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I'm assuming you are interested in using Java RTS (Sun's implementation of JSR-01) since you posted to this forum.
Java RTS has more than enough predictability to simulate (and in fact replace in production) any PLC.
My suggestion is that you use Java RTS for the complete simulation. It's much simpler since the complete logic can be executed in a single JVM no PLC would be required.
If you need proof that Java RTS is so capable check out these videos.
http://www.youtube.com/watch?v=xH1yUXd9krU (JavaOne 2007)
http://www.youtube.com/watch?v=g5Ky2ApC4Y4 (JavaOne 2008)
You can download Java RTS here
Note that for academic work there is no fee to use JavaRTS.
Please stay in touch and let us know more about your porject. Traffic signaling and control is an area in which I am interested and for which, we believe, Java RTS offers significant advantages.