Free energy calculations of conformational transitions in supramolecules and amphiphilic bilayers

In this thesis we report on free energy calculations for calix[4]arenes and amphiphilic bilayers by using molecular dynamics simulations. The calix[4]arene is a bowl-shaped molecule consisting of four phenol rings, which can rotate around the connecting methylene bridges. The isomerization of calix[4]arene studied in the rst part of this thesis concerns the rotation of one of the phenol rings, while the orientation of the three other phenol rings remains unchanged. An amphiphilic bilayer is a membrane resulting from the self-assembly of amphiphilic molecules dissolved in water. This property reects the chemical nature of amphiphilic molecules, consisting of a hydrophilic head and a hydrophobic tail. In experiments, bilayers can not support a large mechanical stress. As a result, bilayers rupture or pores are opened. The second part of the thesis is devoted to pore formation in an amphiphilic bilayer under different stretching conditions.