Nanoscale particles have become promising materials in various biomedical applications,however, in order to stimulate and facilitate these applications, there is an urgent need for the understanding of their nanotoxicity and other related risks to human health.In this talk, I will discuss some of our recent molecular modeling work on nanotoxicity with IBM Blue Gene supercomputer.We show that carbon-based nanoparticles (carbon nanotubes, graphene nanosheets, and fullerenes) can interact and disrupt the structures and functions of many important proteins.