Description of Matthew's Research

My son, Matthew, is in the PhD program for physics at Brandeis University in Boston. I know there are some relatives out there wondering what he is up to so I thought I'd get the scoop from him and write something up in this blog. Hmmmm... where to begin? It's pretty complicated. Oh bother. I'm just going to quote him. Here it is:

"I'm studying part of the assembly process of bacteriophage MS2 (a bacterial virus). MS2 is made up of 180 "dimers" with 90 of them being what I'll call type "A" and 90 being type "B". They form a protective protein shell (made of "dimers") around the viral genetic code, a strand of RNA. A "dimer" is just two proteins (called "monomers"), and a protein is just a large molecule (made up of around 2,000 atoms). Viruses typically take milliseconds to seconds to form once all their parts are present. However, this is a very long time for computer simulations that use straightforward algorithms; in fact, it would take thousands of processors at least a lifetime to simulate problems of interest. This means that it's necessary to use special tricks to figure out what's going on during assembly. Experimentalists have the opposite problem. Often, experiments cannot capture the specifics of what's happening because it occurs so quickly.

An added complication to this process is that the "dimers" switch types during formation (remember there are 90 of each type "A" and "B" in the MS2 virus). The fact that they switch types is an important part of their formation allowing the virus to assemble much more quickly. Some experimentalists believe that RNA binding to the "dimer" drives this switching process, but this is based off of indirect evidence. The goal of my research is to see how the presence/absence of RNA binding to the "dimer" affects its ability to switch types. This will hopefully lead to predictions that can be measured by experimentalists. This research is important because relatively little is known about the assembly process of viruses, and a better understanding of this process could lead to the development of antiviral drugs that target this stage of infection. The antiviral treatments that have the most effect are the ones that target multiple stages of the virus's assembly."

Cool, ha? He's like a super hero or something saving us from the evil viruses.