First Billion-atom Biomolecular Simulation

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 genes 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 human body 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 model 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.

Science Advances – Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long‐range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. A novel algorithm was implemented for nonbonded interactions to increase single instruction multiple data (SIMD) performance, reducing memory usage for ultra large systems. Memory usage for neighbor searches in real‐space nonbonded interactions was reduced by approximately 80%, leading to significant speedup. Using experimental data describing physical 3D chromatin interactions, we constructed the first atomistic model of an entire gene locus (GATA4). Taken together, these developments enabled the first billion‐atom simulation of an intact biomolecular complex, achieving scaling to 65,000 processes (130,000 processor cores) with 1 ns/day performance.

SOURCES – Los Alamos, Science Advances
Written By Brian Wang,


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