This research project investigated promoting student understanding of the Particulate Nature of Matter (PNM) through Inquiry Based Learning (IBL), visualization and modelling. A Practitioner Action Research methodology was employed and student performance at junior second level school was measured using diagnostic and summative testing. A module on this topic was prepared which included a student workbook and a teaching manual. Student and teacher reflections on the learning issues experienced were obtained through interviews and repertory grid analysis based on Kellyian Personal Construct Psychology (PCP) principles. Repertory grid analysis was used to highlight and rate aspects of students’ affective and cognitive learning experiences. Furthermore, in conjunction with PCP, student drawings provided as exam answers when they were asked to think critically within a novel problem scenario were investigated. This exploratory approach enabled the systematic metering of student comprehension of chemistry constructs and served to detect the learning gaps in their construct hierarchy.