Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers
Abstract
We quantify the excitonic coupling in the homodimer of the dimeric Venus fluorescent protein using a quantum-classical hybrid workflow. Because the anionic chromophore carries appreciable double-excitation character, we obtain its site energy from domain-based local-pair-natural-orbital similarity-transformed equation-of-motion coupled-cluster theory (DLPNO-STEOM-CCSD), which places the in-protein bright ππ* state at 523.90 nm, in good agreement with the experimental absorption maximum near 515 nm and validated against an explicit triples-corrected EOM-CCSD(fT) benchmark; single-excitation time-dependent density functional theory (TDDFT) blueshifts this state. Applying a transition-density coupling (TDC) formalism to the STEOM transition density and simulating the VenusA206 tandem-dimer construct (two β-barrels covalently joined by an inter-domain linker), the covalent tether holds the A206 interface docked throughout 1 ns of room-temperature dynamics. We obtain a thermally averaged coupling of J = 32.8 ± 1.6 cm−1 across the $1000$-frame trajectory (Davydov splitting 2|J| = 65.6 ± 3.1 cm−1), representing a 19% near-field enhancement over the ensemble point-dipole estimate (JPDA = 27.6 ± 1.3 cm−1) at the 24.69 ± 0.32 Å chromophore centroid separation. Furthermore, we argue that a separation of timescales resolves the apparent theoretical tension between intermediate experimental excitonic couplings and the highly decoherent biological environment. While it has been hypothesised that the fluorescent protein β-barrel scaffold sustains coupling by shielding the chromophore from thermal fluctuations, we emphasise that the separation of timescales applies irrespective of the exact degree of environmental decoherence and dissipation.
Versions
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BibTeX
@misc{christie2026nonequilibrium,
title = {{Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers}},
author = {Robson Christie and Cerys Murray and Youngchan Kim and Jaewoo Joo},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2605.00027},
eprint = {2605.00027},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2605.00027},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers
AU - Robson Christie
AU - Cerys Murray
AU - Youngchan Kim
AU - Jaewoo Joo
PY - 2026
DA - 2026/09/24
PB - arXiv
DO - 10.48550/arxiv.2605.00027
UR - https://arxiv.org/abs/2605.00027
AB - We quantify the excitonic coupling in the homodimer of the dimeric Venus fluorescent protein using a quantum-classical hybrid workflow. Because the anionic chromophore carries appreciable double-excitation character, we obtain its site energy from domain-based local-pair-natural-orbital similarity-transformed equation-of-motion coupled-cluster theory (DLPNO-STEOM-CCSD), which places the in-protein bright ππ^* state at 523.90 nm, in good agreement with the experimental absorption maximum near 515 nm and validated against an explicit triples-corrected EOM-CCSD(fT) benchmark; single-excitation time-dependent density functional theory (TDDFT) blueshifts this state. Applying a transition-density coupling (TDC) formalism to the STEOM transition density and simulating the VenusA206 tandem-dimer construct (two β-barrels covalently joined by an inter-domain linker), the covalent tether holds the A206 interface docked throughout 1 ns of room-temperature dynamics. We obtain a thermally averaged coupling of J = 32.8 ± 1.6 cm^−1 across the $1000$-frame trajectory (Davydov splitting 2|J| = 65.6 ± 3.1 cm^−1), representing a 19% near-field enhancement over the ensemble point-dipole estimate (J_PDA = 27.6 ± 1.3 cm^−1) at the 24.69 ± 0.32 Å chromophore centroid separation. Furthermore, we argue that a separation of timescales resolves the apparent theoretical tension between intermediate experimental excitonic couplings and the highly decoherent biological environment. While it has been hypothesised that the fluorescent protein β-barrel scaffold sustains coupling by shielding the chromophore from thermal fluctuations, we emphasise that the separation of timescales applies irrespective of the exact degree of environmental decoherence and dissipation.
ER -