I am developing a scientific application used to perform physical simulations. The algorithms used are O(n3), so for a large set of data it takes a very long time to process.
Simplest way to distribute computing on a Linux cluster is to use MPI. I'd suggest you download and look at MPICH2. It's free. their home page is here
If your simulations are completely independent, you don't need most of the features of MPI. You might have to write a few lines of C to interface with MPI and kick off execution of your script or Java program.