Digital Chloroplast: Computational models of the organization, phase behaviour and function of the photosynthetic membrane

   School of Biological and Behavioural Sciences

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  Dr Christopher Duffy, Prof Conrad Mullineaux, Dr Guy Hanke  No more applications being accepted  Awaiting Funding Decision/Possible External Funding

About the Project

  • Supervisor: Dr Christopher Duffy, Prof Conrad Mullineaux and Dr Guy Hanke  
  • Funding: China Scholarship Council (CSC)
  • Deadline: 31st January 2024
  • Expected Start Date: Sept 2024

Research environment

The School of Biological and Behavioural Sciences at Queen Mary is one of the UK’s elite research centres, according to the 2021 Research Excellence Framework (REF). We offer a multi-disciplinary research environment and have approximately 180 PhD students working on projects in the biological 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.

The Duffy Lab is a member of the Digital Environment Research Institute (DERI) at Queen Mary. A successful candidate will join an active team of PhD student and Research Associates who apply techniques from theoretical physics, computational biology, and machine learning to uncover the 'rules'of photosynthetic light-harvesting. Current research projects involve algal biotechnology and astrobiology.

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.

In the Duffy Lab a PhD student will receive considerable training in computational modelling of complex systems, biophysics, and data analysis. 

Project description

Photosynthetic (thylakoid) membranes are nature’s solar cell. They must self-organise to perform multiple complex functions simultaneously, from light-harvesting and electron transport to regulation, biogenesis and repair. A grand challenge in biology is comprehending how millions of diverse proteins, lipids and small molecules combine themselves into systems from which complex functions emerge.

Thylakoid membranes not only represent an interesting example of this self-organisation problem but are extremely relevant to solar and algal biotechnology. The aim of the project is to take the first steps in constructing a predictive model of the thylakoid membrane, a ‘digital twin’ that will allow us to probe the fundamental limits of photosynthesis, develop new strategies for optimizing photosynthesis, and design nanodevices that mimic its function.

We know that the densely-packed protein landscape of the thylakoid membrane is constantly reconfigured according to environmental cues. The balance between order and fluidity must be crucial for the multiple functions of the membrane, but we have little insight into the way that the self-organisation maintains this balance. “Non-Photochemical Quenching’ (NPQ) is a relatively well-understood mechanism in plant thylakoids which switches the membrane from a light-harvesting to a photoprotective state over a timescale of a few minutes. We have previously shown using freeze-fracture electron microscopy that this adaptation is accompanied by a significant re-organisation of the photosynthetic light-harvesting complexes, but it is unclear how this controls energy migration and photoprotection. 

The project will be computational in nature but will work closely with (and be co-supervised by) experimentalists, who will provide us with a large volume of data. Electron and fluorescence microscopy measurement will give us snap-shots of the membrane organization and fluidity. Time resolved spectroscopy data will allow us to characterize light-harvesting efficiency and photoprotective capacity.

We will then develop a detailed computational model that will connect structure and function, and give a prediction of the mesoscale dynamics that are currently inaccessible to experiment. This model will be multi-scale and combine molecular dynamics simulations, lattice diffusion models and Fluctuating Finite Element Analysis (FFEA), a new computational approach that has never been applied to thylakoid membranes but shows great promise for modelling of such a system at the mesoscale.

Eligibility and applying

Applicants must be:

- Chinese students with a strong academic background.

- Students holding a PR Chinese passport.

- Either be resident in China at the time of application or studying overseas.

- Students with prior experience of studying overseas (including in the UK) are eligible to apply. Chinese QMUL graduates/Masters’ students are therefore eligible for the scheme.

Please refer to the CSC website for full details on eligibility and conditions on the scholarship. 

Applications are invited from outstanding candidates with or expecting to receive a first or upper-second class honours degree physics, mathematics, computer science, or any subject that involves computational modelling of complex systems. A masters degree is desirable, but not essential.

Experience in coding is essential, familiarity with photosynthesis is deiserable but not essential (as training will be given).

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:   

Informal enquiries about the project can be sent to Dr Christopher Duffy at [Email Address Removed] 

Formal applications must be submitted through our online form by 31st January 2024 for consideration, including a CV, personal statement and qualifications. You must meet the IELTS/ English Language requirements for your course and submit all required documentation (including evidence of English Language) by 14th March 2024. You are therefore strongly advised to sit an approved English Language test as soon as possible. 

Shortlisted applicants will be invited for a formal interview by the supervisor. If you are successful in your application, then you will be issued an QMUL Offer Letter, conditional on securing a CSC scholarship along with academic conditions still required to meet our entry requirements. Once applicants have obtained their QMUL Offer Letter, they should then apply to CSC for the scholarship by in March 2024 with the support of the supervisor.

Only applicants who are successful in their application to CSC can be issued an unconditional offer and enrol on our PhD programme. For further information, please go to: 

Apply Online

Biological Sciences (4) Mathematics (25) Physics (29)

Funding Notes

This studentship is open to students applying for China Scholarship Council funding. Queen Mary University of London has partnered with the China Scholarship Council (CSC) - to offer a joint scholarship programme to enable Chinese students to study for a PhD programme at Queen Mary. Under the scheme, Queen Mary will provide scholarships to cover all tuition fees, whilst the CSC will provide living expenses for 4 years and one return flight ticket to successful applicants.


C Gray, L Kailas, PG Adams, CDP Duffy (2023) "Unravelling the fluorescence kinetics of light-harvesting proteins with simulated measurements", Biochimica et Biophysica Acta (BBA)-Bioenergetics 1865 (1), 149004