Scientists from Los Alamos national laboratory have created the most complete to date computer model of the entire DNA gene, which required a simulation of one billion atoms. Experts note that their model will help researchers better understand and develop drugs for diseases such as cancer, according to a press release published on the portal Phys.org.
“It is important to understand DNA at this level of detail because we want to know exactly how genes are turned on and off. The knowledge of how this happens may reveal the secrets of the development of many diseases,” says Carissa Sanbonmatsu, a structural biologist at the Los Alamos national laboratory.
The modeling of genes on the atomistic level is the first step to obtaining a full explanation of how DNA expands and contracts, what controls the genetic switch on and off.
Biologist Sanbonmatsu Carissa and her team of researchers conducted a revolutionary simulation on a supercomputer Trinity in Los Alamos, the sixth performance in the world today.
DNA is the basis for all life and contains genes that encode the structure and activities of the human body. In the human body enough DNA to wrap the Earth 2.5 million times, which means that it is sealed very accurately and orderly.
Long threadlike DNA molecule is wound on a network of tiny molecular coils. Then as these coils rotate and spin, which directly affects the switching on and off of genes. When the DNA more compact, the genes turn off, and when DNA is expanding, genes included. Researchers do not yet understand how and why this happens.
Although atomistic model is the key to the mystery, modelling DNA at this level is challenging and requires huge computing performance.
“Right now, we have been able to model a gene with the help of a supercomputer Trinity. In the future we can use Exascale supercomputers, which will enable us to simulate the whole genome”, says Anna Lappala, a physicist from the labs in Los Alamos.
Exascale is a new generation of supercomputers capable of performing calculations many times faster than modern machines. With such huge computing capabilities, researchers will be able to simulate entire human genome, providing more information about how genes are turned on and off.
In a new study published in the Journal of Computational Chemistry, a team of scientists from Los Alamos teamed up with researchers from the Japan Center for computational science RIKEN, scientists from new Mexico and University of new York to collect a large number of different experimental data and connect them together to create a fully atomic model, which is consistent with these data.
Computer modeling of this sort is based on the experiments, including the capture of the conformation of chromatin, cryoelectron microscopy and x-ray crystallography and a range of sophisticated algorithms, computer simulation, created by specialists of Javon by Yong from RIKEN and Chan shun the Tung of Los Alamos.
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