One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis.

In this work, we study the effects of non-Condon vibronic coupling on the quantum coherence of excitation energy transfer, via the exact dissipaton-equation-of-motion evaluations on excitonic model systems. Field-triggered excitation energy transfer dynamics and two dimensional coherent spectroscopy are simulated for both Condon and non-Condon vibronic couplings. Our results clearly demonstrate that the non-Condon vibronic coupling intensifies the dynamical electronic-vibrational energy transfer and enhances the total system-and-bath quantum coherence. Moreover, the hybrid bath dynamics for non-Condon effects enriches the theoretical calculation, and further sheds light on the interpretation of the experimental nonlinear spectroscopy.

We consider the hybrid system-bath dynamics, based on the Yan's dissipaton formalism [Y. J. Yan, J. Chem. Phys. 140, 054105 (2014)]. This theory provides a unified quasi-particle treatment on three distinct classes of quantum bath, coupled nonperturbatively to arbitrary quantum systems. In this work, to study the entangled system and bath polarization and nonlinear Fano interference, we incorporate further the time-dependent light field, which interacts with both the molecular system and the collective bath dipoles directly. Numerical demonstrations are carried out on a two-level system, with comparison between phonon and exciton baths, in both linear and nonlinear Fano interference regimes.