Simulating the Role of Molecular Binding to Mineral Surfaces: from Biomineral Growth to Cell Attachment

The interactions between organic molecules and minerals is fundamental to the under- standing of processes such as biomineralisation, the attachment of bacteria to surfaces and the design of synthetic materials within biomimetics. This thesis shows how molec- ular dynamics simulations can be employed to study the organic - inorganic interactions and give new insights into the molecular binding at mineral surfaces that play a role in these processes. The incorporation of amino acids within calcium carbonate crystals was simulated and show a high energy associated with the incorporation of these molecules. The amino acids get incorporated in-between the lattice planes of the crystal, causing small anisotropic distortions to the crystal. The inclusion of these molecules occurs via a goodness-of-fit principle, where disruptions to the crystal lattice should be kept to a minimum. These simulations show good agreement with experimental X-ray data. Simulations of multiple tripeptides show a different conformational behaviour of the peptides in solution than on the surface of calcium carbonate. Whereas the pep- tides exhibit a flexible behaviour in solution, binding to the mineral surface induces a disorder-to-order transition and the peptides become rigid. These changes in con- formational behaviour offer insight into the structure and behaviour of intrinsically disordered proteins. The polymer poly acrylic acid was simulated to analyse its conformational behaviour. In the presence of counter ions the polymer exhibits a flexible, extended conformation, whereas a coiled conformation is found in the absence of counter ions. The simulations in this work agree well with experimental spectroscopy studies. The binding of the polymer to a mineral surface is not only governed by the number of functional groups, but also the flexibility of the polymer. These results give an insight in how such molecules can aid the attachment of bacteria to surfaces.