IBM researchers at Watson Labs are taking an interest in how 3-D environments work. In particular, how can Second Life be utilized to pursue serious scientific research?

Zha Ewry is in the Research Division of Watson Labs pursuing the overall question of use of SL for research. She is the owner of ThorneBridgeTown, the IBM Research Shared Work Island, one of several IBM research islands showcasing some of the projects going on within IBM research. She, along with others in her group, feels that work in SL is important enough to pursue in addition to their day jobs.

“Watson Research is part of the Labs which worry about longer term, somewhat more fundamental research, so we’re trying to look at similar questions in SL,” Ewry said. “Can we do visualization and if so, how well and then, how can we exploit that? We’re also deeply interested in looking at the longer term here: how collaboration and interaction change in 3-D space.”

Scientist Rez Tone added “In 1999, IBM announced the Blue Gene hardware project, which was to be the next generation of the world’s fastest supercomputers. The fastest supercomputer is now the Blue Gene installation at Lawrence Livermore National Labs, with 64 racks of Blue Gene (each rack holds 1024 nodes, or 2048 processors). The installation at IBM Watson Research Labs in NY, now the third fastest supercomputer in the world, is dedicated to research collaborations between internal scientists, such as myself, and outside academic and government labs.”

The present project being tested is a giant rhodopsin membrane protein which has been built on the island. (Rhodopsin is the protein that is responsible for night vision.) The SL build resulted from simulations starting from experimental coordinates done on the Blue Gene supercomputer. This large build took 5500 prims and originally had scripts that rotated the rhodopsin. The colors indicate which particular atom or element lies at the tube junctions: green is carbon, white is hydrogen, red is oxygen, blue is nitrogen and yellow is sulphur. Common to all vision is a small molecule attached to the protein core called retinal, which actually captures a photon of light.

“Rhodopsin is a member of the class of signally proteins known as G-protein coupled receptors (GPCRs). Over half (>50%) of the drugs on the market today target GPCRs. GPCRs represent the most important class of therapeutic targets for the treatment of disease,” Tone said. “Rhodopsin is, however, the only GPCR where the structure is experimentally known in atomic detail. This allows detailed studies of rhodopsin to uncover secrets about how it works, and perhaps gain functional insight into the broader class of GPCRs.”

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