Vanilla Markdown and Markdown Extra don't support mathematics. However, kramdown and MultiMarkdown do very easily, and there's an extension for PHP Markdown Extra that you can use. The syntax is different for each, so it depends on which you're using.
In short, in kramdown, use $$ double dollar signs $$
, and in MultiMarkdown or the PHP Markdown Extra Math extension, use \[ LaTeX-style brackets \]
for display and \(LaTeX-style parentheses\)
for inline mathematics.