Peer instruction (PI) involves interaction between students and provides opportunities for students to reveal their own ideas, articulate their thinking, and facilitate construction of their knowledge with social interaction. Since the classroom environment of PI provides a rich information for students to discuss scientific phenomena, this research examined how students' mental models interacted with Peer Instructional elements in an undergraduate level physics course. After the identification of students' mental models of wave-particle duality in the first step of the project, the analyses of several data sources showed that some group-related issues, such as the explanatory based annotations before classes, good performance answering conceptual questions, and discussion of additional concepts during classes, were important for scientific understanding. When students have similar group environments (i.e. peers in the same group), then individual pre-class preparation had a positive influence on students' scientific mental models of wave-particle duality. In addition, students having scientific models indicated that the satisfaction with their knowledge and the importance of conflict with their peers for their learning. All students in the classroom stated they benefited from peer discussions in different ways such as by recalling and reinforcing their knowledge, by getting feedback, and by reconstructing their knowledge. Both pre-class preparation and discussion of additional concepts and conflicting ideas in peer groups should be promoted in physics classes for facilitation of construction of scientific mental models.