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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. 

We report a high-finesse bow-tie cavity designed for atomic physics experiments with Rydberg atom arrays. The cavity has a finesse of 51,000 and a waist of 7.1μm at the cesium D2 line (852 nm). With these parameters, the cavity is expected to induce strong coupling between a single atom and a single photon, corresponding to a cooperativity per traveling mode of 35 at the cavity waist. To trap and image atoms, the cavity setup utilizes two in-vacuum aspheric lenses with a numerical aperture (NA) of 0.35 and is capable of housingNA = 0.5 microscope objectives. In addition, the large atom-mirror distance ( $\gtrsim <\#comment/>1.5$cm) provides good optical access and minimizes stray electric fields at the position of the atoms. This cavity setup can operate in tandem with a Rydberg array platform, creating a fully connected system for quantum simulation and computation.