We studied the use of online molecular dynamics simulations (MD) to enhance student abilities to understand the atomic processes governing plastic deformation in materials. The target population included a second-year undergraduate engineering course in the School of Materials Engineering at Purdue University. The objectives of the study were to help students (i) understand the atomic-level processes that govern plastic deformation in metals, and (ii) develop a more intuitive understanding of how materials look and behave in atomic scales. The treatment consisted of traditional lectures followed by inquiry-based simulation lab activities powered by research-grade computational tools. Two lectures by the instructor reviewed the topic of plastic deformation and presented the basic physics of modeling MD to provide a description of materials with atomic resolution of the forces. Next, the students used a simulated laboratory experience to conduct several inquiry activities using fully interactive online MD simulations. Students needed to use the visualizations provided by the simulation to evaluate the atomic processes responsible for plastic deformation of materials and they computed values of various materials properties. Our first analysis compared differences between students who attended one or two lectures and those who attended no lectures. The results showed that participation in the background and/or pre-laboratory lectures supported student abilities to recall specific facts and behavior of materials explicitly taught during instruction. The lectures did not prepare most students for transferring what they had learned in the lecture or prelab lectures to problems they had not previously encountered, but were first presented in the laboratory activities. However, most students who participated in the laboratory experience demonstrated the ability to transfer what they had learned to predict how an unfamiliar material would behave at the molecular level. This instructional approach can be generalized to other learning experiences designed to help students apply abstract fundamental engineering principles to evaluate a larger context of unfamiliar situations.