Explanations involving submicro levels of representation are central to science education, but known to be difficult for students in secondary school. This study examines students' written explanations of physical and chemical phenomena regarding matter and changes in matter, in a large-scale test. This is done in order to understand linguistic challenges in constructing submicro level explanations involving the particle model of matter. Drawing from systemic functional linguistics, the lexicogrammatics used in explanations for realising experiential meaning in student explanations were analysed. We used answers to two partly constructed response items from the Swedish part of Trends in International Mathematics and Science Studies 2007, grade 8, to sort out explanations referring to the particle model of matter. These answers (86 from 954) were analysed regarding choices of vocabulary and grammar to distinguish between macro and submicro level of representation. The results show that students use a wide variety of lexicogrammatical resources to realise what happens on both macro and submicro level of representation, with greater diversity of verbs on the submicro level of explanation. The results suggest an uncertainty about the distinction between macro and submicro level of explanation.