  Recent experimental achievements have demonstrated the potential of neutral
atom architectures for fault-tolerant quantum computing. These architectures
feature the dynamic rearrangement of atoms during computation, enabling nearly
arbitrary two-dimensional rearrangements. Additionally, they employ a zoned
layout with dedicated regions for entangling, storage, and readout. This
architecture requires design automation software that efficiently compiles
quantum circuits to this hardware and takes care that atoms are in the right
place at the right time. In this paper, we initiate this line of work by
providing, (1) an abstract model of the novel architecture and, (2) an
efficient solution to the routing problem of entangling gates. By this, we aim
to maximize the parallelism of entangling gates and minimize the overhead
caused by the routing of atoms between zones. In addition to that, we keep the
realm of fault-tolerant quantum computing in mind and consider logical qubit
arrays, each of which encodes one logical qubit. We implemented the proposed
idea as a tool called NALAC and demonstrated its effectiveness and efficiency
by showing that it can significantly reduce the routing overhead of logical
entangling gates compared to the naive approach. As part of the Munich Quantum
Toolkit (MQT), NALAC is publicly available as open-source at
https://github.com/cda-tum/mqt-qmap.
