A single-strand DNA entering an alpha hemolysim protein pore.
Image courtesy of SPICE |
Scientists in the UK combine grid computing, high-speed networks, supercomputers and three-dimensional visualization technology to study how biomolecules move through cell and nuclear membranes. Translocation, the process through which a DNA or mRNA fragment moves from the outside of a membrane to the inside through a pore, is important for several scientific disciplines and technological applications.
"Geneticists, biologists and physicists all study this problem," said Shantenu Jha, a physicist from University College London (UCL). "Geneticists are interested in how the DNA unravels, and physicists are interested in translocation as an energy problem. It has technical applications as well—nanotechnology and materials science researchers want to use artificial pores very similar to the natural pore we're investigating to screen thousands of DNA fragments against a test fragment and see what matches."
ss-DNA being pulled through the alpha-hemolysin pore during an interactive simulation.
Image courtesy of SPICE |
Jha collaborates in the SPICE—Simulated Pore Interactive Computing Environment—project, which uses the RealityGrid Steering Library and associated middleware to run interactive simulations on the UK's National Grid Service and TeraGrid in the U.S. The simulations are unique; instead of a one-way flow of simulation data from supercomputer to remote visualization resource, the scientist also uses the visualization to steer the simulation. The bi-directional data flow is made more challenging when the simulation and visualization resources are located hundreds, or even thousands, of miles away.
"We have to take the experiment to high-end supercomputers because the simulations are computationally extremely demanding," said Jha. "The chances of the resources required to do this experiment being all local to the scientist's desktop are essentially zero."
With SPICE, a scientist at UCL uses a visualizer to apply forces to individual atoms in the DNA molecule, "dragging" the DNA through the pore. Information about his actions is sent across high-speed networks to supercomputers connected to the NGS or TeraGrid, where the response is simulated and sent back to UCL. He physically feels the response through a haptic device, and views it in 3D through the use of goggles and a tiled display. The RealityGrid steering framework permits the integration of numerical simulations and instruments to the same grid middleware. Once the simulation is complete, data recorded by the supercomputer is transferred—again using the high-speed networks—to UCL, where it is stored for another set of analyses using local resources.
View a SPICE demonstration video at http://www.realitygrid.org/SPICE/.
—Katie Yurkewicz
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