Biomolecules in open nanotubes.
The project will be an all-atom molecular dynamics simulation of biomolecules in a nanotube using a modified Lennard-Jones potential that allows variable hydrophobic interactions between the nanotube, biomolecules and water molecules. The project will consist learning how to use NAMD software and simulating the secondary structure of biomolecules on the Super Computing Cluster. The video provided above is an example of an NAMD simulation of a 12 Å by 12 Å carbon nanotube enclosed in a periodic box immersed in water molecules at 310 kelvin temperature. Every pause in the simulation is the reverse playback of the simulation.