Computer-based simulations can help students visualize chemical representations and understand chemistry concepts, but simulations at different levels of representation may vary in effectiveness on student learning. This study investigated the influence of computer activities that simulate chemical reactions at different levels of representation in students' conceptual understanding of the particulate nature of matter (PNM). The participants included 170 second semester general chemistry students and were divided into two groups: one interacting with computer simulations at the particulate level and one at the macroscopic level. Students' understanding of the PNM was measured using the Particulate Nature of Matter Assessment. In addition, factor analysis was performed to detect latent concepts in the instrument. Results showed that dynamic simulations at the particulate level helped students understand the PNM in chemistry involving particle motion.