This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This proposal requests CPU time on the terascale computers Cray XT3 (BigBen) at the Pittsburgh Supercomputing Center, Tungsten at the National Center for Supercomputing Applications and Blue Gene at the San Diego Supercomputing Center. The proposed research involves novel large-scale simulations investigating Enzyme Catalysis, Ion Channels and DNA-Carbon Nanotube hybrids. The methods used will include Density Functional Theory based Car-Parrinello molecular dynamics, hybrid quantum mechanics-molecular mechanics and classical molecular dynamics. The work proposed here is currently funded by NSF and NIH.