Simulation of the nucleation and growth of biominerals

• Main Author: Innocenti Malini, Riccardo
• Format: Dissertation
• Language: English
• Published: University of Sheffield 2016

Nature appears to always be a step ahead. Through millions of years of evolution it has developed an incredible array of tools and machinery for a multitude of different applications. Biomineralization is one of those processes. It leads to the formation of a material with functions that include lenses, exoskeletons, grinding tools, mineral reservoirs and shells. All of these materials, are tailor-made for their applications by a complex interplay between the mineral phase and the organic matter. Understanding the fundamental mechanisms leading to the formation of these functional materials would lead to the development of new manufacturing methods to control matter at the nm scale. Nucleation is a process that is still not well understood. Recent investigation suggests the existence of (meta)stable complexes prior to the precipitation of a wide number of mineral systems. Due to the current resolution limit, it is not possible to directly observe the molecular mechanisms involved. In this thesis, Molecular Dynamics simulations have been used to probe the association of calcium phosphate ionic complexes and their aggregation in solution. To obtain the free energy of the reactions, Umbrella Sampling was used. The results partially confirm the experimental observations showing that the [Ca(HPO4)3]4- is stable and can exist in solution. In addition, the aggregation of both the [Ca(HPO4)3]4- and [Ca(HPO4)2]2- complexes were analysed allowing for a step-by-step understanding of one of the potential pathways prior to the nucleation of calcium phosphate minerals. As living organisms have been observed to initially precipitate an amorphous phase prior to the development of crystalline minerals it is important to understand its properties. Hydrous amorphous calcium carbonate is usually the precursor of both calcite and aragonite. As multiple short range structures have been observed for this phase, it is important to sample comprehensively the ensemble of configurations. By studying four models of hydrous ACC obtained in different ways, the structure and role of the water molecules within the structure were analysed. All the structures match experimentally obtained data. Formation of continuous, or percolating, channels was found to be metastable compared to more homogeneous distributions. Additionally the diffusion coefficient of the ions were extremely small suggesting that large scale reorganisation would require a large driving force. Biomolecules, including proteins, proteoglycans, glycosoamminoglycans, amino acids and peptides have the ability to dramatically alter the nucleation and growth process of biominerals. Often they induce the formation of minerals with non-equilibrium geometries. Here the effect of small organic molecules on the association of ions in solution and on the surface of an amorphous intermediate were investigated using Molecular Dynamics. The results show that organic molecules can stabilise ionic complexes, and can have an important effect on the water dynamics associated with ions.