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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. 

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.