PhD Studentship: Quantum and Classical Molecular Dynamics

Project Title: Quantum and Classical Molecular Dynamics – Accelerated Classical Mechanics

Closing Date: 29 April 2024 at 23:59

Eligibility: UK Applicants only

Funding

EPSRC Doctoral Training Partnership Studentship offering the award of fees, together with a tax-free maintenance grant of £19,237 per year for 3.5 years. 

Lead Supervisor’s full name & email address

Professor Dmitry Shalashilin – d.shalashilin@leeds.ac.uk

Co-supervisor name: To be confirmed

Project Summary

The goal of our research is to develop new computational methods for atomistic simulations in chemistry and physics.  These methods should allow us to treat bigger molecular systems faster and more accurately.

This  project is focused on classical molecular dynamics of biological molecules such as proteins for example. Here we disregard quantum effects and only consider classical dynamics. The molecules we are simulating are often comprised of thousands of atoms, which are viewed almost as classical balls connected by springs. The problem with classical molecular dynamics is that for molecules of this size atomistic simulations can be done on the time scale of picoseconds but the time scale of important biological processes such as protein folding for example is microseconds or longer so that at least 6 orders of magnitude of time scale have to be bridged. We developed efficient methods which allow to solve this problem by viewing long time dynamics as a set of short time processes. Therefore one very long simulation is replaced by a number of short ones. An example of such study can be found in ref [1] where we reproduced experimental data on peptide cyclization. With our new methods of accelerated classical dynamics we are looking now at protein folding, drug binding and other problems important in biochemistry in which we reach relevant time scales [1]. 

References

[1] (a) Glowacki, D. R.; Paci, E.; Shalashilin, D. V. J Phys Chem B 113 16603 (2009);  (b) D.V. Salashilin,G.Beddard, E. Paci and D. R. Glowacki, J. Chem. Phys. 137 165102 (2012).

Please state your entry requirements plus any necessary or desired background

First or Upper Second Class UK Bachelor (Honours) or equivalent

Subject Area

Biochemistry, Macromolecular Chemistry, Physical Chemistry

Keywords

Chemistry, Mathematics, Physical Chemistry, Physical Sciences