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Simulation of the HP-model of protein folding

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Awaiting Funding Decision/Possible External Funding
    Awaiting Funding Decision/Possible External Funding

Project Description

The School of Mathematical Sciences of Queen Mary University of London invite applications for a PhD project commencing either in September 2016 (funded students) or at any point in the academic year (self-funded students).

The HP-model, which has rightfully been called the "Ising model of protein folding," serves as a benchmark model for testing the performance of algorithms attempting to compute the density of states of proteins close to their folded ground state. This model provides an ideal testing ground for the comparison of Monte-Carlo algorithms.

The successful applicant will implement several competing algorithms, such as the Wang-Landau Method, and the flat-histogram version of the Pruned and Enriched Rosenbluth Method, to comprehensively analyse performance of these algorithms within the context of the HP model, and to develop improvements for these algorithms.

For an overview of the subject, see this website: http://www.maths.qmul.ac.uk/~tp/talks/PERMandallthat.pdf

For full details, see the project abstract: http://www.maths.qmul.ac.uk/sites/default/files/phd%20projects%202015/DSSP/prellberg.pdf

The application procedure is described on the School website. For further enquiries please contact Prof. Thomas Prellberg ().

This project is eligible for several sources of full funding for the 2016/17 academic year, including support for 3.5 years’ study, additional funds for conference and research visits and funding for relevant IT needs. Applicants interested in the full funding will have to participate in a highly competitive selection process. The best candidates will be eligible to receive a prestigious Ian Macdonald Postgraduate Award of £1000, for which you will be considered alongside your application. The application deadline for full funding is January 31st 2016.

There is also 50% funding scheme available for students who are able to find the matching 50 % of the cost of their studies.
Competition for these half-funded slots will be less intensive, and eligible students should mention their willingness to be considered for them in their application. The application deadline for 50% funding is January 31st 2016.

This project can be also undertaken as a self-funded project, either through your own funds or through a body external to Queen Mary University of London. Self-funded applications are accepted year-round.

Funding Notes

If you wish to apply, please visit the application website and mention that you wish to work on the “Simulation of the HP-model of protein folding” project.

School website: View Website

Related Subjects

How good is research at Queen Mary University of London in Mathematical Sciences?

FTE Category A staff submitted: 34.80

Research output data provided by the Research Excellence Framework (REF)

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