About the Project
Experiments to determine how metals might bind to amyloid beta peptides are difficult and costly to perform. In this light, using computers to simulate how metals bind to amyloid beta peptides and affect their structure and aggregation is an attractive proposition. This project will use modern simulation methods to describe in detail how metals bind to the peptides that cause AD, and the effect different metals have on their structure and aggregation characteristics. A suitable protocol for theoretical description of this important event must be able to properly describe the bonding and d-orbital effects that determine transition metal chemistry, while retaining the computational efficiency required for dynamical simulation of entire biomolecular systems. We have identified ligand field molecular mechanics (LFMM) as the ideal candidate for this task, as it efficiently and transferably captures the behaviour of metals. This project will use LFMM within molecular dynamics simulations to explicitly allow the peptide to change its shape in response to different metals. Crucially, the speed of LFMM coupled with the supercomputing resources available to us means that we can simulate the behaviour of two or more peptides together, and hence to examine the effect of metal on the initial stages of aggregation.
Supervisor: Dr James Platts https://www.cardiff.ac.uk/people/view/38541-platts-jamie
Academic criteria: We require applicants to have a 2.2 BSc or equivalent to be considered for PhD study.
If English is not your first language that you must fulfil our English Language criteria before the start of your studies. Details of accepted English Language qualifications for admissions can be found here https://www.cardiff.ac.uk/study/international/english-language-requirements/postgraduate
HOW TO APPLY
To apply please complete the online application - https://www.cardiff.ac.uk/study/postgraduate/research/programmes/programme/chemistry and state the project title and supervisor name
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