Ab initio quantum mechanical investigation of structural and chemical-physical properties of selected minerals for minero-petrological, structural ceramic and biomaterial applications

The purpose of this thesis is the atomic-scale simulation of the crystal-chemical and physical (phonon, energetic) properties of some strategically important minerals for structural ceramics, biomedical and petrological applications. These properties affect the thermodynamic stability and rule the mineral-environment interface phenomena, with important economical, (bio)technological, petrological and environmental implications. The minerals of interest belong to the family of phyllosilicates (talc, pyrophyllite and muscovite) and apatite (OHAp), chosen for their importance in industrial and biomedical applications (structural ceramics) and petrophysics. In this thesis work we have applicated quantum mechanics methods, formulas and knowledge to the resolution of mineralogical problems ("Quantum Mineralogy”). The chosen theoretical approach is the Density Functional Theory (DFT), along with periodic boundary conditions to limit the portion of the mineral in analysis to the crystallographic cell and the hybrid functional B3LYP. The crystalline orbitals were simulated by linear combination of Gaussian functions (GTO). The dispersive forces, which are important for the structural determination of phyllosilicates and not properly con-sidered in pure DFT method, have been included by means of a semi-empirical correction. The phonon and the mechanical properties were also calculated. The equation of state, both in athermal conditions and in a wide temperature range, has been obtained by means of variations in the volume of the cell and quasi-harmonic approximation. Some thermo-chemical properties of the minerals (isochoric and isobaric thermal capacity) were calculated, because of their considerable applicative importance. For the first time three-dimensional charts related to these properties at different pressures and temperatures were provided. The hydroxylapatite has been studied from the standpoint of structural and phonon properties for its biotechnological role. In fact, biological apatite represents the inorganic phase of vertebrate hard tissues. Numerous carbonated (hydroxyl)apatite structures were modelled by QM to cover the broadest spectrum of possible biological structural variations to fulfil bioceramics applications.

A review of air–ice chemical and physical interactions (AICI): liquids, quasi-liquids, and solids in snow

Snow in the environment acts as a host to rich chemistry and provides a matrix for physical exchange of contaminants within the ecosystem. The goal of this review is to summarise the current state of knowledge of physical processes and chemical reactivity in surface snow with relevance to polar regions. It focuses on a description of impurities in distinct compartments present in surface snow, such as snow crystals, grain boundaries, crystal surfaces, and liquid parts. It emphasises the microscopic description of the ice surface and its link with the environment. Distinct differences between the disordered air–ice interface, often termed quasi-liquid layer, and a liquid phase are highlighted. The reactivity in these different compartments of surface snow is discussed using many experimental studies, simulations, and selected snow models from the molecular to the macro-scale. Although new experimental techniques have extended our knowledge of the surface properties of ice and their impact on some single reactions and processes, others occurring on, at or within snow grains remain unquantified. The presence of liquid or liquid-like compartments either due to the formation of brine or disorder at surfaces of snow crystals below the freezing point may strongly modify reaction rates. Therefore, future experiments should include a detailed characterisation of the surface properties of the ice matrices. A further point that remains largely unresolved is the distribution of impurities between the different domains of the condensed phase inside the snowpack, i.e. in the bulk solid, in liquid at the surface or trapped in confined pockets within or between grains, or at the surface. While surface-sensitive laboratory techniques may in the future help to resolve this point for equilibrium conditions, additional uncertainty for the environmental snowpack may be caused by the highly dynamic nature of the snowpack due to the fast metamorphism occurring under certain environmental conditions. Due to these gaps in knowledge the first snow chemistry models have attempted to reproduce certain processes like the long-term incorporation of volatile compounds in snow and firn or the release of reactive species from the snowpack. Although so far none of the models offers a coupled approach of physical and chemical processes or a detailed representation of the different compartments, they have successfully been used to reproduce some field experiments. A fully coupled snow chemistry and physics model remains to be developed.

An updated synthesis of the observed and projected impacts of climate change on the chemical, physical and biological processes in the oceans

The 5th Assessment Report (AR5) of the Intergovernmental Panel on Climate Change (IPCC) states with very high certainty that anthropogenic emissions have caused measurable changes in the physical ocean environment. These changes are summarized with special focus on those that are predicted to have the strongest, most direct effects on ocean biological processes; namely, ocean warming and associated phenomena (including stratification and sea level rise) as well as deoxygenation and ocean acidification. The biological effects of these changes are then discussed for microbes (including phytoplankton), plants, animals, warm and cold-water corals, and ecosystems. The IPCC AR5 highlighted several areas related to both the physical and biological processes that required further research. As a rapidly developing field, there have been many pertinent studies published since the cut off dates for the AR5, which have increased our understanding of the processes at work. This study undertook an extensive review of recently published literature to update the findings of the AR5 and provide a synthesized review on the main issues facing future oceans. The level of detail provided in the AR5 and subsequent work provided a basis for constructing projections of the state of ocean ecosystems in 2100 under two the Representative Concentration Pathways RCP4.5 and 8.5. Finally the review highlights notable additions, clarifications and points of departure from AR5 provided by subsequent studies.

Chemical characteristics of coal pebbles and Barzas-type coals

Coal pebbles found in 1994 in the Greham Bell Island (Franz Josef Land Archipelago) are made up of Barzas-type cuticular liptobiolith. The coal belongs to the initial stage of catagenesis and is characterized by high content of cutinite (up to 70%) with very low reflectance (Ro = 0.1%). Maceration products show some tegillate elements of Arthropoda and individual Devonian spores. It is supposed that plant cuticle and Arthropoda exocuticle are present in this coal. Obtained data suggest presence of Paleozoic rocks in the sedimentary sequence, although they are not yet recovered. These data complement available information on distribution of specific Devonian coals and allow to have a new insight into zoogenic material involved in coal formation.

(Table 1) Cation exchange capacity and other characteristics of soils common in Lower Saxony, Germany

The chemical and biochemical processes associated with the filtration of rainwater through soils, a step in groundwater recharge, were investigated. Under simulated climatic conditions in the laboratory, undisturbed soil columns of partly loamy sands, sandy soils and loess were run as lysimeters. A series of extraction procedures was carried out to determine solid matter in unaltered rock materials and in soil horizons. Drainage water and moisture movement in the columns were analysed and traced respectively. The behaviour of soluble humic substance was investigated by percolation and suspension experiments. The development of seepage-water in the unsaturated zone is closely associated with the soil genetic processes. Determining autonomous chemical and physical parameters are mineral composition and grain size distribution in the original unconsolidated host rock and prevailing climatic conditions. They influence biological activity and transport of solids, dissolved matter and gases in the unsaturated zone. Humic substances, either as amorphous solid matter or as soluble humic acids play a part in diverse sorption, solution and precipitation processes.

Physico-chemical characteristics and ikaite content of brine and ice samples taken during SIPEX and DDU campaigns in East Antarctica, 2007

Calcium carbonate precipitation in sea ice is thought to potentially drive significant CO2 uptake by the ocean. However, little is known about the quantitative spatial and temporal distribution of CaCO3 within sea ice, although it is hypothesized that high quantities of dissolved organic matter and/or phosphate (common in sea ice) may inhibit its formation. In this quantitative study of hydrous calcium carbonate as ikaite, sea ice cores and brine samples were collected from pack and land fast sea ice between September and December 2007 during two expeditions, one in the East Antarctic sector and the other off Terre Adélie. Samples were analysed for CaCO3, salinity, dissolved organic carbon/nitrogen, inorganic phosphate, and total alkalinity. No relationship between these parameters and CaCO3 precipitation was evident. Ikaite was found mostly in the uppermost layers of sea ice with maximum concentrations of up to 126 mg ikaite per litre melted sea ice being measured, although both the temporal and horizontal spatial distributions of ikaite were highly heterogeneous. The precipitate was also found in the snow on top of the sea ice at some of the sampling locations.

Physical properties, mineral and chemical compositions, and accumulation rates of Holocene and Upper Pleistocene bottom sediments from the Sea of Okhotsk

Mineral and chemical compositions and physical properties of diatomaceous clayey-siliceous sediments from the Sea of Okhotsk are studied. Accumulation rates of silica are determined. Their compositional model based on silica content is similar to that of Late Jurassic and Olenekian-Middle Anisian cherts from the Sikhote Alin region. Thickness of Holocene siliceous unit and accumulation rates of siliceous deposits depended on bioproductivity in the upper water layer and seafloor topography. Accumulation rates of amorphous SiO2 (0.05-5.7 g/cm**2/ka) and free SiO2 (0.5-11.6 g/cm**2/ka) are minimal on seamounts and maximal in depressions near foothills. These values match accumulation rates of free SiO2 in Triassic and Late Jurassic basins of the Sikhote Alin region (0.33-3 g/cm**2/ka). Comparison of composition and accumulation rates of silica shows that Triassic and Late Jurassic siliceous sequences of Sikhote Alin could accumulate in a marginal marine basin near a continent.

Physical properties, compressional-wave velocity and consolidation characteristics of ODP Holes 133-815B and 133-817B

Sites 815 and 817 were drilled near the Townsville Trough during Leg 133 of the Ocean Drilling Program. The physical properties, compressional-wave velocity, and consolidation characteristics indicate that the periplatform carbonate sediments maintain more water content and lower compressional velocity near the Queensland Plateau than the clayey hemipelagic sediments, which have a clay content of up to 60%. Bulk density, void ratio or porosity, water content, and compressional-wave velocity are shown to have a linear relationship with burial depth. Between 3.5 and 5 Ma (about 100-500 mbsf), these physical properties maintained a constant rate vs. the depth in core because of the fast sedimentation-rate effect at Site 815. However, compressionalwave velocity still increases downward in this section. The clay content in this section causes an increase of bulk modulus and compaction effect. At Site 817, scarce terrigenous mud content and abundant carbonate content (88%-97%) cause a straight line relationship between physical properties and burial depth. During the consolidation test, we show that dominant micritic particles may cause faster acoustic velocity than sediments composed mainly of coccoliths. The bulk modulus ratio increasing rate in the clay-rich carbonate sediments is almost 4.5 times higher than in the clay-free periplatform carbonate sediments.

Mean chemical characteristics and volcano signatures of ice cores from Belukha, the Everest and three Svalbard sites

Ice cores from outside the Greenland and Antarctic ice sheets are difficult to date because of seasonal melting and multiple sources (terrestrial, marine, biogenic and anthropogenic) of sulfates deposited onto the ice. Here we present a method of volcanic sulfate extraction that relies on fitting sulfate profiles to other ion species measured along the cores in moving windows in log space. We verify the method with a well dated section of the Belukha ice core from central Eurasia. There are excellent matches to volcanoes in the preindustrial, and clear extraction of volcanic peaks in the post-1940 period when a simple method based on calcium as a proxy for terrestrial sulfate fails due to anthropogenic sulfate deposition. We then attempt to use the same statistical scheme to locate volcanic sulfate horizons within three ice cores from Svalbard and a core from Mount Everest. Volcanic sulfate is <5% of the sulfate budget in every core, and differences in eruption signals extracted reflect the large differences in environment between western, northern and central regions of Svalbard. The Lomonosovfonna and Vestfonna cores span about the last 1000 years, with good extraction of volcanic signals, while Holtedahlfonna which extends to about AD1700 appears to lack a clear record. The Mount Everest core allows clean volcanic signal extraction and the core extends back to about AD700, slightly older than a previous flow model has suggested. The method may thus be used to extract historical volcanic records from a more diverse geographical range than hitherto.

Physical properties and AMS characteristics of ODP Site 185-1149 sediments

During Ocean Drilling Program Leg 185, we studied progressive changes of microfabrics of unconsolidated pelagic and hemipelagic sediments in Holes 1149A and 1149B in the northwest Pacific at 5818 m water depth. We paid particular attention to the early consolidation and diagenetic processes without tectonic deformation before the Pacific plate subduction at the Izu-Bonin Trench. Shape, size, and arrangement of pores were analyzed by scanning electron microscope (SEM) and were compared to anisotropy of magnetic susceptibility (AMS) data. The microfabric in Unit I is nondirectional fabric and is characterized by large peds of ~10-100 µm diameter, which are made up of clay platelets (mainly illite) and siliceous biogenic fragments. They are ovoid in shape and are mechanically packed by benthic animals. Porosity decreases from 0 to 60 meters below seafloor (mbsf) in Unit I (from 60% to 50%) in association with macropore size decreases. The microfabric of coarser grain particles other than clay in Unit II is characterized by horizontal preferred orientation because of depositional processes in Subunit IIA and burial compaction in Subunit IIB. On the other hand, small peds, which are probably made of fragments of fecal pellets and are composed of smectite and illite (3-30 µm diameter), are characterized by random orientation of clay platelets. The clay platelets in the small peds in Subunit IIA are in low-angle edge-to-face (EF) or face-to-face (FF) contact. These peds are electrostatically connected by long-chained clay platelets, which are interconnected by high-angle EF contact. Breaking of these long chains by overburden pressure diminishes the macropores, and the clay platelets in the peds become FF in contact, resulting in decreases in the volume of the micropores between clay platelets. Thus, porosity in Subunits IIA and IIB decreases remarkably downward. The AMS indicates random fabric and horizontal preferred orientation fabric in Units I and II, respectively. This result corresponds to that of SEM microfabric observations.In Subunit IIB, pressure solutions around radiolarian tests and clinoptilolite veins with normal displacement sense are seen distinctively below ~170 mbsf, probably in correspondence to the transition zone from opal-A to opal-CT.

(Table 1) Results of measurements of productive characteristics of phytoplankton and environmental parameters in the Barents Sea in September-October 1997

The described studies were carried out in the eastern part of the sea during the end of the summer seasonal succession from September 1 to October 12, 1997. Concentration of chlorophyll a in the surface layer varied from 0.09 to 1.24 mg/m**3; it tended to increase in the southern regions (<74°N). Primary production in the water column (P_p) varied from 24 to 214 mg C/m**2/day and was on average 91 mg C/m**2/day. The low level of P_p seems to result from combination of physical and chemical environmental factors unfavorable for photosynthesis (e.g. deficiency of nutrients and low values of insolation and temperature) and intensive grazing of phytoplankton by zooplankton. The lower boundary of the photosynthetic layer in open waters was located at depth 60-75 m; irradiance there was 0.1-0.5% of incident irradiance. In deep-water regions (>200 m) the subsurface maximum of chlorophyll occurred in the layer at 20-40 m; usually this maximum resulted in formation of additional maxima of primary production.

Physical properties, velocity and attenuation characteristics, and mineralogy of gabbros from ODP Hole 176-735B

Laboratory compressional wave (Vp) and shear wave (Vs) velocities were measured as a function of confining pressure for the gabbros from Hole 735B and compared to results from Leg 118. The upper 500 m of the hole has a Vp mean value of 6895 m/s measured at 200 MPa, and at 500 meters below seafloor (mbsf), Vp measurements show a mean value of 7036 m/s. Vs mean values in the same intervals are 3840 m/s and 3857 m/s, respectively. The mean Vp and Vs values obtained from log data in the upper 600 m are 6520 and 3518 m/s, respectively. These results show a general increase in velocity with depth and the velocity gradients estimate an upper mantle depth of 3.32 km. This value agrees with previous work based on dredged samples and inversion of rare element concentrations in basalts dredged from the conjugate site to the north of the Atlantis Bank. Laboratory measurements show Vp anisotropy ranging between 0.4% and 8.8%, with the majority of the samples having values less than 3.8%. Measurements of velocity anisotropy seem to be associated with zones of high crystal-plastic deformation with predominant preferred mineral orientations of plagioclase, amphiboles, and pyroxenes. These findings are consistent with results on gabbros from the Hess Deep area and suggest that plastic deformation may play an important role in the seismic properties of the lower oceanic crust. In contrast to ophiolite studies, many of the olivine gabbros show a small degree of anisotropy. Log derived Vs anisotropy shows an average of 5.8% for the upper 600 m of Hole 735B and tends to decrease with depth where the overburden pressure and the age of the crustal section suggests closure of cracks and infilling of fractures by alteration minerals. Overall the results indicate that the average shear wave splitting in Hole 735B might be influenced by preferred structural orientations and the average value of shear wave splitting may not be a maximum because structural dips are <90°. The maximum fast-wave orientation values could be influenced by structural features striking slightly oblique to this orientation or by near-field stress concentrations. However, flexural wave dispersion analyses have not been performed to confirm this hypothesis or to indicate to what extent the near-field stresses may be influencing shear wave propagation. Acoustic impedance contrasts calculated from laboratory and logging data were used to generate synthetic seismograms that aid in the interpretation of reflection profiles. Several prominent reflections produced by these calculations suggest that Fe-Ti oxides and shear zones may contribute to the reflective nature of the lower oceanic crust. Laboratory velocity attenuation (Q) measurements from below 500 m have a mean value of 35.1, which is consistent with previous vertical seismic profile (VSP) and laboratory measurements on the upper 500 m.