Quantum error correction (QEC)1,2 is essential for the realization of large-scale quantum computers3,4. However, owing to the complexity of operating on the encoded ‘logical’ qubits5,6, understanding the physical principles for building fault-tolerant quantum devices and combining them into efficient architectures is an outstanding scientific challenge. Here we use reconfigurable arrays of up to 448 neutral atoms to implement the key elements of a universal, fault-tolerant quantum processing architecture and experimentally explore their underlying working mechanisms. We first use surface codes to study how repeated QEC suppresses errors6,7, demonstrating 2.14(13)x below-threshold performance in a four-round characterization circuit by leveraging atom loss detection and machine learning decoding8,9. We then investigate logical entanglement using transversal gates and lattice surgery10–12 and extend it to universal logic through transversal teleportation with three-dimensional [[15,1,3]] codes13,14, enabling arbitrary-angle synthesis with polylogarithmic overhead5,15. Finally, we develop mid-circuit qubit reuse16, increasing experimental cycle rates by two orders of magnitude and enabling deep-circuit protocols with dozens of logical qubits and hundreds of logical teleportations17–20 with [[7,1,3]] and high-rate [[16,6,4]] codes while maintaining constant internal entropy. Our experiments show key principles for efficient architecture design, involving the interplay between quantum logic and entropy removal, judiciously using physical entanglement in logic gates and magic state generation, and leveraging teleportations for universality and physical qubit reset. These results establish foundations for scalable, universal error-corrected processing and its practical implementation in neutral atom systems.
