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One of the goals of science education is to help students make sense of the world around them. To that end, it is critical that students understand the central ideas in each discipline like, in chemistry, energy and interactions. These ideas are of particular importance because they are directly related to one another and are relevant across other science disciplines. Unfortunately, researchers have found that students often struggle to develop a deep understanding of these ideas. To uncover better ways to support students' learning, I explored how students understand interactions and energy in both chemistry and biology. In this dissertation, I focused on London dispersion forces (LDFs), a type of intermolecular force (IMF) which occurs between all atoms and molecules. Specifically, I used the lens of causal mechanistic reasoning to think about students' knowledge. That is, how students connect the properties and behaviors of the underlying entities to the overall phenomenon. If we can help students to develop this type of understanding, they may be able to make powerful predictions about new, unfamiliar phenomena in which IMFs play an important role. Additionally, I explored how students thought about the energy changes which result from the formation of LDFs. Lastly, I designed assessments to elicit and characterize explanations of protein-ligand binding, a biological phenomenon governed by IMFs. To explore these questions, I used a mix of qualitative and quantitative techniques. I designed tasks to elicit causal mechanistic responses from students, using students' responses to refine the task design. I also developed coding schemes to characterize students' engagement in causal mechanistic reasoning. Furthermore, I developed and used automated resources to analyze thousands of responses in a matter of minutes. In these studies, I focused primarily on undergraduate students enrolled in Chemistry, Life, the Universe, and Everything (CLUE), a transformed, core-idea centered general chemistry curriculum. From these studies, I found that the majority of CLUE students could leverage electrostatic ideas to explain LDFs, and that a meaningful proportion of those students could provide a full causal mechanistic account. This highlights the importance of emphasizing these interactions, and the mechanism by which they form, throughout the general chemistry course sequence. Additionally, students who used causal mechanistic reasoning to discuss LDFs were more likely to use that same reasoning in the context of the associated changes in potential energy. However, this relationship was weaker among those providing a partially causal mechanistic response. This suggests that more work needs to be done to find ways of supporting students to connect the ideas of interactions and energy. Additionally, in this thesis, I describe the process by which I used iterative design to develop a task eliciting causal mechanistic explanations of a biological phenomenon. In future work, these materials can be used to explore how broader groups of students engage with this task in an effort to foster interdisciplinary coherence. [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.]