Supercomputer Builds a Virus Simulation

One of the world’s most powerful supercomputers has simulated a moment in the life of a real virus. The simulation is the first to capture a whole biological organism in such intricate molecular detail.

“Computational Biology has finally reached the level of sophistication and utility of the 1970’s video game Pong.

But it sounds like we should reach beyond Space Invaders and Pac Man levels in 5 years…. Maybe we’ll actually have the bioinfo equivalent of Excel by then.”

Running on a machine at the National Center for Supercomputing Applications, Urbana, the program calculated how each of the million or so atoms in the virus and a surrounding drop of salt water was interacting with almost every other atom every femtosecond, or millionth of a billionth of a second.

The team managed to model the entire virus in action for 50 billionths of a second. Such a task would take a desktop computer around 35 years, says Schulten. “This is just a first glimpse,” he says. “But it looks gorgeous.”

The model shows that the virus coat collapses without its genetic material. This suggests that, when reproducing, the virus builds its coat around the genetic material rather than inserting the genetic material into a complete coat. “We saw something that is truly revolutionary,” Schulten says.

Ultimately, computational biologists would like to simulate larger viruses such as influenza or the complex biological systems in a cell - and for longer periods, such as the thousandths of a second that it might take to observe proteins in a cell switch a gene off. These computer models should allow researchers to discover details about such processes that they may miss by observing a real virus.

But such simulations will not become possible until the next generation of supercomputers are built in the next five years, Schulten says.

Source: Nature