Funding
Unfunded
An ATLAS for understanding carbohydrate chemistry
School of Mathematics and Physics | PHD
Reference Number
2026/032
Application Deadline
13 February 2026
Start Date
1 October 2026
Overview
Carbohydrates and sugars are biological molecules, which adopt various geometrices. In cells, carbohydrates change conformation when they bind to proteins. This project aims to develop methods for simulating the binding of sugars to proteins on a computer and to understand how these proteins function. Machine learning will be used to compare the conformers the sugar adopts when it is bound with the conformations that it adopts when it is unbound. Traditionally function in molecular biology is inferred from structure. However, dynamics are increasingly seen to play an important role. Developing tools for systematically studying these effects is thus critical.
Carbohydrates, also known as saccharides, glycans, or sugars, are the most abundant and diverse set of biological molecules on Earth. The fundamental unit of these molecules are monosaccharides, which bind to form polysaccharides [1]. Carbohydrates are implicated in biological functions ranging from structure and energy storage to signalling, with many of these functions being linked to carbohydrates’ interactions with proteins [1]. A better understanding of protein–carbohydrate interactions is thus essential for many fields. For example, glycoside hydrolases are thought to function by distorting the carbohydrate ring geometries in ways that make the cleavage of glycosidic bonds more favourable [2]. To understand protein–carbohydrate interactions we thus need more than the static crystal structures of these complexes that are found in the protein data bank. We also need to understand the effect proteins have upon the dynamical behaviour of the carbohydrate molecules that bind to them so that we can better understand how these proteins facilitate carbohydrate reactivity.
Carbohydrates can adopt a number of distinct metastable configurations and will interconvert between these configurations over a microsecond timescale [3]. Consequently, when we say that binding to a protein affects the dynamics of the carbohydrate one or several of four things must be occurring:
1. Binding stabilizes metastable configurations that are unstable when the carbohydrate is unbound.
2. Binding changes the relative free energies of the various metastable configurations that the carbohydrate can adopt both when it is bound and when it is unbound.
3. Binding changes the rates at which the carbohydrate interconverts between the various conformers.
4. When the carbohydrate binds the way that it fluctuates while it is trapped in the metastable configurations changes.
It is difficult to determine which of these mechanisms proteins are using to change the behaviours of carbohydrates because it is computationally expensive to run the microsecond-long molecular dynamics simulations that would be required to observe the interconversions between the metastable states that the carbohydrates can adopt. In addition, because the simulator defines what constitutes a metastable state, it can be difficult to locate the boundaries between them.
In this project, we will apply our recently-developed ATLAS technique [4] to study the effect of protein binding on the dynamics of carbohydrates using molecular dynamics (MD) simulations. ATLAS is ideally suited to this problem because it uses machine learning to analyze trajectories and find the basins of attraction that correspond to the various metastable states. In other words, the trajectory is used to fit a Gaussian mixture model (GMM). This probability distribution is then used to construct a bias potential that is similar to that used in metadynamics [5] and which enhances the sampling of phase space. By using this technique, we are thus able to study long-timescale processes using relatively short MD simulations.
The great strength of ATLAS is that the Gaussian mixture is a probability distribution. We can thus use this probability distribution to calculate the likelihood that a given trajectory frame is a representative example of a particular conformer. Consequently, we can use a Gaussian mixture model that is fit based on simulations of an unbound carbohydrate to analyse a simulation of a carbohydrate that is bound to a protein. The likelihood information that we obtain from this analysis tells us whether item (1) in the list above occurs for the system of interest, i.e. if the protein stabilises configurations of the carbohydrate that would not be stable for the unbound carbohydrate. Furthermore, this likelihood information also makes partitioning the trajectory between the various metastable configurations straightforward and thus allows us to also determine the effect the protein has on the relative free energies of the conformers and whether binding has affected the local dynamics.
We can even potentially use ATLAS to determine when the system is transitioning between states. The underlying kinetics can be obtained by using the infrequent metadynamics technique. Furthermore, the GMM provides us with an obvious set of states that we can use when constructing a Markov state model of the interstate dynamics.
In this initial project, where we are adapting the ATLAS method for this application we will first study proteins such as the asialoglycoprotein receptor [6], FimH Adhesin carbohydrate-binding domain [7], MhLap carbohydrate-binding domain [8] and L-fucokinase/GDP-fucose pyrophosphorylase [9] that bind to mono and disaccharides. These small saccharides can adopt fewer metastable configurations and the proteins they bind to only have a few hundred residues. These systems are small enough to study with our local computational cluster and are well suited to a proposal whose principal aim is to develop new methodologies. We will run long MD simulations of the mono and disaccharides that bind to these proteins in water and use machine learning to extract representations of the trajectories that can be used to construct an ATLAS bias potential. We will then run ATLAS simulations in the presence and absence of the protein and do the analysis described above.
We would note that there are many problems in biochemistry that, like the saccharide binding we are studying here, involve small, flexible molecules binding to larger, less-flexible macromolecules. Consequently, all the methodologies we develop in this project will be implemented in the PLUMED plugin for molecular dynamics [10]. Example input files for all the calculations that appear in our published papers will be deposited in the PLUMED nest [11], while tutorials on how to use the method will be provided through PLUMED tutorials [12].
Our overall objective is to provide a quantitative framework for determining the effect the environment has on the dynamics of molecules. As discussed in the section on why the Leverhulme Trust, the function of biomolecules is not solely determined by their structures. Dynamics are increasingly seen as providing a critical role. The impact of this project will be to provide a quantitative lens that can be used to probe biomolecular dynamics. This lens leverages the power of machine learning. However, the insight obtained from the algorithms is comprehensible by human users as the model used by it is based on a physical model that assumes the molecule can be in a small number of distinct metastable states. A coarse grained model for the behaviour of the biomolecule can thus be obtained by extracting relative free energies for these states and the transition rates between them.
References
1. Essentials of Glycobiology. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor (NY), 2022).
2. Mayes, H. B., Broadbelt, L. J. & Beckham, G. T. How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis. J. Am. Chem. Soc. 136, 1008–1022 (2014).
3. Guvench, O., Martin, D. & Greene, M. Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins. Int. J. Mol. Sci. 23, 473 (2022).
4. F. Giberti, G. A. Tribello and M. Ceriotti, Global free-energy landscapes as a smoothly joined collection of local maps. J. Chem. Theory Comput. 17 3292-3308 (2021)
5. G. Bussi and A. Laio. Using metadynamics to explore complex free-energy landscapes. Nature Reviews Physics 2, 200-212 (2020)
6. Meier, M., Bider, M. D., Malashkevich, V. N., Spiess, M. & Burkhard, P. Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor. J. Mol. Biol. 300, 857–865 (2000).
7. Vanwetswinkel, S. et al. Study of the Structural and Dynamic Effects in the FimH Adhesin upon α-D-Heptyl Mannose Binding. J. Med. Chem. 57, 1416–1427 (2014).
8. Vance, T. D. R., Guo, S., Assaie-Ardakany, S., Conroy, B. & Davies, P. L. Structure and functional analysis of a bacterial adhesin sugar-binding domain. PLOS ONE 14, e0220045 (2019).
Physics overview
The scientific research within the School of Mathematics and Physics was highly rated in the 2021 REF peer-review exercise, with 90% of research being judged as internationally excellent or world-leading. Physics and Astronomy at Queen's has been ranked 14th in the UK (Complete University Guide 2025) and joint 9th in the UK for Graduate Prospects (Complete University Guide 2025).
Physics research activity in the School is focused into three specific Research Centres; all members of academic staff belong to one of these Research Centres, listed below.
Astrophysics Research Centre (PhD/MPhil)
Find out more below, or email Professor Mihalis Mathioudakis (m.mathioudakis@qub.ac.uk)
Centre for Light-Matter Interactions (PhD/MPhil)
Find out more below, or email Professor Brendan Dromey (b.dromey@qub.ac.uk) or Professor Hugo Van Der Hart (h.vanderhart@qub.ac.uk)
Centre for Quantum Materials and Technologies (PhD/MPhil)
Find out more below, or email Dr Amit Kumar (a.kumar@qub.ac.uk)
Registration is on a full-time or part-time basis, under the direction of a supervisory team appointed by the University. You will be expected to submit your thesis at the end of three years of full-time registration for PhD, or two years for MPhil (or part-time equivalent).
Physics Highlights
Career Development
- Queen's graduates from Physics have secured employment through a number of companies such as Allstate, AquaQ Analytics, Citigroup, Deloitte, First Derivatives, PwC, Randox, Seagate, Teach First and UCAS. In addition, Belfast has been ranked as the world’s most business friendly small-medium sized city (Financial Times’ fDi Intelligence, 2018)
- 91% of Queen’s graduates were in employment and/or further study 15 months after completing their course (HESA Graduate Outcomes, 2021/22).
World Class Facilities
- Since 2014, the School has invested over £12 million in new world-class student and staff facilities. Maths and Physics students have their own teaching centre that opened in 2016, housing brand experimental physics laboratories, two large computer rooms plus a student interaction area with a new lecture theatre and study rooms. In addition to this, Belfast is the UK’s most affordable student city (Natwest Student Living Index 2024)
Internationally Renowned Experts
- Physics and Astronomy has been ranked joint 9th in the UK for Graduate Prospects (Guardian University Guide 2025). The School has a continually growing international community of both undergraduate and postgraduate students and staff. Our research is conducted and recognised as excellent across the world. Staff are involved in cutting-edge research projects that span a multitude of fields.
Student Experience
- Physics and Astronomy at Queen's has been voted 8th in the UK for student experience (Times and Sunday Times Good University Guide 2025)
Queen’s is a lead UK university in tackling the unequal representation of women in science and engineering. The School currently holds a Silver Athena SWAN Award.
Key Facts
- Students will have access to our facilities, resources, study space and dedicated staff. Research students are encouraged to play a full and active role in relation to the wide range of research activities undertaken within the School.
- The School of Maths & Physics is one of the largest Schools in the University. Staff are involved in cutting-edge research that spans a multitude of fields.
Course content
Research Information
Research Themes
Astrophysics (PhD/MPhil)
You’ll be involved in the search for distant supernovae and where they came from; study the asteroid and comet population in the Solar system; look for planets orbiting other stars in our Galaxy; study flares and other dynamic processes in the atmosphere of the Sun. You’ll have the opportunity to spend extensive periods at world-leading research centres such as the European Southern Observatory and NASA Goddard Space Flight Center.
At Queen’s we lead major European consortia and are supported by a multi-million pounds portfolio of research grants from a range of sources, including the UK Science and Technology Facilities Council, the Royal Society, and European Union.
Research Themes
Centre for Quantum Materials and Technologies (PhD/MPhil)
Human history is defined by the materials we use to underpin our technology: stone, bronze, iron, silicon. As we enter the emerging Quantum era, this impetus on materials and their link to technologies becomes even stronger. As a PhD student in Centre for Quantum Materials Technologies, you will be playing a part in the development of materials systems which will, in some way, define our technology for the future. How can this not be exciting? You will seek to reveal the physics of material behaviour at the boundary of current global knowledge and quantum limits, at the same time, become proficient in techniques for Quantum computation, materials growth, patterning, characterisation and theoretical modelling.
These skills are highly valued in high-tech companies and commercial research institutions, as well as in academic research settings. Our laboratories and computational facilities are extremely well-equipped for international-level research and our links to other research teams throughout the world in both academia and industry are strong and you should expect to travel, should you wish to, as part of your PhD experience.
Research Themes
Centre for Light Matter Interactions (PhD/MPhil)
Your research will involve identifying, and responding to, major open problems in laser- and electrically-produced plasmas, ultra-fast atomic and molecular physics, the interaction of ionising radiation and plasmas with matter (including biological systems), the physics of antimatter interactions with atoms and molecules, and the description of strong field laser interactions with atoms and molecules.
You will address fundamental and/or practical questions related to the description of electronic excitations, optical properties of matter, and the interaction between electric currents, heat and light. Your theoretical activity will imply the development and programming of novel simulation methodologies to model such processes. Experimentally, you will employ local, national and international facilities, including some of the most powerful laser systems worldwide ,while benefiting from transferring your research findings into the industrial and medical sectors.
Career Prospects
Alumni Success
Many of our PhD graduates have moved into academic and research roles in Higher Education while others have progressed into jobs such as Data Scientist, Software Engineer, Financial Software Developer, IT Graduate Associate, Technology Consultant, Research Physicist, Telescope Operator and R&D Engineer.
People teaching you
Dr Amit Kumar
Head of Research Centre - Centre for Quantum Materials and Technologies
School of Maths and Physics
Prof Brendan Dromey
Co-Head of Research Centre - Centre for Light-Matter Interactions
School of Maths and Physics
Prof Hugo Van Der Hart
Co-Head of Research Centre - Centre for Light-Matter Interactions
School of Maths and Physics
Prof Mihalis Mathioudakis
Head of Research Centre - Astrophysics Research Centre
School of Maths and Physics
Course structure
There is no specific course content as such. A PhD programme runs for 3-4 years full-time or 6-8 years part-time. Students can register for a writing up year should it be required.The PhD is open to both full and part time candidates and is often a useful preparation for a career within academia or consultancy.
Application Process
Please review the eligibility criteria on the webpages. If you believe that you meet these criteria then follow the steps below:
Select ONE potential supervisor from our list of Academic Staff: https://www.qub.ac.uk/courses/postgraduate-research/find-a-phd-supervisor/ and send an email to that supervisor advising that you are interested in studying for a PhD, stating when you would start, and how you would plan to fund the research. It would be helpful to provide a a brief statement of the research question or interest, and how you think the question could be investigated. The potential supervisor may invite you to meet with them or they may invite you to apply formally.
Assessment
Assessment processes for the Research Degree differ from taught degrees. Students will be expected to present drafts of their work at regular intervals to their supervisor who will provide written and oral feedback; a formal assessment process takes place annually.
This Annual Progress Review requires students to present their work in writing and orally to a panel of academics from within the School. Successful completion of this process will allow students to register for the next academic year.
The final assessment of the doctoral degree is both oral and written. Students will submit their thesis to an internal and external examining team who will review the written thesis before inviting the student to orally defend their work at a Viva Voce.
Feedback
Supervisors will offer feedback on draft work at regular intervals throughout the period of registration on the degree.
Facilities
Our world-class facilities support research and teaching across a diverse range of areas designed to fulfil specific activities. The School contains 4,700m2 of purpose-built laboratory space which includes the ANSIN materials research hub, the Ewald Microscopy Facility (EMF) and the Taranis laser facility. The Teaching Centre includes experimental physics laboratories, two large computer rooms and plenty of student study (recently updated) and interaction space. Our laboratories and equipment are looked after by a dedicated team of technicians and are used by our researchers, students and industry.
PhD students can benefit from the new interaction space 'Old Physics Lounge' and the refurbished foyer area of the Maths & Physics Teaching Centre.
Students can benefit from the Nursing Mother and Parents' Room & Quiet Room. This room can be used for quiet reflection which also helps support Neurodivergent Individuals.
PhD students have access to a bookable private office space for quiet work or teams meetings.
Entrance requirements
Graduate
The minimum academic requirement for admission to a research programme is normally an Upper Second Class Honours degree from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School of Mathematics and Physics.
International Students
For information on international qualification equivalents, please check the specific information for your country.
English Language Requirements
Evidence of an IELTS* score of 6.0, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required. *Taken within the last two years
International students wishing to apply to Queen's University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes.
For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs.
If you need to improve your English language skills before you enter this degree programme, INTO Queen's University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree.
Tuition Fees
| Northern Ireland (NI) 1 | TBC |
| Republic of Ireland (ROI) 2 | TBC |
| England, Scotland or Wales (GB) 1 | TBC |
| EU Other 3 | £28,000 |
| International | £28,000 |
1 EU citizens in the EU Settlement Scheme, with settled or pre-settled status, are expected to be charged the NI or GB tuition fee based on where they are ordinarily resident, however this is provisional and subject to the publication of the Northern Ireland Assembly Student Fees Regulations. Students who are ROI nationals resident in GB are expected to be charged the GB fee, however this is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
2 It is expected that EU students who are ROI nationals resident in ROI will be eligible for NI tuition fees. The tuition fee set out above is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
3 EU Other students (excludes Republic of Ireland nationals living in GB, NI or ROI) are charged tuition fees in line with international fees.
All tuition fees quoted relate to a single year of study unless stated otherwise. All fees will be subject to an annual inflationary increase, unless explicitly stated otherwise.
More information on postgraduate tuition fees.
Physics costs
Depending on the area of research chosen there may be extra costs which are not covered by tuition fees.
Additional course costs
All Students
Depending on the programme of study, there may also be other extra costs which are not covered by tuition fees, which students will need to consider when planning their studies . Students can borrow books and access online learning resources from any Queen's library. If students wish to purchase recommended texts, rather than borrow them from the University Library, prices per text can range from £30 to £100. Students should also budget between £30 to £100 per year for photocopying, memory sticks and printing charges. Students may wish to consider purchasing an electronic device; costs will vary depending on the specification of the model chosen. There are also additional charges for graduation ceremonies, and library fines. In undertaking a research project students may incur costs associated with transport and/or materials, and there will also be additional costs for printing and binding the thesis. There may also be individually tailored research project expenses and students should consult directly with the School for further information.
Bench fees
Some research programmes incur an additional annual charge on top of the tuition fees, often referred to as a bench fee. Bench fees are charged when a programme (or a specific project) incurs extra costs such as those involved with specialist laboratory or field work. If you are required to pay bench fees they will be detailed on your offer letter. If you have any questions about Bench Fees these should be raised with your School at the application stage. Please note that, if you are being funded you will need to ensure your sponsor is aware of and has agreed to fund these additional costs before accepting your place.
How do I fund my study?
1.PhD OpportunitiesFind PhD opportunities and funded studentships by subject area.
2.Funded Doctoral Training ProgrammesWe offer numerous opportunities for funded doctoral study in a world-class research environment. Our centres and partnerships, aim to seek out and nurture outstanding postgraduate research students, and provide targeted training and skills development.
3.PhD loansThe Government offers doctoral loans of up to £26,445 for PhDs and equivalent postgraduate research programmes for English- or Welsh-resident UK and EU students.
4.International ScholarshipsInformation on Postgraduate Research scholarships for international students.
Funding and Scholarships
The Funding & Scholarship Finder helps prospective and current students find funding to help cover costs towards a whole range of study related expenses.
How to Apply
Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply.
Find a supervisor
If you're interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions.
To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here.
You might be asked to provide a short outline of your proposal to help us identify potential supervisors.