Computational approaches have brought powerful new techniques to understand chemical reactions and material physics as well as experimental and theoretical methods, and they are playing a crucial role in nano technology. Growth in applications of codes enabled us to show the properties of molecular and atoms interacting with surrounding complex environment and new material finding. We developed Molecular modeling codes based on tight binding (TB) approach, conventional density functional method (DFT) and time-dependent DFT. These codes have used for many phenomena as the need arose. As for nano material design, we have challenged large scale simulations up to ten thousand atoms without the spatial symmetry and homogeneous condition. The TB method is suitable for treatment of a large number of atoms. Thus at first we concentrated on the TB code for optimizations. The Carbon-Recursive-Technique-Molecular-Dynamics (CRTBD) is a tight binding software specialized for Carbon systems with Order-N scaling. Through efficient optimization by the parallelization and vectorization on the Earth Simulator, we achieved the performance of 7.1 Tera Flopes on 435 nodes (3480 processors) in the simulation of thermal conductivity of carbon nanotube with 48600 atoms. Earth Simulator could give a possibility of large-scale realistic simulations in finding and creating novel nano materials.