We analyze the dynamics of atom-laser interactions for atoms having multiple,closely spaced, excited-state hyperfine manifolds. The system is treated fullyquantum mechanically, including the atom's center-of-mass degree of freedom,and motion is described in a polarization gradient field created by athree-dimensional laser configuration. We develop the master equationdescribing this system, and then specialize it to the low-intensity limit byadiabatically eliminating the excited states. We show how this master equationcan be simulated using the Monte Carlo wave function technique, and we providedetails on implementation of this procedure. Monte Carlo calculations of steadystate atomic momentum distributions for two fermionic alkaline earth isotopes,$^{25}$Mg and $^{87}$Sr, interacting with a three-dimensional lin-$\perp$-linlaser configuration are presented, providing estimates of experimentallyachievable laser-cooling temperatures.
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