Improving molecular dynamics of biomolecules

We are a research group at the MRC Laboratory of Molecular Biology in Cambridge, UK working on improving molecular simulations.

Molecular dynamics has shown success in obtaining biological insights by providing mechanistic interpretations of experimental data. However, the force fields used to describe how the atoms interact lack accuracy and can fail for example when applied to disordered proteins or protein aggregation.

We aim to improve force fields for biomolecular simulation in two ways. The first is to use graph neural networks and data from quantum mechanics and experiments to learn fast molecular mechanics force fields. The aim is to replace the existing manual approach focused on specific types of molecule with a reproducible, easy to train model that applies equally to all molecules found in biology.

The second approach is to develop machine learning interatomic potentials (MLIPs) that are fast enough to simulate biomolecules. Recently MLIPs have been developed that rival the accuracy of quantum mechanics, but scaling them to the number of atoms and simulation times relevant to biology has been challenging. We will use simpler models and GPU programming to address this problem, with the eventual aim of simulating enzyme reactions.

The next few decades will see compute resources increase to the point where simulations at biologically relevant length and time scales become routine. It is crucial that we have accurate physical models available to take advantage of this and to probe the molecular basis of life.

We also have a page on the LMB website.

Joining the group

We are currently looking to grow the group!

If you are interested in a postdoc position, please contact Joe informally. We welcome applicants with experience in programming, computational chemistry, physical simulation or machine learning. We are also interested in helping people apply for fellowships to obtain their own funding.

PhD applications are handled as part of the LMB PhD program. Applications are currently closed.

University of Cambridge students can also apply to do part III or masters projects in the group.

Contact

jgreener at mrc-lmb.cam.ac.uk

Joe Greener
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge
CB2 0QH
United Kingdom
tel: +44 (0)1223 267068