In order to defeat an enemy one must understand the enemy. This traditional military maxim also holds true in the field of biomedicine.

Computational biologists at the University and crystallographers at the University of California at Irvine recently simulated a virus for the first time. This view into the dynamics of a virus revealed the key, physical properties of a viral particle and is part of a broader effort to understand viral infections and how to prevent them.

“The next step is to go toward more health-oriented viruses – maybe the polio virus,” said Klaus Schulten, a Swanlund professor of physics who co-authored a report of the research team’s findings.

The polio virus is three times larger than the virus studied, the satellite tobacco mosaic virus, linearly and has 27 times as many atoms, University researchers said.

With a better understanding of the virus structure, assembly and disassembly, University researchers hope to pave the way for improvement of anti-viral drugs.

The collaborating researchers were able to do this by applying “reverse engineering.” This is a technique often used to design and test ships, planes and cars on a computer before they are built.

“(Reverse engineering) is a general technology in biomedicine used to describe with a computer the molecular machines in living organisms,” Schulten said.

Collaborators were successful in reverse engineering the tobacco mosaic virus, which was chosen because of its small size and simplicity. A virus is a tiny particle that hijacks a biological cell; infecting the cell and eventually making it produce many new viruses from the original. Viruses have evolved elaborate mechanisms of proliferation and departure from host cells, according to the research team’s Web site.

The technology to achieve biomedical reverse engineering only recently became available by way of local innovators.

“All the software was developed at the University,” said Peter Freddolino, a graduate student who worked with Schulten.

The computer simulation allowed the researchers to examine, for a short period of time, the genetic material within the virus. This first time look illuminated the interior structure of the virus and its assembly, which together with a drop of salt water included more than a million atoms.

“Ten years ago it was a very big challenge to simulate 10,000 atoms,” said Anton Arkhipov, a fellow researcher and graduate student.

The tobacco mosaic virus, however, is only a serious threat to tobacco plants. Researchers hope that in the future they will be able to simulate more, complex viruses. As of now there are technical issues that severely limit the duration of time researchers can observe the virus.

The research was supported by the National Institutes of Health and by computing time from the National Center for Supercomputing Applications through its National Science Foundation funding.