Figuring out viruses

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Figuring out viruses

Postby dignan » Fri Mar 17, 2006 10:17 am

Hopefully one day in the not-too-distant future they can apply this technology to some of the viruses implicated in MS like EBV and HHV6a.

Supercomputer builds a virus - Vast simulation captures molecules in motion.

Nature - 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.

Klaus Schulten at the University of Illinois, Urbana, and his colleagues built a computer model of the satellite tobacco mosaic virus, a tiny spherical package of RNA.

Their success depended on the latest version of a computer program called NAMD, which Schulten and his colleagues have built over the past decade to simulate biological molecules. The program allows the several hundred different processors within a supercomputer to work in parallel on the same problem.

Running on a machine at the National Center for Supercomputing Applications, Urbana, the program calculated how each of the million or so atoms in the virus and a surrounding drop of salt water was interacting with almost every other atom every femtosecond, or millionth of a billionth of a second.

The team managed to model the entire virus in action for 50 billionths of a second. Such a task would take a desktop computer around 35 years, says Schulten. "This is just a first glimpse," he says. "But it looks gorgeous."

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 breathing1.

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.

Computer scientists have simulated viruses before, but they often had to limit themselves to one part of a virus and assume that the rest behaves in the same way.

Other biologists study how proteins fold by harnessing many idle desktop computers. But Schulten says that this would not work for the virus simulation, because all the atoms must be modelled simultaneously.

Ultimately, computational biologists would like to simulate larger viruses such as influenza or the complex biological systems in a cell - and for longer periods, such as the thousandths of a second that it might take to observe proteins in a cell switch a gene off. These computer models should allow researchers to discover details about such processes that they may miss by observing a real virus.

But such simulations will not become possible until the next generation of supercomputers are built in the next five years, Schulten says. ... 313-4.html
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Postby dignan » Thu May 11, 2006 9:34 am

Another story on the same research team at U of Illinois.

Scientists claim atomic-level simulation of living organism - 11 May 2006 - Researchers in Illinois have created what is believed to be the first atomic-level computer-based simulation of a complete functioning organism.

According to the scientists, the breakthrough has the potential to speed development of new drugs to combat viruses in plants, animals and, ultimately, people.

A research team led by Professor Klaus Schulten at the University of Illinois at Urbana-Champaign simulated a plant virus with as many as one million moving atoms.

The achievement is described by the team as historic due to the sheer complexity of the problem. Had the researchers relied on today's desktop computer systems, they would not have finished until 2041.

Professor Schulten's team used part of an SGI Altix 3700 Bx2 system located at the National Center for Supercomputing Applications. The Altix system allowed them to calculate how all the atoms interact every femtosecond, or one-millionth-of-a-billionth of a second.

Although the virus is so small that biologists refer to it as a particle, the ability to simulate the organism as it functions holds tremendous promise for medical research.

"It allows us to see how the virus assembles and disassembles," said Peter Freddolino, a member of the Illinois research team which also includes physicist Anton Arkhipov.

"Because assembly and disassembly are two of the key steps in the viral life cycle, understanding these events could lead to the development of drugs designed to attack them at these vulnerable points."

The project, reported in the March issue of the scientific journal Structure, is the first successful case of biological reverse-engineering of a complete virus. "This is on the highest end of what is feasible today," said Professor Schulten.

"The approach is something that we learned from engineers: reverse engineer the subjects you're interested in and test fly them in the computer to see if they work in silico (or simulated on a computer) the way they do in vivo (in the body).

"Naturally, deeper understanding of the mechanistic properties of other more complicated viruses will eventually contribute to public health and medicine."

The smallest natural organisms known, viruses contain intricate mechanisms for infecting host cells. The Illinois researchers simulated one of the tiniest and most primitive viruses in an attempt to recreate the process of infection and propagation.

The satellite tobacco mosaic virus attacks tomato plants throughout the US, and relies on a host cell and a host virus to reproduce.

While they simulated the activity of the viral organism over just 50 nanoseconds of time, the researchers were able to determine that the virus, which appears symmetrical, actually pulses in and out in an asymmetrical pattern.

"We observed that each part of the viral structure moves a little bit on its own," noted Arkhipov, who has worked with Freddolino and Professor Schulten since the project's inception a little more than a year ago.

The team's simulated findings support observations made by others in traditional laboratory work. Those earlier observations, however, left researchers wondering what caused the behaviour - something that remained a mystery until today. ... rst-atomic
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