Scientists celebrate first billion-atom simulation of entire DNA gene

23 Apr 2019

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Cancer research has been bolstered with news that scientists have created the largest simulation to date of an entire gene of DNA.

In our quest to fully understand the human body down to the smallest level, researchers at Los Alamos National Laboratory have churned through huge amounts of information to create a model of 1bn atoms. This is no simple collection of atoms, but the largest simulation ever of an entire gene of DNA.

In doing so, researchers will now better understand how to develop treatments – and even cures – for the most common of diseases, such as cancer. This is an important first step towards creating a complete image of how DNA expands and contracts.

“It is important to understand DNA at this level of detail because we want to understand precisely how genes turn on and off,” said Karissa Sanbonmatsu, a structural biologist at Los Alamos. “Knowing how this happens could unlock the secrets to how many diseases occur.”

Publishing their findings in the Journal of Computational Chemistry, the researchers created the simulation using the centre’s Trinity supercomputer – the sixth-fastest in the world – which was also used to monitor the US’s vast nuclear weapons stockpile.

Within a DNA molecule, there is a network of tiny, molecular spools called histone proteins. Depending on how these wind and unwind, they can turn genes on and off. So, when DNA is more compacted genes are turned off, and when expanded they are turned on.

How or why this happens has remained a mystery, which is why the researchers turned to supercomputers to help solve it. However, in order to be able to model an entire genome in the future, scientists will require exascale supercomputers that can make a quintillion calculations a second.

With this achieved, future healthcare could quickly compare a healthy genome with that of a patient who may have a particular type of cancer. According to Sanbonmatsu, it could even help us develop research on autism and intellectual disabilities.

Colm Gorey was a senior journalist with Silicon Republic