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We model the energy transfer and trapping kinetics in PSI. Rather than simply applying Förster theory, we develop a new approach to self-consistently describe energy transfer in a complex with heterogeneous couplings. Experimentally determined spectral densities are employed to calculate the energy transfer rates. The absorption spectrum and fluorescence decay time components of the complex at room temperature were reasonably reproduced. The roles of the special chlorophylls (red, linker, and reaction center, respectively) molecules are discussed. A formally exact expression for the trapping time is derived in terms of the intrinsic trapping time, mean first passage time to trap, and detrapping time. The energy transfer mechanism is discussed and the slowest steps of the arrival at the primary electron donor are found to contain two dominant steps: transfer-to-reaction-center, and transfer-to-trap-from-reaction-center. The intrinsic charge transfer time is estimated to be 0.8 approximately 1.7 ps. The optimality with respect to the trapping time of the calculated transition energies and the orientation of Chls is discussed.

We introduce a sparse-matrix algorithm that allows for the simulation of two-dimensional infrared (2DIR) spectra in systems with many coupled chromophores. We apply the method to bulk water, and our results are based on the recently developed ab initio maps for the vibrational Hamiltonian. Qualitative agreement between theory and experiment is found for the 2DIR spectra without the use of any fitting or scaling parameters in the Hamiltonian. The calculated spectra for bulk water are not so different from those for HOD in D(2)O, which we can understand by considering the spectral diffusion time-correlation functions in both cases. We also calculate the ultrafast anisotropy decay, which is dominated by population transfer, finding very good agreement with experiment. Finally, we determine the vibrational excitation diffusion rate, which is more than two orders of magnitude faster than the diffusion of the water molecules themselves.

We calculate theoretical IR and Raman line shapes for the OH stretch region of liquid water, using mixed quantum/classical and electronic-structure/molecular-dynamics methods. Our approach improves upon the time-averaging approximation used earlier for the same problem, and our results are in excellent agreement with experiment. Previous analysis of theoretical results for this problem considered the extent of delocalization (over local OH stretch excitations) of the instantaneous vibrational eigenstates. In this work we present a complementary analysis in the time-domain, by decomposing the appropriate response functions into diagonal and off-diagonal contributions (in the local mode basis). Our analysis indicates that all vibrational spectra show signatures of coherent vibrational energy transfer. This is manifest in different (IR, isotropic and depolarized Raman) experiments to different extents, because of the competition between coherent energy transfer and rotational disorder.