Computer builds virus

This is too cool.

One of the world's most powerful supercomputers has conjured a fleeting moment in the life of a virus. The researchers say the simulation is the first to capture a whole biological organism in such intricate molecular detail.

The simulation pushes today's computing power to the limit. But it is only a first step. In future researchers hope that bigger, longer simulations will reveal details about how viruses invade cells and cause disease.

(Continued below)

The fleeting simulation, published in this month's Structure, reveals that although the virus looks symmetrical it pulses in and out asymmetrically, as if it were breathing.

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.

Two comments. One, man, this is just such cool stuff. It's amazing what can be simulated on the computer, and the kind of insight we can gain from it. But two--this isn't meant to necessarily supersede what we see in the "real world"--it's meant to complement it. When something in the model contradicts what we see in the "real world," that opens up a new area for investigation--was the data that was entered faulty in some way? Was one of the assumptions incorrect? Where are we lacking information that could allow us to more correctly understand the phenomenon we're investigating? Computer models are just that--models, even the most powerful ones. They can greatly improve our understanding, but they're only as good as the information they're based on--"garbage in, garbage out," as they say. Still, I'm excited to hear about advancements in this area, since viral (or bacterial) invasion of cells is an area that's obviously difficult to observe in real-time, much less to sort apart all the different genes and cascades in both the microbe and the host that facilitate such invasion.

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The fleeting simulation, published in this month's Structure, reveals that although the virus looks symmetrical it pulses in and out asymmetrically, as if it were breathing.

Symmetry breaking! Like in particle physics! Wow!

By Roman Werpachowski (not verified) on 19 Mar 2006 #permalink

I wonder if the viral walls exert a pressure that assists with the injection of DNA into the cell? Or are we too micro-level for that? :)

I would say that this is significant, if not for any other reason that as a person with an MD background, I would have loved to be part of such a project. This is just the start. Large, multi-scale simulations are going to play a big role as we move from simulating invidual proteins and biological components to large complexes and cellular machinery.

It's extremely cool. But it's just 10^-10 second (give or take order of magnitude) in the life of the virus. And that took several supercomputers 2 weeks. I sure hope that the exponential increase in computing power continues for a while longer. It would be so nice to see a day in the life of a bacterium simulated (but I guess 1 bacterium might be millions by that time)

It would appear this new computr contraption would be the ideal place to place the leftover hiv viruses that Rebecca Culshaw couldn't get into her adding machine whilst working on mathematical models for AIDs. Think of it, you could get a computr with AIDs and then toss in some of David Rasnick's
vitamin cures and heal the computr. Just an experimental thought. I'm shur it wouldn't work.

By McKiernan (not verified) on 19 Mar 2006 #permalink

Anyone else having a Matrix moment?

Very very cool and interesting.

In the mid 80's, i worked for Purdue University. They had cold virus simulations on a Cyber 205. Hot machine at the time. 16 MB RAM, 35 MIPS, 400 megaflops. $15,000,000 of machine. The word processor on my desk has more resources. Unfortunately, i don't know any of the details of what was attempted back then.

When weather forecasting was claimed to be 'fast enough for real time' - that is, you get a 24 hour forecast, but it takes 24 hours to run... that was exciting, since it was clear that it wouldn't be long. Now 24 hour point casting for 2,000 sites is performed by a PC.

They don't say what machine did the work. Simple calculations suggest that a 1,000 CPU machine ran for two weeks.

The headline of this week's Weekly World News is Computer Virus Crosses Over to Humans - or somesuch.

Fiction... or fact?
(cue dramatic music)

So, I don't know what they were running this on either, but I manage two large compute clusters, and we've just gotten into the business of running these large simulations for the Medical Research groups attached to our Med. School. Right now we're trying small mutation simulations. It is a challenge to keep up with the data throughput demands...but it fuels our research in grid computing environments.

By montepellier (not verified) on 21 Mar 2006 #permalink