Slovak Grid NGI will set up NGI virtual centre of excellence for application development and consultancy to researchers from various application domains to improve their adoption of EGI e-Infrastructure services. Our work has been focused on Grid application activities such as analysis of Case Studies and solving of either ready simulation programs or development of software packages. Researchers and involved research communities have varying requirements on the e-Infrastructure services and resources and so far eleven Case Studies have been worked out in details, all differing in specific scientific demands and nanotechnology applications. From the selected Case Studies, the Case Study " Nanoscale modelling and structure optimization " which uses OOMF and MagPar simulation SW packages will be presented more in details. New phenomena and exotic magnetic arrangements like vortices or skyrmions are investigated in this Case Study for practical applications like information storage. Simulations of dynamical processes in magnetic devices are quite CPU time consuming and new algorithms are developing for increasing simulations speed and efficiency. Related to this Case Study, the nanotechnology portal is already developed as a pivot step to make easier access for end-users toward high performance applications on Grid.