Do you have any experience with Conway's Game of Life? It might not be the most realistic model, but it has clear rules and often is used for learning automata. There is an example on Processing's website here:  http://processing.org/learning/topics/conway.html

The chapter in the Nature of Code is also a pretty good introduction to the subject:

http://natureofcode.com/book/chapter-7-cellular-automata/

If I search for cellular automata in Google it was as I expected, I got loads of hits related to Coways Game Of Life and you couldn't use these to ' simulate a human cell in its natural aqueous environment'. In fact I am not sure what you mean because thre are many types of ' human cell' and what is its ' natural aqueous evnvironment'

I assume that you are looking for something more scientific. If that is the case then this is what I suggest.

First thing - Forget about programming, model the system instead.

When developing software It is always easier if the design and implementation activities are kept separate and the design is done first.
Many programming newbies attempting to create something like this would attempt to write some code without fully understanding what is required so invariably ends up back tracking on what they have done.

The System Model

1. make a list of the things that you want to know about the cell e.g. temperature, electrolyte balance etc. These are called attributes and should be nowns. (If you have verbs in your list then see 2)
2. make a list of the things the cell does (these should be verbs)
3. same as 1 but for the environment
4. same as 2 but for the environment
5. define the rules of the simulation i.e. cause and effects how the cell and enviroment interact
   

Once you have this then you can consider programming and in this case I would suggest two Java classes Cell and Enviroment.

Once there is a clear model there many people on the forum that could help you with the classes.

Ok first of all thanks for the reply's.

I was thinking about the rules a bit more in detail. Basically each cell (or lipid vesicle as it is in this demonstration) needs to:

Looks more like managing particles (several Processing libraries manage them well) rather than a cellular automata (generally implying a continuous medium and in place changes).