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Photosynthetic Light Harvesting: Computational approaches to studying the relationship between light-harvesting, photochemistry, photo-damage, and repair

  • Supervisor: Dr Christopher Duffy
  • Funding: open to external funding sources
  • Deadline: external funding deadlines apply

Project description

Background: The primary events of photosynthesis are the absorption of light energy by the photosynthetic antenna complexes and delivery of this excitation energy to the reaction centres where it is used to drive photochemistry and ultimately carbon fixation. The harvesting of light by plants is not only far more efficient than any artificial system but remarkably flexible in the face of light environment that changes rapidly and strongly.

Plant light-harvesting is regulated by a process known as non-photochemical quenching (NPQ), in which photo-damage to the photosystem II (PSII) reaction centres (RCs) is limited by the light-induced formation of energy-dissipating traps in the antenna [1, 2]. However, the nature of these traps, their precise location within the PSII supercomplex and their mechanism, of formation are still matters of debate. Recently, my group published the first complete theoretical model of the major PSII light-harvesting complex LHCII. Based on this model we have proposed that NPQ involves the slow capture of excitation energy by the carotenoid lutein, followed by rapid non-radiative decay of the excitation [3, 4].

Aims: This project will extend this theoretical approach beyond isolated light-harvesting complexes to PSII as a complete system. The aim to establish the fundamental theoretical foundations of the interplay between light-harvesting, photosynthesis, photo-damage, repair and NPQ. Recent work has revealed new features (without offering any insight into the details of the mechanism)

1. NPQ is economic. The kinetics of NPQ are (counter intuitively) slow, offering protection without impeding photosynthetic function [5].
2. NPQ is related to PSII repair. In addition to offering defence against damage, NPQ promotes repair of damaged PSII RCs.
3. NPQ is general and robust. No single component of PSII appears to be the site of NPQ. NPQ seems to be a general feature of systems containing carotenoids.

Approach: Current models of light harvesting are based on the stochastic Master Equation approach2. These models are highly abstract (based on the diffusion of occupation probability) and non-visual, are based on arbitrary parameters rather than structural and physical insight, and cannot account for dynamic processes such as a natural, varying light environment, the finite rate of photochemistry in the RCs, and the cycle of photo-damage and repair. In this project we will Continuous Time Random Walk approach (CTRW). While yielding all of the experimental/statistical parameters (fluorescence lifetime, quantum yield, O2 evolution, electron transport rate, etc.) given by the Master Equation approach (via ensemble calculations), CTRW is a closer representation of the actual dynamics of light-harvesting in a dynamic system. The effects of real processes such as photochemistry and the damage/repair cycle can be probed and conditions (light intensity, connectivity between protein sub-units, etc.) can be altered during the simulation. The most striking advantage is that results of these calculations can be rendered graphically, yielding physically meaningful movies of light-harvesting in the chloroplast membrane. Ultimately, we aim to release a quantitative computational application that will aid experimentalists in understanding the molecular basis of light harvesting phenomena.

Impact: This project aims as establishing the molecular mechanisms of photosynthetic light-harvesting, photosynthesis, photo-damage, repair and regulation, a goal that the purely experimental approach has consistently failed to achieve. Additionally, the project will result in visual but quantitative computational tools for the study of the factors determining kinetics of natural solar energy collection. The mathematical and computational framework is entirely general to biological diffusion processes and a long term goal is the production of a suite of bio-computational tools for studying diffusive processes in molecular biology.

Funding notes

Project is open to students seeking external funding through various funding schemes.


[1] Duffy CD, Ruban AV (2015) Dissipative pathways in the photosystem-II antenna in plants. J Photochem Photobiol B 152, 215-226.
[2] Duffy CD, Valkunas L, Ruban AV (2013) Light-harvesting processes in the dynamic photosynthetic antenna.Phys Chem Chem Phys. 15, 18752-18770.
[3] Chmeliov J, Bricker WP, Lo C, Duffy CDP (2015) An ‘all pigment’ model of excitation quenching in LHCII.Phys. Chem. Chem. Phys. 17, 15857-15867.
[4] Duffy CD, Chmeliov J, Macernis M et al. (2013) Modelling of fluorescence quenching by lutein in the plant light-harvesting complex LHCII.J Phys Chem B 117, 10974-10986.
[5] Belgio E, Kapitonova E, Chmeliov J et al. (2014) Economic photoprotection in photosystem II that retains a complete light-harvesting system with slow energy traps. Nat. Commun. 5, 10.1038/ncomms5433.

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