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We derive the low energy effective theory for two brane system with bulk complex scalar fields. Then we find that higher order corrections to the effective equation for scalar fields on the brane lead us to the baryon number(B) violating process if the complex scalar field is regarded as a particle carrying the baryon number current. We see that the motion of the brane leads us the baryon number violation via the current-curvature coupling even if the potential for scalar fields do not exist. We also estimate the net baryon number assuming a C/CP violating interaction.

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