HPCwire: The Computational Microscope

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March 21, 2008

The Computational Microscope

by Aaron Dubrow

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Ranger's parallel computing power enables researchers to model the largest biomolecular apparatus to date

In the 300 years since Dutch scientist Antonie van Leeuwenhoek first discovered living cells with his homemade lenses in 1674, microscopes have grown hundreds of thousands of times more powerful. Employing new methods and techniques, from electron beams and atomic probes to x-rays, the frontier of magnification has moved from the cell to the molecule, trillions of which work in tandem to create life.

"All life forms are actually a society of molecules, a very hierarchical society," Klaus Schulten, preeminent molecular biologist and professor of physics at The University of Illinois at Urbana-Champaign, explained. "But we're also more than molecules. Water is made of molecules, but it cannot repair or duplicate itself. The point about molecules in living systems is they form teams and work together."

To truly understand the human body, and to design effective medicines and treatments, it is necessary to grasp the operations of cellular molecules from the atomic level up. While the functions of biomolecules, like proteins and DNA, are well known, certain aspects of the proteins' actions elude researchers -- even when using the most powerful microscopes.

Schulten has spent his career extending the limits of microscopy by applying the immense power of supercomputers to molecular imagery. His "computational microscope" takes information from laboratory tests and turns it into dynamic, three-dimensional images with a powerful program Schulten created called NAMD (NAnoscale Molecular Dynamics, pronounced "NAM-dee"). Joining electron microscopy, x-ray crystallography, quantum chemistry and multi-scale molecular dynamics, with the massive parallel processing power of Ranger, the most powerful supercomputer in the world for open science research, Schulten's molecular simulations are opening new realms of research that help us understand fundamental aspects of how life exists on earth.

Schulten uses a football game as an analogy to explain how the computational microscope combines diverse microscopy techniques. "Crystallography," Schulten said, "is like football players listening to the national anthem before the game. They stand there, and if you take a good photograph, you can see them all precisely."

But during the game, the players (molecules) are in motion, interacting, bumping into one another, which is where electron microscopy plays a role. "Here, you can capture the biomolecules in action, but not with the same resolution as in the crystal," Schulten explained. "You don't see every detail, but you see enough that you can match the straight standing players to the actors on the field and learn what are they doing -- where are their legs? where are their heads? do they have the football?"

Combining these two methods tells you what you're looking at from the outside. But to see the molecule from the inside out and to understand how it forms and what it does, you need an all-atom representation of the protein. "Only when you know the chemical detail can you make sense of what is actually happening," Schulten said. "In football language, who has the ball? who kicks the ball? who throws the ball? You can reconstruct this detail through the application of the computational microscope."

Ranger, the newly launched supercomputer at the Texas Advanced Computing Center (TACC), will integrate the data from these varied methods on thousands of parallel processors, and output movies of the molecular machinery in motion. These information-rich visualizations, in turn, will help fuel the next round of molecular dynamics breakthroughs.

Coming from Schulten, it sounds simple, but in reality, this process is the product of more than two decades of coding and refinement, and $20 million in funding from the National Institute of Health (NIH). Today, Schulten's parallel molecular dynamics program, NAMD, is the leader for large-scale simulations of biomolecular systems (more than 100,000 atoms) and one of the most capable parallel scientific codes ever run on a supercomputer.

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