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\usepackage{xepersian}
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\begin{document}
\title{...}
\author{-}
\maketitle

\section{.1}
 ‎\begin{equation}‎
 \begin{split}
‎‎‎Y=‎
\dfrac{1}{2}
\left( {\begin{smallmatrix}
 \dfrac{1}{\varepsilon_{3}}e^{\dfrac{ika_{0}}{2}}(2\cos\dfrac{\mu\pi}{n}+e^{\dfrac{-3ika_{0}}{2}})&\qquad &  \dfrac{1}{\varepsilon _{4}}e^{\dfrac{ika_{0}}{2}}(2\cos\dfrac{\mu\pi}{n}+e^{\dfrac{-3ika_{0}}{2}})\\[4pt]
1&\qquad &1\\[4pt]
\dfrac{1}{\varepsilon _{1}}e^{i(\dfrac{\mu\pi}{n}+\dfrac{ka_{0}}{2})}(2\cos\dfrac{\mu\pi}{n}-e^{\dfrac{-3ika_{0}}{2}})&\qquad &\dfrac{1}{\varepsilon _{2}}e^{i(\dfrac{\mu\pi}{n}+\dfrac{ka_{0}}{2})}(2\cos\dfrac{\mu\pi}{n}-e^{\dfrac{-3ika_{0}}{2}})\\[4pt]
-e^{\dfrac{i\mu\pi}{n}}&\qquad &e^{\dfrac{i\mu\pi}{n}}\\
 \end{smallmatrix}}
 \\
{ \begin{smallmatrix}
 \dfrac{1}{\varepsilon _{1}}e^{\dfrac{ika_{0}}{2}}(-2\cos\dfrac{\mu\pi}{n}+e^{\dfrac{-3ika_{0}}{2}})&\qquad & \dfrac{1}{\varepsilon_{2}}e^{\dfrac{ika_{0}}{2}}(-2\cos\dfrac{\mu\pi}{n}+e^{\dfrac{-3ika_{0}}{2}})\\[4pt]
1&\qquad &1\\[4pt] 
\dfrac{1}{\varepsilon _{3}}e^{i(\dfrac{\mu\pi}{n}+\dfrac{ka_{0}}{2})}(2\cos\dfrac{\mu\pi}{n}+e^{\dfrac{-3ika_{0}}{2}})&\qquad &\dfrac{1}{\varepsilon _{1}}e^{i(\dfrac{\mu\pi}{n}+\dfrac{ka_{0}}{2})}(2\cos\dfrac{\mu\pi}{n}+e^{\dfrac{-3ika_{0}}{2}})\\[4pt]
-e^{\dfrac{i\mu\pi}{n}}& \qquad &e^{\dfrac{i\mu\pi}{n}} 
 \end{smallmatrix}}
 \right) 
 \end{split}
\end{equation}
\end{document}
