Dissertations / Theses on the topic 'Biomineral'

Biomineralisation is the process by which living things produce hard mineral tissues with unique physical properties. The study of this process can help us produce biomimetic materials, reproducing such properties, with the study of nucleation and crystallisation of the materials being particularly important. I have used molecular simulation techniques to help gain a greater understanding of these processes, focussing particularly on identifying the conformations and solid phases available to nanoparticles of two biomineral compounds. The bones and teeth of mammals are made largely of calcium phosphates. I have used metadynamics to study nanoparticles of tricalcium phosphate (TCP) and have identified high and lower order configurations. To facilitate this work I reviewed the extant empirical potentials for calcium phosphate systems, selecting the most appropriate for TCP. Calcium carbonate, found in examples throughout the animal kingdom, has three crystalline polymorphs relevant to biomineralisation: calcite, aragonite and vaterite. While nanoparticles of calcite have been extensively studied the other polymorphs have been neglected to date. In this work I present a technique for predicting crystalline morphologies for all three polymorphs across a range of sizes, and compare the energetic ordering. In water the energetic ordering of the nanoparticles is heavily dependent on nanoparticle size. Furthermore, I present work calculating the surface enthalpies of a variety of calcium carbonate surfaces, many of which are negative. It appears that entropic penalty of ordered water is key to understanding the stability of nanocrystals. Also presented is an application of the nudged elastic band method to study transitions between nanoparticle crystal conformations. Between all three crystal polymorphs the nanoparticles passed through an amorphous region of phase space. These results have also been used to evaluate order parameters for use in metadynamics simulations.

It has been proposed that geochemical and biomolecular palaeontological information can be obtained from biomineral associatedli pids. The location of lipidic material within the inorganic structureo f molluscan shells has previously been unknown, with important implications for long term survival of lipids and post-depositional contamination from the environment. Discrete experimental stages have been investigated and the different mechanical and chemical methods combined for the removal of contaminating material prior to the release and analysis of surficial, intercrystalline and intracrystalline lipids. Three extraction protocols have been compared using Recent Patella vulgata shells. Sequential stages of cleaning and extraction treatments identify n-alkanes, cholesterol (free and bound) and bound fatty acids. The n-alkanes are indigenous to the shell, but laboratory contamination can be significant, and highlights the need for experimental blanks. Bound fatty acids are extracted from intercrystalline and intracrystalline fractions. Cholesterol is extracted throughout the sequential methodology. The extraction of these compounds after extensive cleaning treatments illustrates the protective role of the inorganic biomineral. An experimental protocol for sequentially extracting protected lipids from the shells of Recent molluscs has been tested to distinguish the indigenous shell lipids from laboratory contamination and postdepositional ingress. The use of a calcium carbonate blank reveals the phthalate plasticisers extracted from the shells are due to laboratory contamination. Pristane, phytane and free fatty acids were rarely extracted which limits their use for interpretation. The n-alcohols, bound fatty acids, ß-hydroxy fatty acids, cholesterol and other steroids are extracted from the shells in higher yields than the calcium carbonate blanks and are considered indigenous to the shells. Multivariate statistical analysis is used to compare the distributions of bound fatty acids and steroids extracted from different shell locations with the reported fatty acids and steroids for the soft tissues of the same species. The reported values for the soft tissues were used to indicate the original shell lipid composition. The shells lack the unsaturated bound fatty acids reported in the soft tissues. The saturated bound fatty acids of Littorina littorea shells also differ in the carbon number distributions to the reported saturated fatty acids of the soft tissues. Surficial shell extracts are characterized by steroidal ketones, representing sterols which have been oxidised by the cleaning treatments used. The steroids from both intercrystalline and intracrystalline shell locations in Littorina littorea are most similar to the soft tissues. However, the intercrystalline steroids are different to the intracrystalline steroids which may indicate a different original composition. Potential Class level phylogenetic differences between the shells of Recent molluscs are revealed by their steroidal and bound saturated fatty acid compositions. The bivalves (n=3) have bound saturated fatty acids with a carbon number maximum of C16 whilst the gastropods (n=8) have a maximum of C16 or C18 and exhibit higher yields. ß-hydroxy fatty acids may indicate phylogenetic differences below the Class level for the Gastropoda. Principal component statistical analysis of the shell steroidal composition indicates differences at the Class level. Steroidal markers indicating the dietary intake have been found in the shells. The application of a methodology for the sequential extraction of lipids from molluscan shells has been used in a preliminary analysis of shell material for the presence of hydrocarbon pollutants. The shell nalkanes require comparison of carbon number distributions and yields with an experimental calcium carbonate blank to ensure indigeneity. Different n-alkane distributions within two Artica islandica shell samples are attributed to the different sampling locations. Differences between Patella vulgata and Littorina littorea shells from the same environment have also been observed, indicating different n-alkane uptake by different species. Polyaromatic hydrocarbons and sterane biomarkers reported to be present in the soft tissues of Patella vulgata exposed to the Braer oil spill have been searched for in the shells of an exposed sample. These compounds have not been detected. No increase in the shell n-alkane yields or similarity in carbon number distribution with the spilt oil is observed. This suggests no hydrocarbon incorporation or deputation pathway into the shell. Quaternary aged mollusc shells yield n-alkanes, n-alcohols, bound fatty acids and cholesterol. These have been extracted from both intercrystalline and intracrystal line locations within the shells. When compared with the extracts from Recent shells the yields of these lipids from fossil shells are significantly lower. The n-alkanes extracted from Quaternary shells are dominated by laboratory contamination, although some indigenous intracrystalline n-alkanes have been extracted. The bound fatty acids from intercrystalline sites within the fossils maintain their carbonn umber distribution but decreasein yields with increasinga ge; no diagenetic products were observed. The previously reported phylogenetic distinctions based on the bound fatty acids betweent he gastropodsa nd bivalves are maintainedf or fossils. However,t he information obtained from this analysis is limited by the small diversity of lipid distributions found in these fossil shells.

La biosphère océanique module la concentration de CO2 atmosphérique via la pompe biologique (transfert vertical de carbone organique particulaire - POC - de l'océan de surface vers le fond) et la contre-pompe des carbonates (émission de CO2 lors de la précipitation du carbone inorganique particulaire - PIC). Cette thèse a pour but (1) d'identifier la contribution de différents groupes planctoniques à l'export de POC et PIC à échelle annuelle dans des zones de production contrastée de l'océan Austral et (2) de comprendre comment cette diversité influence la stœchiométrie et la labilité du matériel exporté.Des déploiements de pièges à particules à proximité les iles Kerguelen et de la Géorgie du Sud montrent que la fertilisation naturelle en fer augmente l'intensité mais pas l'efficacité de l'export de POC. Les spores de résistance de diatomées pilotent une fraction importante (40-60 %) de l'export annuel de POC dans chacun des sites productifs. L'analyse taxonomique des diatomées mène à l'identification de groupes consistants qui impactent la séquestration préférentielle du C ou du Si. Lors d'une campagne estivale, nous associons l'abondance relative de diatomées et dinoflagellés à la stœchiométrie N:P de la matière organique et soulignons l'importance des couches de transition pour le découplage des cycles du C et Si. L'étude de la composition en lipides du matériel exporté nous permet d'identifier les spores de diatomées comme des vecteurs de matière organique contenant des acides gras riches en énergie. A Kerguelen, la faible contre-pompe des carbonates est due à dominance des coccolithophoridés dans l'export de PIC au Sud du Front Polaire
Marine biosphere impacts the atmospheric CO2 concentration by two main processes: the biological pump (vertical transfer of particulate organic carbon - POC - from the surface to the deep ocean) and the carbonate counter pump (CO2 emission during particulate inorganic - PIC - precipitation). The objectives of this PhD are (1) to identify the relative contribution of different plankton groups to POC and PIC export at annual scale in regions of contrasted productivity in the Southern Ocean and (2) to understand how this diversity impacts the elemental stoichiometry and lability of the exported material.Annual sediment trap deployments in the vicinity of the Kerguelen and South Georgia island plateaus have demonstrated that natural iron fertilisation increases the intensity but not the efficiency of export. Diatom resting spore formation drives an important fraction (40-60 %) of the annual carbon export in the productive sites. The taxonomic analyses of exported diatoms lead to the identification of consistent groups that impact the preferential export of C or Si. During a summer cruise, we associate the relative abundance of diatoms and dinoflagellates to the N:P stoichiometry of particulate organic matter and highlight the importance of transition layers for C and Si uncoupling. The study of the lipid composition of export leads to the identification of diatom resting spore as preferential vectors for the export energy-rich fatty acids. At Kerguelen, the low carbonate counter-pump is due to the dominance of coccolithophores contribution to PIC export south of the Polar Front

The Ingurtosu Pb-Zn deposit (Sardinia, Italy) was exploited for about a century until 1968. Huge amounts of tailings were abandoned, resulting in long-term harmful metal dispersion processes in both soils and waters. The maximum Zn concentration in waters from the Naracauli stream catchment area attains several hundreds of mg per litre, whereas Cd and Pb concentrations are in the order of thousands of μg per litre, despite the near neutral to slightly alkaline pH values (6.2-8.4). Zn concentration in waters is positively correlated with Pb, Cd, Ni and Co concentrations. The strongest correlation was observed between Zn and Cd, with a constant Zn/Cd ratio (close to 100) among samples that could suggest the weathering of a relatively uniform composition of sphalerite from tailings and mine wastes. Waters from tributaries show the lowest concentrations of contaminants. The highest contents in harmful and toxic elements were observed in waters that drain flotation tailings and mine wastes. Metals concentrations change under different seasonal conditions. The highest concentrations were observed under high-flow condition (October-April), probably due to the high runoff through the tailings and to aqueous transport of these metals in association with very fine particles, i.e. <0.4 μm. Zn, Pb, Cd, Cu and Ni concentrations in waters of the Naracauli stream, the main stream of the area, are abated by the seasonal bioprecipitation of hydrozincite, Zn5(CO3)2(OH)6. Hydrozincite precipitation is promoted by a microbial community made up of a filamentous cyanobacterium (Scytonema sp.) and a microalga (Chlorella sp.). Hydrozincite could be used in a controlled process to attenuate metal pollution in mining waters. Information on environmental conditions that promote the biomineralization process is fundamental for the development of remediation strategies. This work aims to investigate the variables controlling the biomineralization process, and the hydrochemical factors that affect hydrozincite precipitation. According to field observations, correlated with speciation and equilibrium calculations, the optimum condition for hydrozincite precipitation occurs in late spring of rainy years, when the hydraulic regime in the stream reaches stationary conditions, and SI values with respect to hydrozincite and pH reach the highest values, in agreement with the higher stability of the hydrozincite solid phase in contact with slightly alkaline waters. Concomitantly, Zn 2+/CO32- molar ratio reaches values close to 1, indicating that kinetic processes have a role on the hydrozincite biomineralization process. Conversely, heavy rain events occurring in late spring appear to inhibit biomineralization, likely due to the decrease in the SI values resulting from the dilution effect of rain water. Results from morphological analysis show that hydrozincite morphology varies, and depends on the environmental conditions. Changes were observed between samples collected in late spring and samples collected in summer, and among samples precipitated under different water flow conditions. Hydrozincite samples collected in summer are characterized by globules with a larger diameter than those collected in spring, this variation can be ascribed to a difference in the production of external mucilage sheaths by cyanobacteria colonies in response to stress conditions. Considering influence of water flow, it was observed that hydrozincite sheaths precipitated under low flow condition have more or less a constant diameter, whereas under high flow conditions sheaths become thinner at the final ends. This particular morphology is due to the influence of hydrodynamics on the structure of the biofilm and, consequently, on biomineral shape. Diel cycles in dissolved Zn, Co, Ni and Mn were found to occur in a selected station along the Naracauli stream. The highest change in concentration was observed for Zn: the difference between the minimum (3 mg/l) and maximum (4.7 mg/l) Zn concentrations is 1.7 mg/l (about 35%). The minimum values occurred at h 17:00 and maxima between h 02:00 and h 05:00. The timing of diel cycles in Co and Ni is very similar to that for Zn, but the ranges of Co and Ni concentrations are much smaller than Zn. Increased nocturnal concentrations could result from a combination of geochemical and biological processes. Considering the relations among temperature, pH and Zn contents, temperature and pH would seem to be the parameters that control variations in Zn concentration. Water temperature shows a well defined diurnal cycle. Maximum water temperature was observed between the h 13:00 and h 17:00. Water temperature varies due to change in air temperature and incident solar radiation. The pH values vary between 7.7 and 8.1; the highest values were observed during the sunny hours and the lowest during the night or early morning. The diel pH cycle derives from photosynthesis (predominant during the day) and respiration (predominant during the night). Obtained results may be explained by adsorption-desorption reactions (onto colloids, carbonates, bacterial surfaces and biofilms) and/or different rates of mineral precipitation between the morning and the night time. Diurnal metal cycles should be taken into account to evaluate environmental conditions, potential risks and cleanup of contaminated sites

It is important to evaluate periodic fluctuations in environment or climate recorded through time to better understand the nature of Earth's history as well as to develop ideas about what the future may hold. There exist numerous proxies by which these environmental patterns can be demonstrated and analyzed through various time scales; from sequence stratigraphic bundles of transgressive-regressive cycles that demonstrate eustatic changes in global sea level, to the geochemical composition of a skeleton that records fluctuations in ocean temperature through the life of the biomineralizing organism. This study examines some of the methods by which we can analyze environmental fluctuations recorded at different time scales. The first project examines the methods by which extrabasinal orbital forcing (i.e. Milankovitch cycles) can be tested in the rock record. In order to distinguish these patterns, computer generated carbonate rock records were simulated with the resulting outcrops tested using common methods. These simulations were built upon eustatic sea level fluctuations with periods similar to what has been demonstrated in the rock record, as well as maintaining the many factors that affect the resultant rock composition such as tectonics, subsidence, and erosion. The result demonstrated that substantially large sea level fluctuations, such as those that occur when the planet is in an icehouse condition, are necessary to produce recognizable and preservable patterns that are otherwise overwhelmed by other depositional factors. The second project examines the temporal distribution of the bivalve Semele casali from Ubatuba Bay, Brazil by using amino acid racemization (AAR) calibrated with ¹⁴C radiometric dates. This data set is one of the largest ever compiled and demonstrates that surficial shell assemblages in the area have very long residence times extending back in time 10,000 years. The area has had very little change in sea level and the AAR ratios which are highly temperature dependent could be calibrated across sites varying from 10 to 53 meters in water depth. Long time scales of dated shells provide us with an opportunity to study climate fluctuations such as El Niño southern oscillation. The third project describes a newly developed method for estimating growth rates in organisms using closely related species from similar environments statistically analyzed for error using a jackknife corrected parametric bootstrap. As geochemical analyses get more precise while using less material, data can be collected through the skeleton of a biomineralizing organism, thus revealing information about environmental shifts at scales shorter than a year. For such studies, the rate of growth of an organism has substantial effects on the interpretation of results, and such rates of growth are difficult to ascertain, particularly in fossilized specimens. This method removes the need for direct measures of growth rates and even the most conservative estimates of growth rates are useful in constraining the age ranges of geochemical intra-skeletal studies, thus elucidating the likely time period under analysis. This study assesses the methods by which periodic environmental fluctuations at greatly varying time scales can be used to evaluate our understanding of earth processes using rigorous quantitative strategies.
Ph. D.

Diatoms are unicellular photosynthetic algae that display intricately patterned cell walls made of amorphous silicon dioxide (silica). Long-chain polyamines and highly phosphorylated proteins, silaffins and silacidins, are believed to play an important role in biosilica formation. The phosphate moieties on silaffins and silacidins play a significant role in biomineral formation, yet no kinase has been identified that phosphorylates these biomineral forming proteins. This dissertation describes the characterization of a novel kinase from the diatom Thalassiosira pseudonana, tpSTK1, which is upregulated during silica formation. A recombinantly expressed histidine-tagged version of tpSTK1 was capable of phosphorylating recombinant silaffins but not recombinant silacidin in vitro. Through establishing methods for subcellular fraction of T. pseudonana membranes in combination with antibody inhibition assay, it was discovered that native tpSTK1 phosphorylates silaffins but not silacidins in vitro (i.e. it exhibits the same substrate specificity as recombinant tpSTK1). As tpSTK1 is an abundant protein in the ER lumen (~ 0.5 % of total ER protein) it seems highly likely to function as a silaffin kinase in vivo. TpSTK1 lacks clear sequence homologs in non-diatom organisms and is the first molecularly characterized kinase that appears to be involved in biomineralization. The predicted kinase domain (KD) of tpSTK2, the only T. pseudonana homolog of tpSTK1, was recombinantly expressed and tested for phosphorylation activity. Recombinant tpSTK2-KD and native tpSTK2 exhibited detectable activity with myelin basic protein, but did not phosphorylate silaffins or silacidins in vitro. Western blot analysis demonstrated that native tpSTK2 was not present in the ER, but associated with the cytosol and Golgi membrane containing subcellular fractions.

The interactions between organic molecules and minerals is fundamental to the under- standing of processes such as biomineralisation, the attachment of bacteria to surfaces and the design of synthetic materials within biomimetics. This thesis shows how molec- ular dynamics simulations can be employed to study the organic - inorganic interactions and give new insights into the molecular binding at mineral surfaces that play a role in these processes. The incorporation of amino acids within calcium carbonate crystals was simulated and show a high energy associated with the incorporation of these molecules. The amino acids get incorporated in-between the lattice planes of the crystal, causing small anisotropic distortions to the crystal. The inclusion of these molecules occurs via a goodness-of-fit principle, where disruptions to the crystal lattice should be kept to a minimum. These simulations show good agreement with experimental X-ray data. Simulations of multiple tripeptides show a different conformational behaviour of the peptides in solution than on the surface of calcium carbonate. Whereas the pep- tides exhibit a flexible behaviour in solution, binding to the mineral surface induces a disorder-to-order transition and the peptides become rigid. These changes in con- formational behaviour offer insight into the structure and behaviour of intrinsically disordered proteins. The polymer poly acrylic acid was simulated to analyse its conformational behaviour. In the presence of counter ions the polymer exhibits a flexible, extended conformation, whereas a coiled conformation is found in the absence of counter ions. The simulations in this work agree well with experimental spectroscopy studies. The binding of the polymer to a mineral surface is not only governed by the number of functional groups, but also the flexibility of the polymer. These results give an insight in how such molecules can aid the attachment of bacteria to surfaces.

The morphological diversity and complexity of naturally occurring forms and patterns have been a motivation for humans to copy and adopt ideas from Nature to achieve functional, aesthetic and social value. Common biogenic materials, such as biominerals, constructed with mineral phases and an organic matrix exhibit delicate structure with unusual optimal chemical-physical, morphological and mechanical properties, and have inspired ideas for the design and synthesis of biomimetic functional materials. The organic templates play an important role in directing assembly of the mineral/organic composites, and in controlling the nucleation and subsequent crystallization. Consequently, knowledge about the molecular interactions at mineral/organic interfaces is essential for understanding the principles of the organic-matrix-mediated biomineralization process. The microscopic properties of biomineral hydrozincite [Zn₅(CO₃)₂(OH)₆] from Naracauli Creek (SW Sardinia) were investigated by using X-ray Diffraction (XRD), Fourier Transform Infrared (FT-IR), Nuclear Magnetic Resonance (NMR), Scanning Electron Microscopy (SEM), and High-Resolution Transmission Electron Microscopy (HR-TEM) and the organic matrix present has been extracted and characterized by using Fourier Transform Infrared (FT-IR). In the context of molecular interactions at mineral/organic interfaces we describe an experimental study of the interaction of Bis(2-ethylhexil)phthalate (DEHP) with hydrozincite. This interaction, under controlled laboratory experiments, was investigated by using Fourier Transform Infrared (FT-IR) and Nuclear Magnetic Resonance Spectroscopy (NMR).

Due to their high biodiversity and widespread distribution in the Phanerozoic oceans, brachiopods are very important tools for research in palaeontology and related fields in Earth Sciences to investigate the past and present global change. Their biominerals have been considered the best carbonate archives of proxies for extending climate and environmental records on a broad geographical scale over long periods of time. Their fidelity as archives is supported by the following: 1) they record the physical and chemical composition of the seawater in which they live without, or with very limited, vital effects; 2) they precipitate a low-Mg calcite shell, which withstands post-depositional alteration; and 3) they are low metabolic and physiologically unbuffered animals sensitive to change in the physicochemical composition of the ambient seawater. However, there is still insufficient knowledge of the microstructures of these biomineral archives and their biomineralization processes during the evolutionary history of the phylum. The aims of the present thesis, focused on solving these issues, are to: 1) examine the micro- and morpho- structural diversity of modern and fossil brachiopods, 2) assess the microstructure variation in different environmental conditions; and 3) reconstruct the evolutionary changes and fabric differentiation of the main brachiopod classes through geological time. A multidisciplinary approach was used for the microstructural analyses: 1) a comprehensive dataset was established based on detailed microstructural observations of modern and fossil brachiopods analysed by Scanning Electron Microscopy (SEM); 2) new measurement methods were developed based on SEM observations to quantitatively describe the morphology and size of the structural units (fibres) of the shell secondary layer, the thickness of the primary layer, and the density and size of endopunctae of modern brachiopod shells; 3) new measurement methods were developed to describe the structural units (laminae and fibres) of fossil brachiopod shells; 4) statistical analyses of the acquired data were performed, i.e. independent-sample t-tests, frequency distribution plots, principal component analysis, and symmetric and asymmetric variants analyses; 5) stable isotope compositions (δ13C and δ18O) were tested from the secondary shell layer along shell ontogenetic increments in both dorsal and ventral valves of modern brachiopod shells; and 6) Transmission Electron Microscope (TEM) and Electron Backscatter Diffraction (EBSD) were performed in collaboration with other researchers to investigate the micro- and nanoscale features of modern brachiopod shells. Through these approaches, details of microstructural patterns were described and compared of twenty-nine specimens of six recent brachiopod species [Notosaria nigricans (Sowerby, 1846), Liothyrella neozelanica (Thomson, 1918), Liothyrella uva (Broderip, 1833), Magasella sanguinea (Leach, 1814), Gryphus vitreus (Born, 1778), Calloria inconspicua (Sowerby, 1846)] from different environmental conditions. Based on the morphology and size of the shell secondary layer fibres, the following conclusions were reached: 1) There was no significant difference in the shape and size of the fibres between ventral and dorsal valves of the same specimen; 2) An ontogenetic trend in the morphology of the fibres was found, as they become larger, wider, and flatter with increasing age. This change in size and shape indicated that the animal produced a fibrous layer with a different organic content during the ontogeny. 3) The relationship between size and shape of fibres and environmental conditions was clear when comparing two species of the same genus (L. neozelanica, L. uva) living in seawater with different carbonate saturation state and temperature, i.e. the fibres of L. uva are narrower and rounder than those of L. neozelanica. This in turn indicated a higher shell organic content in L. uva. Additional investigations were performed on the species Magellania venosa (Dixon, 1789), grown in the natural environment and in controlled culturing experiments in different pH conditions (7.35 to 8.15 ±0.05), and led to following conclusions: 1) Under low pH conditions, M. venosa produced a more organic-rich shell with larger and higher density endopunctae, and smaller secondary layer fibres, when subjected to about one year of culturing. 2) Increasingly negative δ13C and δ18O values were recorded by the shell produced during culturing and are related to the CO2–source in the culture setup. 3) Both the microstructural changes and the stable isotope results supported the value of brachiopods as robust archives of proxies for studying ocean acidification events in the geologic past. Finally, the measurements made on the size of structural units (laminae/fibres) of Cambrian to Devonian fossil brachiopod shells coupled with very detailed qualitative micro-scale observations, allowed the following conclusion: 1) The fossil organocarbonate brachiopod shells produced two main secondary layer fabrics: a laminar fabric in the Strophomenata, and a fibrous fabric in the Rhynchonellata. The Strophomenata laminar fabric shells appeared to be more variable and complex in their structural organization, but the thickness of the laminae was rather uniform and much thinner than that of the fibres. The Rhynchonellata fibrous fabric was more simple and uniform in its organization, but the size of the fibres was much more variable and comparable to the fabric of modern brachiopods. 2) Brachiopods with a fibrous secondary layer were mostly associated with biconvex shells, whereas brachiopods with a laminar secondary layer are associated with a variety of shell shapes. 3) Detailed microstructural studies were shown to be a very useful tool to construct the phylogenetic tree of the Phylum Brachiopoda. For example, the recorded gradual change in thickness of laminae from Billingselloidea to Productida could be important evidence to support the hypothesis that taxa with laminar microstructure diverged from the Billingsellida. Microstructural observation on the Chonetidina suggested that their shells had already evolved a laminar fabric during the Devonian. In summary, this new multidisciplinary and quantitative approach to describe the microstructure of brachiopod shells is a powerful tool to interpret microstructural variations of brachiopod shells in different ontogenetic stages and environmental conditions. Moreover, using the microstructure of brachiopod shells as a biomineral archive is a very promising tool for studying climate and environmental change and reconstructing the state of the oceans over the long history of geological time, and may be used to constrain the evolutionary history of the Phylum Brachiopoda.

Die unter dem Einfluss von Organismen entstehenden Minerale können entweder lediglich ein Nebenprodukt des Metabolismus sein oder aber eine Funktion aufweisen, wofür ihre Eigenschaften und Morphologie gezielt vom Organismus gesteuert werden. Der erstere Fall der bioinduzierten Mineralisation wurde in dieser Arbeit bei der Fällung des Minerals Schwertmannit (Fe8O8(OH)6SO4) durch den Bakterienstamm Leptospirillum ferrooxidans angetroffen. Die ursprünglich als bio-spezifisch eingeschätzte Morphologie des Minerals konnte in abiotischen Experimenten unter geeigneten Bedingungen erhalten werden. Die in dieser Arbeit am Beispiel der calcitischen Brachiopodenschalen, Seeigelstacheln und Seeigelzähne untersuchten Produkte der gesteuerten Biomineralisation sind Kompositwerkstoffe, deren Eigenschaften aus der Kombination von weichen organischen und harten mineralischen Komponenten entstehen. Sie sind funktionsangepasste Strukturen, für die ein anorganischer Bildungsmechanismus nicht in Frage kommen kann. Die Bildung der Minerale und deren Eigenschaften wurden mit Hilfe von Rasterelektronenmikroskopie, Rückstreuelektronenbeugung, Transmissionselektronenmikroskopie, Röntgenbeugung, Mikrohärtenmessungen nach Vickers und Nanoindentation untersucht. Durch Messungen mit niedriger Beschleunigungsspannung konnte die laterale Auflösung der Rückstreuelektronenbeugung verbessert werden. Eine Verbesserung der Winkelgenauigkeit der Rückstreuelektronenbeugung wurde durch einen statistischen Ansatz erreicht. Durch vergleichende biotische und abiotische Syntheseexperimente wurde die Bildung von Schwertmannit durch Leptospirillum ferroooxidans als Prozess einer bioinduzierten Mineralisation identifiziert. Die abiotischen Synthesewege beinhalten sowohl zweiwertige als auch dreiwertige Eisenlösungen als Ausgangsmaterial und nutzen verschiedene Wege der Oxidation und/oder Präzipitation von Schwertmannit. Die so gefällten Proben zeigten unterschiedliche Morphologien des Minerals, worunter aber auch die "Igelmorphologie" zu finden war, die in der Literatur als mit Schwertmannit-Nadeln überwachsene Zellen angesehen worden war. Rietveld-Anpassungen des Röntgenbeugungsprofils des amorphen bis nanokristallinen Minerals zeigen, dass die Kristallitgröße anisotrop ist. Sie ist je nach Bildungsbedingungen 2-2.5 nm senkrecht und als 5-11 nm parallel zu Kanälen, die durch das Netzwerk von [FeO6]3- -Oktaedern in der Struktur gebildet werden. Die Untersuchungen des Aufbaus calcitischer Brachiopodenschalen zeigen, dass Brachiopodenschalen, je nach Spezies, aus bis zu drei distinkten Mikrostrukturen bestehen können: Kolumnare Schicht, faserige Schicht und Primärschicht. Die Mikrostruktur und Textur der kolumnaren Schicht kann durch einen kompetitiven Wachstumsprozess erklärt werden, der auch bei anorganischen Prozessen angetroffen werden kann. Eine Erklärung der Mikrostruktur der fasrigen Schicht und der Primärschicht ist hingegen nicht durch Prozesse, die aus anorganischen Systemen bekannt sind, möglich. Die Mikrostruktur der Primärschicht, die in dieser Arbeit erstmalig mit Hilfe von räumlich hochauflösender Rückstreuelektronenbeugung aufgeklärt wurde, ähnelt dendritischen Strukturen. Eine derartig stark verzahnte und hochwiderstandsfähige Mikrostruktur ist bisher bei keinem anderen einphasigen Material bekannt und wird durch einen Entstehungsprozess aus einem amorphen CaCO3 (ACC) Precursor erklärt, der seinerseits eine Agglomeration von ACC-gefüllten Vesikeln entstand. Die Vickerhärten der einzelnen Schichten in Brachiopodenschalen schwanken zwischen 200 und 520 HV (0.005/10) und sind damit deutlich härter als bei anorganisch geformtem Calcit (150-170 HV 0.005/10). Mikrostruktur, Textur und Anordnung der Schichten innerhalb von Brachiopodenschalen maximieren deren Bruchfestigkeit. Seeigel bilden Calcit mit einem starken Grad an kristallographischer Vorzugsorientierung. Diese Vorzugsorientierung ist bei Seeigelstacheln so hoch, dass diese hochporösen Konstrukte als Einkristalle bezeichnet werden. Eine genaue, räumlich aufgelöste Messung der Orientierung der Kristallite mit Hilfe von Rückstreuelektronenbeugungsmessungen mit hoher Winkelauflösung zeigten, dass es interne Verkippungen bis zu 0.5° gibt. Diese Verkippungen in Seeigelstacheln erlauben Rückschlüsse auf deren Bildung. Die räumlich aufgelöste chemische Analyse in Kombination mit räumlich aufgelöster mechanischer Charakterisierung zeigt, dass der Mg Gehalt (molares Mg/Ca Verhältnnis 1-6 %) in Seeigelstacheln nicht mit Nanohärte (4-4,5 GPa) und E-Modulus (50-80 GPa) korrelierbar ist. Die Nanhohärte von Seeigelstacheln liegt deutlich höher als bei anorganisch gebildetem Calcit (3.0 +/- 0.2\,GPa), während deren E-Moduli ähnlich sind (70 +/- 5\,GPa). Diese Arbeit untersucht erstmals die Mikrostruktur von Seeigelzähnen mit Rückstreuelektronenbeugung. Die Untersuchungen zeigen, dass die großen strukturellen Einheiten, Steinteil, lamellarer Nadel Komplex, Prismen, Primär-, Sekundär- und Karinarplatten, 3-5° gegeneinander verkippt sind. Diese Bereiche selbst sind wieder in Untereinheiten strukturiert, beispielsweise einzelne Platten, die 1-2° gegeneinander verkippt sind. Diese Untersuchungen zeigen jedoch auch, dass die Bereiche ineinandergreifen können und eine strikte Unterscheidung nicht immer möglich ist. Für dieses Material wird der Begriff des Kompositkristalls vorgeschlagen. Das molare Mg/Ca Verhältnis der untersuchten Seeigelzähne liegt bei 10-25 % und ist positiv mit der Nanohärte (4-8 GPa) korreliert. Die Kombination der Messung der präzisen kristallographischen Orientierung, mikrostrukturellen, chemischen und mechanischen Eigenschaften trägt zu einem tiefergehenden Verständnis des Selbstschärfungsmechanismuses der Seeigelzähne bei. So konnte beispielsweise der häufig diskutierte Einfluss der prominenten 104-Spaltfläche von Calcit ausgeschlossen werden.
Minerals formed by organisms may either be simply a side-product of the metabolism or they carry a function, for which their properties and morphologies are controlled by the organism. The first case, bioinduced mineralisation, was encountered in this work in the case of the precipitation of the mineral schwertmannite (Fe8O8(OH)6SO4) by the bacterial strain \textit{Leptospirillum ferrooxidans}. In the literature the characteristic morphology of the mineral had been viewed as bio-specific. However, in this work, in could be produced in abiotic syntheses with appropriate conditions. Products of biocontrolled mineralisation investigated in this work were brachiopod shells, sea urchin spines and sea urchin teeth. These products are hybrid composite materials consisting of soft organic and hard mineral components. For their complex, highly characteristic, and purpose-oriented microstructures an inorganic mechanism can not be envisaged. The formation of the minerals and their properties has been investigated with scanning electron microscopy, electron backscatter diffraction, transmission electron microscopy, x-ray diffraction, Vickers microhardness indentation and nanoindentation. The use of a low accelerating voltage allowed the increase of the lateral resolution of electron backscatter diffraction. The angular resolution of electron backscatter diffraction could be increased by a statistical approach. Comparative biotic and abiotic synthesis experiments identified schwertmannite precipitation in cultures of Leptospirillum ferrooxidans as a process of bioinduced mineralisation. Different abiotic synthesis started from ferric or ferrous-solutions and used various methods of oxidation and/or precipitation to produce schwertmannite. The samples prepared by these methods led to a variety of morphologies of the mineral, including the "hedgehog" morphology which had been adressed as cell overgrown with schwertmannite needles in the literature. Rietveld refinements of the diffraction profile of the amorphous-to-nanocrystalline schwertmannite show that the crystallite size is anisotropic. It varies depending on the growth conditions and is between 2-2.5 nm perpendicular and 5-11 nm parallel to channels created by the network of [FeO6]3- -octahedra in the structure. The analyses of calcitic brachiopod shells show that, depending on the species, a distinction of up to three microstructures are present: columnar layer, fibrous layer and primary layer. The microstructure and texture of the columnar layer of the brachiopod shell can be explained by a process of competitive growth, which can also be found in inorganic systems. However, the formation of the fibrous and the primary layer can not be described by processes known from inorganic systems. The microstructure of the primary layer, which was correctly resolved in this thesis for the first time by high spatial resolution electron backscatter diffraction, resembles dendritic structures. Such a high interdigitated and highly resistive microstructure is not known from any other single phase material. Its formation is explained in terms of a precursor of amorphous CaCO3 (ACC) which has formed as an agglomeration of ACC-filled vesicles. Vickers hardnesses of the bachiopod shell layers vary between 200-520 HV (0.005/10) and are thus much harder as inorganic formed calcite (150-170 HV 0.005/10). Microstructure, texture and arrangement of the shell layers maximises the fracture toughness of brachiopod shells. Sea urchins form calcite with a high degree of crystallographic preferred orientation. The preferred orientation in sea urchin spines is so high that these highly porous structures are referred to as single crystals. A precise, spatially resolved measurement of the crystallographic orientation of sea urchin spines gives information on their formation. The spatially resolved chemical analyses of sea urchin spines in combination with spatially resolved mechanical characterisation shows that Mg content (molar Mg/Ca ratio: 1-6 %) is not correlated with the nanohardness(4-4.5 GPa) and Young's modulus (50-80 GPa). The nanohardness of sea urchin spines is higher than that of inorganically formed calcite (3.0 +/- 0.2\,GPa), while the Young's moduli of sea urchin spines and inorganically formed calcite (70 +/- 5\,GPa) are similar. The present thesis analyses the microstructure of sea urchin teeth for the first time with electron backscatter diffraction. The data shows that the major structural units (i.e. stone, lamellar needle complex, prisms, primary plates, secondary plates and carinar process plates) are misoriented 3-5°. These units are assembled of sub-units, e.g. plates, that are misoriented 1-2°. The data furthermore shows that the units can interdigitate and that a distinction is not always possible. The term "composite crystal" is suggested for these materials. The molar Mg/Ca ratio of the investigated sea urchin teeth is 10-25 % and it is positively correlated with nanohardness(4-8 GPa). The combination of precise measurement of the crystallographic orientation, microstructural, chemical and mechanical analyses lead to a deeper understanding of the self-sharpening mechanism of sea urchin teeth. It could be shown that the 104-clevage of calcite does not influence the self-sharpening.

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.

The practice of soil stabilization has become an essential part of present day geotechnical engineering projects. However, it is a matter of growing concern that popular chemical stabilizers possess high carbon footprint and adversely affect the eco-system. With the emergence of bio-geotechnology as an environmentally benign alternative to chemical stabilization, there is a paradigm shift in the field of soil stabilization. This thesis is a novel attempt to underpin the effect of bacterial biopolymers and biomineralisation on stabilization of soil.

Dental enamel consists mainly of calcium-deficient hydroxyapatite (CDHA). The formation and evolution of enamel is a progressive and complex process the final stage of which is post-eruptive maturation (PEM), when mineralisation is completed following tooth eruption and exposure to oral fluids. Although PEM is directly correlated with decrease in caries susceptibility, a complete model to describe the whole process does not exist. Several reports have recently suggested that the previously observed caries decline, which started with the introduction of F- in drinking water and dental products, has stopped and is in some cases in reverse. New research approaches are therefore needed, which will focus on caries prevention and not treatment. This project monitored the in vitro effects of simulated PEM on the physicochemical properties of dental enamel and proposed a model which describes the whole process. For this purpose, primary and permanent bovine enamel was tested, using a suitably designed demineralisation/remineralisation laboratory protocol as well as characterisation techniques. The results were applied to the synthesis of enamel proxies, which could mimic the physicochemical properties of dental enamel; these proxies were evaluated for their potential to be used as enamel substitutes in dental research.

Marine biomineralizing organisms provide a fundamental link between biology and environment. Calcified structure are important archives that can provide us main means of understanding organism adaptation, habits, environmental characteristics, and to look back in time and explore the past climate and their evolutionary history. In fact, biomineralized structures retain an unparalleled record of current and past ocean conditions through the investigation of their microchemistry and isotopes. This thesis considers aspects of two different biomineralization systems: fish otolith and coral skeletons at macro-, micro- and nanoscale, with the aim to understand how their morphology, structural characteristics and compositions can provide information of their functionality, and the environmental, behavioural, and evolutionary context in which organisms are framed. To this end, I applied a multidisciplinary approach in the scope to investigate calcified structures as “information recorders” and as models to study the phenotypic plasticity.

The iron and calcium biominerals of the major lateral teeth of the chitons, Acanthopleura hirtosa, Acanthopleura echinata, Plaxiphora albida, Cryptoplax striata, Ischnochiton australis, and Acanthopleura rehderi, have been characterised in situ at all stages of mineralization, with laser Raman microscopy. Mature teeth do not contain goethite and ferrihydrite, both of which have been isolated in early stage teeth. Deposition of magnetite in the posterior region of tooth cusp occurs on two fronts simultaneously, from both the anterior and posterior. In contrast, the lepidocrocite region, where present, is formed by aggregation over the whole extent of the interior surface. A thin veneer of ferrihydrite over the posterior surface of the magnetite prevents this region from undergoing oxidation prior to use. The first evidence for conditions favouring the deposition of hematite over goethite in biological systems is shown. Hematite is uniquely located in micro-domains of teeth at a critical stage of development, at the transition between iron and calcium biomineralisation. The Raman spectrum of biogenically produced hematite is distinctly differently from geological and synthetic material. Calcium biomineralisation in the major lateral teeth of Acanthopleura echinata takes place as an ordered process from the top of the tooth core under the tab region, down its interior surface and down the lepidocrocite layer, before extending outwards to the anterior surface at the junction zone. Mineralization is not initiated until the lepidocrocite layer has isolated the core from the magnetite cap. The junction zone, previously shown to be a region of high ion density, is shown to be free of mineral deposits. In contrast to previous work, the cores of P. albida, C. striata, and I. australis, are shown to contain amorphous ferric iron oxide minerals and not the previously described ferric phosphate. Mineral deposition progresses in the same manner as all other chitons studied, from posterior to anterior and from tooth tip towards the base.

Thesis (M.S.)--School of Computing and Engineering. University of Missouri--Kansas City, 2006.
"A thesis in civil engineering." Typescript. Advisor: Ganesh Thiagarajan. Vita. Title from "catalog record" of the print edition Description based on contents viewed Oct. 30, 2007. Includes bibliographical references (leaves 72-73). Online version of the print edition.

Studying calcium carbonate (otoliths) and calcium phosphate (fins, scales, bones) hard structure chemistry has numerous applications in the fisheries field for both freshwater and marine environments. The overall thesis objectives were: 1.) to provide an integrated and multidisciplinary approach to understanding the incorporation of trace elements and isotopes into biomineralized hard structures, and 2.) to apply this multidisciplinary perspective in the examination of element marking, stock discrimination, and migration in teleost fish species found within the Canadian Polar North. Varying physiological mechanisms within fishes control the uptake of essential and non-essential trace elements and isotopes during biomineralization processes. Essential life elements such as zinc and magnesium are controlled by their own uptake regulation systems whereas non-essential elements such as strontium and barium are controlled primarily by calcium uptake at the gills driven by internal calcium homeostasis. Secondarily, environmental trace elements compete with calcium and with each other for uptake at the gills. The ability of certain hard structures such as bones, fins, and scales to remobilise calcium and associated calcium-like elements, plays a role in the prolonged high concentrations of strontium that were observed in otolith marking of Greenland Halibut, Reinhardtius hippoglossoides. High doses of strontium chloride resulted in a prolonged expulsion of excess strontium. Strong associations of Dolly Varden Char, Salvelinus malma malma, with groundwater allowed discrimination of populations among studied river systems using otolith strontium and barium, and strontium isotopes. Calculation of otolith strontium freshwater baselines allowed for a quantitative method to examine migration histories of Arctic Char, S. alpinus, in Canada and western Greenland. Migration seaward was related to ease of access to estuary and marine habitats. Easy access to estuaries resulted in migration at a young age and small size whereas longer rivers resulted in a delay of migration to older ages and larger sizes. Understanding the role of fish physiology in association with calcium homeostasis provided a stronger basis for understanding the incorporation and presence of trace elements and isotopes found within biomineralized hard structures. These studies underscore the utility of microchemical studies for elucidating biological phenomena, thus linking the aspects of biology, physiology, and geology.
February 2017

Magíster en Gestión para la Globalización
El presente estudio corresponde al plan de internacionalización de AguaMarina S.A., una empresa chilena de biotecnología con foco en la biominería, específicamente, en biolixiviación de pilas. Este plan abarca distintos aspectos para el negocio, como son los análisis estratégicos para la selección del país con mayores condiciones favorables para invertir, los análisis Porter y FODA, las estrategias de entrada al mercado escogido y sus respectivas proyecciones de venta y análisis financiero. Cabe destacar el alto desempeño y reconocimiento que ha tenido AguaMarina en el mercado chileno, donde ha sido premiada por BHP Billiton dentro de su programa Clúster Minero, reconocida como el primer proveedor de servicios en la etapa de Innovación e I&D, lo anterior sumado con el reducido número de competidores internacionales, le ofrece una gran ocasión para su expansión en nuevos mercados. De acuerdo a los distintos parámetros evaluados como índices de inversión en minería, facilidad de hacer negocios, corrupción, ubicación entre otros, el mercado recomendado para invertir es el peruano, el cual entre otras características, es el segundo productor mundial de cobre y posee sobre MUSD$22.000 como inversión estimada en minería hasta el 2017. El análisis de competitividad de Porter muestra que en la biominería en Perú no existen participantes privados locales y solo presencias esporádicas de participantes internacionales y universidades. La estrategia recomendada es asociarse con un local, como por ejemplo Laboratorios Analíticos del Sur (LAS), quién ya tiene una cartera de clientes y una red de contacto que pueden ser futuros clientes. LAS posee los servicios e infraestructura de un laboratorio de minerales y está acreditado al igual que AguaMarina con altos estándares de calidad, como por ejemplo la acreditación en ISO17025.Of2005. Por otro lado, LAS está ubicado en Arequipa, el cual corresponde a una ubicación estratégica por tiempos de respuesta y por poseer el 52% de la producción de cobre de biolixiviación y/o flotación que es el proceso alternativo. Las estrategias recomendadas son mantener su batería de productos, haciendo énfasis en la calidad y las ventajas de estos con respecto a la competencia y a los procesos alternativos. Con respecto a la promoción se recomienda ingresar a una entidad como Promisur, quien se encarga de la participación de sus miembros en ferias, exposiciones, congresos y revistas especializadas. Considerando una intervención de 1/3 del volumen de servicios al quinto año para 3 unidades mineras, se proyectan ventas de MUSD$ 2,5 y los parámetros de análisis VAN con una tasa de 20% de MUSD$ 1,92 y un TIR al quinto año de 296%, lo que refleja la alta rentabilidad de este proyecto. Los valores mostrados corresponden a resultados antes de proyectar una asociación con algún local y el margen de asociación entre estos debe ser menor a 1/3 de los ingresos por venta, con lo cual se alcanza un TIR de 63%.

On appelle biominéraux l’ensemble des minéraux fabriqués par le vivant. Ce sont des matériaux essentiels, présents dans la quasi-totalitédes espèces vivantes. Néanmoins les caractéristiques structurales, chimiques ainsi que les mécanismes de formation, et l’évolution de cesmatériaux sont encore fortement débattus. Cela s’explique notamment par les difficultés à étudier expérimentalement des espèces chimiquesévoluant en milieux biologiques.Bien que tout aussi complexe, une approche théorique, à l’échelle moléculaire, peut aider à la caractérisation de ces matériaux biologiqueset notamment la caractérisation de leurs interfaces formées avec les milieux biologiques environnants. Cela étant essentiel pour une meilleurecompréhension de la formation et de l’évolution de ces minéraux.Les oxalates de calcium constituent une famille de biominéraux très importante dans le monde du vivant. Ils constituent notamment les principales espèces cristallinesrencontrées dans les calculs rénaux où ils peuvent exister sous trois phases possédant différents degrés d'hydratation. Au cours de cette thèse, nous avons effectuéles simulations des propriétés spectroscopique IR et RMN des ces trois phases, ce qui permet d'obtenir une signature propre à chacune d'entre elle, aidant ainsi àl'identification de ces phases à partir des spectres obtenus expérimentalement.Les phosphates de calcium font aussi partie des biominéraux. Ils composent la majeure partie du minéral osseux des mammifères. Ce minéral se trouvesous la forme de nanoparticules décrites comme possédant un cœur cristallin d’hydroxyapatite substituées entourée d'une couche hydratée et désordonnée en surface.Durant ce travail de thèse, nous nous sommes intéressés à ces deux composantes. Concernant le cœur cristallin des particules, nous avons étudié en particulierle cas des substitutions par des carbonates car il s'agit de la substitution prédominante dans les apatites biologiques. En couplant ce travail à des expériencesde RMN solide nous pouvons proposé une localisation précise de ces substituants au sein de la maille d’hydroxyapatite.La couche désordonnée de surface est encore très mal comprise à l'heure actuelle et de nombreux modèles structuraux sont proposés dans la littérature pour la décrire. Nous avonsconsidéré un certain nombre d'entre eux pour lesquels nous avons modélisé les propriétés RMN, qui confrontées à celle issues de l'expérience nous ontpermis d'identifier les points forts et faibles des différentes hypothèses
Biominerals are all the minerals produced by living organisms. They are essential materials, present in almost all living species. Nevertheless,the structural, chemical properties and, formation mechanisms and the evolution of these materials are still heavily debated. This is due in particular to thedifficulties of experimentally studying chemical species evolving in biologicalenvironments. Although, equally complex, a theoretical approach at the molecular level can help in the characterization of these biological materialsand in particular the characterization of their interfaces formed with the surrounding biological media. This is essential for a better understandingof the formation and evolution of these minerals.Calcium oxalates are essential biominerals that are very common in the living world. They constitute the main crystalline speciesencountered in kidney stones where they can exist in three phases possessing different degrees of hydration. In this, thesis we carried outsimulations to predict the IR and NMR spectroscopic properties of these three phases. Thsi enabled us to obtain specificsignature of each polyhydrate, and thus makes it possible to obtain a signature specific to each of them, thus helpingthe identification of these phases from the experimentally spectra obtained.Calcium phosphates are part of the bio/biological minerals. They make up the major part of the bone mineral of mammals. This mineral is in the form of nanoparticles havinga crystalline core of hydroxyapatite and a hydrated and disordered surface layer.During this thesis we were interested in these two components. Concerning the crystalline core of the particles, we studied in particularthe case of carbonate substitutions because of its predominant substitution in biological apatites. By combining this work with solid state NMR experimentswe can propose a precise localization of these substituents within the hydroxyapatite crystalline cell.The disordered surface layer is still very poorly understood and many structural models are proposed in the literature to describe it. We haveconsidered a number of them for which we have modeled the NMR properties which were then confronted with experimental results. The comparaisonmade it possible to identify the strengths and weaknesses of the various hypotheses

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.

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.
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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

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. ...