This study has been designed to examine the difficulties grade 7-9 students encounter in the process of developing a model for understanding the concept of particles as part of their instruction in the particulate nature of matter. Seeking also to discover how these difficulties change over time, the study further sets out to establish what acquired knowledge by students about the subject and to determine the extent of the shift between assimilated knowledge and knowledge to be taught, attempting at the same time to discuss this shift and make recommendations for solutions. The instrument was administrated to a total of 163 grade 7-9 students and the data collected was qualitatively analyzed. The study determined which ideas the students based their particle model on. It was seen that there was no overlap between assimilated knowledge and knowledge to be taught. In addition, the study revealed 8 misconceptions so far not covered in the literature.