As Hype is not a 3D app, a key issue is handling an object that moves in front of something and then in back of it. The only way to do this is to have duplicates front and back and turn them on and off in sync with the motion.
Here's an example of foreground/background transition. (Ideal for those who feel like popping a dramamine, putting on some sitar music, and staring at the screen for half an hour.) Note that the pink object is tilted back on the X axis.
The objects have been split into sections with individual sections appearing and disappearing. Try putting an object between the layers and the two will appear to be swimming around it.
SimpleSwirl.hype.zip (33.6 KB)
Another key issue is that flat is flat. Hype won't let you put object one inside object two, rotate object 2 in the X axis and counter rotate object one on the X.
The clunky way to handle the atomic concept would be to use curved path segments for from at back and have the proton (or whatever) scale up and down at a convincing ratio (the opposite of ease in / out).