Technology

Scientists have created the most complete computer model of the gene of DNA

Scientists from Los Alamos National Laboratorycreated the most complete computer model of the entire DNA gene to date, which required the simulation of one billion atoms. Experts point out that their model will help researchers better understand and develop medicines for diseases such as cancer, according to a press release published on Phys.org.

"It is important to understand DNA at this level of detail,because we want to know exactly how the genes turn on and off. Knowing how this happens can reveal the secrets of how many diseases develop, ”comments Karissa Sanbonmatsu, a structural biologist at the Los Alamos National Laboratory.

Atomic-level gene modeling is the first step to getting a full explanation of how DNA expands and shrinks, which controls genetic activation and deactivation.

Biologist Carissa Sanbonmatsu and her team of researchers conducted a revolutionary simulation on the Trinity supercomputer at Los Alamos, the sixth fastest-performing computer in the world today.
DNA is the basis for all life and containsgenes that encode the structure and activity of the human body. There is enough DNA in the human body to wrap the Earth 2.5 million times, which means that it is compacted very precisely and orderly.

A long, filamentous DNA molecule is wound on a net.tiny molecular coils. The way these coils spin and spin, directly affects the switching on and off of genes. When the DNA is more compact, the genes turn off, and when the DNA expands, the genes turn on. Researchers do not yet understand how and why this happens.

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Although the atomistic model is the key to unraveling the mystery, DNA modeling at this level is not an easy task and requires tremendous computational performance.

“Right now we were able to model the whole gene withusing the Trinity supercomputer. In the future, we will be able to use Exascale supercomputers, which will enable us to model the entire genome, ”comments Anna Lappala, a physicist at a laboratory in Los Alamos.

Exascale is a new generation of supercomputers,able to perform calculations many times faster than modern machines. With such enormous computational power, researchers will be able to simulate the entire human genome at once, providing even more information about how genes are turned on and off.

In a new study published in editionThe Journal of Computational Chemistry, a team of scientists from Los Alamos teamed up with researchers from the Japanese Center for Computational Sciences RIKEN, scientists from New Mexico and the University of New York to collect a large number of different experimental data and connect them together to create a completely atomic model, which is consistent with this data.

Computer simulation of this kind is basedon experiments, including the capture of chromatin conformation, cryoelectron microscopy and X-ray crystallography, as well as a number of sophisticated computer simulation algorithms created by experts Jayvong Yong from RIKEN and Chan-Shun Tang from Los Alamos.

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