Computer Simulations of Biological Macromolecules

PGR-P-173

Key facts

Type of research degree: PhD
Application deadline: Ongoing deadline
Project start date: Wednesday 1 October 2025
Country eligibility: International (open to all nationalities, including the UK)
Funding: Competition funded
Additional supervisors: Dr Sarah Harris
Schools: School of Physics and Astronomy

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

Computational models are invaluable for visualisation in molecular biology, as they employ our best quantitative physical understanding of biomolecules and their interactions to predict their dynamics, which is often missing from biophysical experiments. Now that biophysical techniques are revealing highly organised supermacromolecular architectures at the length-scale directly above that of single molecules, which was invisible until very recently, there is a need for new computational tools to intepret these experiments. We are developing two lines of research in supermacromoleular biology – one for DNA, and one for proteins. While it is well known that DNA is the molecule of heredity and that the sequence of bases in DNA encodes the genetic information that defines an organism, the way in which genomes are regulated is not understood. Recent experimental data shows that the physical arrangement of DNA within the nucleus is critical to genetic control. We have developed a model system involving small DNA circles that we can analyse both by experimental methods and atomistic computer modelling using well established computer programs to understand how the packaging of DNA helps in the control and regulation of the cell, and how it influences recognition by other molecules, such as proteins and drug molecules. We are also writing our own modelling software that provides a continuum mechanics description of proteins, and which uses experimental electron microscopy data as input to the calculations. The model uses the Finite Element algorithm that we have generalised to include thermal fluctuations, known as Fluctuating Finite Element Analysis (FFEA), we are using this program to model the action of molecular motors such as myosin and dynein, and are improving our physical description of biomolecules and their interactions by adding more accurate representations of the hydrodynamic environment Our approach is highly multidisciplinary, and we can adapt projects to suit researchers with backgrounds as diverse as physics, maths, chemistry, biology and computer science. Collaborative projects including experimental work are also available.

<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 the Planned Course of Study that you are applying for PHD Physics & Astronomy FT and in the research information section that the research degree you wish to be considered for is Computer Simulations of Biological Macromolecules as well as <a href="https://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=SAH">Dr Sarah Harris</a> as your proposed supervisor and in the finance section, please state clearly the funding that you are applying for, if you are self-funding or externally sponsored. 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 on an ongoing basis. 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 Monday 3 February 2025 if applying for Leeds Doctoral Scholarship or Tuesday 1 April 2025 for Leeds Opportunity Research Scholarship. If you are applying with external sponsorship or you are funding your own study, please ensure you provide your supporting documents at the point you submit your application: <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>

Self-Funded or externally sponsored students are welcome to apply. UK – The <a href="https://phd.leeds.ac.uk/funding/138-leeds-doctoral-scholarship-2025-faculty-of-engineering-and-physical-sciences#:~:text=Key%20facts&text=One%20Leeds%20Doctoral%20Scholarship%20is,rata%20for%20part%2Dtime%20study.">Leeds Doctoral Scholarship</a> (closing date: Monday 3 March 2025) and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> (closing date: Tuesday 1 April 2025) are available to UK applicants. The <a href="https://phd.leeds.ac.uk/funding/102-bell-burnell-scholarship-award-awarded-by-the-iop">Bell Burnell Scholarship Award</a> is available to support applicants who are from groups that are currently under-represented in physics (awarded by the IOP) (now closed for October 2025 entry). <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. Non-UK – The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a> is available to nationals of China (now closed for October 2025 entry). The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds. You will be responsible for paying the overtime fee in full in your writing up/overtime year (£320 in Session 2024/25), but the scholarship maintenance allowance will continue to be paid for up to 6 months in the final year of award. 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 your application, please contact PGR Admissions by email to <a href="mailto:EMAIL@leeds.ac.uk">m</a><a href="mailto:maps.pgr.admissions@leeds.ac.uk">aps.pgr.admissions@leeds.ac.uk</a> For further information about this project, please contact Dr Sarah Harris by email to <a href="mailto:S.A.Harris@leeds.ac.uk">S.A.Harris@leeds.ac.uk</a>