[yogi]

first - strings are made of energy. energy and mass are convertible.
so the "shake hands" of strings should be same as our's (humans) . when we shake hands do we exchange elementory particles or strings ? (electron, protons any other discovered particle lately). we dont know !. but until we become so tiny at the level of strings, we can not answer the question, only thing we can do is speculate. it all depends on the observer.
answer to your second question - it is posssible to have n-number of universes within an atom because they are existing in totally different dimensions. Brian Green talks about this, i have found a story written 5000 years ago talking the same phenomena. i am in the process of getting this short story peer reviewd and then release it for public.

yogi