This is a clear case for Blender in my opinion. Freeware, super-robust, Linux, Mac and Windows, and exceptionally powerful and flexible - enough so that despite being freeware, it's finding acceptance in the 3D industry in commercial pipelines - because it does what it does quite well.
Hope that helps.
It is a bit hard to say what particular physics/biological processes do you want to model, so I will give a more general recommendation:
Wiki page on software for molecular mechanics modeling
In particular, I would point you to LAMMPS that is suited for distributed systems and is very popular.
What about software-as-a-service offers? With https://www.circuitlab.com/ you can run simulations in your Browser. It is commercial software, subscription-based.
I don't know how well this can scale up. Maybe the web can handle only simple circuits.
You didn't say which platform you're on, but if it's Windows, you could use AutoHotkey for this.
You can have it open (or activate) your editor or IDE if you like. Then use Send to send keystrokes. You can adjust the speed at which it spits out characters using SetKeyDelay. You can have it control the mouse too, if you like. Pretty much anything you can do ...
I would suggest trying Houdini. You can create an inflatable balloon object out of a mesh with any properties you desire. There is actually a beginners level tutorial that shows how to do exactly what you are talking about. An apprentice edition with very few restraints is available for free.
Here are a couple free online simulations, although they don't let you view interactions with objects they do allow viewing interaction between sources and let you vary parameters of the sources.
What kind of protocol(s) are you using? If RPL is an option, then you can quickly start with Contiki OS, which has a simulator (Cooja) to run your experiment. NS2 (for Linux) is a much more open and general simulator with very big capabilities.
You want Selenium
Selenium automates browsers. That's it! What you do with that power is entirely up to you. Primarily, it is for automating web applications for testing purposes, but is certainly not limited to just that. Boring web-based administration tasks can (and should!) be automated as well.
Selenium has the support of some of the largest browser ...