Technological advances in neutral-atom platforms have opened a new path toward designing efficient protocols for fault-tolerant quantum computing (FTQC). However, each physical operation is still orders of magnitude slower than on other platforms, such as superconducting qubits. Therefore, architects must identify fast and efficient FTQC architectures, which require reliable modeling tools to explore various design choices across the software, classical hardware, and quantum device stacks of neutral-atom platforms. In this paper, we propose NAQsim, an open-source simulation framework for neutral-atom FTQC architectures based on transversal gates. As its key feature, NAQsim enables detailed full-stack architecture evaluation that opens opportunities to explore previously overlooked performance bottlenecks. As a first use case for NAQsim, we identify one such bottleneck, patch rotations, perform full-stack co-optimization, and finally derive a near-rotation-free architecture (D3-ROT). For practical FTQC benchmark workloads, D3-ROT achieves a 2.27x speedup from this single bottleneck alone, with minimal footprint overhead. These results point to a much broader space of full-stack optimizations that NAQsim makes accessible for transversal surface-code architectures and beyond.

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