Postgraduate research opportunities Molecular simulations of lipid interactions with bacteria

We'll use bio-molecular simulations to understand how lipid bilayer structures interact with bacteria, to aid the interpretation of experiments and understand the functionality of lipids produced by Abitec Corp.

The Academic Supervisors, Dr Paul Mulheran and Dr Valerie Ferro, have collaborated for ten years, co-supervising a number of PhD students working on a range of biotechnology projects including vaccines [1], antibodies [2], and biopolymers for antimicrobial applications. They use molecular simulation to help guide and interpret experiments, and as a design tool for new technology [3]. They will be complemented by Dr Donald Kelemen from Abitec as the Industrial Adviser, who will provide context and direction for the project development.

We'll employ Molecular Dynamics simulations, using open source software packages (NAMD, CHARMM and VMD) to design a series of computational experiments. The work will be performed on the ARCHIE-WeSt High Performance Computer at the University of Strathclyde, for which Mulheran is Director.

The project will also be supported by Dr Karina Kubiak-Ossowska, who is the Training Officer at the supercomputer centre and a bio-molecular simulation expert. In the project, the simulations will be designed to model the lipid structures of direct relevance to ongoing experimental work supported by Abitec in SIPBS, and how these interact with bacterial structures such as the peptidoglycan layer and the outer membrane of gram-negative bacteria. This will provide a unique molecular-scale view of the activity of the lipids.

This project will complement, inform and add to ongoing work as part of an international consortium between the University of Strathclyde (UK), Abitec (US), ABVista (UK), Sungkyunkwan University (South Korea), Larodan (Sweden) and Karolinska Institute (Sweden).

Understanding the mechanism of action at the molecular level will inform biophysical, in vivo and field work, driving towards product development.

References

[1] DJ Connell et al, Rationalising drug delivery using nanoparticles: a combined simulation and immunology study of GnRH adsorbed to silica nanoparticles, Sci. Rep. 8;17115 (2018).

[2] MM Al Qaraghuli et al, Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response, Sci. Rep. 10;13696 (2020).

[3] MAH Farouq et at, Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019, Current Opin. Coll. & Interface Sci. 54;101461 (2021).

In addition to undertaking cutting-edge research, students are also registered for the Postgraduate Certificate in Researcher Development (PGCert), which is a supplementary qualification that develops a student’s skills, networks and career prospects.

Find out more about the Department of Chemical & Process Engineering and the Department's Research.