From: Richard Willey on
> Because they are collected at different conditions. Therefore they are not
> the same. The function Y(t) takes in a set of known parameters that
> characterize the condition. So strictly speaking, the Y(t) are not the
> same for each set of data but they are correlated.
> Please let me know if the question is clear now.

Have you looked into a nonlinear mixed effects model?

http://www.mathworks.com/access/helpdesk/help/toolbox/stats/nlmefit.html