I've been working on a homebrew fantasy world in my spare time for years. It'll probably never go anywhere, but it's fun to think about! One of the things I've wanted to nail down for a long time was the magic physics of the world, what elements made up reality in this extremely magical world.
I had a few requirements to keep in mind when developing this.
First and foremost, it had to be "complex". By this I mean--well, it's easiest to explain by contrast. In the real world, physics is "simple". The fundamental units of reality (quarks, photons, etc) have basically nothing to them. They're just a few numbers that combine together in trivial ways. The complexity of our world comes not from any fundamental complexity, but rather from enormous numbers of these super-simple things combining together. Even tho each individual thing has no complexity at all, and neither does the way they interact, the aggregate is capable of displaying tons of complexity.
Magic, on the other hand, is always "complex" at its root. It generally assumes the existence of minds as a fundamental unit of reality (whereas in the real world minds are just one of the patterns that vast quantities of unthinking particles can arrange themselves into). Sometimes it has "morality" baked in as a physical force; often it has complex things like "fire" or "earth" as core concepts. This makes magic easier to comprehend at a surface level, because it's made out of "big" things we can wrap our minds around, which combine in ways that are complex and ideosyncratic, but don't involve the dizzying amounts of data that the real world's fundamentals do. The elements of magic thus have to reflect this.
Secondly, it has to involve fives. Five is a good number of things, mentally and spiritually significant. So early on, long before I knew what anything would be, I knew I'd have five spheres of five atoms each.
So let's dive in!
The Sphere of Elements
Fire, Water, Earth, Wind, Wood
This was the simplest of all. I knew I needed to involve the classical "elements" of fire/water/earth/air, and I had a few common choices for what to make the fifth. I chose to go for "wood" for a few reasons. One, it's very physical, and helps tie together "elemental" magic with a druid-ish theme. Two, I already knew from my fantasy races that I wanted elves to have wooden skeletons, and for this to be properly mystically significant, I'd need wood to be a fundamental force. Three, wood is usually mystically significant in stories, which means its likely to be pretty core to the magic system, so I had to include it somewhere. Some other common choices I rejected are "metal" (already served by "earth"), "void" (too abstract/encompassing for what's supposed to be only one sphere of the world, also this feels a little sci-fi-y and I ended up letting Energies have that), and "heart" (very non-physical, so it doesn't fit well, and it's more over in the mental sphere that I knew I wanted to do).
A wrinkle: atoms can be "hard" or "soft"; the "hard" ones are suitable for making magical staffs with that aid in channeling related atoms. The hard/soft dichotomy is pretty literal, so Wood and Earth are both hard. This explains why staffs are commonly wood or metal, and/or contain gems (which are Earth) - they help channel elemental magic!
The Sphere of Energies
Heat/Light, Electricity/Magnetism, Kinetic, Entropy, Void
Lacking any hard atoms to make staves from, the energies are somewhat difficult to channel directly, particularly in the heat of combat. Instead they're usually admixed with an appropriate element, to aid in using an elemental staff to channel them. This produces the so-called "Wizard's Elements": Fire (Heat+Fire, or something Heat+Earth or Heat+Air), Lightning (Electricity+Air/Earth), Thunder (Kinetic+Air), Acid (Entropy+Water, or sometimes Entropy+Earth for Corrosion), and Cold (Void+Water/Air).
This one started out easy. I knew I wanted the D&D damage types, because I intended this world to be D&D-based, and what do you know, there are five common damage types. I also wanted to somehow include some slightly science-y things, but it seemed too on-the-nose to make them a sphere of their own, and I couldn't come up with a decent pentad for them anyway. I was pretty happy when I realized I could combine those two and get a more flexible sphere out of the deal.
The Sphere of Biology
Flesh, Blood, Bone, Elan, Soul
Flesh, Blood, and Bone are fairly self-explanatory. They cover all the things bodies are made of: cartilage and bone are both Bone; skin, muscle, and organs are mostly Flesh; mucus, blood, tears, and other liquids are variations on Blood.
Soul is the thinking substance, that our identities and selves are made of. Brains are a Flesh/Soul melange, for example.
Elan is "life energy", the animating force that distinguishes living things from dead. Without Elan infusing it, flesh is inert, and decomposes. With Elan, it's vital, active, and growing. Many simple healing spells are nothing more than increasing Elan in the body and letting natural healing take place, albeit at an accelerated pace.
Biology has more complex atomic interactions than the previous spheres. Bone is another "hard" atom, and thus suitable for making staffs with that aid in channeling, particularly other Biology atoms. But curiously, Bone is almost impervious to Elan; healing bone breaks is very difficult unless you have skill in Bone, and a Bone staff is absolutely worthless for channeling Elan. This has curious consequences! For one, healers are stuck using elemental staffs, at lower efficiency, which partially explains why it's always easier to harm than to heal. For two, it means that Biology specialists carrying Bone wands are definitely not healers, and the second most common use of Biology is... necromancy. (Note: Bone instruments are useful to actual surgeons, who have real training in Flesh/Blood/Bone beyond just "throw Elan at it until it's better".)
Necromancy uses all the non-Elan parts of Biology to do its work, warping bodies and souls in unnatural ways. (They can't use Elan, actually - it encourages natural growth and forms, which would unravel the work they're doing.) Bone is great for necromancers, then, as it enhances all of their spells.
This split in Biology carries over to its interactions with the Energies. Bone has a strong affinity to Void and Entropy; necromancers are well-known for an Entropy/Flesh blend known as "Necrotic energy", and some specialize in a powerful Void/Entropy blend known as "Uttercold". Flesh and Electricity have a unique affinity as well, such that some necromancers use it as an alternative animating energy. On the other hand, Elan has a strong affinity with Light, blending to produce the popular "Radiant energy" that is particularly damaging to undead.
The Sphere of Psionics
I haven't fully nailed these down yet, and the concepts I'm mulling over aren't really named yet. My initial throwaway idea is to lean on the M:tG colors to make it about the mental states that each color can produce, but that seems like a huge cop-out, particularly since I know I'm using the same conceit for the Divine sphere. I just need to do more work here.
The Sphere of the Divine
White, Blue, Black, Red, Green
Divine magic flows directly from the gods, and comes bundled with each god's own idiosyncratic preferences and restrictions. Within that chaos, tho, arcanists have discovered five consistent aspects. Not only do gods themselves tend to organize around these aspects, but entire pantheons tend to stabilize around filling the five aspects equally. As such, most arcanists consider the five divine aspects to be the fifth atomic sphere, thus completing the pentad.
[snip explanation, they're the Magic: the Gathering color-wheel philosophies]
These can manifest in dramatically different ways. For example, one of the more popular pantheons is the Unconquered Sun, a triune deity preaching Right Thoughts (Blue), Right Body (Green), and Right Heart (White), opposed by the twin evils of the quick death (murder, Red) and the slow death (decay, Black). On a very different spectrum, the Garlandite pantheon is led by Garland, god of blood and pain (cast as the good god of this pantheon, believe it or not), opposed by the Four Distractions, each associated with one of the other four aspects.
"Arc" pantheons that center in one aspect but embrace the two neighboring ones are common. Druidic religions, for example, are almost always centered in Green with a reverence for nature, but embrace both organization (White) and savagery (Red), while typically fighting against death/corruption (Black) and technology/artifice (Blue). The Unconquered Sun's White-centered arc structure is common in many folk pantheons.
Destiny scholars suggest that the Divine sphere, more than any other, is strongly self-balancing. If a particular aspect becomes strong in an area, it automatically draws strong opposition from its enemy aspects to counter it. There is no known instance of a stable, long-lived religion that did not incorporate the five aspects in major positions, whether good or evil, balanced in some significant way.
This requirement for balance can manifest in fairly simple dualities, like the Unconquered Sun's pantheon, or in vastly more intricate pantheons, like the ten carefully intertwined cults of Ravnican society, each embracing a different pair of aspects and all serving a vital role in the maintenance of the Infinite City, or the five unbalanced "wedges" (two neighboring aspects and their mutual enemy) exemplified by the Dragonlords.