The development of new and effective drug delivery systems is of fundamental importance to improve the pharmacological profiles of many classes of therapeutic molecules. However, in comparison with drug design work, very few molecular modelling studies have focused on drug delivery systems. Mathematical modelling methods have been used to investigate the properties of bulk systems. The aim of this chapter is to describe the application of modelling methods to probe drug delivery systems at the atomic level and therefore these mathematical methods are beyond the scope of this chapter. Readers interested in mathematical methods are referred to the excellent review paper by Siepmann and Siepmann.