UC Berkeley

This dissertation focuses on understanding the ultrafast dynamics in photosystem II (PSII) and connecting the PSII dynamics with its functions to reveal its design principles. Specifically, we begin the study with the smallest subunit of PSII and gradually increase the size to the C2S2M2-type PSII supercomplex (PSII-SC). In Chapter 1, we discuss photosynthetic light-harvesting and how energy conversion efficiency needs to be balanced with photoprotection. We also briefly discuss the implications the structure of the PSII-SC has on the ultrafast dynamics and the experimental and theoretical methods—two-dimensional electronic-vibrational (2DEV) spectroscopy and energy transfer theories—used to study the ultrafast dynamics. In Chapter 2, we apply 2DEV spectroscopy on the smallest functional units of the PSII, the PSII reaction center and the PSII core complex. The improved resolution afforded by 2DEV spectroscopy allows detailed charge separation dynamics in the PSII reaction center to be revealed. The application of 2DEV spectroscopy on the PSII core complex shows how energy is transferred from the core antennae to the reaction center. In Chapter 3, we use both 2DEV spectroscopy and structure-based modeling to understand how energy flows in the C2S2-type PSII-SC. We show that energy can initially flow in both directions between the PSII core and the peripheral antenna system, which allows the PSII-SC to achieve a balance between efficient energy conversion and photoprotection. In Chapter 4, we extend the structure-based model to the C2S2M2-type PSII-SC and combine the model with kinetic Monte Carlo simulations. We perform first passage time and dwell time analyses on “computational mutants” to understand the functional roles of the subunits in the PSII-SC. We also construct a free energy landscape for the PSII-SC which allows us to discuss the mechanism of its kinetic network. The analyses allow us to connect the microscopic energy transfer dynamics in the PSII-SC to its macroscopic function. In the final chapter, we propose higher-order experiments and single-trajectory simulations to understand ultrafast dynamics in light-harvesting involved in different scales. We also propose methods to quantify entropy involved in the energy transfer dynamics, which is potentially a mechanism that facilitates the control of energy flow for balancing efficiency and photoprotection in the PSII-SC.