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In this work we study the CP violation for and up to leading and next-to-leading order QCD corrections in the standard model, two-Higgs-doublet model and the minimal supersymmetric extension of the standard model. We also study the effect of new physics on the branching ratios of these two decay modes. We find that within the parameter space constrained by the observation of the decay , new physics does not affect the CP asymmetries greatly, and the prediction of new physics to the branching ratios of and $\bar{B^0}\to \phi K_s$ is the same as that of the standard model up to a minor discrepancy as far as the Yukama couplying constants are perturbative.

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