Transforming Science – “Petascale Day” – Celebrating “In Silico”
("This illustration depicts DNA molecules (light green), packaged into nanoparticles by using a polymer with two different segments…. [Researchers’] tests showed that a nanoparticle’s shape could dramatically affect how effectively it delivers gene therapy to the cells." (Credit: Wei Qu, Northwestern University, simulation cartoons; Xuan Jiang, Johns Hopkins University, microscopic images)
An update on a prior post about the University of Illinois continuing to blaze new trails in supercomputing, and a new example of the medical treatment research results generated from combining supercomputing and molecular biology.
The update begins with "Petascale Day" on October 15, 2012. That’s the day designated for celebration by the National Center for Supercomputing Applications at the University of Illinois. It’s a celebration of the U of I’s "Blue Waters" supercomputer going online with "petascale" numbers of calculations. Blue Waters ties together about 265 Cray supercomputing devices. It used to be that the cutting edge national operations had just one Cray.
So, how big is "petascale"? I had no clue. NCSA explains:
"Petascale" refers to computing and data in the quadrillions, like the more than 11 quadrillion calculations Blue Waters will be able to perform and the more than 380 quadrillion bytes that will be available in NCSA’s new tape archive. In scientific notation, 1 quadrillion is 10 to the 15th (1015). So on 10.15 (October 15) NCSA will celebrate PETASCALE DAY!
Supercomputing already is changing lives today through genomics. For example, a couple of decades ago, my molecular biologist sister, Melissa, used gels and hand work to sequence individual genes her group was studying at Salk Institute, and they were out on the cutting edge. In contrast, today, computers sequence entire human genomes in just hours.
Blue Waters and other newly announced supercomputers (e.g. at Indiana University and at Ohio State University) will change more lives in the near tomorrow. And for the tomorrow a bit further out, there will be quantum computing at some point, a future anticipated by this year’s Nobel Prizes. Vast computing power is incredibly important because it makes it possible to undertake massive calculations that allow researchers to run computer simulations of actions in nature, and find answers far faster than just doing lab experiments. Indeed, the future is so promising that Gordon Moore contributed $ 600 million to Caltech to increase the pace of research (Mr. Moore is one the cofounders of Intel and the creator of Moore’s law of computing power.)
As it happens, Petascale Day coincides nicely with a new example from ScienceDaily of the power of research conducted "in silico." Also described in a press release from Northwestern University in Chicaga, the example is a new paper on researchers using massive computer simulations/calculations to figure out why nanoparticles take on various shapes, and why some shapes of nanoparticles with DNA go into cells very well, but other shapes do not go in well. Why care? Because that nanoparticle delivery of DNA may slow or stop a tumor, or help fix a genetic problem that creates vulnerability to Alzheimers, to name but a couple of the possible examples. Key excerpts explain the points in more detail:
"Our computer simulations and theoretical model have provided a mechanistic understanding, identifying what is responsible for this shape change," Luijten said. "We now can predict precisely how to choose the nanoparticle components if one wants to obtain a certain shape."
The use of computer models allowed Luijten’s team to mimic traditional lab experiments at a far faster pace. These molecular dynamic simulations were performed on Quest, Northwestern’s high-performance computing system. The computations were so complex that some of them required 96 computer processors working simultaneously for one month.
In their paper, the researchers also wanted to show the importance of particle shapes in delivering gene therapy. Team members conducted animal tests, all using the same particle materials and the same DNA. The only difference was in the shape of the particles: rods, worms and spheres.
"The worm-shaped particles resulted in 1,600 times more gene expression in the liver cells than the other shapes," Mao said. "This means that producing nanoparticles in this particular shape could be the more efficient way to deliver gene therapy to these cells."
The particle shapes used in this research are formed by packaging the DNA with polymers and exposing them to various dilutions of an organic solvent. DNA’s aversion to the solvent, with the help of the team’s designed polymer, causes the nanoparticles to contract into a certain shape with a "shield" around the genetic material to protect it from being cleared by immune cells. (underlining added)