NOTE - This does NOT mean the Quarks (red/blue/yellow/green floaty things)
Once you get through the tutorial level and past the Quark pond there is a sign that says
Gluons - 233
Leptons - 69
Bosons - 13
This is the amount of those creatures that is currently loose in the Zoo (there's actually more than that but this is what you're tasked with collecting).
At the beginning and end of each stage there is also a mini version of the above that may say something like :
Gluons - 14
Leptons - 4
Bosons - 1
This is how many of those creatures there are loose in that particular stage (or area). You have to make them all read :
Gluons - 0
Leptons - 0
Bosons - 0
For the achievement to pop, I suggest that you get everyone in a stage before progressing it's not difficult. If you press
then the map will zoom out and arrows will point to any near press
again to zoom out.
The only time that you will not be able to do that is when you face the end of the act, that usually involves the sideways run with an enemy chasing you. Those levels you need all the quarks to get through it, however, once you have gotten through it any damage etc you make to a level remains meaning you can redo the levels and this time use your nets to capture the creatures as you should have spare Quarks. The damage also stays on the race levels which is handy. Also NOTE that when running through the habitat levels you can also sometimes JUMP the checkpoints meaning that you don't deposit your Quarks so you have spares.
Also when you pass through specific habitats for the Gluon etc. I can't be sure that you can collect all of those and it will decrease the total at the beginning but as you have to play the game to get all the charms you may as well clear the stages as you go. The Boson habitat contains the last Charm anyway so it's not as if you can grind it out early.
Edit - Whilst I can't vouch that the following will work if you're missing 1 boson, Fury87 did have the following to say :
"I had 1 boson left and it was the very first one you capture right after leaving the quark pond. After resetting the area tons of times and not being able to get him to respawn so my counter would tick down I was ready to give up. I decided I would try and reset another area with bosons to see if I could trick the game into thinking I got my last boson that way. I went to the beginning of chapter 3 and reset it and went right to the very first 2 bosons and captured them both and no achievement. I thought that was it so I went back to the nucleus to finish the game and lo and behold the board by the nucleus showed that I had collected all of the loose creatures. I went back to the beginning of chapter 3 to see if I finished clearing the area would make the achievement pop. I was about half way done and I got the Absolute Zero achievement. Hope this helps someone so they can avoid playing the whole game again to get this achievement."