  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.
