Supercomputer Simulates Virus

Supercomputer Builds Virus

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

The simulation pushes today’s computing power to the limit. But it is only a first step. In future researchers hope that bigger, longer simulations will reveal details about how viruses invade cells and cause disease.

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.”

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.

This is a good example of the growing importance of simulations in medicine. Simulations are basically the future of medicine, simply because it is more practical to study a simulation on a computer than it is to study a physical virus that exists in real life.

In real physical life, you have no control over time and viewing angles like you do in simulations. In simulations, you get to decide when the programs runs, when it halts, or when it should rewind a bit. You are also free to define an arbitrary number of camera’s inside a simulation, which can point in any direction and at any zoom-level.

In the near future, medical simulations will help a great deal in speeding up medical discoveries, which directly translates into a healthier body and longer life for all of us.

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