there are many challenges when you look for micro or nano structure analysis. First the micro or nano structures are not stable in nature and in most cases doesn't have solid shape as they take randam orientation. Second it requires huge computational capacity.  

Dear Hussien Abdel Baky

I agree with you, but these reasons are already found but in other forms of difficulty in many fields of other sciences like GR or nuclear physics, but at least there are models there to describe what's happening. In the case of nano nothing standard until now!!!

meshing with having nano structures in the model would take ages .. I was thinking to use scaling options to fix this issue.

Dear Munir

I agree with you scaling might make it easier, but in a condition if it's based on strong physical evidences, because It's not only a geometrical process.

Dear Eck

You put a right assessment  to the the problem. I think this originally is related to the absence of a real physical model that can describe what's going on in these dimensions, which lead most researches towards geometrical and numeric solutions.

It could be done using material modeling that represents the nano structure instead of meshing as it happen in crystal plasticity models for metals and Microplane for concrete. However developing such a model is not an easy so far

Material modelling software such as Nanotube Modeler, Surface Builder tool of Material Studio etc can be used for structural modelling of nanomaterials. This approach is versatile and the model in most cases does not require meshing if finite element analysis will be conducted. For details on modeling nanosheets and nanotubes, refer to the attached file or link.

http://file.scirp.org/Html/5-2610135_48842.htm