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Supercomputer Performs Simulation of Virus
moller writes to tell us Red Herring is reporting that researchers from the University of California at Irvine and the University of Illinois at Urbana-Champaign have announced that they created a computer simulation of a virus. From the article: "Using one of the world's fastest computers at the U.S. National Center for Supercomputing Applications, located at the University of Illinois at Urbana-Champaign, the researchers ran a computer program devised to reverse engineer the dynamics of all atoms making up the virus particle and a tiny drop of water containing it." Nature also has an interesting write up on the research surrounding this project.
This is just fascinating, and precisely why we do high performance scientific computing. This quote piqued my interest in particular:
The model also shows that the virus coat collapses without its genetic material. This suggests that, when reproducing, the virus builds its coat around the genetic material rather than inserting the genetic material into a complete coat. "We saw something that is truly revolutionary," Schulten says.
So, by doing this simulation of a tiny span of time, the team was able to get new insight into the process of viral replication that would be extremely difficult to come by with experimental techniques. It also is fascinating, since we often think of viruses as little static particles that float around until they interact with a cell, and yet the simulation showed the surface pulsing. Very cool! -- Paul
OpenSource.MathCancer.org: open source comp bio
The virus later choked to death on a SMTP configuration file.
It must have been something you assimilated. . . .
Dear Sir or Madam: This letter is to notify you, pursuant to the provisions of the Digital Millennium Copyright Act, that we believe one of your humans is infringing God's copyrighted materials. Specifically, God is the owner of the copyright and trademarked materials, wich includes all life forms. The aforementioned human reverse engineered a virus without authorization, thereby infringing upon God's copyrights and trademarks. Accordingly, God demands that you act expeditiously immediatelly stop and remove all acquired data from that procedure in order for you to claim a safe harbor under the DMCA from liability for contributory and vicarious copyright infringement. Sincerely, God
Bigger problems, and bigger computers to solve them on. This is certainly a fun example, and aesthetically pleasing as well.
Unfortunately, we're still a few generations of supercomputer off from being able to simulate ribosomes (at which point most of the cellular machinery will be suitable for in-silicio biochemical investigation), but this is an excellent step along the way. It's also a good to showcase Schulten's group's work on efficient parallelization of complex simulations. He's had to solve a lot of algorithmic issues in order to be able to run that simulation, so this is not just an example of "wait for a bigger computer". If you check out their web-page http://www.ks.uiuc.edu/, you'll find discussions of the underlying technology, which has required collaboration between biophysicists and computer science. My hat is off to them, especially as they not only achieved the proof of concept (we can simulate a small virus), but also gained biochemical insights (we didn't know they collapsed without the genetic payload). Bully for the Biophysicists!
Note: I don't work for them, but I admire the scale of simulations they do, and their willingness to make available to the community the tools they use.
the more accurate the calculations became, the more the concepts tended to vanish into thin air. R. S. Mulliken
I realize that the /. crowd is going to fellate any researcher who uses high-performance computing to draw pretty pictures, but from the Nature summary this sounds like a classic scientific case of showboating.
The researchers were using a technique called molecular dynamics, which attempts to model the movements of atoms in a 3D structure by integrating over Newton's equations. Force, however, is calculated using a coarse, empirical function of atom positions and their chemical properties. This model is weak, and it fails to produce physically-reasonable results on a whole variety of smaller problems, so it's an exaggeration to suggest that this simulation produced anything of physical or experimental relevance. And drawing strong physical conlusions from it? That's just crazy.
Before I get flamed by the MD crowd, I'll say that I am NOT suggesting that MD is useless. It's just that, it has a very short track record on problems of this size, and even in much smaller systems (i.e. fewer atoms), it's success rate is questionable. We can't even predict the dynamics of a single protein with this stuff -- it's absurd to suggest that it will work on an entire virus.
In short: don't be fooled. This experiment got into Nature because of its hubris and glamour, not necessarily because of its science.
P.S. I work in this field, so I'm posting anonymously.
Finally, I can say this for real: Imagine a Beowulf cluster (link is to Biowulf) of these!
The modeling software they used is called NAMD, free open source "parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems" that will run on commodity clusters of tens of Linux PCs on gigabit ethernet. In other words, you too can run the virus simulation on your own Beowulf cluster, if you don't mind it taking some years to run. According to NCSA's own press release about the virus simulation, it "only" took 35 processor-years, so if you have a 100 fast Linux PCs on a gigabit network lying around you can do it yourself in not much more than 4 months.
1. The full research page for this project is here. This is a lot better than the stuff linked through Nature and such.
2. The image was actually generated by our group, and specifically Anton Arkhipov, using our software package VMD. NCSA didn't have anything to do with it.