Conceptual understanding of the particulate nature of matter (PNM) has been shown to be critical for success in learning chemistry. In this study, a newly developed instrument called the Particulate Nature of Matter Assessment (ParNoMA) was used as a pretest and posttest to measure students' conceptual understanding of the PNM regarding phases of matter and phase changes. The capacity of animations of molecular-level water to remediate PNM misconceptions held by students from middle school through college was investigated and the results of male and female students were compared. The data indicate that molecular-level animations helped students to improve their scores on the ParNoMA. Pretest scores for male students were significantly higher than those for female students; the posttest scores for the students who viewed the animations were equivalent for males and females. Watching the animations seemed to improve the posttest scores of female students, closing the gender gap that existed prior to the int...