Hi Geowai!
This sounds a little more complex than I may be able to help you with.
The Tinkard link (by the way: thanks for mention this site – I had not heard of them before!) gave me an “410 – The requested page has expired” error 
To have LEDs move smoother you’ll either need a more potent controller, maybe something like a Raspberry Pi?
OR … use the approach I suggested.
The Arduino isn’t really designed for doing multiple things at the same time.
So having the nucleus and the atoms move at almost the same time you’d need to come up with a “task switching” mechanism, which makes the sketch much more complicated.
A good example (also showing the increased complexity) can be found here.