Bi$_2$Se$_3$, a layered three dimensional (3D) material, exhibits topological insulating properties due to presence of surface states and a band gap of 0.3 eV in the bulk. We study the effect hydrostatic pressure $P$ and doping with rare earth elements on the topological aspect of this material in bulk from a first principles perspective. Our study shows that under a moderate pressure of P$>$7.9 GPa, the bulk electronic properties show a transition from an insulating to a Weyl semi-metal state due to band inversion. This electronic topological transition may be correlated to a structural change from a layered van der Waals material to a 3D system observed at $P$=7.9 GPa. At large $P$ density of states have significant value at the Fermi-energy. Intercalating Gd with a small doping fraction between Bi$_2$Se$_3$ layers drives the system to a metallic anti-ferromagnetic state, with Weyl nodes below the Fermi-energy. At the Weyl nodes time reversal symmetry is broken due to finite local field induced by large magnetic moments on Gd atoms. However, substituting Bi with Gd induces anti-ferromagnetic order with an increased direct band gap. Our study provides novel approaches to tune topological transitions, particularly in capturing the elusive Weyl semimetal states, in 3D topological materials.
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