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In the early Universe it it's believed that matter and anti-matter annihilated one another till there was but a remaining 1% left. In a matter/anti-matter collision, is there not an explosion of energy left behind? According to basic Newton principals the energy can't be destroyed. My question is: what exactly happened to the energy of this reaction? Can it be a contender for the explanation of the origin of dark matter or dark energy?

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Most of it would've become radiation- mostly photons and some neutrinos. Some of that can be seen in the cosmic microwave background. The rest would've gone into the kinetic energy of remaining matter particles (i.e., heat). We don't actually know what dark matter is made of, but we do know what the reaction products of matter/anti-matter annihilation are for the kinds of particles and anti-particles that we do know about, and none of them are candidates for dark matter (it's just more regular matter particles- again, mostly photons and some neutrinos in the end, sometimes with pions or other heavy particles as an intermediate step).

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The word energy tends to be used in a rather vague way, and typically to mean something exotic. In the context of particle reactions energy either means photons or the kinetic energy of the particles leaving the reaction.

For example an electron and anti-electron annihilate to produce two photons. By contrast the annihilation of a proton and anti-proton is a generally messy business because the proton is quite a complicated object with internal structure. The annihilation produces not just photons but a spray of other particles with kinetic energy.

So the energy produced by annihilation couldn't be dark energy or indeed anything mysterious.

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