Supercomputer simulation could show us how to stop COVID

13 August 2020

The vital work examining how the coronavirus invades our cells could also unlock potential drug treatments.

In the battle against COVID-19 you need as many weapons as possible in your armoury. And it doesn't hurt if you have Australia and the Southern Hemisphere's most powerful and fastest supercomputer.

That's what ANU researcher Asssociate Professor Megan O'Mara has at her fingertips. She's using Gadi, housed at the National Computational Infrastructure (NCI Australia) on the ANU campus to help understand how the coronavirus invades human cells.

So powerful is Gadi, it has been named a member of the elite US-led COVID-19 High Performance Computing Consortium. It also allows Associate Professor O'Mara and her team members, Dr Katie Wilson and Dr Stephen Fairweather, to run simulations on 800,000 atoms in a key receptor in our bodies that the coronavirus is exploiting to attack our cells.

Using 48 processors running over 19 days to complete 64 simulations at the molecular level, her research will spend around 13 million hours of computing time in the coming months. In contrast, the same work would take a human around 1,500 years on one single computer doing constant calculations. If Fortnite is more your thing, what Gadi will do in less than three weeks is equal to 26.5 years of non-stop use on a high-end gaming machine.

Professor O'Mara will use the findings from the computer simulations to understand the first step of infection by the virus. She says this vital work will not only help us understand how the virus invades our cells, but could lead to targeted drug design to stop it.

"It is only with high-resolution modelling that accurately replicates the true behaviours of these receptors that we can figure out where vulnerabilities in the virus' binding process are," Associate Professor O'Mara says.

"Targeting the interaction between the human receptors and the coronavirus binding protein might well be a useful direction for drug design. This project will produce world-first vital information about regions of the receptors that could be potential vaccine or drug targets.

"We will use the computer to screen drugs that bind to the receptor complex and can thus prevent the changes necessary for virus binding. Our goal is to identify drugs that can stop the virus from infecting human cells.

"This allocation from NCI is absolutely essential for our research: the receptor complex is so large and intricate that NCI's new Gadi supercomputer is the only supercomputer in the Southern Hemisphere powerful enough to do these simulations."

NCI's Gadi supercomputer is named in the local Ngunnawal language meaning "to search for". Commissioned in late 2019, Gadi ranked #24 in the June 2020 TOP 500 - a ranking of the fastest supercomputers around the world. Gadi was funded by a $70M investment from the Australian Government.

Overnight, The White House Office of Science and Technology named Gadi and CSIRO's Pawsey Supercomputer Centre's Nimbus as members of the US-led COVID-19 High Performance Computing Consortium. As the "Australian HPC COVID-19 Rapid Response (NCI Australia and Pawsey Supercomputing Centre)", the two supercomputers will be available to researchers from around the world who are tacking COVID-19 from multiple angles.

The US consortium is a unique private-public effort spearheaded by the White House Office of Science and Technology Policy, the US Department of Energy and IBM to bring together federal government, industry, and academic leaders who are volunteering free compute time and resources on their world-class machines.