The Secret of Zoom by Lynne Jonell

Christina's parents are scientists but now she lives alone with her father. Her mother was blown up in a science experiment a few years before. Christina's father keeps her safe and isolated as he is worried about her winding up in the orphanage next door. One day Taft, an orphan boy befriends Christina and convinces Christina to find the secret tunnel that will help him escape from the orphanage where the children are starved and abused. Soon, she and Taft embark on a journey filled with mystery, crazy scientists and flying planes.