National Computational Infrastructure

NCI

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Molecular movies

Every nine minutes approximately one Australian is diagnosed with Alzheimer’s disease.

ARC Future Fellow Associate Professor Aaron Oakley from the University of Wollongong and his team are using Raijin to simulate how a key protein in Alzheimer’s Disease interacts with other biological molecules in the brain.

The protein, Apolipoprotein-D (apoD), appears to protect against Alzheimer’s Disease and is also linked to brain cancer, says A/Prof Oakley.

“Biological molecules aren’t static; they’re moving all the time,” he explains.

“At the moment there are no microscopes available that will allow us to see in atomic detail how biological molecules moving around. We can work out the 3D shapes of the molecules, but we struggle to see them moving.

“We’re basically using Raijin to generate ‘molecular movies’ to see how ApoD moves and interacts with other molecules.”

Using chemistry techniques, researchers can work out the shapes of the molecules and how they’re positioned relative to each other in the lab. They can then feed this information into Raijin, which performs calculations to figure out how they are likely to move next.

“Raijin is literally calculating how the atoms within the molecules will move in response to the forces around them. We can then turn that data into animations and watch how the molecules move and bind to one another over time,” says A/Prof Oakley.

“That’s really important for understanding how they work and how they’re involved in disease.”

The simulations require huge number-crunching power, says A/Prof Oakley, as Raijin recalculates atomic positions and forces in femtosecond steps.

“The longest movies we’ve made are only about 2 microseconds long, but in terms of atomic fluctuations, that’s a very long time,” explains A/Prof Oakley. “Atoms move on the scale of femtoseconds, and a femtosecond is to a second what a second is to 31.7 million years.”

A/Prof Oakley, who has been using NCI facilities for almost 10 years, says that without Raijin the sheer number of calculations required would be overwhelming.

“It’s the sort of thing you could run on your home computer, but it would take decades.”

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