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Using advanced MD simulation for understanding biomolecular mechanism (HAYWARDSU19SF)

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  • Full or part time
    Dr S Hayward
  • Application Deadline
    No more applications being accepted
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

Many biomolecules act as molecular machines and have a precise mechanism. Understanding how biomolecules work in detail could bring great advances in medicine and other biotechnologies. However, our understanding of mechanism, even for biomolecules that have been studied extensively, is very incomplete.

Like all machines biomolecules undergo shape change when they function. For example substantial parts of the biomolecule may undergo a relative movement when binding another molecule. The PhD project concerns understanding the energetics and the specific role of these kinds of movements.

The project will be carried out in collaboration with Dr Danilo Roccatano at the School of Mathematics and Physics, University of Lincoln, and will involve the use of Molecular Dynamics simulation. In particular we will use sampling techniques, such as umbrella sampling, to determine the energetics of functional movements in selected biomolecules, such as those that are targets for the development of therapeutic interventions in cancer.

Project start date: October 2019
Mode of Study: Full-time
Entry requirement: minimum UK 2:1.
Acceptable first degree: Physics, Chemistry, Biochemistry, Computer Science, Mathematics, Engineering or other numerate discipline.

Funding Notes

This PhD project is offered on a self-funding basis. It is open to applicants with funding or those applying to funding sources. Details of tuition fees can be found at

A bench fee is also payable on top of the tuition fee to cover specialist equipment or laboratory costs required for the research. The amount charged annually will vary considerably depending on the nature of the project and applicants should contact the primary supervisor for further information about the fee associated with the project.

The project may be filled before the closing date, so early application is encouraged.


HJC Berendsen and S Hayward, “Collective protein dynamics in relation to function” Current opinion in structural biology 10 (2), 165-169, 2000.

ii) H Ishida, S Hayward, “Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome”, Biophysical journal 95 (12), 5962-5973, 2008.

iii) D Taylor, G Cawley, S Hayward, “Quantitative method for the assignment of hinge and shear mechanism in protein domain movements” Bioinformatics 30 (22), 3189-3196, 2014.

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