Towards Understanding Underlying Principles for Efficient Energy Transport in Biological Complexes

Abstract

Light harvesting complexes are a type of biological complex found in photosynthetic bacteria and plants. They perform a critical role in the photosynthetic pathway – transporting energy absorbed from sunlight to the reaction centre – and do so with exceptional efficiency. Understanding the root of this however has proved difficult due to the large size and the complexity of the systems. The wide structural variability of these complexes further complicates matters, raising the question of optimality of the complexes: is the exceptional efficiency by chance or design? This work aims to aid the description of the underlying principles of energy transport in these complexes and move towards answering the question of chance versus design. A force matching method to develop molecular mechanics forcefields for use in studies combining molecular dynamics with higher level methods (a strategy regularly employed in biophysical research) is outlined. This method reduces errors resulting from the methodology and lessens computational demand of developing forcefields, making the study of multiple complexes more feasible. Resulting forcefields lead to notable differences in subsequent spectral density computations. Structure-function relationships and the role of environment is investigated by examining spectral densities of rigid chromophores of several complexes with different functions. Analysis of the results reveals the environment to be unspecific in regard to function. Examining the exciton dynamics of several light harvesting complexes may uncover important characteristics of light harvesting. In order to study this the excitonic Hamiltonian of several complexes is computed and their dynamics propagated using a Lindblad master equation. The results indicate the protein likely plays little role in exciton dynamics with the most influential component being the solvent. The exciton dynamics are found to be determined solely by the static disorder of the system and the results suggest relative arrangement of LHCs is more important for efficiency than internal arrangement of chromophores.