Abstract

Photosynthesis, the fundamental process converting light energy into chemical energy, is intrinsically linked to the integrity and function of the thylakoid membrane within the chloroplast. This study aims to develop a comprehensive mathematical model to simulate the dynamic interplay between light-harvesting, electron transport, and the resulting proton gradient across the thylakoid membrane. The model integrates key cellular components, including the photosystems (PSII and PSI), the cytochrome b6f complex, and the ATP synthase, focusing on the biophysical constraints imposed by membrane structure and ion transport kinetics. Methods involved a system of coupled ordinary differential equations (ODEs) to describe the flow of electrons and protons, with parameters calibrated against experimental data on chlorophyll fluorescence and P700 oxidation. Key findings reveal that the efficiency of the proton motive force generation, a process highly dependent on thylakoid membrane permeability and ultrastructure, is a critical bottleneck determining overall photosynthetic rate. Furthermore, the model accurately predicts the impact of environmental stressors, such as varying light intensity, on the regulation of non-photochemical quenching (NPQ) mechanisms, which are crucial for protecting the delicate membrane machinery. The analysis provides a quantitative framework for understanding how cellular-level membrane dynamics scale up to influence whole-plant productivity, offering valuable insights for optimizing crop yield and engineering more efficient photosynthetic systems.