I am not sure if you use window.open you are creating a page class that inherits from the master page.
So JQuery is probabaly not included in that pop up. In addition popups aren't nice. people download all kind of things so they don't open. but it can be done like this:
protected void Button1_Click(object sender, EventArgs e)
{
string queryString =
"http://localhost:39208/TreeView.aspx?param1="
+ TextBox1.Text.Trim();
string newWin =
"window.open('" + queryString + "');";
ClientScript.RegisterStartupScript
(this.GetType(), "pop", newWin, true);
}
ClientScript.RegisterStartupScript will bring your jquery in the pop up