Deconstructing biofilms

About the Project

Lead supervisor:Dr Agnes Noy

Co-supervisors:Dr Martin Fascione and Prof Gavin Thomas

The student will be registered with the Department of Physics, Engineering and Technology

Antimicrobial resistance (AMR) is one of the greatest challenges facing modern medicine, already responsible for millions of deaths worldwide each year. A major contributor to this crisis is the formation of bacterial biofilms. Within biofilms, bacteria are embedded in a protective extracellular matrix composed primarily of polysaccharides, proteins, and DNA. This matrix acts as a molecular shield, preventing effective antibiotic penetration and enabling persistent infections, particularly in clinical settings. To overcome biofilm-associated resistance, it is essential not only to develop new antibiotics but also to design anti-biofilm strategies that can destabilize or dismantle these protective matrices.

This PhD project aims to uncover and disrupt the molecular interactions that stabilize bacterial biofilms using state-of-the-art computational simulations. You will model the complex interplay between DNA, proteins, and polysaccharides in biofilm matrices to identify structural features that can be exploited as drug targets. Using in silico drug-design, you will develop and test potential small molecules capable of disrupting these interaction — paving the way for new anti-biofilm therapeutics.

Supervisory Team

• Dr. Agnes Noy – an expert in biomolecular simulations, with a strong track record in modelling DNA–protein interactions and biofilm-related systems [1-2].
• Prof. Gavin Thomas – a microbiologist specializing in bacterial physiology and biofilm formation [3].
• Dr. Martin Fascione – a biological chemist working on biofilm polysaccharides [3].

Together, this supervisory team will provide you with an interdisciplinary and supportive research environment, combining cutting-edge computational methods with experimental insight.

You will join the Postgraduate Programme in Biomedical Sciences, a prestigious interdisciplinary programme at the University of York. As a PhD student, you will join a vibrant interdisciplinary cohort and take part in a wide range of tailored training opportunities, including workshops, scientific seminars, and cohort-wide events designed to support your professional and personal development.

Training and Career Development

You will gain:

• Expertise in widely-used molecular modelling software employed across the pharmaceutical, biotech and chemical industries.
• Strong programming and data analysis skills, opening potential career paths in data science, and software engineering.
• Broad interdisciplinary knowledge spanning biology, chemistry, and physics.

This is an exceptional opportunity to contribute to the global fight against antimicrobial resistance while developing a versatile and highly sought-after skill set. To learn more about the main supervisor Dr. Agnes Noy, please visit:

• https://agnesnoylab.wordpress.com
• http://www.linkedin.com/in/agnesnoy
• X (@ANoylab)
• Bluesky @agnesnoy.bsky.social

Do not hesitate to make informal enquiries to agnes.noy@york.ac.uk

This project is open-ended and can be adapted for MSc by Research or PhD level candidates. Dr. Noy has experience in publishing articles with master students [4]

[1] EW Chan, MC Leake and A Noy (2025) JACS Au, ASAP articles. https://pubs.acs.org/doi/10.1021/jacsau.5c00800

[2] SB Yoshua et al (2021) Nuc Acids Res, 49,8684-8698 https://doi.org/10.1093/nar/gkab641

[3] T Keenan et al (2024) Structure, 32, 2399-2409.e4. https://www.cell.com/structure/fulltext/S0969-2126(24)00386-1

[4] T Gardasevic and A Noy (2024) Nanoscale, 16, 18410-18420 https://doi.org/10.1039/D4NR02571G

The University of York is committed to recruiting future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and we have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Entry Requirements: Students with, or expecting to gain, at least an upper second class honours degree, or equivalent, are invited to apply. The interdisciplinary nature of this programme means that we welcome applications from students with any biological, chemical, and/or physical science backgrounds.

Programme: PhD in Biomedical Science (3 year)

Start Date: 21 September 2026