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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 Suppressing errors is the central challenge for useful quantum computing¹, requiring quantum error correction (QEC)^2–6for large-scale processing. However, the overhead in the realization of error-corrected ‘logical’ qubits, in which information is encoded across many physical qubits for redundancy^2–4, poses substantial challenges to large-scale logical quantum computing. Here we report the realization of a programmable quantum processor based on encoded logical qubits operating with up to 280 physical qubits. Using logical-level control and a zoned architecture in reconfigurable neutral-atom arrays⁷, our system combines high two-qubit gate fidelities⁸, arbitrary connectivity^7,9, as well as fully programmable single-qubit rotations and mid-circuit readout^10–15. Operating this logical processor with various types of encoding, we demonstrate improvement of a two-qubit logic gate by scaling surface-code⁶distance fromd = 3 tod = 7, preparation of colour-code qubits with break-even fidelities⁵, fault-tolerant creation of logical Greenberger–Horne–Zeilinger (GHZ) states and feedforward entanglement teleportation, as well as operation of 40 colour-code qubits. Finally, using 3D [[8,3,2]] code blocks^16,17, we realize computationally complex sampling circuits¹⁸with up to 48 logical qubits entangled with hypercube connectivity¹⁹with 228 logical two-qubit gates and 48 logical CCZ gates²⁰. We find that this logical encoding substantially improves algorithmic performance with error detection, outperforming physical-qubit fidelities at both cross-entropy benchmarking and quantum simulations of fast scrambling^21,22. These results herald the advent of early error-corrected quantum computation and chart a path towards large-scale logical processors.