductions of 1.4$\times$, 27.7$\times$, and6.3$\times$ in circuit depth for 100-qubit random, quantum simulation, and QAOAcircuits, respectively.

Q-Pilot: Field Programmable Quantum Array Compilation with Flying Ancillas