Hi Mirko,
there are a couple of things in your post ...
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[li][b]Loop-breaker[/b]: indeed, it may happen that an algebraic loop be detected due to a controller, i.e. the controlled variable is directly dependent on the measured variable.
Unfortunately, there is no such thing as a loop breaker block for signals (red lines); and the only way to solve the issue is to place a normal loop breaker on a blue connection (flux) in a position such that the data loop is also broken[/li]
[li][b]flow through the membrane[/b]: it's not entirely correct that Qout is constant. The outflow is regulated by the flux through the membrane (J12) which is a manipulated variable, i.e. can be controlled[/li]
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If you need / prefer to directly control Qout, the only way is to re-write the model somehow in reverse, so that it exposes directly Qout (as an input) and e.g. the flux as an output.