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Scientists create the first biomolecular simulation of billions of atoms



  Scientists create the first biomolecular simulation of billions of atoms
A Los Alamos-led team created the largest ever simulation of an entire DNA gene that required a billion atoms to model it. Picture credits: Los Alamos National Laboratory

Researchers at the Los Alamos National Laboratory have created the largest ever simulation of an entire DNA gene, a feat for which one billion atoms had to be modeled, and will help researchers better understand diseases such as cancer and develop healing modalities.

"It's important to understand DNA at this level of detail because we want to know exactly how to turn genes on and off," said Karissa Sanbonmatsu, a structural biologist in Los Alamos. "Knowing how this happens could reveal the secrets of how many diseases are occurring."

Modeling of genes at the atomic level is the first step on the way to a full explanation of how DNA expands and contracts, controlling the on / off of genes. 1

9659005] Sanbonmatsu and her team performed the breakthrough simulation on the Trinity supercomputer of Los Alamos, the sixth fastest in the world. Trinity's capabilities primarily support the National Nuclear Security Administration's warehousing program, which ensures the safety, security and effectiveness of the nation's nuclear inventory.

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

The long, strand-like DNA molecule is in a network of tiny molecular coils. The way these coils wind up and down activates the genes. Exploring this coil network is known as epigenetics, a new, growing science area that explores how bodies develop in the womb and how diseases develop.


As DNA becomes more compressed, genes are shut down and as DNA expands, genes are turned on. The researchers do not yet understand how and why this happens.

While the atomistic model is the key to solving the puzzle, the simulation of DNA at this level is not an easy task and requires massive computing power.

"At the moment, we were able to model a complete gene using the Trinity supercomputer in Los Alamos," said Anna Lappala, a polymer physicist in Los Alamos. "In the future, we will be able to use exascale supercomputers to model the complete genome."

Exascale computers are the next generation of supercomputers and perform calculations much faster than previously machines. With this kind of computing power, researchers can model the entire human genome to gain even more insight into gene turning on and off.

In the new study published in the Journal of Computational Chemistry . On April 17, the Los Alamos team teamed up 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 types of experimental data and make it into an all-atom Composite model that agrees with this data.

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


Los Alamos to get new supercomputer


Further information:
Jaewoon Jung et al. Scaling of Molecular Dynamics Over 100,000 Cores for Biophysical Large-Scale Simulation, Journal of Computational Chemistry (2019). DOI: 10.1002 / jcc.25840

Provided by
Los Alamos National Laboratory




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Scientists create first biomolecular simulation of billions of atoms (2019, April 23)
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