Elements are combined together to create the next more complex "compound" in the system. For example, a button with no label is an atom, but when you add a label it becomes a molecule. I find this works very well when you are trying to organize and manage your digital assets, especially if you are using a storage area like the Creative Cloud or Google Drive and Dropbox.
You can organize the folders or areas in the storage medium by their element type, making it easy to generate style guides and other baseline assets when needed. I was using this in the ClassFlow 3.0 project at Promethean, by creating a folder set in Adobe's Creative Cloud library.
Each folder contained the atomic building blocks for the app. Carrying this further you could use apps like Zeplin,Avocode, or Frontify.com to create your app's style guide and DAM (digital asset management) system. (Editor Note: I contacted a couple of the aforementioned to see if they were planning on importing assets from CC libraries, but nothing has been developed yet.)
I find that when you start thinking in terms of atomic modeling for your apps, it helps keep microinteraction's at the forefront of your thoughts, just by the nature of the process. When you are thinking in terms of individual elements and their combination to create more complex elements, the next natural step for a designer is to think about user interaction with those elements (ok, that's the way this designer thinks about it).
Whatever method you use to organize your assets, it's worth considering using the atomic method - it's elementary (couldn't resist).