I loved the application of the theme, and the use of physics to cause chain reactions of decay. The physics also worked surprisingly smoothly at large scales. Was that the built-in physics engine, or did you use a physics plugin? The sound effects and music were also nice.
I tried to the juggling act a few times of using the rods, but I would always eventually meltdown. Eventually, I tried filling the whole screen with neutrons from the very beginning, so they immediately reacted with any atoms that spawned in. Then it just became a game of picking the right upgrades until my reactor had no more heat producing atoms.
This was still a joy to watch unfold, but not as fun to play. Maybe some upgrades should stack by multiplication instead of addition so the player never reaches 100%. [Edit: just saw the comment below, nothing new here :-P]
Overall, though, I still enjoyed this quite a lot! Great first submission to GWJ! I hope to see more :-)