Broad, Alexander; (2023) Tuning the Growth and Mechanical Properties of Calcite Using Impurities: Insight from Molecular Simulation. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Over many millions of years, evolution has provided living organisms with the tools to control the growth and properties of materials from the molecular scale upward. One of the many ways this is achieved is through the introduction of impurities into the solution in which these materials grow. A long-term goal of materials scientists is to harness nature's control mechanisms and apply them in the world of engineering. However, these mechanisms of growth control are highly complex, and understanding them requires insight into physical processes at the molecular scale. While experiments are so-far unable to offer such a high resolution, computer simulations can be used to directly model these physical process with no limit on the resolution. Throughout this thesis, an array of computational methodologies is applied to calcite in an attempt to understand how impurities are able to drive the growth process, and ultimately alter the mechanical properties of the crystal. A series of metadynamics simulations are applied to calcite kink sites, revealing a more complex growth mechanism in which kink-terminating ions do not initially occupy their crystal lattice sites, and only do so upon the adsorption of an additional solute. A combination of metadynamics and Kinetic Monte Carlo simulations are used to examine the adsorption free energies and growth inhibiting properties of amino acids and polyamines, the results of which are compared directly to experiment. This offers a robust insight into the molecular mechanisms that underpin how organic molecules are able to tune the growth of calcite. Simulations are also applied to two case studies of impure calcite. By examining lattice spacings, determining stress distributions and simulating a series of crack propagation events, insight into mechanisms through which biogenic crystals exhibit superior mechanical properties is found. Finally, the nature of non-Markovianity when using reaction coordinates -such as those used in rare event methodologies applied throughout this thesis- are investigated. By introducing non-Markovianity into the system, barrier crossing rates in a coarse-grained system more closely resemble those in the original two-dimensional system. Furthermore, we study the breakdown in rare-events sampling when a poor reaction coordinate is used, and identify which rare-events sampling techniques are more appropriate for detecting poor reaction coordinate choices.

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