dorsal/arxiv
View SchemaExcitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study
| Authors | Ana Damjanovic, Ioan Kosztin, Klaus Schulten |
|---|---|
| Categories | |
| ArXiv ID | physics/0107064 |
| URL | https://arxiv.org/abs/physics/0107064 |
| DOI | 10.1103/PhysRevE.65.031919 |
Abstract
The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.
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"abstract": "The dynamics of pigment-pigment and pigment-protein interactions in\nlight-harvesting complexes is studied with a novel approach which combines\nmolecular dynamics (MD) simulations with quantum chemistry (QC) calculations.\nThe MD simulations of an LH-II complex, solvated and embedded in a lipid\nbilayer at physiological conditions (with total system size of 87,055 atoms)\nrevealed a pathway of a water molecule into the B800 binding site, as well as\nincreased dimerization within the B850 BChl ring, as compared to the\ndimerization found for the crystal structure. The fluctuations of pigment (B850\nBChl) excitation energies, as a function of time, were determined via ab initio\nQC calculations based on the geometries that emerged from the MD simulations.\n From the results of these calculations we constructed a time-dependent\nHamiltonian of the B850 exciton system from which we determined the linear\nabsorption spectrum. Finally, a polaron model is introduced to describe quantum\nmechanically both the excitonic and vibrational (phonon) degrees of freedom.\nThe exciton-phonon coupling that enters into the polaron model, and the\ncorresponding phonon spectral function are derived from the MD/QC simulations.\nIt is demonstrated that, in the framework of the polaron model, the absorption\nspectrum of the B850 excitons can be calculated from the autocorrelation\nfunction of the excitation energies of individual BChls, which is readily\navailable from the combined MD/QC simulations. The obtained result is in good\nagreement with the experimentally measured absorption spectrum.",
"arxiv_id": "physics/0107064",
"authors": [
"Ana Damjanovic",
"Ioan Kosztin",
"Klaus Schulten"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph"
],
"doi": "10.1103/PhysRevE.65.031919",
"title": "Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study",
"url": "https://arxiv.org/abs/physics/0107064"
},
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