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Out of the logo suggestions so far, I was able to work on the theme proposed by Anoop Nair in his answer, thanks to him making it available for collaboration on GitHub.

This is what I have so far, but I'm open to changing the words used, or adding more equations, or putting more images in the background (I wanted that DNA double-helix to be a protein in tertiary structure, but couldn't find one that was black-and-white):

Smaller Logo

Stack Logo Uploaded to Imgur (apparently wrong size)

Please feel free to add suggestions or comments or disagreements in the answers, or to contribute on GitHub! You can change the image here then push to the GitHub repository for the above image to automatically change.

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I've improved upon Nike'suggestion.enter image description here

I've taken the keywords used, from Nike's version of the logo and from the tags in MM. So that the logo will have a part contributed by almost every user (I couldn't include every tag ). May be it could be done :) Looking for more feedback on the same :)

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    $\begingroup$ I like the double M being incorporated into the logo, but I worry it might be a little too densely packed with tag names. I don't know what the right number would be, but probably closer to the ~10 in Nike's version rather than the ~30 in this one. We need to strike a balance between showing off the broad range of topics available on the site while still highlighting the areas that will draw in new users. $\endgroup$
    – Tyberius Mod
    May 14 at 18:07
  • $\begingroup$ @Tyberius Yes youre right! it does look congested. So what should be done ?? :). Pranoy's logo does look aesthetically pleasing!! $\endgroup$ May 16 at 15:19
  • $\begingroup$ @AnoopANair This looks beautiful, and I appreciate all the time and energy you put into it! I think we can definitely use it for some things. For example, maybe I'll put it in a slide during my talks, as I usually like to have 1 slide advertising MMSE when I give a talk. I may point out that maybe not all these tags are necessary to include in the logo, e.g. you have both KS-DFT and DFT. As for what to do next? Well we currently have your logo with my added text on several sites, and to get our site advertised on other sites: $\endgroup$ May 20 at 22:41
  • $\begingroup$ we need at least 6 upvotes on our ad, please click through our ads on each site here if you'd like to help with that: mattermodeling.meta.stackexchange.com/q/259/5 ! I also liked Pranoy's logo too. We can also use that too. I've been spending all my energy during my "spare" time on the main site's Q/A and the chat rooms (especially with trying to get things answered so that users come back, and recommend us to their colleagues), so I haven't had time to do anything with Pranoy's logo yet (it also took me months to do anything with yours!), but it's great to see so many community $\endgroup$ May 20 at 22:44
  • $\begingroup$ members involved. $\endgroup$ May 20 at 22:44
  • $\begingroup$ @NikeDattani HI! I've up-voted the ads! You're right the image does in fact have a few redundant tags; The image I've attached can be edited via this link, feel free to add in all thats necessary :) : docs.google.com/drawings/d/… $\endgroup$ May 20 at 22:57

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