I'll be honest, I don't think integrating '3DS' into many project names works well. It just feels a bit clumsy to me. If you put it at the end, e.g. 'Project Name 3DS' then that's fine as it makes it clear. I integrated '3DS' into a project name with 3DSafe because the word 'safe' is not only relevant to the project but starts with 's' so blended well with '3DS'. However, I think trying to embed '3DS' into the name of the project can look messy and difficult to read if the letters don't match up and if the word chosen doesn't match well with the purpose of the project (i.e. it was chosen just because it can be blended with '3DS').
If this was for DS, then you could call it NeuTRino - neutrinos are particles hence relevant to physics, and the capitalisation hints at NTR (the model number for the DS). Perhaps 'NeuTRino 3D' - so you've got neutrino, the NTR hint, plus 3D to indicate it's for 3DS not DS.