Not Anti-matter
“Dark matter” and “dark energy”
In the question you ask, “It’s all atoms isn't it?”
Well, no.
It’s not even protons and electrons. Nor muons, pions, positrons or any other sub-atomic particle or anti-particle (the stuff of which anti-matter is made). That stuff (both matter and anti-matter) makes up only 5% of the total mass of the universe (probably).
The rest is “Dark matter” and “dark energy”
But don’t ask me what that is. I can tell you something about what it is not. But I can’t tell you what it is.
Actually, I can. It’s a fudge. A frig. A subterfuge. But one that stands up to some heavy mathematical rigour.
Back in the day (the 1990s), physicists made estimates of the total amount of matter in the universe. Once you have that number, it’s possible to work out how fast the universe should be expanding, or how that rate of expansion should be changing with time.
When you do the sums, things don’t add up. There’s not enough matter in the visible universe to make the expansion and rate of change of the expansion behave according to the observations.
It’s even more problematic than that. The universe appears to be expanding at an ever-faster rate. Gravity ought to slow the acceleration down, at the very least. However, careful observations show that there appears to be something at work that reverses the effects of gravity. Something that appears to break the known laws of physics.
This being quite a big deal, people thought long and hard about it, checked the data; did more independent experiments using different datasets and so on.
All that effort did nothing except confirm the observations of accelerating expansion.
The observationists were a bit shocked at this, so handed it over to the theoreticians to see if they could come up with an explanation that could be tested by observation.
There’s a few ways the theoreticians can explain the apparent accelerating expansion. You can propose that free space has some kind of energy through the ‘quantum foam’ of constant creation and destruction of particles and anti-particles. But when you do those sums very accurately, you end up with way too much energy.
You can invoke the controversial ‘Cosmological Constant’ in Einstein’s General Relativity, but that is so offensive (“inelegant”) to many physicists, that they came up with the idea that there is a lot of energy and matter in the universe that we can’t see or understand or explain.
This is Nobel prize-winning stuff (Physics 2011). The reason it is Nobel Prize-winning thinking is that this ‘Dark Energy” solves some other problems around the origins and development of the universe, such as the distribution of galaxies and galaxy-clusters along filaments of matter in a universe that appears to be made up mostly of huge volumes of nothingness called supervoids.
But this dark matter still doesn’t account for all the gravity-reversing weirdness.
So they came up with dark energy. Mass and energy being sort of equivalent, a large amount of energy distorts space-time in the same way that a large amount of mass does.
So it is a bit of a fudge, but a quite brilliant, Nobel-prize winning fudge.
Nails, you can ask more questions, but this is science that is still being developed; still being tested by a combination of theory and observation. Still undergoing fierce debate.
Further reading (in addition to the links above):
https://www.sciencedaily.com/releases/2009/11/091102121644.htm
https://www.livescience.com/16367-nobel-physics-universe-expansion-accelerating.html
https://www.geek.com/news/geek-answers-how-do-we-know-dark-matter-and-dark-energy-exist-1574942/