@prisoner849 yep, you are absolutely correct, for better performance, I did create a point cloud version of it, with lots of your help actually 
(Display sprites correctly with customized Points material?, Instancing Point Cloud - #11 by lxiangyun93)
It’s a great alternative if there are more atoms, However, people still prefers actual spheres and it would be great if we could make this work as well. Again, the rendering performance with actual sphere is great, it’s only the overhead that’s too costly currently
I did a quick test, showing sphereTemplate.clone() along takes ~ 70-100 ms out of the 300ms total time, maybe we could bypass it somehow? or maybe the way I combined the buffergeometries were not ideal?