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The National Research Council (2012) recently published A Framework for K-12 Science Education that describes a vision for science classrooms where students engage in three dimensions--scientific and engineering practices, crosscutting concepts, and disciplinary core ideas--to explain phenomena or observations they can make about the universe around them. This vision of science instruction is a significant shift from current classroom instruction. This dissertation provides detailed examples of how students developed and used models to build causal explanations of phenomena. I co-taught classes that focused on having students develop and revise models of electric fields and atomic structure using a curriculum that was designed to align with the three-dimensional vision of learning. I developed case studies of eleven students from these classes. I analyzed the students' responses and interviewed the students throughout the school year. By comparing and contrasting the analysis across the analysis of students' interviews, I identified four themes: 1) students could apply their ideas to explain novel and abstract phenomena; 2) students struggled to connect changes in their atomic models to evidence, but ended up with dynamic models of atomic structure that they could apply to explain phenomena; 3) students developed models of atomic structure that they applied to explain phenomena, but they did not use models of electric fields in this way; and 4) too much focus on details interfered with students' ability to apply their models to explain new phenomena. This dissertation highlights the importance of focusing on phenomena in classrooms that aim at aligning with three-dimensional learning. Students struggled to focus on specific content and apply their ideas to explain phenomena at the same time. In order to apply ideas to new context, students had to shift their focus from recalling ideas to applying the ideas they do have. A focus on phenomena allowed students to show their understanding through applying their ideas to new context. During this transition, students struggled, and in particular, had a hard time using evidence from experiments to justify the changes they made to their models of atomic structure. While the changes students made looked unproductive at times, by the end of the semester, students had developed models of atomic structure that incorporated relationships among charged components that they could apply to explain complex phenomena. Asking students to explore and evaluate their own ideas supported their development of models that they could apply to explain new context they experience in their future. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]