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The neutral atom array has gained prominence in quantum computing for its scalability and operation fidelity. Previous works focus on fixed atom arrays (FAAs) that require extensive SWAP operations for long-range interactions. This work explores a novel architecture reconfigurable atom arrays (RAAs), also known as field programmable qubit arrays (FPQAs), which allows for coherent atom movements during circuit execution under some constraints. Such atom movements, which are unique to this architecture, could reduce the cost of longrange interactions significantly if the atom movements could be scheduled strategically. In this work, we introduce Atomique, a compilation framework designed for qubit mapping, atom movement, and gate scheduling for RAA. Atomique contains a qubit-array mapper to decide the coarse-grained mapping of the qubits to arrays, leveraging MAX k-Cut on a constructed gate frequency graph to minimize SWAP overhead. Subsequently, a qubit-atom mapper determines the fine-grained mapping of qubits to specific atoms in the array and considers load balance to prevent hardware constraint violations. We further propose a router that identifies parallel gates, schedules them simultaneously, and reduces depth. We evaluate Atomique across 20+ diverse benchmarks, including generic circuits (arbitrary, QASMBench, SupermarQ), quantum simulation, and QAOA circuits. Atomique consistently outperforms IBM Superconducting, FAA with long-range gates, and FAA with rectangular and triangular topologies, achieving significant reductions in depth and the number of two-qubit gates. 

Neutral atom arrays have become a promising platform for quantum computing, especially the field programmable qubit array (FPQA) endowed with the unique capability of atom movement. This feature allows dynamic alterations in qubit connectivity during runtime, which can reduce the cost of executing long-range gates and improve parallelism. However, this added flexibility introduces new challenges in circuit compilation. Inspired by the placement and routing strategies for FPGAs, we propose to map all data qubits to fixed atoms while utilizing movable atoms to route for 2-qubit gates between data qubits. Coined flying ancillas, these mobile atoms function as ancilla qubits, dynamically generated and recycled during execution. We present Q-Pilot, a scalable compiler for FPQA employing flying ancillas to maximize circuit parallelism. For two important quantum applications, quantum simulation and the Quantum Approximate Optimization Algorithm (QAOA), we devise domain-specific routing strategies. In comparison to alternative technologies such as superconducting devices or fixed atom arrays, Q-Pilot effectively harnesses the flexibility of FPQA, achieving reductions of 1.4x, 27.7x, and 6.3x in circuit depth for 100-qubit random, quantum simulation, and QAOA circuits, respectively. 

Dynamically field-programmable qubit arrays (DPQA) have recently emerged as a promising platform for quantum information processing. In DPQA, atomic qubits are selectively loaded into arrays of optical traps that can be reconfigured during the computation itself. Leveraging qubit transport and parallel, entangling quantum operations, different pairs of qubits, even those initially far away, can be entangled at different stages of the quantum program execution. Such reconfigurability and non-local connectivity present new challenges for compilation, especially in the layout synthesis step which places and routes the qubits and schedules the gates. In this paper, we consider a DPQA architecture that contains multiple arrays and supports 2D array movements, representing cutting-edge experimental platforms. Within this architecture, we discretize the state space and formulate layout synthesis as a satisfiability modulo theories problem, which can be solved by existing solvers optimally in terms of circuit depth. For a set of benchmark circuits generated by random graphs with complex connectivities, our compiler OLSQ-DPQA reduces the number of two-qubit entangling gates on small problem instances by 1.7x compared to optimal compilation results on a fixed planar architecture. To further improve scalability and practicality of the method, we introduce a greedy heuristic inspired by the iterative peeling approach in classical integrated circuit routing. Using a hybrid approach that combined the greedy and optimal methods, we demonstrate that our DPQA-based compiled circuits feature reduced scaling overhead compared to a grid fixed architecture, resulting in 5.1X less two-qubit gates for 90 qubit quantum circuits. These methods enable programmable, complex quantum circuits with neutral atom quantum computers, as well as informing both future compilers and future hardware choices.