new browser no session merge

new browser no session merge

I have application A and application B deployed in two different app servers.
B is launched in a new browser window    when user clicks on a link in A .
So application B   starts as a  popup.
the problem I am facing is if I logout in B, automatically  A also logouts and  vice versa.
this may be happening becasue of session merge, when new window is called , i am need help please suggest me is there any way in java script or jquery to open   a new browser window   without passing  the session information ?