The results presented here derive from a longitudinal study of Swedish upper secondary science students' (16-19 years of age) developing understanding of key chemical concepts. The informants were 18 students from two different schools. The aim of the present study was to investigate the mental models of matter at the particulate level that learners develop. Data were collected using semi-structured interviews based around the students' own drawings of the atom, and of solids, liquids, and gases. The interview transcripts were analysed to identify patterns in the data that offer insight into aspects of student understanding. The findings are discussed in the specific curriculum context in Swedish schools. Results indicate that the teaching model of the atom (derived from Bohr's model) commonly presented by teachers and textbook authors in Sweden gives the students an image of a disproportionately large and immobile nucleus, emphasises a planetary model of the atom and gives rise to a chain of logic leading to immobility in the solid state and molecular breakdown during phase transitions. The findings indicate that changes in teaching approaches are required to better support learners in developing mental models that reflect the intended target knowledge.