The flow of nematic liquid crystals in tightly confined systems was simulated using a molecular theory and an unsymmetric radial basis function collocation approach. When a nematic liquid crystal is subjected to a cavity flow, we find that moderate flows facilitate the relaxation of the system to the stable defect configuration observed in the absence of flow. Under more extreme flow conditions, e.g., an Ericksen number Er=20, flows can alter the steady-state defect structure observed in the cavity. The proposed numerical method was also used to examine defect annihilation in a thin liquid crystal film. The flows that arise from shear stresses within the system result in a higher velocity for s = +1∕2 defect than for the defect of opposing charge. This higher velocity can be attributed to reactive stresses within the deformed liquid crystal, which result in a net flow that favors the motion of one defect. These two examples serve to illustrate the usefulness of radial basis functions methods in the context of liquid crystal dynamics both at and beyond equilibrium.