Well., I dont know about matlab. If you were using python, you could have built a prototype first using python., then start optimizing it by converting the bottlneck modules to C++/C.

See whether Matlab provides something like that. If it does not., you'll be wasting a lot of time converting it all to C++ and then continuing research on a C++ base., which means half your R&D team would have to be re-educated.

http://mail.python.org/pipermail/python-list/1999- November/016220.html

The above link should be of help.