Coarse‐graining kinetic networks in photosynthetic energy transport

Abstract

AbstractPhotosynthetic systems utilize hundreds of chlorophylls to collect sunlight and transport the energy to the reaction center with remarkably high quantum efficiency, however, the large size of the system together with the complex interactions among the components make it extremely challenging to understand the dynamics of light harvesting in large photosynthetic systems. To shed light on this problem, we present a structure‐based theoretical framework that can be used to calculate transition rate matrix describing energy transport in photosynthetic systems and network clustering methods that provide simplified coarse‐grained model revealing key structures guiding the light harvesting process. We constructed an effective model for energy transport in a Photosystem II supercomplex and applied several network clustering methods to generate coarse‐grained kinetic cluster models for the system. Furthermore, we evaluated the performances of the network clustering methods, and show that a spectral clustering method and a minimum cut approach produce accurate coarse‐grained models for the PSII‐sc system. The results indicate that finding bottlenecks of energy transport is a crucial factor for reduced representations of photosynthetic light harvesting, and the overall work presented in this paper should provide a comprehensive theoretical framework to elucidate the dynamics of light harvesting in photosynthetic systems.