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arXiv:2610.26471

End-to-End Optimization of Partial Fault Tolerance in Neutral-Atom Arrays

Stefano Veroni, Aydin Deger, Andrew J. Daley

quant-phcond-mat.quant-gasphysics.atom-phSubmitted Oct 19, 2026• Announced Oct 20, 2026• 0 citations
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Abstract

Fault-tolerant (FT) quantum computation offers a pathway to quantum advantage, but its realization is hindered by its significant overhead. The partially FT "STAR" architecture reduces the cost of universal computation at the price of relaxing FT requirements for non-Clifford operations, increasing exposure to hardware noise. Therefore, maximizing its performance and applicability demands careful co-design with the underlying hardware. In this work we investigate the co-design of the STAR architecture with neutral-atom platforms, connecting the underlying atomic physics to logical error modeling and application-level performance. At the physical level, we identify a favorable noise bias in $^{171}\mathrm{Yb}$ Rydberg gates, and show how it can be enhanced through error-selective pulse optimization. At the logical level, we identify an intrinsic error suppression mechanism, yielding vanishing logical coherent noise in leading order. Detailed circuit-level simulations of surface code implementations show more than an order of magnitude reduction in logical error relative to previous estimates. As a concrete target application, we focus on the Fermi-Hubbard model with periodic boundaries, for which we design a simulation circuit particularly suited to early implementations. We quantify the resource tradeoff of partially and fully FT approaches to gate synthesis, with the former showing approximately an order of magnitude reduction in state-injection depth, and an even larger reduction in Clifford resources. Comparing with classical and fully FT approaches, we identify regimes where partial fault tolerance provides both lower overheads and lower error rates. In our estimates, this is accessible with moderate error rates $p\sim 10^{-3}$ and a few thousand qubits, underlining that for these types of problems, partial FT approaches provide a compelling pathway to early quantum advantage.

Comments
42 pages, 9 figures

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Fault-tolerant (FT) quantum computation offers a pathway to quantum advantage, but its realization is hindered by its significant overhead. The partially FT "STAR" architecture reduces the cost of universal computation at the price of relaxing FT requirements for non-Clifford operations, increasing exposure to hardware noise. Therefore, maximizing its performance and applicability demands careful co-design with the underlying hardware. In this work we investigate the co-design of the STAR architecture with neutral-atom platforms, connecting the underlying atomic physics to logical error modeling and application-level performance. At the physical level, we identify a favorable noise bias in 171Yb^{171}\mathrm{Yb}171Yb Rydberg gates, and show how it can be enhanced through error-selective pulse optimization. At the logical level, we identify an intrinsic error suppression mechanism, yielding vanishing logical coherent noise in leading order. Detailed circuit-level simulations of surface code implementations show more than an order of magnitude reduction in logical error relative to previous estimates. As a concrete target application, we focus on the Fermi-Hubbard model with periodic boundaries, for which we design a simulation circuit particularly suited to early implementations. We quantify the resource tradeoff of partially and fully FT approaches to gate synthesis, with the former showing approximately an order of magnitude reduction in state-injection depth, and an even larger reduction in Clifford resources. Comparing with classical and fully FT approaches, we identify regimes where partial fault tolerance provides both lower overheads and lower error rates. In our estimates, this is accessible with moderate error rates p∼10−3p\sim 10^{-3}p∼10−3 and a few thousand qubits, underlining that for these types of problems, partial FT approaches provide a compelling pathway to early quantum advantage.
Partially fault-tolerant quantum computing (FTQC) has recently emerged as a promising approach for the execution of megaquop-scale circuits with millions of logical operations. In this work, we demonstrate the strengths and the limitations of this approach by conducting quantum resource estimation (QRE) of the space--time-efficient analog rotation (STAR) architecture using realistic hardware specifications for superconducting processors, and compare it against the QRE of the full FTQC architecture. We show how the performance of the STAR architecture's protocols is affected by hardware improvements. We also reduce the space requirements for partial FTQC by developing a procedure leveraging code growth to decrease the size of a factory producing analog rotation states. Our results reveal a non-trivial dependence of the optimal pre-growth code distance on the rotation angle with respect to post-growth infidelity. Further, we analyze space--time trade-offs between the factory size and the error-mitigation overhead, and observe that in an application-agnostic setting, there is a Goldilocks zone for circuits in the regime of roughly 10510^5105--10610^6106 small-angle rotation gates. We show that quantum simulation of 2D Fermi--Hubbard model systems is a particularly well-suited application for the STAR architecture, requiring only hundreds of thousands of physical qubits and runtimes on the order of minutes for modest system sizes. Due to its favourable algorithmic scaling to larger system sizes, utility-scale simulation of the 2D Fermi--Hubbard model could potentially be attained using partial FTQC.
Quantum computing experiments have made remarkable progress in demonstrating key components of error-corrected quantum computing, a prerequisite for scalable quantum computation. While we anticipate the near-term arrival of early fault-tolerant quantum hardware capable of a million reliable quantum operations, the cost of preparing low-noise “magic resource states,” which are necessary for performing universal quantum computation, presents a formidable challenge. The recently proposed partially fault-tolerant architecture based on a space-time efficient analog rotation (STAR) approach attempts to address this challenge by using postselection to prepare low-noise, arbitrary small-angle magic states. Its proposed physical implementation, however, assumes fixed qubit connectivity, resulting in implementation costs closer to leading fully fault-tolerant approaches. In this work, we propose the transversal STAR architecture and co-design it with neutral-atom quantum hardware, deriving explicit and significant savings in logical layout, time, and space overhead. Through detailed circuit-level simulations, we derive the logical noise model for surface-code-based transversal STAR gadgets and verify their composability. At its limit, the transversal STAR architecture with neutral atoms can efficiently simulate local Hamiltonians with a total simulation volume exceeding 600, defined as the product of the number of logical qubits and Hamiltonian evolution timescales. Achieving this limit would require approximately 10 000 physical qubits at a physical error rate of 10 − 3 . This is equivalent to a fully fault-tolerant computation requiring over 10 6 – 10 7 T gates and a potential > 100 × saving on space-time volume for equivalent simulation over current, state-of-the-art protocols. Finally, we extend the transversal STAR architecture to high-rate quantum low-density parity-check codes, demonstrating how a limited set of highly parallel transversal Clifford gates and generalized small-angle magic injection can be utilized for effective quantum simulation. We anticipate that the co-designed transversal STAR architecture could substantially reduce the physical resources necessary for early fault-tolerant quantum simulation at the megaquop scale.
Recent advancements in neutral atom platforms have enabled exploration of early fault-tolerant (FT) architectures for applications with quantum advantage, such as quantum dynamics simulations. An efficient fault-tolerant architecture has both spatially efficient quantum error correction codes (low qubit overhead), and efficient methodologies (transversal based gates, extractor based gates, etc.) for logical computation, to minimize overall execution time. Achieving the right balance between space and time can be critical for enabling early FT demonstrations of quantum advantage. In this work, we identify bottlenecks in existing spatially efficient schemes, which tend to be very serial, and do not take advantage of unutilized space. We introduce a teleportation-based scheme that leverages the reconfigurable connectivity of neutral atoms to parallelize logical operations. Our approach achieves up to \textbf{∼3×\mathbf{\sim 3 \times}∼3× speedup} over extractor architectures at no extra space cost and achieves the best spacetime performance among other viable architectures before accounting for external \textit{resource-states}. To rigorously evaluate performance, we construct explicit quantum advantage benchmarks and \textit{simulate} compilation to a fault-tolerant instruction set, including low-level gate scheduling and shuttling patterns, and resource-state nondeterminism. We find that our speedups still apply and report exact space-time cost along with success probabilities, identifying architectures capable of achieving quantum advantage \textbf{with as little as 11,495\mathbf{11,495}11,495 atoms and a runtime of ∼15\mathbf{\sim 15}∼15 hours}.
Fault-tolerant quantum simulation is approaching a phase where encoding overhead, logical Clifford operations, magic-state preparation, and rotation synthesis must be optimized together for efficient implementation. Space-Time efficient Analog Rotation (STAR) architectures reduce two of these costs by preparing small-angle rotation magic states directly, and the transversal STAR variant further lowers the Clifford overhead. Existing concrete implementations, however, largely inherit the low O(1/d2)O(1/d^2)O(1/d2) encoding rate of the surface code, while high-rate codes have not yet been integrated into comparably explicit architectures. Here, we introduce a high-rate STAR architecture for local lattice Hamiltonian simulation based on a symmetry-driven co-design of the algorithm, QEC code, and neutral-atom hardware. Translation symmetries of the target lattice determine the choice of bicycle chain codes, a tunable family of self-dual bivariate bicycle codes that natively implement Clifford gates required for lattice simulation. Disjoint logical representatives allow STAR injections to be performed in parallel on all kkk logical qubits in a code block, amortizing resource state preparation and enabling practical post-selection rates. On neutral-atom platform, the same translation symmetry compiles the key logical operations into low-depth, hardware-native acousto-optic-deflector shifts. End-to-end estimates show that an 8×88 \times 88×8 transverse-field Ising simulation to T∗≈8(zJ)−1T^* \approx 8 (zJ)^{-1}T∗≈8(zJ)−1 requires 224022402240 physical qubits and ∼200\sim 200∼200 s per shot, a ∼5.5×\sim 5.5\times∼5.5× space reduction relative to a surface code STAR baseline at comparable speed; for Fermi-Hubbard dynamics to T∗≈4(zt)−1T^* \approx 4 (zt)^{-1}T∗≈4(zt)−1, the corresponding estimates are ∼6300\sim 6300∼6300 physical qubits and ∼200\sim 200∼200 s per shot. These results provide a concrete route toward early fault-tolerant quantum simulation with high-rate codes.
Neutral-atom arrays are a leading qubit technology for large-scale, fault-tolerant quantum computing (FTQC). A dominant error source on this platform is qubit loss, which accrues with every operation and movement. The presence of loss undermines the promises of existing architectural work. Standard error correction targets stochastic Pauli errors and cannot correct loss, so most FTQC performance analyses are not directly compatible with it. Moreover, compilation and routing decisions, which strongly affect overall loss, are typically optimized against Pauli-error cost models and often remain loss-agnostic, potentially increasing exposure to the loss channel. In this work, we comprehensively model the effect of qubit loss on neutral-atom FTQC and develop a loss-tolerant transversal-gate architecture. We treat loss not as a predetermined error parameter but as a dynamic budget spent across a whole program, allowing us to control it by co-designing layout, compilation, and decoding. We target a physical implementation with no separate storage and entangling zones, eliminating the repeated SLM-AOD handoffs and long-distance shuttling that dominate loss in other layouts. We develop compiler optimizations that maximize gate parallelism while respecting the RF tone budget and AOD bandwidth constraints. Our work couples these with a loss-aware, delayed-erasure decoder and an end-to-end loss-aware magic state cultivation protocol. Overall, we improve accumulated loss per syndrome-extraction round by up to 2.15X against a zoned baseline and reduce logical error rates by over two orders of magnitude versus current architectures. Our framework also informs concrete device targets such as continuous reloading rates, AOD counts, and shuttling trajectory choices. We expect these insights to matter for system architects as neutral-atom hardware scales.
Resource estimation is a significant challenge in evaluating fault tolerant quantum computers. Existing approaches often rely on either fixed architectural assumptions or coarse analytical models that fail to capture the interaction between hardware constraints and circuit compilation. This challenge is particularly acute for neutral atom quantum computers, where architectural features such as atom movement, measurement zones, and multi-species arrays introduce a broad design space for implementing fault tolerant computation. Addressing the need for a tighter feedback loop between hardware design and practical application development, we present a compilation-driven framework for quantum resource estimation that translates arbitrary quantum circuits into logical primitive operations with known physical resource costs. This framework allows for easily configurable hardware assumptions that enable rapid comparison of different architectural design choices. We apply our approach to two early fault tolerant quantum simulation and optimization workloads, assuming the use of the surface code, revealing several architectural trends. While the production of magic states continues to be the dominant source of overhead for these benchmarks, access to movement can save time on cultivation and important transversal gates. As problem size grows, routing and qubit movement become dominant bottlenecks, highlighting the need for movement-aware compiler optimizations and frugal routing strategies. Finally, our results suggest that neutral atom architectures combining dual-species arrays with controlled qubit movement offer a promising path toward near-term advantage on fault tolerant devices.