{
  "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 $523.90~\\mathrm{nm}$, in good agreement with the experimental absorption maximum near $515~\\mathrm{nm}$ 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 $1~\\mathrm{ns}$ of room-temperature dynamics. We obtain a thermally averaged coupling of $J = 32.8 \\pm 1.6~\\mathrm{cm^{-1}}$ across the $1000$-frame trajectory (Davydov splitting $2|J| = 65.6 \\pm 3.1~\\mathrm{cm^{-1}}$), representing a $19\\%$ near-field enhancement over the ensemble point-dipole estimate ($J_{\\mathrm{PDA}} = 27.6 \\pm 1.3~\\mathrm{cm^{-1}}$) at the $24.69 \\pm 0.32~\\textÅ$ 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.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "Journal reference: Journal of Physical Chemistry B (2026)",
  "arxiv": "2605.00027",
  "author_total": 4,
  "authors": [
    {
      "name": "Robson Christie"
    },
    {
      "name": "Cerys Murray"
    },
    {
      "name": "Youngchan Kim"
    },
    {
      "name": "Jaewoo Joo"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3adbsvpe4w9x5.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2605.00027",
  "fulltext_url": null,
  "id": "3adbsvpe4w9x5",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2605.00027",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "physics.bio-ph"
    ],
    [
      "arxiv",
      "physics.chem-ph"
    ],
    [
      "arxiv",
      "quant-ph"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://arxiv.org/pdf/2605.00027",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-24",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3adbsvpe4w9x5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:11Z",
      "native_id": "2605.00027",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2605.00027"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "arxiv:physics.chem-ph",
      "subfield": "physical"
    },
    {
      "field": "physics",
      "origin": "arxiv:physics.bio-ph",
      "subfield": "biological-medical"
    },
    {
      "field": "physics",
      "origin": "arxiv:quant-ph",
      "subfield": "quantum"
    }
  ],
  "title": "Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers",
  "title_text": "Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:11Z",
  "url": "https://research.draconitic.com/paper/3adbsvpe4w9x5",
  "venue": "arXiv",
  "versions": [
    {
      "doi": "10.1021/acs.jpcb.6c05048",
      "pid": null,
      "relation": "published-as",
      "title": null,
      "venue": null
    }
  ]
}