Pause a Simulation from MATLAB

Hi,

I have a SIMULINK System consisting of 2 models. I'm trying to control them programmatically using a MATLAB script. I keep checking for some flag values (Consider them to be just some MATLAB variables for simplicity. One for each model) based on which I try to pause the corresponding SIMULINK model. When I use the customary pause function, its freezing the entire MATLAB application and so the other model is stopping too. Is there a way in which I can pause only the corresponding model like the thread.sleep command executed in Java and other platforms?

Thanks in advance.