| Smashable bit | 13 |
| Smallest unit of an element | 27 |
| Small energy source | 19 |
| Small amount of gold | 20 |
| Science class topic | 19 |
| Radical member | 14 |
| Quark's milieu | 18 |
| Quark place | 11 |
| Quark locale | 12 |
| Quantum mechanics unit | 22 |
| Quantum mechanics model | 23 |
| Proton's spot | 17 |
| Proton spot | 11 |
| Powerful particle | 17 |
| Place for positrons | 19 |
| Place for a proton | 18 |
| Physics focus | 13 |
| Physicist's topic | 21 |
| Physicist's subject of study | 32 |
| Physicist's focus | 21 |
| Particle for a physicist | 24 |
| Particle depicted on an Emmy | 28 |
| Particle Ani DiFranco sings about | 33 |
| Participant in a collision | 26 |
| Orbit site | 10 |
| Oppenheimer subject | 19 |
| One of trillions in a single human body | 39 |
| One of three for H20 | 20 |
| One is depicted in the Emmy statuette | 37 |
| Oft-split item | 14 |
| Oft-smashed particle | 20 |
| Nucleus locale | 14 |
| Nucleus + electrons etc. | 25 |
| Nuclear-energy source | 21 |
| Nuclear component | 17 |
| Niels Bohr's subject | 24 |
| Niels Bohr's study | 22 |
| Niels Bohr's concern | 24 |
| Neutron's place | 19 |
| Neutron's home | 18 |
| Neutrino's place | 20 |
| Nanotechnology subject | 22 |
| N preceders? | 12 |
| Mr. ___, radioactive enemy of Captain Marvel | 44 |
| Mote; bit | 9 |
| Molecule portion | 16 |
| Molecule piece | 14 |
| Molecule mite | 13 |
| Molecule element | 16 |
| Molecule builder | 16 |
| Molecule bit | 12 |
| Molecular unit | 14 |
| Moat anagram | 12 |
| Mite that might blight | 22 |
| Minuscule particle | 18 |
| Minimum amount of an element | 28 |
| Minimal molybdenum | 18 |
| Minimal matter | 14 |
| Minimal amount of gold or platinum | 34 |
| Mini-powerhouse | 15 |
| Mighty particle | 15 |
| Might split at best show of your life? | 38 |
| Microphysics particle | 21 |
| Matter unit | 11 |
| Maker of bonds | 14 |
| Lord Rutherford's concern | 29 |
| Little powerhouse | 17 |
| Little bit of matter | 20 |
| Literally, "indivisible" | 34 |
| Lepton site | 11 |
| Label on the first of two file drawers? | 39 |
| Label on the first of two file drawers, maybe | 45 |
| Lab particle | 12 |
| Jot or bit | 10 |
| Its diameter is measured in picometers | 38 |
| Item studied by Niels Bohr | 26 |
| Item once thought indivisible | 29 |
| Item for Bohr | 13 |
| It's smashed in a particle accelerator | 42 |
| It's small but lethal | 25 |
| It's often split | 20 |
| It's a little matter | 24 |
| It was smashed in the 40's | 30 |
| It splits energetically | 23 |
| It may get smashed or split | 27 |
| It may be ionized | 17 |
| It gets smashed | 15 |
| It can get smashed | 18 |
| It can be viewed with a scanning tunneling microscope | 53 |
| Isotope, e.g. | 13 |
| Infinitesimal bit | 17 |
| Home to a muon or pion | 22 |
| Hadron's place | 18 |
| Fundamental matter? | 19 |
| Focus of Heisenberg's research | 34 |
| Fluke: "___ Bomb" | 27 |
| Fissionable particle | 20 |
| Fission bit | 11 |
| First half of the files? | 24 |
| Film director Egoyan | 20 |