Dorothy M. Duffy

Computational Techniques at the Organic−Inorganic Interface in Biomineralization

Just over ninety years ago, the first edition of D’Arcy Thompson’s book On Growth and Form appeared. Much of it is long out of date, but D’Arcy Thompson makes a point of fundamental importance in his discussion of the morphology of inorganic crystals in biological systems. He points out that the deposition of minerals in the living body, the complex shapes and symmetries often seen, cannot be explained by simple ideas of crystal packing. He speculates (and in 1919 it could be no more than speculation) on the importance of “directing forces”, using the analogy of ordering in liquid crystals discussed in the work of Lehman. In some cases, it was already clear that a pre-existing template controlled the growth of the inorganic material and D’Arcy Thompson shows how the complex forms of the silicate skeletons of sponges and radiolarians can be explained using simple models based on froths and bubbles that somehow constrain the growth of the inorganic material in their interstices. This presence of some controlling growth mechanism distinguishes two kinds of biomineralization process. Biologically induced mineralization occurs when minerals form as a byproduct of the activity of cells or their interaction with the surrounding environment. The morphologies and phases observed are usually similar to those seen in nonbiological systems. Biologically controlled mineralization is regulated by the organism, and the resulting structures have a physiological function (or sometimes functions). In this review, we are concerned only with the second case, biologically controlled mineralization. * Address for corresponding author: Department of Engineering Materials, Sir Robert Hadfield Building, University of Sheffield, Mappin St., Sheffield S1 3JD, U.K. Telephone: +44 114 222 5957. Fax: +44 114 222 5943. E-mail: j.harding@sheffield.ac.uk. Chem. Rev. 2008, 108, 4823–4854 4823

The nature of high-energy radiation damage in iron

Understanding and predicting a materials performance in response to high-energy radiation damage, as well as designing future materials to be used in intense radiation environments, requires knowledge of the structure, morphology and amount of radiation-induced structural changes. We report the results of molecular dynamics simulations of high-energy radiation damage in iron in the range 0.2-0.5 MeV. We analyze and quantify the nature of collision cascades both at the global and the local scale. We observe three distinct types of damage production and relaxation, including reversible deformation around the cascade due to elastic expansion, irreversible structural damage due to ballistic displacements and smaller reversible deformation due to the shock wave. We find that the structure of high-energy collision cascades becomes increasingly continuous as opposed to showing sub-cascade branching as reported previously. At the local length scale, we find large defect clusters and novel small vacancy and interstitial clusters. These features form the basis for physical models aimed at understanding the effects of high-energy radiation damage in structural materials.

Metadynamics simulations of calcite crystallization on self-assembled monolayers

We show that recent developments in the application of metadynamics methods to direct simulations of crystallization make it possible to predict the orientation of crystals grown on self-assembled monolayers. In contrast to previous studies, the method allows for dynamic treatment of the organic component and the inclusion of explicit surface water without the need for computationally intensive interfacial energy calculations or prior knowledge of the interfacial structure. The method is applied to calcite crystallization on carboxylate terminated alkanethiols arrayed on Au (111). We demonstrate that a dynamic treatment of the monolayer is sufficient to reproduce the experimental results without the need to impose epitaxial constraints on the system. We also observe an odd-even effect in the variation of selectivity with organic chain length, reproducing experimentally observed orientations in both cases. Analysis of the ordering process in our simulations suggests a cycle of mutual control in which both the organic and mineral components induce complementary local order across the interface, leading to the formation of a critical crystalline region. The influence of pH, together with some factors that might affect the range of applicability of our method, is discussed.

The challenge of biominerals to simulations

Biomaterials are hierarchical systems whose structure and properties represent a major challenge to simulation. We briefly discuss the remarkable experimental data now available both on the structure, formation and properties of biominerals. In the light of this we discuss current attempts to simulate biomaterials at atomic and meso length scales and timescales and the range of physical effects that are important in producing biomaterials. We emphasise the importance of obtaining robust forcefields for these systems and the sensitivity of simulations to the forcefields used. We conclude by suggesting future directions for the field and remaining problems to be solved.

Simulations of calcite crystallization on self-assembled monolayers.

This paper presents simulations of calcium carbonate ordering in contact with self-assembled monolayers. The calculations use potential-based molecular dynamics to model the crystallization of calcium carbonate to calcite expressing both the (00.1) and (01.2) surfaces. The effect of monolayer properties: ionization; epitaxial matching; charge density; and headgroup orientation on the crystallization process are examined in detail. The results demonstrate that highly charged surfaces are vital to stimulate ordering and crystallization. Template directed crystallization requires charge epitaxy between both the crystal surface and the monolayer. The orientation of the headgroup appears to make no contribution to the selection of the crystal surface.

Modelling the interfaces between calcite crystals and Langmuir monolayers

Langmuir monolayers are good model systems for investigating the use of organic templates to control the growth and morphology of calcium carbonate. We investigate the structure of the organic–mineral interface using molecular dynamics methods. The monolayer consists of octadecanoic (stearic) acid molecules; the calcium carbonate is the calcite phase. Seven interfaces were chosen to demonstrate the various types of behaviour possible. We show that simple epitaxial arguments based on the ideal, unrelaxed monolayer and mineral surfaces can be very misleading, particularly when considering polar directions. Furthermore, such arguments cannot predict the relative stability of the various interfaces. We show that the polar (001) direction (with a Ca termination) produces the most stable interface and discuss the implications for mineral growth on organic monolayers.

Electronic effects in high-energy radiation damage in iron

Electronic effects have been shown to be important in high-energy radiation damage processes where a high electronic temperature is expected, yet their effects are not currently understood. Here, we perform molecular dynamics simulations of high-energy collision cascades in α-iron using a coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We subsequently compare it with the model employing electronic stopping only, and find several interesting novel insights. The 2T-MD results in both decreased damage production in the thermal spike and faster relaxation of the damage at short times. Notably, the 2T-MD model gives a similar amount of final damage at longer times, which we interpret to be the result of two competing effects: a smaller amount of short-time damage and a shorter time available for damage recovery.

Strain-relief by single dislocation loops in calcite crystals grown on self-assembled monolayers

Most of our knowledge of dislocation-mediated stress relaxation during epitaxial crystal growth comes from the study of inorganic heterostructures. Here we use Bragg coherent diffraction imaging to investigate a contrasting system, the epitaxial growth of calcite (CaCO3) crystals on organic self-assembled monolayers, where these are widely used as a model for biomineralization processes. The calcite crystals are imaged to simultaneously visualize the crystal morphology and internal strain fields. Our data reveal that each crystal possesses a single dislocation loop that occupies a common position in every crystal. The loops exhibit entirely different geometries to misfit dislocations generated in conventional epitaxial thin films and are suggested to form in response to the stress field, arising from interfacial defects and the nanoscale roughness of the substrate. This work provides unique insight into how self-assembled monolayers control the growth of inorganic crystals and demonstrates important differences as compared with inorganic substrates.

Oriented crystal growth on organic monolayers

Ordered organic substrates influence the crystallisation of minerals and different crystal morphologies and polymorphs can be stabilised by varying the properties of the substrates. The mechanisms behind this crystallisation control are not always apparent; however in recent years results from molecular modelling studies have led to an increased level of understanding. We present a review of the experimental evidence for crystallisation control by organic self-assembled monolayers and discuss the modelling methods that have been used to study these effects. We give an overview of the contribution modelling has made to the field of mineral crystallisation on organic substrates. The focus is on calcium carbonate because of its importance as a biomineral and, consequently, the large number of experimental and modelling studies that have been performed for this mineral.

Electronic effects in high-energy radiation damage in tungsten.

Although the effects of the electronic excitations during high-energy radiation damage processes are not currently understood, it is shown that their role in the interaction of radiation with matter is important. We perform molecular dynamics simulations of high-energy collision cascades in bcc-tungsten using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We compare the combination of these effects on the induced damage with only the effect of electronic stopping, and conclude in several novel insights. In the 2T-MD model, the electron-phonon coupling results in less damage production in the molten region and in faster relaxation of the damage at short times. These two effects lead to a significantly smaller amount of the final damage at longer times.