In this paper, one student's learning process in a course on quantum atomic physics in grade 13 of a German gymnasium (secondary school) is described. The course lasted 16 weeks for a total of approximately 80 lessons. The aim of the present study is to elaborate the student's cognitive system for atomic physics as a hypothetical pragmatic model to describe, analyse and explain his thinking and learning while interacting with the teaching input. In this paper, the student's learning pathway is described as a sequence of several meta-stable conceptions of the atom, starting from a planetary model. His final cognitive element 'atom' following teaching is displayed as an association of three parallel conceptions including his initial planetary model, a state-electron model and an electron-cloud model. These different conceptions influence his thinking in different 'strengths' and 'status'. In addition, the student's meta-cognitive beliefs on physics and the way they are affected by a quantum world view are briefly described.