Scientists create first billion-atom biomolecular simulation

Scientists create first billion-atom biomolecular simulation
A Los Alamos-led team created the largest simulation to date of an entire gene of DNA, a feat that required one billion atoms to model. Credit: Los Alamos National Laboratory

Researchers at Los Alamos National Laboratory have created the largest simulation to date of an entire gene of DNA, a feat that required one billion atoms to model and will help researchers to better understand and develop cures for diseases like cancer.

"It is important to understand DNA at this level of detail because we want to understand precisely how 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."

Modeling genes at the atomistic level is the first step toward creating a complete explanation of how DNA expands and contracts, which controls genetic on/off switching.

Sanbonmatsu and her team ran the breakthrough simulation on Los Alamos' Trinity supercomputer, the sixth fastest in the world. The capabilities of Trinity primarily support the National Nuclear Security Administration stockpile stewardship program, which ensures safety, security, and effectiveness of the nation's nuclear stockpile.

DNA is the blueprint for all living things and holds the genes that encode the structures and activity in the human body. There is enough DNA in the to wrap around the earth 2.5 million times, which means it is compacted in a very precise and organized way.

The long, string-like DNA molecule is wound up in a network of tiny, molecular spools. The ways that these spools wind and unwind turn genes on and off. Research into this spool network is known as epigenetics, a new, growing field of science that studies how bodies develop inside the womb and how diseases form.

When DNA is more compacted, genes are turned off and when the DNA expands, genes are turned on. Researchers do not yet understand how or why this happens.

While atomistic is key to solving the mystery, simulating DNA at this level is no easy task and requires massive computing power.

"Right now, we were able to model an entire gene with the help of the Trinity supercomputer at Los Alamos," said Anna Lappala, a polymer physicist at Los Alamos. "In the future, we'll be able to make use of exascale supercomputers, which will give us a chance to model the full genome."

Exascale computers are the next generation of supercomputers and will run calculations many times faster than current machines. With that kind of computing power, researchers will be able to model the entire human genome, providing even more insight into how genes turn on and off.

In the new study published in the Journal of Computational Chemistry April 17, the Los Alamos team partnered with researchers from the RIKEN Center for Computational Science in Japan, the New Mexico Consortium and New York University to collect a large number of different kinds of experimental data and put them together to create an all-atom model that is consistent with that data.

Simulations of this kind are informed by experiments, including chromatin conformation capture, cryo- and X-ray crystallography as well as a number of sophisticated computer modeling algorithms from Jaewoon Jung (RIKEN) and Chang-Shung Tung (Los Alamos).


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More information: Jaewoon Jung et al. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations, Journal of Computational Chemistry (2019). DOI: 10.1002/jcc.25840
Citation: Scientists create first billion-atom biomolecular simulation (2019, April 23) retrieved 23 May 2019 from https://phys.org/news/2019-04-scientists-billion-atom-biomolecular-simulation.html
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Apr 23, 2019
Storing apparently redundant genes

It appears the storage of genes has been found
what we thought were redundant genes are actually genes compacted turned off in storage
as
when these genes are required their expanded from storage so turned on bringing into use
A longstanding view that these genes are redundant is a view to change
also
is removing genes from our human genome for when these genes are needed to be turned

Apr 23, 2019
1 billion atoms modeled, another ~200 billion atoms to go. Trinity has a peak speed of ~40 PetaFLOPs, so to model the entire DNA molecule at roughly the same amount of time (after the software for the entire thing had been coded, i.e. taking into account only computer modeling speed) a x200 supercomputer speed would be required. 40 PFLOPs times 200 is 8 ExaFLOPs. Such a supercomputer will take quite a while to be built. My guess is it will show up between 2026 and 2028.

Of course the full genome could also be modeled with 4 ExaFLOPs in twice the time. Or with 2 ExaFLOPs four times slower etc So, assuming they could afford so much supercomputer time, they could perhaps do it even with a 1 ExaFLOP supercomputer, which would stretch the modeling time quite far (8 times slower) but perhaps not too far, depending on the time they spent modeling that gene with Trinity.

Apr 25, 2019
Awesome work, but pity the video didn't show the actual motion of the DNA structure and how it unwinds, interacts and recombines.

Apr 28, 2019
The whole universe is inside a spherical picture tube connected to a computer in a larger universe. This explains the BIG BANG.

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