We investigate the effects of vortex interaction on the formation of interference patterns in a coherent pair of two-dimensional Bose condensed clouds of ultra-cold atoms traveling in opposite directions subject to a harmonic trapping potential. We identify linear and nonlinear regimes in the dipole oscillations of the condensates according to the balance of internal and centre-of-mass energies of the clouds. Simulations of the collision of two clouds each containing a vortex with different winding number (charge) were carried out in these regimes in order to investigate the creation of varying interference patterns. The interaction between different vortex type can be clearly distinguished by those patterns.
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