I don't know if this is what you're referring to, but a common application for government-owned supercomputers is simulating the degredation of nuclear warheads. The degradation of the fissile material as well as its surroundings is highly critical to a nation's security, and also very hard to model well.

Of course in an ideal world those cycles would be used to help cure cancer, but given that these warheads exist, it's probably a good idea to invest resources into getting an idea of what shape they're in.