Basically, here in the Theoretical Biophysics group we use the computer to simulate the physics behind biological processes. We know that a lot of biological processes happen, but we don't know how they happen. Researchers in the group are trying to figure some of these things out. We are have people interested in drug design; making sure that the drug is going to be accepted in a cell and things of that nature. Also working with diseases to figure out how they work.

We have another main area in the group, and that is writing software packages to help the researchers do their work. And not just researchers in our group. All of the software that we produce here is freely available. You can go to our website and download any of this software free of charge and use it.

I want to go into some more detail on some of the software packages that we are working on. The first is VMD which stands for Visual Molecular Dynamics. VMD is basically a very good graphics program that the researchers can use to view the molecules and systems that they are interested in.

VMD will run on Windows as well as virtually any unix platform that has a graphical display. It is actually one of the very very few graphics programs in this field that will run on Windows. You can see a number of the pictures that can be produced with VMD on the VMD homepage. A person can download VMD and then download the protein information and create things like that. VMD has been out a few years now, and is used by literally thousands of researchers around the world.

The group develops another software package called NAMD. NAMD is basically a molecular dynamics simulator. It actually calculates the physics. It figures out all of the forces on each atom and how they interact with each other. This is extremely computationally intensive. Because of this, NAMD is designed to run well on the fastest Cray supercomputers, or SGI Origins, etc. It also, however, runs on a linux box. So, it will run on the very high end machines, but it will also run on a relatively low end machine.

Recently the group started working on another software package called BioCoRE. We wanted a way to tie our software programs (VMD, NAMD), as well as other software programs not produced by us, together more tightly than they have been in the past. BioCoRE is a "collaboratory for structural biology". The term "collaboratory" means: Laboratory without walls. When a person is doing research in this field (or virtually any other field these days) all of the people that you need to work with are NOT going to be in the same room as you. They might be in Germany, or California, or New York... But they probably are NOT going to be exactly where you are. So, we wanted to work on a way to make research easier. To make people feel as though they WERE sitting in the same room with each other. And, we chose to do this over the computer.

Just this past week we released the first version of BioCoRE, and I want to show you a little bit about what we can do with it. BioCoRE has a Notebook tool that lets you send messages back and forth, similar to what you could do with email or a newsgroup. It is searchable so that you can look up information that has been discussed in the past. The Notebook also stores other sessions in BioCoRE.

BioCoRE also has a monitoring tool that can be used to monitor the progress of NAMD runs. Before this tool became available, the typical way that a simulation worked was this: The person started the simulation, waited the days, weeks, or months for the simulation to finish. Then, they look at the output files and check to see whether or not things worked right. If, for some reason, things were not working right, all of this computer time was essentially wasted.

With this tool, the users can check the status of their simulations AS IT IS RUNNING. We can find out information about the processor usage, temperature and energy information of the system, and we can even pull up animations that show how the system is changing over time. This can be quite useful, because I might look at this simulation and realize that it isn't working properly. I can then terminate the simulation, fix what was wrong, and restart it. By doing this, I have saved many many hours of computation time on the supercomputers. And, time is money.

BioCoRE also gives the ability to start VMD runs. I'm going to turn it over to Justin now who is going to talk about Interactive Molecular Dynamics, which is another way that we are putting the scientists in control of their running simulations.

IMD gives us immediate feedback and finer control over our simulations. The haptic is a natural interface for IMD because force feedback gives us a strong impression of being "part" of the simulation, helping to guide our movements.

Lac Repressor: Docking is a process in which a smaller molecule referred to as a ligand binds to binding site of a larger molecule called a receptor. Since all drugs must bind to particular receptors in our bodies in order to function, understanding the docking process is of great interest to the pharmaceutical industry. The Lac Repressor system shown here is of interest not only as a paradigm for small-molecule docking, but as an example of how a cell uses feedback loops to control its metabolism.