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Photosynthetic organisms utilize sophisticated pigment-protein complexes(PPCs)to achieve remarkable near-unity quantum efficiency in the light reactions of photosynthesis.Motivated by recent experimental and theoretical investigations into excitation energy transfer(EET)in photosynthetic systems,we apply molecular dynamics(MD)simulations to study chromophore-protein interactions in chlorophyll-binding PPCs.We demonstrate that a semi-classical charge-density coupling model combined with a time-windowing algorithm allow us to probe protein-modulated electronic fluctuations based on a MD trajectory,giving spectral-density functions that are in reasonable agreement with experimental spectrum.The results also show that diagonal fluctuations in excitation energies play a major role in EET,while off-diagonal fluctuations in excitonic couplings are too small to be consequential.In addition,we have developed a coherent modified-Redfield theory(CMRT)for spectroscopy and EET dynamics of photosynthetic systems.Combined with spectral densities obtained from MD simulations,the CMRT method has been applied to simulate coherent excitation energy transfer processes in model photosynthetic light-harvesting complexes,and the dynamics predicted by the new method are in reasonable agreement with experiments.More importantly,the results allowed us to identify several key elements that play important roles in the speedup of energy trapping in photosynthesis.In summary,we have developed an effective approach that combines quantum chemical calculations,MD simulations,and the CMRT method for describing spectra and coherent energy transfer dynamics in PPCs.This framework should be applicable to general organic molecular aggregates and useful for the design of efficient light-harvesting materials.