Looping DNA for Nanotechnology and Biomedicine Using Computer Simulations

About the Project

DNA is often depicted as a perfect double helix, yet inside living cells it is constantly bent, twisted, and supercoiled to perform essential genetic functions. These looping and supercoiling processes play key roles in gene regulation, replication, and genome organization. Despite their importance, the physical mechanisms controlling DNA looping remain poorly understood.

Beyond its biological significance, DNA is also a powerful material for nanotechnology. Its precise base-pairing (A:T and C:G) enables the creation of highly programmable nanoscale structures and molecular machines. However, the potential of DNA’s mechanical properties—such as looping and bending—remains largely untapped for engineering applications.

In this project, you will use computational simulations and artificial intelligence to investigate the physical factors that control DNA looping. You will:

• Explore how DNA sequence and supercoiling affect looping behavior.
• Study how specific proteins remodel DNA.
• Apply your findings to both biomedical systems (e.g., loops within disease-related genes) and nanotechnological applications (e.g., mechanically switchable DNA loops).

Your research will therefore bridge molecular biophysics, computational biology, and nanotechnology, contributing to both fundamental science and applied innovation.

Research Environment

This project will be supervised by Dr. Agnes Noy, who has been a pioneer in the modelling of DNA looping [1-3]. There will also be opportunities to collaborate with Prof. Mark Leake (University of York) to test theoretical predictions experimentally [4], providing hands-on exposure to biophysical and biochemical techniques.

As a PhD student, you will become part of the vibrant and interdisciplinary Physics of Life Group at the University of York. You will also benefit from a wide range of tailored training opportunities, including workshops, summer schools, and scientific seminars, all designed to support your professional and personal development. These activities will take place both at York and through the UK-wide Physics of Life network (www.physicsoflife.org.uk), providing you with valuable opportunities to connect and collaborate with researchers across the country.

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.
• Experimental training in microbiology and biochemistry, enhancing your versatility as a researcher.

This is an exceptional opportunity to contribute to the future of bioengineering and biotechnology while developing a versatile and highly sought-after skill set.

You will find more information of Dr. Noy’s research at:

• Website: agnesnoylab.wordpress.com
• X (Twitter): @ANoyLab
• LinkedIn: linkedin.com/in/agnesnoy

Do not hesitate to make informal enquiries to Dr. Agnes Noy (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 [2].

1. M Burman and A Noy (2025) “Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA” Phys Rev Lett, 134, 038403 https://doi.org/10.1103/PhysRevLett.134.038403.

Focus article: Ingrid Fadelli (2025) “Molecular simulations provide new insights into the dynamics of supercoiled DNA” Phys.org

https://phys.org/news/2025-02-molecular-simulations-insights-dynamics-supercoiled.html

2. T Gardasevic and A Noy (2024) “The impact of sequence periodicity on DNA elasticity: investigating the origin of A-tract’s curvature” Nanoscale, 16, 18410 – 18420 https://doi.org/10.1039/D4NR02571G

3. GD Watson, EW Chan, MC Leake, A Noy (2022) “Structural interplay between DNA-shape protein recognition and supercoiling: the case of IHF” Comput Struct Biotech J, 20, 5264-5274 https://doi.org/10.1016/j.csbj.2022.09.020

4. JW Shepherd, S Guilbaud, Z Zhou, J Howard, M Burman, C Schaefer, A Kerrigan, C Steele-King, A Noy, and MC Leake (2024) “Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiram biopolymers such as DNA” Nat Commun, 15, 2748 https://www.nature.com/articles/s41467-024-47126-6

Entry requirements:

Candidates should have (or expect to obtain) a minimum of a UK upper second class honours degree (2:1) or equivalent in Physics, Chemistry, Biology, Computer Science, Mathematics, or a closely related subject.

How to apply:

Applicants should apply via the University’s online application system at https://www.york.ac.uk/study/postgraduate-research/apply/. Please read the application guidance first so that you understand the various steps in the application process.

This project is open-ended making it suitable for MSc by Research and PhD level

Funding Notes

This is a self-funded project and you will need to have sufficient funds in place (eg from scholarships, personal funds and/or other sources) to cover the tuition fees and living expenses for the duration of the research degree programme. Please check the School of Physics, Engineering and Technology website for details about funding opportunities at York.