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Simulation of the HP-model of protein folding


School of Mathematical Sciences

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Dr T Prellberg Applications accepted all year round

About the Project

The School of Mathematical Sciences of Queen Mary University of London invite applications for a PhD project commencing in September 2020 for self-funded students.

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 [Email Address Removed].

Funding Notes

This project can be undertaken as a self-funded project. Self-funded applications are accepted year-round for a January, April or September start.

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.

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
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