The bigger picture in all of this? Making a game in which the player is an explorer of sorts, investigating various planets for human colonization. Part sim, part RPG, all based on real science. For designing the atomic structure specifically? The player will be able to get perform experiments on various samples gotten from the planet, and then “deep dive”, visually speaking, into what makes up that sample, from seeing what compounds make up the sample, to the molecular structure of those compounds, to the atomic structure for those molecules, all the way down to the quantum structure. There will also be fires and explosions of course, can’t make a game without having explosions, can we? 
On the smaller scale, the scientific subsystem I’m designing for that game, will be released as a project for free (see my Chemistry! thread in WIP). This will, or rather, should be, a good project for e-learning, testing, real-time visualizations, and calculations. This is only the first part of the project, chemistry. I also need to work on systems for astronomy, biology, geology, oceanography, Newtonian physics, planetary science, and quantum physics.