Re: expected ammount of protein production

Well, this is a very complex system you are trying to model.  Hard to
really get a feel for things through a small email as above but can offer
some suggestions at best.  If  you simplify this system * A LOT * then the
model wouldn't be that hard to code.  You  mention that you know the amount
of protein present yet you are trying to find the amount of protein
produced?  Surely I am reading this wrong (again, limited information :-).
 OK, so the question is how much protein is produced by a gene that can be
turned 'off' or 'on' by a substituent.  If you assume a linear throughput
then the system would be easy to model by, as you said, just coming up with
the length of the bind for each at what rate then calculating the amount of
protein produced.  If you have a binding algorithm then you may be able to
solve for length of bind of each substiuent then calculate the amount of
time the gene is turned 'on' and the rate at which the protein is produced.
 this will provide the amount of protein produced over time t.  But, often
translation isn't at a linear rate, it is highly dependent on many *MANY*
other factors (as I am sure you know) so it really depends on how complex
you want to make it.  If you are dividing the total time up into slices and
measuring the amount of protein produced over each period then one
suggestion would be to look at a monte carlo solution.   Hmmm, a good
starting point for this is http://osu.orst.edu/instruct/ch490/lessons/lesson15.htm
or better
yet http://osu.orst.edu/instruct/ch490/index.html
which is a good reference
point for programming such a system (FORTRAN is my preference though PERL
would be a  nice choice as well).

All in all, you seem to have the general impression of what you want and
how to get there.  To do it you will have to make some assumptions on
certain things (e.g. rate at which translation occurs, etc.) then go from
there.  You can do this without using differential equations by making such
assumptions.  BUT, DiFe was devloped  largely in response to the idea of
not making such assumptions.  :-)  If this is your system, feel free to do so.

Best of luck!!