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Quantum error correction (QEC) is believed to be essential for the realization of large-scale quantum computers. However, due to the complexity of operating on the encoded `logical' qubits, understanding the physical principles for building fault-tolerant quantum devices and combining them into efficient architectures is an outstanding scientific challenge. Here we utilize reconfigurable arrays of up to 448 neutral atoms to implement all key elements of a universal, fault-tolerant quantum processing architecture and experimentally explore their underlying working mechanisms. We first employ surface codes to study how repeated QEC suppresses errors, demonstrating 2.14(13)x below-threshold performance in a four-round characterization circuit by leveraging atom loss detection and machine learning decoding. We then investigate logical entanglement using transversal gates and lattice surgery, and extend it to universal logic through transversal teleportation with 3D [[15,1,3]] codes, enabling arbitrary-angle synthesis with logarithmic overhead. Finally, we develop mid-circuit qubit re-use, increasing experimental cycle rates by two orders of magnitude and enabling deep-circuit protocols with dozens of logical qubits and hundreds of logical teleportations with [[7,1,3]] and high-rate [[16,6,4]] codes while maintaining constant internal entropy. Our experiments reveal 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 with neutral atom systems. 

Abstract The ability to perform entangling quantum operations with low error rates in a scalable fashion is a central element of useful quantum information processing¹. Neutral-atom arrays have recently emerged as a promising quantum computing platform, featuring coherent control over hundreds of qubits^2,3and any-to-any gate connectivity in a flexible, dynamically reconfigurable architecture⁴. The main outstanding challenge has been to reduce errors in entangling operations mediated through Rydberg interactions⁵. Here we report the realization of two-qubit entangling gates with 99.5% fidelity on up to 60 atoms in parallel, surpassing the surface-code threshold for error correction^6,7. Our method uses fast, single-pulse gates based on optimal control⁸, atomic dark states to reduce scattering⁹and improvements to Rydberg excitation and atom cooling. We benchmark fidelity using several methods based on repeated gate applications^10,11, characterize the physical error sources and outline future improvements. Finally, we generalize our method to design entangling gates involving a higher number of qubits, which we demonstrate by realizing low-error three-qubit gates^12,13. By enabling high-fidelity operation in a scalable, highly connected system, these advances lay the groundwork for large-scale implementation of quantum algorithms¹⁴, error-corrected circuits⁷and digital simulations¹⁵.