The new research field of Nanoplasmonics has recently showed a great potential to become a new area in future photonic materials. Applications are vast, ranging from integrated photonic circuits, through Nanolasers, to optical detection and manipulation of individual atoms and molecules. This progress notwithstanding lacks a clear fundamental picture of how quantum systems, such as an ensemble of atoms and/or molecules, interact with metal surfaces of different topologies. In this project we combine the finite-difference time-domain technique that allows us to solve Maxwell equations on a grid with a dynamics of quantum systems, treating the latter from the first principles. With the help of the home-built supercomputer Plasmon located at the Polytechnic campus we perform numerical experiments on how atoms interact with various plasmonic materials.