Hydroxyapatite (HA, Ca₁₀(PO₄)₆(OH)₂) is one of the most abundant materials in mammal bone. It crystallizes in an aqueous environment within spaces between tropocollagen protein chains. However, despite its abundance and possible usefulness in the medical field this complex physical system remains poorly understood to date. We present a theoretical study of the energetics of hydroxyapatite, its electronic, mechanical and thermodynamic properties. Our mechanical and thermodynamic properties from first principles are in excellent agreement with the rare available experimental data. The monoclinic and hexagonal phases are lowest in energy. A comparison of the phonon dispersions of these two phases reveals that a phase transition occurs due to a difference in vibrational free energy. The transition is of order-disorder type. Our calculated phase transition temperature is 680 K, in decent agreement with the experimentally determined 470 K. An alternative theoretical model yields 882 K. The phase transition is mediated by OH libration modes. We also report for the first time on a peculiarity in the phonon spectrum of hexagonal and monoclinic HA. When studying the Lyddane-Sachs-Teller shifts in the spectrum close to the [Gamma]-point we identify two vibration modes showing a systematically increasing Lyddane-Sachs-Teller shift in frequency with decreasing dielectric constant. In experiment, the dielectric constant varies between 5 and 20 depending on the Ca/P ratio in the sample. The frequency shifts in the affected modes are as large as 20 cm⁻¹ as one spans the range of the dielectric constant. Thus, a simple spectroscopic analysis of a sample of bone may determine the quality of the sample in a physiological sense. We also identify the chemically stable low energy surface configurations as function of the OH, PO₄ and Ca concentration. In the experimentally relevant OH-rich regime we find only two surfaces competing for lowest energy. The surface most stable over almost the entire OH-rich regime is OH-terminated, and is currently being investigated in the presence of water and atomic substitutions on the HA surface. / text

abstract: The potential of using bio-geo-chemical processes for applications in geotechnical engineering has been widely explored in order to overcome the limitation of traditional ground improvement techniques. Biomineralization via urea hydrolysis, referred to as Microbial or Enzymatic Induced Carbonate Precipitation (MICP/EICP), has been shown to increase soil strength by stimulating precipitation of calcium carbonate minerals, bonding soil particles and filling the pores. Microbial Induced Desaturation and Precipitation (MIDP) via denitrification has also been studied for its potential to stabilize soils through mineral precipitation, but also through production of biogas, which can mitigate earthquake induced liquefaction by desaturation of the soil. Empirical relationships have been established, which relate the amount of products of these biochemical processes to the engineering properties of treated soils. However, these engineering properties may vary significantly depending on the biomineral and biogas formation mechanism and distribution patterns at pore-scale. This research focused on the pore-scale characterization of biomineral and biogas formations in porous media. The pore-scale characteristics of calcium carbonate precipitation via EICP and biogenic gas formation via MIDP were explored by visual observation in a transparent porous media using a microfluidic chip. For this purpose, an imaging system was designed and image processing algorithms were developed to analyze the experimental images and detect the nucleation and growth of precipitated minerals and formation and migration mechanisms of gas bubbles within the microfluidic chip. Statistical analysis was performed based on the processed images to assess the evolution of biomineral size distribution, the number of precipitated minerals and the porosity reduction in time. The resulting images from the biomineralization study were used in a numerical simulation to investigate the relation between the mineral distribution, porosity-permeability relationships and process efficiency. By comparing biogenic gas production with abiotic gas production experiments, it was found that the gas formation significantly affects the gas distribution and resulting degree of saturation. The experimental results and image analysis provide insight in the kinetics of the precipitation and gas formation processes and their resulting distribution and related engineering properties. / Dissertation/Thesis / Doctoral Dissertation Civil, Environmental and Sustainable Engineering 2019

Continuous efforts have been directed towards controlled calcium carbonate biomineral synthesis in recent years. Compared to their inorganic counterparts, biominerals are more tensile in industrial applications, biocompatible with scientific designs, and sustainable for the environment. Most current approaches for synthetic biomineral production rely heavily on sophisticated engineering techniques to constrain the physical property of their crystals, which limits the adaptability of these products. Here, we proposed a novel approach to synthesize calcium carbonate biominerals by reproducing skeletogenesis of the sea urchin larva in vitro using common cellular and molecular methods. Skeleton formation in Lytechinus variegatus sea urchin embryos is a highly coordinated event, where ectodermal cells in different domains express distinct patterning cues that are received by adjacent primary mesenchyme cells (PMCs), which in turn secrete the skeleton. Our group and others have identified a range of skeletal patterning cues, and based on our current understanding of the mechanism, we envisioned a synthetic ectoderm culture using defined ectodermal lineages that, when combined with PMCs, will direct the synthetic production of skeletal structures. Here we have developed a detailed protocol for establishing such as ectoderm culture and have begun initial experiments towards this goal. Future deployment of this protocol will provide invaluable insights into the mechanism of skeletal patterning in sea urchins, as well as an unprecedented system for customized synthetic calcium carbonate biomineral production. Finally, improving our mechanistic understanding of skeletal patterning in echinoderms has the potential to shed light on analogous biomineralization processes in other species as well. / 2024-10-03T00:00:00Z

In this thesis, geometry is used as a basis for conducting experiments aimed at growing and arranging inorganic minerals on curved interfaces. Mineralisation is directed using crystalline and liquid-crystalline metallic soaps and surfactant/water systems as templates.¶ A review of the history, syntheses, structure and liquid crystallinity of metallic soaps and other amphiphiles is presented as a foundation to understanding the interfacial architectures in mesostructured template systems in general.¶ In this study, a range of metallic soaps of varying chain length and cation type are synthesised and characterised to find potentially useful templates for mineral growth. These include alkaline-earth, transition metal, heavy metal and lanthanide soaps. These are systematically characterised using a variety of analytical techniques, including chemical analyses, x-ray diffraction (XRD) infrared spectroscopy (IR) and differential scanning calorimetry (DSC). Their molecular and crystal structures are studied using transmission electron microscopy (TEM), cryo-TEM, electron diffraction (ED), electron paramagnetic spin resonance (EPR), absorption spectroscopy (UV-VIS), high resolution laser spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance spectroscopy, scanning electron microscopy (SEM), electron dispersive x-ray analysis (EDXA), thermal gravimetric analysis (TGA) and magnetic measurements. Models for the molecular and crystal structures of metallic soaps are proposed. The soaps are predominantly lamellar crystalline or liquid crystalline lamellar rotor phases with tilted and/or untilted molecular constituents. These display evidence of varying degrees of headgroup organisation, including superstructuring and polymerisation. A single crystal structure is presented for a complex of pyridine with cobalt soap. Simple models for their structure are discussed in terms of their swelling properties in water and oils. Experiments are also presented to demonstrate the sorbent properties of aluminium soaps on oil spills.¶ The thermotropic liquid crystallinity of alkaline earth, transition metal, heavy metal and lanthanide soaps is investigated in detail. This is done to assess their suitability as templates, and to document their novel thermotropic behaviour, particularly the relatively unknown lanthanide soaps. Liquid crystalline behaviours are studied using high-temperature XRD (HTXRD), hot-stage optical microscopy and DSC. Models for a liquid crystalline phase progression from crystals to anisotropic liquids are discussed in terms of theories of self-assembly and interfacial curvature. The terminology required for this is drawn from various nomenclature systems for amphiphilic crystals and liquid crystals. General agreement with previous studies is reported for known soaps, while liquid crystallinity is demonstrated in the lanthanide and some non-lanthanide soaps for the first time. A general phase progression of crystalline lamellar through liquid crystalline lamellar to non-lamellar liquid crystalline is discussed in terms of models concerned with the molecular and crystal structures of the soaps and their phase transitions via headgroup and chain re-arrangements.¶ Experiments aimed at guiding growth of metal sulfides using metallic soaps as templates are described, and a model for this growth is discussed. Metal sulfides have been successfully grown by reacting crystalline and liquid crystalline transition metal and heavy metal soaps with H2S gas at room temperature and at elevated temperature. These have been characterised using XRD, TEM, ED and IR. Sulfide growth is demonstrated to be restricted and guided by the reacting soap template architecture. Zinc, cadmium, indium and lead soaps formed confined nanoparticles within the matrix of their reacting soap template. In contrast, curved and flat sheet-like structures, some resembling sponges were found in the products of sulfided iron, cobalt, nickel, copper, tin and bismuth soaps. A model to explain this behaviour is developed in terms of the crystal and liquid crystal structures of the soaps and the crystal structures of the metal sulfide particles.¶ Liquid crystalline iron soaps have been subjected to controlled thermal degradation yielding magnetic iron oxide nanoparticles. Some XRD and TEM evidence has been found for formation of magnetic mesostructures in heat-treated iron soaps. Models for the molecular and liquid crystalline structure of iron soaps, their thermotropic phase progression and eventual conversion to these magnetic products are discussed. Systematic syntheses of mesoporous silicates from sheeted clays are discussed.¶The templates that have been used are cationic surfactants and small, organic molecular salts. Experiments are reported where a cooperative self-assembly of surfactant/water/kanemite plus or minus salt and oils yields 'folded sheet materials' (FSM'S). Templating of kanemite has also been achieved using cobalt cage surfactants. A theoretical prediction of the specific surface areas and specific volumes of homologous sets of FSM's gave excellent agreement with measured values. The geometry and topology of the mesostructures are discussed. A theoretical model is also discussed regarding the curvature found in the sheets of natural clays , and results of templating clays and silica using metallic soaps are presented. Experiments and a model for low temperature nucleation and growth of microporous silicalite-1 are described in terms of silica templating by water clathrates.¶ Finally, the problem of finding minimal surface descriptions of crystal networks is addressed. Combinatoric methods are used to disprove the existence of possible embeddings of type I and II clathrate networks in non-self intersecting periodic minimal surfaces. The crystal network of the clathrate silicate, melanophlogite is successfully embedded in the WI-10 self-intersecting surface. Details of a previously unreported, genus-25 periodic surface with symmetry Im3m are discussed.