Prenucleation Cluster Pathway is Inconsistent with CaCO3 Kinetics.

It has been debated whether CaCO3 nucleates classically with the attainment of a critical cluster size or nonclassically with the restructuring of a prenucleation cluster (PNC). Here, we determine from the nucleation kinetics of CaCO3 that the transition state is composed of about 10 formula units, irrespective of the supersaturation. Crucially, the size of the transition state is considerably smaller than the average PNC size estimated from experimental characterization. This size discrepancy suggests the PNCs are uninvolved in nucleation, and the kinetics indicate that if CaCO3 nucleates classically, the transition state must be an abnormally unstable (antimagic) cluster.

Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling.

Molecular reactions in solution typically involve solvent exchange; for example, a surface must partly desolvate for a molecule to adsorb onto it. When these reactions are simulated, slow solvent dynamics can limit the sampling of configurations and reduce the accuracy of free energy estimates. Here, we combine Hamiltonian replica exchange (HREX) with well-tempered metadynamics (WTMD) to accelerate the sampling of solvent configurations orthogonal to the collective variable space. We compute the formation free energy of a carbonate vacancy in the calcite-water interface and find that the combination of WTMD with HREX significantly improves the sampling relative to WTMD without HREX.

Calcite Kinks Grow via a Multistep Mechanism.

The classical model of crystal growth assumes that kinks grow via a sequence of independent adsorption events where each solute transitions from the solution directly to the crystal lattice site. Here, we challenge this view by showing that some calcite kinks grow via a multistep mechanism where the solute adsorbs to an intermediate site and only transitions to the lattice site upon the adsorption of a second solute. We compute the free energy curves for Ca and CO3 ions adsorbing to a large selection of kink types, and we identify kinks terminated both by Ca ions and by CO3 ions that grow in this multistep way.

Calcite Kinetics for Spiral Growth and Two-Dimensional Nucleation.

Calcite crystals grow by means of molecular steps that develop on {10.4} faces. These steps can arise stochastically via two-dimensional (2D) nucleation or emerge steadily from dislocations to form spiral hillocks. Here, we determine the kinetics of these two growth mechanisms as a function of supersaturation. We show that calcite crystals larger than ∼1 µm favor spiral growth over 2D nucleation, irrespective of the supersaturation. Spirals prevail beyond this length scale because slow boundary layer diffusion creates a low surface supersaturation that favors the spiral mechanism. Sub-micron crystals favor 2D nucleation at high supersaturations, although diffusion can still limit the growth of nanoscopic crystals. Additives can change the dominant mechanism by impeding spiral growth or by directly promoting 2D nucleation.

Critical Step Length as an Indicator of Surface Supersaturation during Crystal Growth from Solution.

The surface processes that control crystal growth from solution can be probed in real-time by in situ microscopy. However, when mass transport (partly) limits growth, the interfacial solution conditions are difficult to determine, precluding quantitative measurement. Here, we demonstrate the use of a thermodynamic feature of crystal surfaces-the critical step length-to convey the local supersaturation, allowing the surface-controlled kinetics to be obtained. Applying this method to atomic force microscopy measurements of calcite, which are shown to fall within the regime of mixed surface/transport control, unites calcite step velocities with the Kossel-Stranski model, resolves disparities between growth rates measured under different mass transport conditions, and reveals why the Gibbs-Thomson effect in calcite departs from classical theory. Our approach expands the scope of in situ microscopy by decoupling quantitative measurement from the influence of mass transport.

Magnesium-rich nanoprecipitates in calcite: atomistic mechanisms responsible for toughening in Ophiocoma wendtii.

The brittlestar Ophiocoma wendtii is theorised to employ a technique already used in metallurgy in order to optimise the mechanical properties of calcitic microlenses within their skeletons. These microlenses contain arrays of Mg-rich nanoprecipitates, which are proposed to inhibit crack propagation through the compression of the local host lattice. Here, we employ classical molecular dynamics in order to study the effects of Mg-rich nanoprecipitates on lattice strain, stress distributions and crack propagation in calcite. Our quantitative results on lattice strain and stress induced on the host matrix are compatible with empirical estimates. Simulations of crack propagation demonstrate that the inclusion of a Mg-rich region results in an increase in stress required to fracture the crystal, as well as higher residual stress in the fractured crystal. This is the result of an inhomogeneous stress distribution causing a more disordered fracture, as well as deflections of the crack away from the lowest energy (10.4) surface. The results agree with the proposal that the compression of the host lattice inhibits propagation, and offer insight into other mechanisms through which the nanoprecipitates affect crack propagation.

Hydroxyl-rich macromolecules enable the bio-inspired synthesis of single crystal nanocomposites.

Acidic macromolecules are traditionally considered key to calcium carbonate biomineralisation and have long been first choice in the bio-inspired synthesis of crystalline materials. Here, we challenge this view and demonstrate that low-charge macromolecules can vastly outperform their acidic counterparts in the synthesis of nanocomposites. Using gold nanoparticles functionalised with low charge, hydroxyl-rich proteins and homopolymers as growth additives, we show that extremely high concentrations of nanoparticles can be incorporated within calcite single crystals, while maintaining the continuity of the lattice and the original rhombohedral morphologies of the crystals. The nanoparticles are perfectly dispersed within the host crystal and at high concentrations are so closely apposed that they exhibit plasmon coupling and induce an unexpected contraction of the crystal lattice. The versatility of this strategy is then demonstrated by extension to alternative host crystals. This simple and scalable occlusion approach opens the door to a novel class of single crystal nanocomposites.

Amino Acid Assisted Incorporation of Dye Molecules within Calcite Crystals.

Biomineralisation processes invariably occur in the presence of multiple organic additives, which act in combination to give exceptional control over structures and properties. However, few synthetic studies have investigated the cooperative effects of soluble additives. This work addresses this challenge and focuses on the combined effects of amino acids and coloured dye molecules. The experiments demonstrate that strongly coloured calcite crystals only form in the presence of Brilliant Blue R (BBR) and four of the seventeen soluble amino acids, as compared with almost colourless crystals using the dye alone. The active amino acids are identified as those which themselves effectively occlude in calcite, suggesting a mechanism where they can act as chaperones for individual molecules or even aggregates of dyes molecules. These results provide new insight into crystal-additive interactions and suggest a novel strategy for generating materials with target properties.

Unravelling the Molecular Basis of High Affinity Nanobodies against HIV p24: In Vitro Functional, Structural, and in Silico Insights.

Preventing the spread of infectious diseases remains an urgent priority worldwide, and this is driving the development of advanced nanotechnology to diagnose infections at the point of care. Herein, we report the creation of a library of novel nanobody capture ligands to detect p24, one of the earliest markers of HIV infection. We demonstrate that these nanobodies, one tenth the size of conventional antibodies, exhibit high sensitivity and broad specificity to global HIV-1 subtypes. Biophysical characterization indicates strong 690 pM binding constants and fast kinetic on-rates, 1 to 2 orders of magnitude better than monoclonal antibody comparators. A crystal structure of the lead nanobody and p24 was obtained and used alongside molecular dynamics simulations to elucidate the molecular basis of these enhanced performance characteristics. They indicate that binding occurs at C-terminal helices 10 and 11 of p24, a negatively charged region of p24 complemented by the positive surface of the nanobody binding interface involving CDR1, CDR2, and CDR3 loops. Our findings have broad implications on the design of novel antibodies and a wide range of advanced biomedical applications.

Dislocation loop formation by swift heavy ion irradiation of metals.

A coupled two-temperature, molecular dynamics methodology is used to simulate the structural evolution of bcc metals (Fe and W) and fcc metals (Cu and Ni) following irradiation by swift heavy ions. Electronic temperature dependent electronic specific heat capacities and electron-phonon coupling strengths are used to capture the full effects of the variation in the electronic density of states. Tungsten is found to be significantly more resistant to damage than iron, due both to the higher melting temperature and the higher thermal conductivity. Very interesting defect structures, quite different from defects formed in cascades, are found to be created by swift heavy ion irradiation in the bcc metals. Isolated vacancies form a halo around elongated interstitial dislocation loops that are oriented along the ion path. Such configurations are formed by rapid recrystallization of the molten cylindrical region that is created by the energetic ion. Vacancies are created at the recrystallization front, resulting in excess atoms at the core which form interstitial dislocation loops on completion of crystallization. These unique defect structures could, potentially, be used to create metal films with superior mechanical properties and interesting nanostructures.

Novel high-temperature ferroelectric domain morphology in PbTiO3 ultrathin films.

Exotic domain morphologies in ferroic materials are an exciting avenue for the development of novel nanoelectronics. In this work we have used large scale molecular dynamics to construct a strain-temperature phase diagram of the domain morphology of PbTiO3 ultrathin films. Sampling a wide interval of strain values over a temperature range up to the Curie temperature Tc, we found that epitaxial strain induces the formation of a variety of closure- and in-plane domain morphologies. The local strain and ferroelectric-antiferrodistortive coupling at the film surface vary for the strain mediated transition sequence and this could offer a route for experimental observation of the morphologies. Remarkably, we identify a new nanobubble domain morphology that is stable in the high-temperature regime for compressively strained PbTiO3. We demonstrate that the formation mechanism of the nanobubble domains morphology is related to the wandering of flux closure domain walls, which we characterise using the hypertoroidal moment. These results provide insight into the local behaviour and dynamics of ferroelectric domains in ultrathin films to open up potential applications for bubble domains in new technologies and pathways to control and exploit novel phenomena in dimensionally constrained materials.

Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

The influence of the electronic specific heat on swift heavy ion irradiation simulations of silicon.

The swift heavy ion (SHI) irradiation of materials is often modelled using the two-temperature model. While the model has been successful in describing SHI damage in metals, it fails to account for the presence of a bandgap in semiconductors and insulators. Here we explore the potential to overcome this limitation by explicitly incorporating the influence of the bandgap in the parameterisation of the electronic specific heat for Si. The specific heat as a function of electronic temperature is calculated using finite temperature density functional theory with three different exchange correlation functionals, each with a characteristic bandgap. These electronic temperature dependent specific heats are employed with two-temperature molecular dynamics to model ion track creation in Si. The results obtained using a specific heat derived from density functional theory showed dramatically reduced defect creation compared to models that used the free electron gas specific heat. As a consequence, the track radii are smaller and in much better agreement with experimental observations. We also observe a correlation between the width of the band gap and the track radius, arising due to the variation in the temperature dependence of the electronic specific heat.

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.

Stress in titania nanoparticles: an atomistic study.

Stress engineering is becoming an increasingly important method for controlling electronic, optical, and magnetic properties of nanostructures, although the concept of stress is poorly defined at the nanoscale. We outline a procedure for computing bulk and surface stress in nanoparticles using atomistic simulation. The method is applicable to ionic and non-ionic materials alike and may be extended to other nanostructures. We apply it to spherical anatase nanoparticles ranging from 2 to 6 nm in diameter and obtain a surface stress of 0.89 N m(-1), in agreement with experimental measurements. Based on the extent that stress inhomogeneities at the surface are transmitted into the bulk, two characteristic length-scales are identified: below 3 nm bulk and surface regions cannot be defined and the available analytic theories for stress are not applicable, and above about 5 nm the stress becomes well-described by the theoretical Young-Laplace equation. The effect of a net surface charge on the bulk stress is also investigated. It is found that moderate surface charges can induce significant bulk stresses, on the order of 100 MPa, in nanoparticles within this size range.

Correlation between anisotropy and lattice distortions in single crystal calcite nanowires grown in confinement.

Growing nanostructures in confinement allows for the control of their shape, size and structure, as required in many technological applications. We investigated the crystal structure and morphology of calcite nanowires, precipitated in the pores of track-etch membranes, by employing transmission electron microscopy and selected area electron diffraction (SAED). The data showed that the nanowires show no preferred growth orientation and that the crystallographic orientation rotated along the length of the nanowire, with lattice rotation angles of several degrees per micrometer. Finite element calculations indicated that the rotation is caused by the anisotropic crystallographic nature of the calcite mineral, the nanoscale diameter of the wires and the confined space provided by the membrane pore. This phenomenon should also be observed in other single crystal nanowires made from anisotropic materials, which could offer the potential of generating nanostructures with tailored optical, electronic and mechanical properties.

Adhesion of sodium dodecyl sulfate surfactant monolayers with TiO(2) (rutile and anatase) surfaces.

Surfactants are widely used as templates to control the nucleation and growth of nanostructured metal oxides such as titania. To gain insight into the origin of the surfactant-titania interactions responsible for polymorph and orientation selection, we simulate the self-assembly of an anionic surfactant monolayer on various low-index titania surfaces, for a range of densities. We characterize the binding in each case and compute the adhesion energies, finding anatase (100) and rutile (110) to be the strongest-binding surfaces. The sodium counterions in the monolayer are found to dominate the adhesion. It is also observed that the assembly is directed predominantly by surface-monolayer electrostatic complementarity. Incorporating water displacement into the calculations does not alter the general findings but does cause the adhesion energies to fall within a smaller range.

Point defect-grain boundary interactions in MgO: an atomistic study.

The way in which point defects interact with grain boundaries in oxides is important for understanding radiation damage evolution, sintering, and many other technologically important applications. Here, we examine how vacancies interact with three different grain boundaries in MgO, chosen as a model oxide ceramic. Further, we compare the vacancy interaction with both pristine (as constructed) and 'damaged' boundaries, in which excess interstitials are placed in the boundary plane to mimic the structure after a damage event. We find that the excess interstitials significantly change the interaction of the vacancies with the boundaries and that this change is sensitive to the atomic structure of the boundary. We further observe that complex electrostatic effects arise that can dominate the interaction. These results show that, as boundaries absorb defects, their interaction with other defects will change dramatically.