I used OrgMode during graduate school for all my math/science formula heavy papers. Org lets you mix OrgMode outlining (which is very close to Markdown) and LaT

I used OrgMode during graduate school for all my math/science formula heavy papers. Org lets you mix OrgMode outlining (which is very close to Markdown) and LaTeX. I generally write in org mode and then export to whatever I need to. I use it on and off for TODO list management but it is really good for writing.