Supercomputers are the bodybuilders of the computer world. They boast tens of thousands of times the computing power of a desktop and cost tens of millions of dollars. They fill enormous rooms, which are chilled to prevent their thousands of microprocessor cores from overheating. And they perform trillions, or even thousands of trillions, of calculations per second.

All of that power means supercomputers are perfect for tackling big scientific problems, from uncovering the origins of the universe to delving into the patterns of protein folding that make life possible. Here are some of the most intriguing questions being tackled by supercomputers today.

Recreating the Big Bang

It takes big computers to look into the biggest question of all: What is the origin of the universe?

The "Big Bang," or the initial expansion of all energy and matter in the universe, happened more than 13 billion years ago in trillion-degree Celsius temperatures, but supercomputer simulations make it possible to observe what went on during the universe's birth. Researchers at the Texas Advanced Computing Center (TACC) at the University of Texas in Austin have also used supercomputers to simulate the formation of the first galaxy, while scientists at NASA’s Ames Research Center in Mountain View, Calif., have simulated the creation of stars from cosmic dust and gas.

Supercomputer simulations also make it possible for physicists to answer questions about the unseen universe of today. Invisible dark matter makes up about 25 percent of the universe, and dark energy makes up more than 70 percent, but physicists know little about either. Using powerful supercomputers like IBM's Roadrunner at Los Alamos National Laboratory, researchers can run models that require upward of a thousand trillion calculations per second, allowing for the most realistic models of these cosmic mysteries yet.

Understanding earthquakes

Other supercomputer simulations hit closer to home. By modeling the three-dimensional structure of the Earth, researchers can predict how earthquake waves will travel both locally and globally. It's a problem that seemed intractable two decades ago, says Princeton geophysicist Jeroen Tromp. But by using supercomputers, scientists can solve very complex equations that mirror real life.

"We can basically say, if this is your best model of what the earth looks like in a 3-D sense, this is what the waves look like," Tromp said.

By comparing any remaining differences between simulations and real data, Tromp and his team are perfecting their images of the earth's interior. The resulting techniques can be used to map the subsurface for oil exploration or carbon sequestration, and can help researchers understand the processes occurring deep in the Earth's mantle and core.

Folding Proteins

In 1999, IBM announced plans to build the fastest supercomputer the world had ever seen. The first challenge for this technological marvel, dubbed "Blue Gene"?

Unraveling the mysteries of protein folding.

Proteins are made of long strands of amino acids folded into complex three-dimensional shapes. Their function is driven by their form. When a protein misfolds, there can be serious consequences, including disorders like cystic fibrosis, Mad Cow disease and Alzheimer's disease. Finding out how proteins fold — and how folding can go wrong — could be the first step in curing these diseases.

Blue Gene isn't the only supercomputer to work on this problem, which requires massive amounts of power to simulate mere microseconds of folding time. Using simulations, researchers have uncovered the folding strategies of several proteins, including one found in the lining of the mammalian gut. Meanwhile, the Blue Gene project has expanded. As of November 2009, a Blue Gene system in Germany is ranked as the fourth-most powerful su

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