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Simulation of the HP-model of protein folding

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

The School of Mathematical Sciences of Queen Mary University of London invite applications for a PhD project commencing either in September 2019 for students seeking funding, or at any point in the academic year for self-funded students. The deadline for funded applications was the 31 January 2019.

This project will be supervised by Professor Thomas Prellberg.

The HP-model [1], 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 [2], and the flat-histogram version of the Pruned and Enriched Rosenbluth Method [3], 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 http://www.maths.qmul.ac.uk/~tp/talks/PERMandallthat.pdf

The application procedure is described on the School website. For further inquiries please contact Prof. Thomas Prellberg at .

Funding Notes

This project can be 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.

The School of Mathematical Sciences is committed to the equality of opportunities and to advancing women’s careers. As holders of a Bronze Athena SWAN award we offer family friendly benefits and support part-time study. Further information is available here. We strongly encourage applications from women as they are underrepresented within the School.

We particularly welcome applicants through the China Scholarship Council Scheme.

References

[1] K.A. Dill, "Theory for the folding and stability of globular proteins", Biochemistry 24 (1985) 1501–9.

[2] F. Wang, and D.P. Landau, D. P. "Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States", Phys. Rev. Lett. 86 (2001): 2050–2053.

[3] T. Prellberg and J. Krawczyk, “Flat histogram version of the pruned and enriched Rosenbluth method”, Phys. Rev. Lett. 92 (2004) 120602

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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