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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
There are millions to hundreds of millions of atoms in a typical virus. Here is interesting virus simulation info
Oh yeah, I know (hope?) you're joking, but modelling millions of atomic interactions is, as they say, nontrivial.
Man, you really need that seminar!
I once read that if you converted all the sand of the earth into processors, it would still take ages to accurately simulate the folding of a protein. Is this just "zooming out" and ignoring things like protein folding?
10 ?"Hello World" life was simple then
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
From TFA the virus so simple as to need a second more complex virus in order to replicate. Even so, the simulation only covered 50 billionths of a second, or about 50,000 frames. The Nature article stated that in the next 5 years it may be possible to simulate more complex viruses. Its amazing to see how complex life is that even the most powerful computers we have come up short.
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.
What about the fact that virii aren't usually considered to be alive, not being capable of reproduction outside of a host cell?
What is your evidence that life is completely deterministic atlarge scales? If you've figured that out, you've solved problems for a lot of scientists, philosophers, and theologists.
Most large-scale patterns and processes in nature are stochastic and the outcome is one of a distribution of possibilities, similarly to quantum mechanics. In general, the same pattern can result from diverse processes (e.g., banded patterns of vegetation from dispersal dependence or topographical variation), while a single process may give rise to many different patterns (e.g., fire disturbances may result in even-aged forests or mixed-age forests).
Philosophically, however, the question is interesting and has, as most interesting philosophical questions, been discussed before. Look up "Laplace's demon" sometime(the demon being the closest thing an 18th century mathematician could imagine to a supercomputer with access to infinite information): if one assumes that the world is inherently deterministic(from our point of view, this assumes the "hidden variables" interpretation of quantum mechanics) and proposes that some kind of being could in theory have access to unlimited information about it, then concepts such as time lose much of their meaning, since things are "destined" to happen before they actually do happen(and in what absolute sense can they then be said not to have happened already?).
Obviously, free will in the absolute sense is also non-existent from this point of view.
I am a computational chemist, and although this is a good piece of work, it's really not a big deal compared to what everyone else out there is doing. There are also a few caveats here...
First off, this is not actually a virus perse, it's a satallite virion which can only reproduce during cocontaminant Tobacco-Mosaic Virus infection, and does not have the ability to infect anything itself. It is also only a fraction of the size of most viruses.
Second, Molecular Dynamics is a purely emperical, non-precise method for doing molecular simulation. Although to be fair, ab initio or Density functional theory approaches to this kind of a problem are impossible at this time. But there are some QM semi-emperical methods that are gaining popularity in the biology world.
Third, this is a tiny, minute time-scale for such a large chemical system. It's one thing to be working femtosecond timescale when you are simulating electron exchange between to small molecules, but on a system of this size means very little, especially when using an imprecise measure such as MM.
I guess I should also point out that it's not that hard to set up a simulation such as this when you are starting out with a hi-res x-ray crystal structure for you're starting coordinates. It's really just how much computational capacity you have.
Any thoughts?
-Ryan
This is an interesting coincidence because I used to reflect deeply on this exact subject a few years ago: what if a supercomputer could simulate a human ? I'll be honest here: I am literally _astounded_ to discover that this scientific team has successfuly simulated a virus. I didn't thought supercomputers were powerful enough for such a task. I just finished reading some articles about the experience and I now understand why this has been possible: they used some empirical functions instead of implementing exact physical laws (would have required much more computing power) and they also simulated the virus for only 50 billionths of a second. But still, they seem to have successfuly simulated life.
Most people don't realize the significance of this event, it means that given enough computing resources we could theoretically simulate humans ! One day we will have enough computing power to run such a simulation. And when it will be done, this human life simulation will have the potential to prove (or disprove) that humans are "just" a bunch of atoms following physical laws and nothing more.
This is huge. Think about it. I know this may sound sad, but personally I am convinced that any life form, including humans, is just that a complex assembly of atoms following physical laws, there is no soul, no afterlife, etc. This human life supercomputer will prove I am right :)