This work is directed towards promoting students understanding of the Particulate Nature of Matter (PNM) through Inquiry Based Learning (IBL), visualization and modeling. A teaching module on this topic was prepared which included a student workbook and a teaching manual for junior secondary school students. An action-based methodology was employed and student performance was measured using formative and summative testing. Student input was obtained on the learning issues experienced by them via interviews and repertory grid analysis based on Kellyian Personal Construct Psychology principles. Initial results point towards a better comprehension of PNM by the intervention group as opposed to their control group peers. Repertory grid analysis was used to highlight and rank aspects of their affective and cognitive learning experiences. This approach has enabled the systematic metering of student comprehension of chemistry constructs and served to detect the learning gaps in the construct hierarchy encountered by the learners.