[font=comic sans ms,cursive]Java 3D? your wasting your time, you'd be much better off learning OpenGL (or using it shall i say) to make simulations rather than Java3D.[/font]
[font=comic sans ms,cursive]I mean can you think of any simulation software developed in Java3D? as far as im concernced there 'might' be some but the ones i know are veyr succesful and made in OpenGL for example: Game engines i.e unity3D(mainly c++ but other languages too e.g C),Blender: Computer Graphics and animations software + GE written in OpenGL and python. [/font]
[font=comic sans ms,cursive] [/font]
[font=comic sans ms,cursive]Well there you go i could give you many more examples.[/font]

[font=comic sans ms,cursive]note: remember im not criticising java but rather Java3D since there are better programming languages for making simulations.[/font]

if it's no the case ignore me but... it totally depends on how detailed your 3d graphics should be, i guess you want to concentrate you developement on the simulation itself rather than on fancy 3d graphics. using opengl will eat alot of time.. better use a simple graphics engine e.g. http://jmonkeyengine.com/ (it's based on opengl)
btw i never heared of java3d, maybe it's what you are looking for