Lipid molecules are schizophrenic. One end likes to hang out with a charged crowd (think water); the other prefers neutral neighbors (think fats). Most of us remember those funky illustrations of the bilayer lipid membrane structure that encloses animal cells from high school biology. Recently, Titan supercomputer was used to show cell membranes may be much more than simple scaffolds for proteins and protective enclosures for cells.
Rather, researchers are starting to see that lipids and proteins can form small patches, similar to a mosaic and this patchiness seems to have functional roles in the life of a cell and in regulating different processes. “Without having access to high-speed computing and neutron experiments, this study would be impossible,” said Oak Ridge National Laboratory researcher Xiaolin Cheng.
Cheng, ORNL researcher John Katsaras, and their respective research groups are collaborating to use the Cray XK7 Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF) and the beam lines at the Spallation Neutron Source (SNS) – both DOE Office of Science User Facilities located at ORNL – to understand membrane organization and how it affects biology. An article describing their work is posted on the ORNL site[i].
A key challenge, not surprisingly, is accurate interpretation of the molecular motion data generated by the spin echo experiments.
“If you want a realistic picture of the bilayer’s undulation motions, you need a system big enough to capture these motions,” Cheng said. “Most of these simulations use hundreds of lipids, so you typically need a 10nm by 10nm grid, but for us, this number of lipids is too small. We had more than 2,000.”
Each 2,000-lipid simulation contains millions of individual that must be tracked, and each time step is 1–2 femtoseconds. Typically, the team’s simulations span hundreds of nanoseconds, or, in some cases, a full order of magnitude increase to a full microsecond. Use of a hybrid CPU/GPU supercomputer was critical; the work would have taken 3 times longer on a traditional CPU-only machine.
“[T]he system we’re studying has thousands of lipids,” Cheng said. “If we want to do the same system for a human cell, it would contain millions. I think the next-generation supercomputers like Summit [the OLCF’s next-generation supercomputer, set to be ready for production in late 2017] will be able to push this forward in the length scale, which will become more biologically relevant, but also in time, because it will allow us to observe phenomena that we can’t observe currently.”
Image Credit: Barmak Mostofian, John Nickels, and Renee Manning