An important goal of your graduate work is to try to get papers published. Here is an idealized procedure.
Write your paper as a LaTeX
Divide it into sections with
and include appendices and bibliography.
Migrate that paper into the larger body of your thesis
If the chapter has an abstract, move it into a
chapterabstract environment. See Section 8.1, “The
If the chapter has an acknowledgement, move it to a
chapterack environment. See Section 8.2, “The
If the chapter has appendices, enclose them in a
Begin each appendix with a
\section command. See Section 8.3, “The
For the chapter-level bibliography, use the
chapterbibliography environment. See Section 8.4, “The