My PhD consists in a double project between Genova - with the Giulia Rossi group - and Lugano - with the Giovanni Pavan group, in the field of Computational Physics of Matter. Both groups use Molecular Dynamics (MD) simulations and advanced sampling techniques, e.g. metadynamics, in order to explore biophysical systems like lipid membranes when they interact with functionalised gold nanoparticles and supramolecular polymers properties respectively.