A heavy-ion collision is in neither the thermodynamic limit of large volumes nor long times. Putting aside questions of whether it is sufficiently equilibrated for thermodynamics to be applicable, there is certainly not enough time for weak interactions to occur, so flavor is conserved, and there are independent chemical potentials for all six quark flavors. The initial conditions (the impact parameter of the collision, the number of up and down quarks in the colliding nuclei, and the fact that they contain no quarks of other flavors) determine the chemical potentials. (Reference for this section:).