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The American Institute of Physics provides a guide for Preparing your Manuscript for authors of AIP journal articles. Although you are not yet writing for publication, the manuscript preparation guidance also applies to your thesis writing.
If you are not using a citation manger to prepare your reference list, be sure to check out the American Physical Society's online Physical Review Style and Notation Guide, especially Section II J: Footnotes and references which provides sample reference list entries in the Physical Review style.
Zotero is a free tool you can use with Firefox or Chrome that collects, manages, and cites research sources. It's easy to use and lives in your web browser where you do your work. Zotero allows you to attach PDFs, notes and images to your citations, organize them into collections (or groups you can share with collaborators) for different projects, and create bibliographies using Word (for Mac or Windows) or OpenOffice.
There are a number of tools that you can use to gather and organize citations that integrate well with LaTeX. In no particular order, they include:
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