Java Molecular Dynamics   :  Performing molecular simulations "on the fly" is now possible with platform independent  JAVA language.   Check this l(growing) list of webpages for some fun with Java MD.   For the nuts and bolts of writing your own applet see our recent article in the CACHE Fall01 newsletter.

MOVIE! of a protein in action: alpha-hemolysin is a bacterial toxin protein.  The crystal structure shows that it is a heptamer which upon self-assembly shows a mushroom-like shape with a stem and an axial pore.  It is hypothesized that the heptamer assembles in the vicinity of a cell membrane, punches a hole in the membrane.  Molecules, such as water, ions etc. are then transported freely leading to cell death/lysis.  The toxin structure is similar to that of anthrax and cholera toxins. This is a semi-sci-fi version of the  hypothesis -- the goal is to get highschoolers excited! (purely educational...)

Open ended single walled carbon nanotubes are ideal model systems that resemble in shape and size to the pores in biological macromolecules, such as transmembrane ion channel proteins.  Simulations of nanotubes in aqueous environments can provide insights into thermydynamics and transport of small solutes in confined geometries (click the image for a movie).