Non-equilibrium simulations of the SARS-CoV2 spike protein
Dr Sofia Oliveira used the HPC clusters BlueCrystal4 and Catalyst, as well as the Oracle cloud, to run equilibrium and nonequilibrium molecular dynamics simulations.
The SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells, mediating membrane fusion. In this project, Dr Sofia Oliveira used dynamical-nonequilibrium molecular dynamics simulations to investigate how the presence of linoleic acid at the fatty acid-binding site, or changes in pH, modulate the behaviour of functionally relevant regions of several spike variants.
Below are some links to more in depth-information on the study:
https://doi.org/10.1101/2021.05.11.443384
https://doi.org/10.1101/2021.11.12.468428
It is noteworthy that the third paper reports the work performed by the team that was a finalist for the Gordon Bell special prize for supercomputing applications to Covid recently. While they didn’t win, it was great to be nominated and part of this exciting and interesting work.
For further details about this research, please see the Oracle blog (Congrats to the finalists of the 2021 ACM Gordon Bell Special Prize! (oracle.com).
You can also check our Gordon Bell trailer and presentation on YouTube.