Daniel Day-Lewis, naturally, went to town. He hit Paul Dano earlier than the intended mark during the scene where Daniel screams at Eli to heal his son. The look of shock when Eli tumbles to the ground is genuine. His hatred of Eli, which he continued even off-camera, led Paul Dano to confess he thought he would actually die during some points of the filming.
During the baptism scene, Paul Dano is actually smacking Daniel Day-Lewis around, bringing it around full-circle.