Depends

some applications allow to tie down the application to a single core. An example is Prime95 where you can specify the physical or even the logical core you assign to run the application. This is done on the software level of the application itself, though. If now further specified, the OS kernel will use some kind of load balancing and that's where you will loose out, especially in situations where a lot of caching is involved which is typical for scientific applications. A lot of the overhead comes from having to write back the data to memory and then fetch it to the other cache.