{
  "annotation_id": "4b20e124-eeee-4881-8bcb-d2205f51e773",
  "date_created": "2026-03-02T18:02:31.098000Z",
  "date_modified": "2026-03-02T18:02:31.098000Z",
  "file_hash": "b37612d0e7d626a625864b06483a1cf7034e736470b55359ba2f095661fc9167",
  "private": false,
  "record": {
    "abstract": "We consider continuum dielectric models as minimal models to understand the\neffect of a surrounding globular protein and solvent on the quantum dynamics of\nelectronic excitations in a biological chromophore. We derive expressions for\nthe frequency dependent spectral density which describes the coupling of the\nelectronic levels in the chromophore to its environment. The magnitude and\nfrequency dependence of the spectral density determines whether or not the\nquantum dynamics is coherent or incoherent, and thus whether on not one can\nobserve quantum interference effects such as Rabi oscillations. We find the\ncontributions to the spectral density from each component of the chromophore\nenvironment: the bulk solvent, protein, and water bound to the protein. The\nrelative importance of each component to the quantum dynamics of the\nchromophore is determined by the dynamics\u0027 time scale. Our results provide a\nnatural explanation and model for the different time scales observed in the\nspectral density extracted from the solvation dynamics probed by ultra-fast\nlaser spectroscopy techniques such as the dynamic Stokes shift and three pulse\nphoton echo spectroscopy. Our results are used to define under what conditions\nthe dynamics of the excited chromophore is dominated by the surrounding protein\nand when it is dominated by dielectric fluctuations in the solvent. We show\nthat even when the chromophore is shielded from the solvent by the protein\nultra-fast solvation can be dominated by the solvent. We suggest that the\nultra-fast solvation recently seen in some biological chromophores should not\nnecessarily be assigned to ultra-fast protein dynamics. Spectral densities\nestimated from our continuum models and extracted from experiment suggest that\nmost quantum dynamics of electronic excitations is incoherent.",
    "arxiv_id": "quant-ph/0609075",
    "authors": [
      "Joel Gilmore",
      "Ross H. McKenzie"
    ],
    "categories": [
      "quant-ph",
      "cond-mat.soft"
    ],
    "title": "Quantum dynamics of electronic excitations in biomolecular chromophores:   role of the protein environment and solvent",
    "url": "https://arxiv.org/abs/quant-ph/0609075"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "969dfa9c-3575-4e61-a080-8c1bb0d66380",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}