Excitonic Coupling and Photon Antibunching in Venus Yellow Fluorescent Protein Dimers: A Lindblad Master Equation Approach

Abstract: Strong excitonic coupling and photon antibunching have been observed together in Venus yellow fluorescent protein (YFP) dimers -- a cryptic combination under prevailing theoretical models. In 2019, Kim et al. demonstrated Davydov splitting in Venus dimer circular dichroism (CD) spectra, revealing large negative dimer coupling energy, while antibunching was confirmed by antibunching-fluorescence correlation spectroscopy (AB/FCS fingerprinting). To explain this coexistence, Venus dimer population dynamics are modeled here within a Lindblad master equation framework, justified by the separation of characteristic coupling, dephasing, and thermal relaxation rates. Simulations predict rapid decoherence, consistent with antibunching, indicating that coherence in both the excitonic and site bases is too short-lived to affect photon emission statistics. Despite the absence of long-lived coherence, Venus dimers provide a tractable platform for probing evolutionary pressures on fluorescent protein photophysics and quantum dynamics. Cryogenic cooling could extend coherence lifetimes into the regime required for quantum gate operations, suggesting a route toward fluorescent protein-based qubits. More broadly, the results highlight a structural design principle -- a "bioexciton motif" -- that links excitonic coupling, decoherence, and protein architecture, pointing to general rules by which biology both constrains and inspires quantum technologies.