Many schools have revised the sequence of high school science courses to be taken in the order physics, chemistry and biology. The Science of Atoms and Molecules is supplemental material, constituting about 10% of the course work and providing a progressive understanding of the centrality of atomic scale phenomena and their implications in each discipline. Upgrading the computational models developed in the Molecular Workbench, the materials allow students to experience the atomic world and build models that can be used to understand and predict macroscopic phenomena. Focused on the concepts of molecular biology, the basic physics of atoms and molecules is developed so that it can be further developed in chemistry. Student understanding of these concepts is leveraged to address ideas in molecular biology. For each of the three disciplines, two topics of two class period duration are developed for each of four strands: motion and energy, atoms and molecules, charge, and light. Professional development teachers need to use the materials and integrate them effectively into their courses is also developed as are assessments.