Abstract
<jats:p> Exciton-exciton annihilation (EEA) is a process by which two excitons combine to form a single high energy excitation. In molecular chromophore aggregates EEA is governed by microscopic two-exciton coherence that depends on long-range coupling and supramolecular geometry, motivating scalable quantum mechanical rate calculations beyond deterministic small-system diagonalization. Here, we develop a Fast Fourier Transform (FFT)-accelerated stochastic method for computing finite temperature EEA rates in large 2D excitonic molecular aggregates. We demonstrated agreement with conventional deterministic matrix diagonalization for small and intermediate systems, while improving the scaling <jats:italic toggle="yes"> O(N <jats:sup>2</jats:sup> logN) </jats:italic> from <jats:italic toggle="yes"> O(N <jats:sup>6</jats:sup> ) </jats:italic> cost. This approach enables large-scale parameter sweeps and structure–function screening in realistic 2D morphologies. We close by exploring the role of uncorrelated and correlated disorder, temperature and inter-exciton coupling in EEA. </jats:p>