For some of the thoughts behind this topic, please see the Avishraa Tirades.
Substance magic is the second most common of the eight types of magic to be found among the Chosen, and consists of the ability to alter the constituents of matter. Users of element magic are referred to in the Citadel as alchemists.
Substance magic, at its fundamental level, consists of the ability to manipulate and transform first-generation fermions, among whose members - or combinations thereof - are the building blocks of atoms and therefore physical matter: protons, neutrons, and electrons. By adding, subtracting, or moving these particles, atoms can be transformed from one element to another or their chemical bonds broken or formed - in short, the transformation of matter from one form to another. (It is not known whether an alchemist could manipulate antimatter in the same way, since they almost never encounter it; fortunately the transformation of matter into antimatter is not possible.)
Alchemists are not consciously aware of the particles they are manipulating; they are too small. An alchemist's perception of the composition of matter bears a certain resemblance to the senses of taste and smell, and the use of their power to alter it is something like the “add salt to taste” instruction found in recipes, except with far more leeway. Likewise, users of Substance magic have some of the same difficulties as those describing smells or tastes, in that the complexity and subjectivity of the sensory input requires a certain amount of analogy, metaphor, and multilayering (“it's a bit like iron, not quite, but with some silvery notes and not as harsh; it'll do for this purpose but I need to make it more blue, it's definitely not blue enough”). Discussions between alchemists, as a result, can be somewhat hard to follow by others when their abilities enter into what is said.
Where alchemists' power differs from that of elementalists, whose power also affects matter, is that the latter are able to shape a particular substance in the aggregate, but generally speaking not to transform it; an alchemist, on the other hand, may turn one substance to another, but has no effective way of shaping it.
The amount of mana used by alchemists in exercising their powers depends on several factors, including how much matter is being affected and what kind of transformation is being made.
Whether a magically induced change to matter remains in effect, of course, depends on whether it is stable in the environment in which it is made. With some effort, an alchemist can cause water to become ice, but if the surrounding temperature is above freezing, it will only melt again as soon as the alchemist's will is withdrawn or their mana is depleted.
The least strenuous tasks for an alchemist involve changing the structure of matter, which is to say the way its molecules are arranged, since molecules are generally not bound to one another as tightly as they are internally. An alchemist can usually (though not quickly) cause solid substances to crumble (like rock into gravel or sand) or amalgamate again, and likewise can usually force a change in the state of matter: gas to liquid, liquid to solid, and so on.
Only slightly more difficult is the movement of electrons, which are shared and moved relatively easily between atoms. In practical terms, this covers the realm of classical chemistry: the forming and breaking of chemical bonds, the building and restructuring of molecules, and the magical catalysis of reactions. (It also, in an overlap with energists' Spark magic, allows the formation of electrical charges and currents, though alchemists cannot do this on nearly the same scale.)
While a certain amount of the alchemist's mana must always be used to cause a chemical reaction, how much depends on the type of reaction, since the mana effectively substitutes for the reaction's energy requirements. Naturally endothermic reactions, which normally draw heat from their surroundings, require more mana, while exothermic reactions, which generate heat, can require a bare minimum (the alchemist is not, however, able to draw the generated heat back in to reuse as mana; only an energist can do that).
The manipulation of protons and neutrons can be somewhat more taxing, in that more effort is involved in overcoming the strong nuclear force to separate protons and neutrons from the nucleus, and also more dangerous, since protons and neutrons freed from a nucleus - singly or in groups - are the source of several kinds of radiation. It is, however, also more valuable, because it's through this process that an alchemist is capable of transmutation: the changing of one element or isotope into another.
A little under one-fifth of all Chosen are solely, or primarily, alchemists.
Unlike elementalists, alchemists have no inherent magical restriction on which kinds of materials they can affect; the difference between one who simply crumbles stone into sand and one who turns lead into gold is simply a matter of practice and sensitivity. For this reason - and because applying Substance magic of any sort to large quantities of material is effort-intensive - alchemists in the Citadel usually at least begin their careers in workshops with other alchemists, where they have opportunities to learn from their elders and hone their own skills. Those deciding to specialize in some low-quantity, high-value transformation may strike out on their own, but rising to a management-like position within the workshop is also possible. Alchemists often work closely with elementalists; the latter can bring the former base ingredients and raw mass to work with, and others can shape what the alchemists produce. The Citadel cannot be said to be a post-scarcity society, but it's because of the alchemists that many things are much less scarce than they should be.
Another way in which alchemists differ from elementalists is that their powers can be used on organic materials as well as on inorganic ones. A pure alchemist attempting to cause chemical changes in an actual living being is likely to cause something harmful, if not actively fatal; any organism is such a complicated collection of chemical reactions that it's too easy to disrupt one. But they will often have better luck with organic byproducts; in the Citadel, alchemists are sought after to improve the composition of soils and the durability of fabrics, and alchemist-made dyes are among the most sought-after.
Those individuals who have two magic types often find that Substance magic, with its extreme versatility, meshes well with their other powers. Elementalist-alchemists can either produce large amounts of the element they control, or gather large amounts of it to produce something else from it. Shifter-alchemists have an uncanny sense of their own body chemistry, and can modify themselves in ways that pure shifters can't. And lifegiver-alchemists have the potential to sculpt living beings to an unparalleled degree.