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

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