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Recent advancements in internal combustion engine due to stricter emission regulations require the turbocharger to function with a higher efficiency over the entire operation range. Furthermore, the need for higher boosting pressure requires the extension of rotation speed margin forcing the inclusion of resonance speeds for high order vibration modes, posing a threat on the reliability of the turbine. This paper introduces new variable geometry nozzle vanes and turbine rotor designed based on the understanding and control of tip leakage flows, utilizing both low and high fidelity CFD simulations. Low fidelity single passage steady state simulations were used for vane profile tuning and high fidelity full-scale unsteady simulations for evaluating stator-rotor interactions respectively. The new vane design is comprised of a three-dimensional stacking in the span wise direction which has been found effective in reducing the nozzle tip leakage loss.