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Researchers create biomolecular simulation of the first billion

A Los Alamos-led law created the largest simulation so far of an entire DNA gene, a performance 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 DNA gene, a performance that required one billion atoms to model and helps researchers better understand and develop cures for diseases such as cancer. "It is important to understand DNA at this level of detail because we want to understand exactly how genes turn on and off," says Karissa Sanbonmatsu, a structural biologist at Los Alamos. "Knowing how this happens can unlock the secrets of how many diseases arise." Modeling genes at atomic level are the first step towards creating a complete explanation of how DNA expands and contracts, which controls genetic on / off switching. 1 9659005] Sanbonmatsu and her team ran the breakthrough simulation on Los Alamos' Trinity supercomputer, the sixth fastest in the world. The Trinity Capacity primarily supports the National Nuclear Security Administration stockpile stewardship program, which ensures the security, safety and efficiency of the nation's core stocks. DNA is the drawing for all living things and keeps genes encoding structures and activity in the human body. There is enough DNA in the human body to wobble around the earth 2.5 million times, which means it is compressed in a very precise and organized way. The elongated DNA molecule is wound up in a network of small, molecular coils. The ways…

A Los Alamos-led law created the largest simulation so far of an entire DNA gene, a performance 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 DNA gene, a performance that required one billion atoms to model and helps researchers better understand and develop cures for diseases such as cancer.

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

Modeling genes at atomic level are the first step towards creating a complete explanation of how DNA expands and contracts, which controls genetic on / off switching. 1

9659005] Sanbonmatsu and her team ran the breakthrough simulation on Los Alamos’ Trinity supercomputer, the sixth fastest in the world. The Trinity Capacity primarily supports the National Nuclear Security Administration stockpile stewardship program, which ensures the security, safety and efficiency of the nation’s core stocks.

DNA is the drawing for all living things and keeps genes encoding structures and activity in the human body. There is enough DNA in the human body to wobble around the earth 2.5 million times, which means it is compressed in a very precise and organized way.

The elongated DNA molecule is wound up in a network of small, molecular coils. The ways in which these coils wind and turn on, turn the genes on and off. Research on this coil network is known as epigenetics, a new growing science area that studies how bodies develop inside the uterus and how diseases are formed.

When DNA is compressed genes are extinguished and when DNA grows, genes are turned on. Scientists do not yet understand how or why this happens.

While the atomist model is the key to solving the mystery, it is not easy to simulate DNA at this level and require massive computer power.

“Right now we were able to model a whole gene with the help of the Trinity supercomputer at Los Alamos,” says Anna Lappala, a polymer physicist at Los Alamos. “In the future, we will be able to use exascal supercomputers, which allows us to model the entire genome.”

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

In the new study published in Journal of Computational Chemistry On April 17, the Los Alamos team collaborated with researchers from the RIKEN Center for Computational Science in Japan, New Mexico Consortium and New York University to collect a large number of different types of experimental data and bring them together to create an allatomical model that is consistent with these data.

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


Los Alamos for getting a new supercomputer


More information:
Jaewoon Jung et al. Scaling molecular dynamics over 100,000 processor cores for large-scale biophysical simulations, Journal of Computational Chemistry (2019). DOI: 10.1002 / jcc.25840

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Los Alamos National Laboratory

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Researchers create biomolecular simulation of first billion (2019, April 23)
April 23, 2019
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