What does temperature look like at the subatomic level?

I am trying to get a better understanding of the definition of temperature at the subatomic level. I have a background in molecular biology with some college physics, but no deep quantum mechanics background.

Everything I've found on the web (Wikipedia, Google Scholar) seems to use 'temperature' very loosely as just "agitation of particles": more movement/agitation of particles equals higher temperature. But what exactly does this mean?

The reason I'm asking is because the use of "particles" in relation to temperature seems to just mean atoms. The increase in agitation of atoms is equal to an increase in temperature. But I am asking because I don't know if this is true.

So atoms are made out of protons/neutrons/electrons. Protons and neutrons are composite particles, each made up of 3 elementary particles: quarks. Also, each of these examples I've mentioned are matter particles, but other particles like photons are massless. So how do they fit into temperature?

Basically, how do the different subatomic particles (both composite and elementary) relate to temperature?

The thermodynamic definition of temperature has been found to be emergent from the underlying particulate nature of matter. It is connected with an average over the kinetic energy of individual particles.

Here v is velocity of a molecule, m its mass, k_B the Bolzman constant and T the temperature

The kinetic energy requires to have a degree of freedom, which is fine in gases. In solids the degrees of freedom are the rotations and vibrations of the molecules, as the molecules themselves are bound and thus do not have degrees of freedom in space. The same for the internal constituents of molecules, atoms , etc. They exist in a bound state and a temperature cannot be defined for them. Their only contribution comes into contributing to the mass of the molecules.

One can stretch the definition by using the kinetic energy of a particle in the formula, and derive a temperature. All one is saying is that "this would be the temperature of an ensemble of particles that have this kinetic energy on average"

Another stretch of definitions is found here.

Thus at the subatomic level there does not exist a temperature for the bound quarks and gluons as no kinetic degree of freedom exists.

In the comment the quark matter subject has been broached. This is a hypothetical state of matter where the energies are such that the QCD asymptotic freedom behavior emerges. This can happen in two ways :

1) during the Big Bang ,

The earliest phases of the Big Bang are subject to much speculation. In the most common models the universe was filled homogeneously and isotropically with an incredibly high energy density and huge temperatures and pressures and was very rapidly expanding and cooling. Approximately 10−37 seconds into the expansion, a phase transition caused a cosmic inflation, during which the universe grew exponentially.[18] After inflation stopped, the universe consisted of a quark–gluon plasma, as well as all other elementary particles.

The temperatures here are defined by the kinetic energies of the hypothesized particles and it is supplied by the energy of the universe as it evolves after the Big Bang

2) and is searched for in ion ion collisions at LHC.

In these heavy-ion collisions the hundreds of protons and neutrons in two such nuclei smash into one another at energies of upwards of a few trillion electronvolts each. This forms a miniscule fireball in which everything “melts” into a quark-gluon plasma.

The temperature here is defined by the kinetic energy of quarks and gluons in the plasma that have degrees of freedom as for a while they are asymptotically free. The energy is supplied by the accelerator.

• Ah that does take it closer to a clearer understanding, thanks. But I still don't feel it's fully answered. For example, the QCD matter. I guess it comes down to I don't understand where the energy is coming from (or going to) to create the vibrations in the quarks. Hmm... any other ways of describing it? Jul 31, 2014 at 6:00
• This is a hypothesis, as is the quark gluon plasma that is being studied now at LHC. One has to hypothesize degrees of freedom for the quarks and gluons so that a temperature can be defined. This is supposed to happen at the early stages of the Big Bang, where the energy of the universe is concentrated in a small volume, and all hypothetical particles are hypothesized free within that volume so a hypothetical temperature can be defined. For quark gluon plasma in the lab the gluons will never be seen but the resulting distributions are expected to be explained by the hypothesis of a plasma Jul 31, 2014 at 6:08
• continued: for the very small time interval where the ion ion elementary interactions take place. Jul 31, 2014 at 6:09

A specific temperature corresponds to an equilibrium population of available states. At normal temperatures the atoms (and quarks) are too tightly bound to have translational degrees of freedom and therefore have no kinetic energy states. Instead the molecules (in gas) have kinetic states. Atomic movements are captured in vibrational (solid) or rotational (gas) states. Electronic movement in a gas has a very large gap between states and therefore won't contribute at room temperature.