Molecular and Topological Modelling of Biopolymer Networks

PGR-P-2129

Key facts

Type of research degree: PhD
Application deadline: Friday 10 January 2025
Project start date: Wednesday 1 October 2025
Country eligibility: International (open to all nationalities, including the UK)
Funding: Funded
Source of funding: University of Leeds
Supervisors: Professor Lorna Dougan and Dr Charley Schaefer
Schools: School of Physics and Astronomy
Research groups/institutes: Molecular and Nanoscale Physics

<h2 class="heading hide-accessible">Summary</h2>

This fully funded PhD project focuses on developing theoretical and computational models to understand biopolymer networks, essential for systems such as intracellular condensates, extracellular matrices, artificial hydrogels, and biological materials like silk. These networks play vital roles in healthcare, sustainable material design, and engineering biology. The project integrates statistical physics and topological network models to bridge molecular and macroscopic scales, tackling challenges in predicting macroscopic properties from disordered protein sequences. Research areas include: • Developing protein models that incorporate structural and elastic properties of folded and disordered states. • Investigating external forces or reactants' effects on viscoelasticity, aggregation, and catalytic activity. • Addressing challenges in cell biology, medicine, and sustainable material development. We seek candidates with strong backgrounds in physics, biophysics, or computational modelling, and a keen interest in theoretical modelling, interdisciplinary research, and analytical methods. Supervised by Dr. Schaefer and Prof. Dougan within the Molecular and Nanoscale Physics Research Group at the University of Leeds, the successful candidate will join a vibrant research community, receive advanced training, and engage in collaborative opportunities.

<h2 class="heading hide-accessible">Full description</h2>

We invite applications for a fully funded PhD position focused on developing theoretical and computational models of biopolymer networks. This interdisciplinary project offers the opportunity to contribute to fundamental research with applications in healthcare, engineering biology, and sustainable materials development. Project Overview: Biopolymer networks play crucial roles in systems ranging from intracellular condensates [1,2] and extracellular materials like blood clots and mucus [3,4] to artificial hydrogels [5] and biological materials such as silk in cocoons and spider webs [6-8]. Understanding their behaviour across molecular and macroscopic scales is key to advancing biotechnology and materials science. However, the theoretical prediction of macroscopic properties of biopolymer networks from the constitutive protein sequence is greatly challenged by intrinsic disorder. This project aims to: <ul> <li class="western" style="margin-bottom: 0cm;">Advance statistical physics and topological network models to bridge atomistic and macroscopic phenomena [2,8].</li> <li class="western" style="margin-bottom: 0cm;">Develop protein models, incorporating structural and elastic properties of folded and disordered states [2,6-8].</li> <li class="western" style="margin-bottom: 0cm;">Investigate the effects of external forces or reactants on viscoelasticity, aggregation, and catalytic activity.</li> <li class="western">Apply our methods to address open challenges in cell biology and medicine [1-5] and sustainable material design [5-8].</li> </ul> References: [1] Jin et al., Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness. Sci. Adv. 7, eabh2929 (2021). [2] Payne-Dwyer et al., Predicting Rubisco-Linker Condensation from Titration in the Dilute Phase. Phys. Rev. Lett. 132, 218401 (2024), [3] Meldrum & Yakubov, Journey of dietary fiber along the gastrointestinal tract: role of physical interactions, mucus, and biochemical transformations, Crit. Rev. Food Sci. Nutr., 1–29 (2024) [4] Feller et al., Fibrinogen αC-region acts as a functional safety latch: Implications for a fibrin biomechanical behaviour model, Acta Biomaterialia 189, 179 (2024) [5] Hughes et al., Competition between cross-linking and force-induced local conformational changes determines the structure and mechanics of labile protein networks, J. Coll. Int. Sci., 678, 1259 (2025) [6] Schaefer et al., Silk protein solution: A natural example of sticky reptation. Macromolecules 53, 2669 (2020) [7] Schaefer & McLeish, Power-law stretching of Associating Polymers in Steady-State Extensional Flow. Phys. Rev. Lett. 126, 057801 (2021). [8] Schaefer & McLeish, Theoretical rheo-physics of silk: Intermolecular associations reduce the critical specific work for flow-induced crystallization. J. Rheol. 66, 515 (2022) Candidate Profile We seek a motivated candidate with a strong background in physics, biophysics, computational modelling, or a related field and who can demonstrate: <ul> <li class="western" style="margin-bottom: 0cm;">Interest in theoretical modelling and method development.</li> <li class="western" style="margin-bottom: 0cm;">A proactive, interdisciplinary approach to research.</li> <li class="western" style="margin-bottom: 0cm;">Strong analytical and computational skills.</li> </ul> This position is ideal for individuals interested in combining molecular dynamics, statistical mechanics, and materials science to address critical scientific questions. Student Experience: You will be based within the Molecular and Nanoscale Physics (MNP) Research Group. The PhD project will be supervised by Dr. Schaefer, with Prof. Dougan as co-supervisor, who will provide training and mentorship in statistical physics modelling and the simulation of biopolymer networks. At Leeds, you will be embedded in a vibrant research community, benefiting from student-led research seminars, graduate-level courses in soft matter and biophysics, an annual research retreat, and exciting opportunities for public engagement and outreach.

<h2 class="heading">How to apply</h2>

Formal applications for research degree study should be made online through the <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University's website</a>. Please state clearly in Planned Course of Study that you are applying for EPSRC DTP Engineering & Physical Sciences, in the research information section that the research degree you wish to be considered for is Molecular and Topological Modelling of Biopolymer Networks, as well as <a href="https://eps.leeds.ac.uk/physics/staff/15426/dr-charley-schaefer">Dr Charley Schaefer</a> as your proposed supervisor. Please state clearly in the Finance section that the funding source you are applying for is EPSRC Doctoral Landscape Award 2025/26: Physics & Astronomy. If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below). As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability. Applications will be considered after the closing date. Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application. We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed. Please note that you must provide the following documents in support of your application by the closing date of Friday 10 January 2025: <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> </ul>

<h2 class="heading heading--sm">Entry requirements</h2>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

<h2 class="heading heading--sm">English language requirements</h2>

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<h2 class="heading">Funding on offer</h2>

A highly competitive EPSRC Doctoral Landscape Award providing full academic fees, together with a tax-free maintenance grant at the standard UKRI rate (£19,237 in academic session 2024/25) for 3.5 years. Training and support will also be provided. This opportunity is open to all applicants. All candidates will be placed into the EPSRC Doctoral Landscape Award Competition and selection is based on academic merit. Important: Please note that that the award does not cover the costs associated with moving to the UK. All such costs (<a href="https://www.leeds.ac.uk/international-visas-immigration/doc/applying-student-visa">visa, Immigration Health Surcharge</a>, flights etc) would have to be met by yourself, or you will need to find an alternative funding source. Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.

<h2 class="heading">Contact details</h2>

For further information about this project, please contact Dr Charley Schaefer by email to <a href="mailto:L.Dougan@leeds.ac.uk">c.schaefer@leeds.ac.uk</a> For further information about your application, please contact PGR Admissions by email to <a href="mailto:maps.pgr.admissions@leeds.ac.uk">maps.pgr.admissions@leeds.ac.uk</a>

<h3 class="heading heading--sm">Linked funding opportunities</h3>