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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
Hmm, now... do I believe the scientists in charge of discovering this, or some random guy on slashdot...
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.
Excuse me, but why is the parent modded as a troll?
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.
Plenty of proteins have been modeled using QM/MM and had the results validated by empirical studies.
Sorry, but as far as I know there has not been a single successful simulation of protein folding. Simulation the general behaviour of a complete protein is not the same as completely understanding the interactions and structure.
Folding@Home.
I agree. It's just another "computer stunt" paper. The supercomputer centers love these things, as they (sort of) justify their existence. I think if they tore apart these big parallel machines and gave a small piece to small research groups around the country, a lot more science would get done. It takes a _lot_ of simulations to really learn anything, not just one moon shot hero run. The idea of these grand challenge computational problems soaking up all of the resources is so 80's. You can load up a 2-way dual core (for 4 cores) system (say, Operton or G5) and load up 16GB of RAM and get a lot of science done. This was even true more than 10 years ago: it was faster to run on a RISC workstation than to submit a job to a remote CRAY somewhere, where it sits in a queue for a few hours of cpu time. And debugging was a lot easier, too. I do think there are a few problems that really do require a large, dedicated system - but not very many.
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.
The folding process can take place over microseconds of time.
Many processes, such as conformational changes, ion flow, and ligand binding can occur much faster (1 to 100 nanoseconds).
So if you start to simulate an already folded protein and watch its dynamics you can still discover what sort of behaviors it may do. Without having folded the protein.
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