We present an improved result of lattice computation of the proton decay matrix elements in $N_f=2+1$ QCD. In this study, the significant improvement of statistical accuracy by adopting the error reduction technique of All-mode-averaging, is achieved for relevant form factor to proton (and also neutron) decay on the gauge ensemble of $N_f=2+1$ domain-wall fermions in $m_pi=0.34$--0.69 GeV on 2.7~fm$^3$ lattice as used in our previous work cite{Aoki:2013yxa}. We improve total accuracy of matrix elements to 10--15% from 30--40% for $prightarrowpi e^+$ or from 20--40% for $prightarrow K bar u$. The accuracy of the low energy constants $alpha$ and $beta$ in the leading-order baryon chiral perturbation theory (BChPT) of proton decay are also improved. The relevant form factors of $prightarrow pi$ estimated through the direct lattice calculation from three-point function appear to be 1.4 times smaller than those from the indirect method using BChPT with $alpha$ and $beta$. It turns out that the utilization of our result will provide a factor 2--3 larger proton partial lifetime than that obtained using BChPT. We also discuss the use of these parameters in a dark matter model.
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