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School of Biological and Behavioural Sciences

The contradictory functions of carotenoid-based light-harvesters: Understanding energy harvesting and dissipation in the Fucoxanthin-Chlorophyll Protein (FCP)

Supervisor: Dr Christopher Duffy

Research environment

The School of Biological and Chemical Sciences at Queen Mary is one of the UK’s elite research centres, according to the 2014 Research Excellence Framework (REF). We offer a multi-disciplinary research environment and have approximately 160 PhD students working on projects in the biological, chemical and psychological sciences. Our students have access to a variety of research facilities supported by experienced staff, as well as a range of student support services. 

Training and development

Our PhD students become part of Queen Mary’s Doctoral College which provides training and development opportunities, advice on funding, and financial support for research. Our students also have access to a Researcher Development Programme designed to help recognise and develop key skills and attributes needed to effectively manage research, and to prepare and plan for the next stages of their career. 

Dr C Duffy is a theoretical biophysicist/biochemist interested in photosynthetic light-harvesting and the photo-physics of carotenoids. With his supervision the student will simulate the structural dynamics of FCP, relate these dynamics to inter-pigment interactions via quantum chemistry, and model energy relaxation and spectral evolution using the theory of quantum dissipative dynamics. Dr Duffy has research connections throughout Europe and is part of a network of photosynthesis researchers based in London. The student will be encouraged to work extensively within these networks. 

Project details

Carotenoids in photosynthetic light-harvesting proteins can both harvest light energy and act as a protective barrier depending on light intensity. This is an emergent behavior where the same pigment can perform both functions depending on a complex network of interactions with other pigments. The FCP photosynthetic algae is a heavily experimentally-probed example but so far there is no general model of this dual behavior. In this project, using theoretical physics, quantum chemistry and biomolecular simulation, we will develop a general theory of how a single protein can be both an ultra-efficient solar panel and an effective sun-screen. 

As light-harvesters carotenoids absorb in the green and transfer this energy to neighbouring chlorophylls. In high light they perform the opposite function, pulling energy from chlorophyll and dumping it safely into the environment as heat (quenching). The latter is the natural behaviour of isolated carotenoids so the light-harvesting behaviour must be an emergent property of large chlorophyll-carotenoid networks. 

In Diatom algae the Fucoxanthin Chlorophyll a/c Protein (FCP) is the major light-harvesting antenna of Photosystem II. It is unusual amongst antenna proteins as its primary pigment is a carotenoid (fucoxanthin). Fucoxanthin transfers absorbed light energy chlorophyll-a with near 100% efficiency, mainly via its short-lived, optically-dark low-lying excited states. How this efficiency is achieved is not completely understood. However, in high light FCP switched to a protective state in which a second carotenoids Diadionxanthin or Diatoxanthin captures and dissipates energy via the same dark state. How two structurally similar pigments carry out opposite functions and how the protein switches between these two states are not well-understood. 

In this project we will:- 
(1) Predict the harvesting and protective structures of FCP. 
(2) Map the network of chlorophyll-carotenoid interactions in each structure. 
(3) Model the emergent energy transfer dynamics within these states. 
(4) Explain the microscopic origin of efficient light-harvesting, effective quenching, and all spectroscopic signatures. 
(5) Develop a set of design rules for light-harvesting, photoprotective, and dual (switching) carotenoid devices. 


This project is open to applicants who have obtained or intend to apply for external funding. Please see our fees and funding page for examples.

Eligibility and applying

Applications are invited from outstanding candidates with or expecting to receive a first or upper-second class honours degree or masters degree in an area relevant to the project, such a Theoretical Physics, Applied Mathematics of Chemistry (with a strong emphasis on quantum and physical chemistry). 

Applicants from outside of the UK are required to provide evidence of their English language ability. Please see our English language requirements page for details.

Interested candidates are invited to contact Dr Duffy at For further information, please see our application process page

The School of Biological and Chemical Sciences is committed to promoting diversity in science; we have been awarded an Athena Swan Bronze Award. We positively welcome applications from underrepresented groups. 


  • V. Balevičius Jr. et al (2018) Fine control of chlorophyll-carotenoid interactions defines the functionality of light-harvesting proteins in plants. Scientific reports, 7, 13956 
  • V Balevičius Jr. et al. (2019) The full dynamics of energy relaxation in large organic molecules: from photo-excitation to solvent heating Chemical Science 10, 4792-4804 
  • W. Wang et al. (2019) Structural basis for blue-green light harvesting and energy dissipation in diatoms. Science 363, eaav0365, DOI: 10.1126/science.aav0365
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