ATLAS: Efficient Atom Rearrangement for Defect-Free Neutral-Atom Quantum Arrays Under Transport Loss

Neutral-atom quantum computers encode qubits in individually trapped atoms arranged in optical lattices. Achieving defect-free atom configurations is essential for high-fidelity quantum gates and scalable error correction, yet stochastic loading and atom loss during rearrangement hinder reliable large-scale assembly. This work presents ATLAS, an open-source atom transport algorithm that efficiently converts a randomly loaded W times W lattice into a defect-free L times L subarray while accounting for realistic physical constraints, including finite acceleration, transfer time, and per-move loss probability. In the planning phase, optimal batches of parallel moves are computed on a lossless virtual array; during execution, these moves are replayed under probabilistic atom loss to maximize the expected number of retained atoms. Monte Carlo simulations across lattice sizes W=10--100, loading probabilities p_occ=0.5--0.9, and loss rates p_loss=0--0.05 demonstrate fill rates above 99\% within six iterations and over 90\% atom retention at low loss. The algorithm achieves sublinear move scaling $propto M^0.55$ and linear growth of required initial size with target dimension, outperforming prior methods in robustness and scalability - offering a practical path toward larger neutral-atom quantum arrays.