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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.
The simulations followed the life of the satellite tobacco mosaic virus, but only for a very brief time,
The nature article mentions a runtime of 50 times a billionth of a second, which I guess is 50 nanosecond, or 50 femtosecond, depending on how you define 'billion'. 50 nanoseconds is pretty good for a simulation nowadays, especially for a system of that size.
Look, it al seems very nice that they did this, fancy pictures and nature paper garantueed, but this really won't help us much further. This is no big scientific step forward. Virus processes happen at least in the micro/millisecond timescale, there's a lot of protein diffusion and refolding going on. Since the short simulation done here was an immense effort, it means that going to the timescales studying the real important processes is still way too far away. But who knows, maybe in ten years.
Right now, you could better use the same computer power used for this single project to study a lot more smaller projects that actually will give us insight into real molecular processes. Or maybe I'm just jealous ;)
molmod.com - computing tips from a molecular modeling
Sorry, but I don't see how this is insightful. Anyone...?
I pretend to know more than I really do by mooching off google and wikipedia.
Also, if you read the actual journal article (Structure, not Nature) you'll note that everything that was found in this study is consistent with experimental results.
Of course it is. I have worked in this field. When you do this kind of thing, you set up the parameters so that you already know that almost everything about it is going to be consistent with experimental results. There are other approaches - called 'ab initio' - in which you make no assumptions, but that involved a phenomenal amount of computing for very small systems. The point of this kind of thing is to set almost everthing to be realistic, with all sorts of approximations and fine-tunings, in order to test your assumptions about small parts of the model.
Folding@Home.
The folding problem is the one of the hardest ones.
I agree.
So don't get all blustery about it not being a solved problem. Cancer hasn't been cured yet either.
My point was that if you can't deal with the folding of even a moderately complex single protein, then to say you have modelled an entire virus to any significant extent is to mislead.