Doing any sort of large-scale computational fluid dynamics or finite element simulations may require a great many cores. For example, you might want to conduct a very detailed simulation of the air flow around a vehicle, airplane, structure, etc. to have a basic understanding of its aerodynamics before spending time and money testing an actual prototype in a wind tunnel. You might also want to look at how very complicated, soft-body structures deform due to a variety of external stimuli. Such information would be crucial for certain materials science applications. Chemical reaction and acoustic simulations may also require a great deal of computing power, especially if you want to have a high spatio-temporal resolution.
Essentially, there are plenty of physical and theoretical science applications that can benefit from massive processing capabilities. There is a lot of fundamental science that is also performed in simulation before any actual tests occur.