Definitely check out the bioperl project, even though it might be geared toward more "real life" biology than simulations, for your specific case. There are resources for other languages as well, so you'll be able to draw your own conclusions. Have a look at the tutorial to see if it is what you need.

Also CPAN is as usual an authentic gold mine: AI::Gene is an example, besides having the whole bioperl distribution, of course.

As a general consideration, simulation often (if not always) involves modelling, and perl is certainly strong in handling flexible data structures, so even if your roll your own, you will certainly have all the basic language features you need.

-- TMTOWTDI