Identification of a sulfide derivative with a bicyclic hydrocarbon skeleton related to squalene. Part II: synthesis of a S-spiro-like dithiolane triterpenoid

A sulfide with a bicyclic squalene hydrocarbon skeleton present in sediments from various depositional settings and of different geological age has been identified by synthesis of a reference compound. In contrast to previous expectations [cf. Schouten, S., Sinninghe Damsté, J.S., de Leeuw, J.W., 1995. A novel triterpenoid carbon skeleton in immature sulphur-rich sediments. Geochimica et Cosmochimica Acta 59, 953–958; Gug, S., Schaeffer, P., Adam, P., Klein, S., Motsch, E., Albrecht, P., 2009. Identification of a sulfide derivative with a bicyclic hydrocarbon skeleton related to squalene. Part I: Synthesis of a dithiane triterpenoid. Organic Geochemistry 40, 876–884.], this sulfide bears two “S-spiro type“ thiolane moities, but not the two thiochromane moieties originally envisaged. The synthesis resulted in the formation of a complex isomeric mixture of compounds, all co-eluting in gas chromatography (GC) in the form of one broad peak, as is the case with the geochemical compound. The spiro-type sulfide was formed by intramolecular sulfurization of a polyunsaturated bicyclic squalene derivative of unknown biological origin. The presence of this sulfide in a number of Triassic to Miocene marine sediments from various and contrasting depositional settings (upwelling environments, shallow continental platforms, lagoonal sub-basins, hypersaline environments), all characterized by strongly anoxic conditions, but with or without photic zone anoxia, indicates that the microorganisms biosynthesizing the precursor bicyclic squalene occupy diverse ecological niches.     

Inverse methods and kinetic models of hydrocarbon generation: I. Theoretical considerations

Several different proposed models of thermocatalytic cracking of kerogen to hydrocarbons are exhibited. The specific models are then combined into a single generic, encompassing framework. For laboratory pyrolysis measurements of kerogen degradation and of thermal generation of hydrocarbons, inverse methods are used to show how to determine the relevant distributions of kinetic parameters consistent with the measured data.     

Synthetic coprecipitates of exopolysaccharides and ferrihydrite. Part I: Characterization

Iron(III) (hydr)oxides formed at extracellular biosurfaces or in the presence of exopolymeric substances of microbes and plants may significantly differ in their structural and physical properties from their inorganic counterparts. We synthesized ferrihydrite (Fh) in solutions containing acid polysaccharides [polygalacturonic acid (PGA), alginate, xanthan] and compared its properties with that of an abiotic reference by means of X-ray diffraction, transmission electron microscopy, gas adsorption (N₂, CO₂), X-ray absorption spectroscopy, ⁵⁷Fe Mössbauer spectroscopy, and electrophoretic mobility measurements. The coprecipitates formed contained up to 37 wt% polymer. Two-line Fh was the dominant mineral phase in all precipitates. The efficacy of polymers to precipitate Fh at neutral pH was higher for polymers with more carboxyl C (PGA ∼ alginate > xanthan). Pure Fh had a specific surface area of 300 m²/g; coprecipitation of Fh with polymers reduced the detectable mineral surface area by up to 87%. Likewise, mineral micro- (<2 nm) and mesoporosity (2-10 nm) decreased by up to 85% with respect to pure Fh, indicative of a strong aggregation of Fh particles by polymers in freeze-dried state. C-1s STXM images showed the embedding of Fh particles in polymer matrices on the micrometer scale. Iron EXAFS spectroscopy revealed no significant changes in the local coordination of Fe(III) between pure Fh and Fh contained in PGA coprecipitates. ⁵⁷Fe Mössbauer spectra of coprecipitates confirmed Fh as dominant mineral phase with a slightly reduced particle size and crystallinity of coprecipitate-Fh compared to pure Fh and/or a limited magnetic super-exchange between Fh particles in the coprecipitates due to magnetic dilution by the polysaccharides. The pH_iep of pure Fh in 0.01 M NaClO₄ was 7.1. In contrast, coprecipitates of PGA and alginate had a pH_iep < 2. Considering the differences in specific surface area, porosity, and net charge between the coprecipitates and pure Fh, composites of exopolysaccharides and Fe(III) (hydr)oxides are expected to differ in their geochemical reactivity from pure Fe(III) (hydr)oxides, even if the minerals have a similar crystallinity.     

Effects of long-term irrigation with treated wastewater. Part I: Evolution of soil physico-chemical properties

The long-term impact of irrigation on a Mediterranean sandy soil irrigated with Treated wastewater (TWW) since 1980 was evaluated. The main soil properties (CEC, pH, size distribution, exchangeable cations and chloride, hydraulic conductivity) as well as the organic matter and Cu, Cr and Pb speciation in an irrigated soil and a non-irrigated control soil at various soil depths were monitored and compared during a 2 years experiment. In this first part, the evolution of the physico-chemical soil properties was described. The irrigation with TWW was beneficial with regard to water and nutrient supplying. All the exchangeable cations other than K⁺ were higher in the irrigated soil than in the reference one. A part of the exchangeable cations was not fixed on the exchange complex but stored as labile salts or in concentrated soil solution. Despite the very sandy soil texture, both saturated and unsaturated hydraulic conductivity exhibited a significant diminution in the irrigated soil, but remained high enough to allow water percolation during rainy periods and subsequent leaching of accumulated salts, preventing soil salinization. In the irrigated soil, exchangeable sodium percentage (ESP) exhibited high values (20% on average) and the soil organic C was lower than in the reference. No significant effect was noticed on soil mineralogical composition due to irrigation.     

Diffusion of Li in olivine. Part I: Experimental observations and a multi species diffusion model

There are an increasing number of studies that focus on the systematics of the distribution of Li and its isotopes among different geochemical reservoirs. These studies have found that Li is relatively mobile compared to many other elements (e.g., Fe, Mg), and diffusion has been considered as a mechanism to generate large isotopic fractionations even at high temperatures. In order to quantify some of these aspects, we have measured Li diffusion rates experimentally along [0 0 1] of single crystals of olivines from San Carlos, Arizona and Pakistan, at 800-1200 °C at a total pressure of 100 kPa and fO₂ ≈ WM buffer. A complex diffusion behavior of Li is observed, indicating that two mechanisms of diffusion (a fast and a slower one) operate simultaneously. The behavior is well described by a model that partitions Li between two different sites in olivine - an octahedral site (Li_Me) and an interstitial site (Li_i). Transport of Li is a combination of hopping within and between each of these kinds of sites involving also vacancies on the octahedral site (V_Me). It is assumed that the homogeneous reaction (Li_Me = V_Me + Li_i) that maintains equilibrium distribution of Li between the sites is instantaneous compared to the timescales of all other processes associated with diffusive transport. One consequence of this mode of transport of Li in olivine is that the shape and length of diffusion profiles depend on the boundary conditions imposed at the surface of a crystal; i.e., the chemical environment (e.g., fO₂, aLi₄SiO₄), in addition to temperature and pressure. Our model describes the variable experimentally determined Li-profile shapes produced at different temperatures and with different boundary conditions, as well as their time evolution, quantitatively. Modeling the observed isotopic fractionation shows that ⁶Li diffuses about 5% faster than ⁷Li on the interstitial site. Inspection of published data on Li distribution in natural olivines that are available until now indicates that the fast (interstitial) mechanism of Li diffusion is unlikely to be dominant in most natural systems; Li rich, oxidizing environments (e.g., fluids?) may be exceptions. However, when it operates it can decouple the equilibration of Li isotopic gradients from the time scale of equilibration of overall Li concentrations. Diffusion dominated by the slower mechanism will occur on the average at a rate that is about an order of magnitude faster than diffusion of Fe, Mg and most other divalent cations in olivine; such diffusion of Li in olivine will be much slower than the rates of diffusion in clinopyroxene and plagioclase crystals at the same conditions. Fractionation of isotopes of Li by diffusion is likely to be a transient phenomenon and is more likely to be observed in crystals showing zoning of Li concentrations.     

Kinetic study of the kaolinite-mullite reaction sequence. Part I: Kaolinite dehydroxylation

The decomposition reaction of kaolinite has been investigated as a function of the defectivity of the starting material and the temperature of reaction. Time resolved energy-dispersive powder diffraction patterns have been measured using synchrotron radiation, both under a constant heating rate (heating rates from 10 to 100° C/min) and in isothermal conditions (in the temperature range 500 to 700° C). The apparent activation energy of the dehydroxylation process is different for kaolinites exhibiting a different degree of stacking fault density. The results of the analysis of the kinetic data indicate that the starting reaction mechanism is controlled by diffusion in the kaolinite particle. The diffusion process is dependent on the defective nature of both kaolinite and metakaolinite. At high temperatures, and at higher heating rates, the reaction mechanism changes and the resistance in the boundary layer outside the crystallites becomes the rate-limiting factor, and nucleation begins within the reacting particle. During the final stage of the dehydroxylation process the reaction is limited by heat or mass transfer, and this might be interpreted by the limited diffusion between the unreacted kaolinite domains and the metakaolinite matrix.     

Automated calibration of advanced soil constitutive models. Part I: hypoplastic sand

Acta Geotechnica - This paper discusses an automated deterministic approach to parameters calibration of the hypoplastic model for sand. The calibration is performed on results from basic...     

Structural and vibrational behaviour of fluorapatite with pressure. Part I: in situ single-crystal X-ray diffraction investigation

Using single-crystal X-ray diffraction from a diamond anvil cell, the compressibility of a synthetic fluorapatite was determined up to about 7?GPa. The compression pattern was anisotropic, with greater change along a than c. Unit cell parameters varied linearly with β _a =3.32(8)?10^?3 and β _c =2.40(5)?10^?3 GPa^?1, giving a ratio β _a :β _c =1.38:1. Data fitted with a third-order Birch-Murnaghan EOS yielded a bulk modulus of K ₀=93(4)?GPa with K′=5.8(1.8). The evolution of the crystal structure of fluorapatite was analysed using data collected at room pressure, at 3.04 and 4.72?GPa. The bulk modulus of phosphate tetrahedron is about three times greater than the bulk modulus of calcium polyhedra. The values were 270(10), 100(4) and 86(3) GPa for P, Ca1 (nine-coordinated) and Ca2 (seven-coordinated) respectively. While the calcium polyhedra became more regular with pressure, the distortion of the phosphate tetrahedron remained unchanged. The size of the channel extending along the [001] direction represented the most compressible direction. The Ca2–Ca2 distance decreased from 3.982 to 3.897?Å on compression from 0.0001 to 4.72?GPa. The anisotropic compressional pattern may be understood in terms of the greater compressibility of the channel size over the polyhedral units. The reduction of the channel volume was measured by the evolution of the trigonal prism, having the Ca2–Ca2–Ca2 triangle as its base and the c lattice parameter as its height. This prism volume changed from 47.3?ų at room pressure to 44.78?ų at 4.72?GPa. Its relatively high bulk moduli, 86(3) GPa, indicated that the channel did not collapse with pressure and the apatite structure could remain stable at very high pressure.     

Geosteranes: Identification and synthesis of a novel series of 3-substituted steranes

A novel series of 3-alkyl and 3-carboxyalkyl-5β(H)-steranes 7–10 along with a full homologous series of carboxyalkyl-sterane (C₁ to C₆) 4–6 with 3α(H)5α(H) configuration have been identified in marine-evaporitic oils from Fazenda Belém, Potiguar Basin (Brazil) on the basis of mass spectral interpretation. The synthesis of enantiomerically pure 3α-alkyl-5β(H)-cholestane and 3β-alkyl-5α(H)-cholestane standards and their coinjection with petroleum fractions confirmed the structural assignments.     

Unravelling the conundrum of river response to rising sea‐level from laboratory to field. Part I: Laboratory experiments

The most recent deglaciation resulted in a global sea‐level rise of some 120 m over approximately 12 000 years. In this Part I of two parts, a moving boundary numerical model is developed to predict the response of rivers to this rise. The model was motivated by experiments at small scale, which have identified two modes describing the transgression of a river mouth: autoretreat without abandonment of the river delta (no sediment starvation at the topset–foreset break) and sediment‐starved autoretreat with abandonment of the delta. In the latter case, transgression is far more rapid and its effects are felt much further upstream of the river mouth. The moving boundary numerical model is checked against experiments. The generally favourable results of the check motivate adaptation of the model to describe the response of the much larger Fly‐Strickland River system, Papua New Guinea to Holocene sea‐level rise; this is done in the companion paper, Part II.     

A computer simulation study of natural silicate melts. Part I: Low pressure properties

In implementing into a molecular dynamics simulation code a simple interionic potential developed to describe the nine component system K₂O-Na₂O-CaO-MgO-FeO-Fe₂O₃-Al₂O₃-TiO₂-SiO₂ (KNCMFATS), it has been possible to reproduce satisfactorily a number of thermodynamic, structural and transport properties of a representative set of natural silicate melts. An important conclusion reached in this study is the good transferability of the potential from felsic to ultramafic compositions although this transferability becomes less accurate with high silica contents (rhyolitic composition and beyond) and with very iron-rich silicates (e.g. fayalite). A key feature of the simulation is to make the link between macroscopic properties of the melt and its microscopic structure and dynamics. We thus obtain a relationship between the molar volume of the melt, the number of network modifiers and the oxygen coordination number. The simulation also allows one to quantify the coordination environment around the cations as function of the melt composition. Furthermore, the electrical conductivity of the high temperature liquid is investigated.     

Experimental growth of quartz in petroleum environment. Part I: Procedures and Fluid Trapping

The quartz-water-oil-gas system has been experimentally studied with the objective of investigating the trapping of petroleum and aqueous inclusions in quartz at different water/oil (W/O) ratios (0/100, 5/95, 10/90, 20/80, 50/50, 100/0). Experiments were carried out in both a gas-pressure autoclave (GPA) under CH₄ pressure control, up to 250°C and 212 bar, and in a fluid-pressure autoclave (FPA) up to 350°C and 400 bar. High p-T conditions have notably allowed the growth of quartz at high oil saturation levels (W/O ratios from 10/90 to 50/50). Petroleum inclusions have been synthesised inside quartz microfractures (W/O ratios from 0/100 to 50/50; 209-350°C; 175-400 bar), and also inside quartz overgrowths (W/O ratios from 10/90 to 50/50; 289-350°C; 350-400 bar). Aqueous inclusions have been synthesised in presence of oil inside quartz microfractures from 185°C-163 bar up to 400°C-400 bar, and inside quartz overgrowth from 277°C-330 bar. Synthesised petroleum inclusions are representative of the parent oil up to 250°C. At 350°C, evidence of a cracking process has been observed with the consequent formation of methane. The segregation of the oil/gas/water column inside the GPA autoclave may also have prevented methane diffusion into the water phase when oil is present. This experimental approach shows that the trapping of fluid inclusions and the formation of quartz cement, under conditions of high oil saturation, have not been suppressed or prevented.     

Coupled HM analysis using zero‐thickness interface elements with double nodes. Part I: Theoretical model

In recent years, the authors have proposed a new double‐node zero‐thickness interface element for diffusion analysis via the finite element method (FEM) (Int. J. Numer. Anal. Meth. Geomech. 2004; 28 (9): 947–962). In the present paper, that formulation is combined with an existing mechanical formulation in order to obtain a fully coupled hydro‐mechanical (or HM) model applicable to fractured/fracturing geomaterials. Each element (continuum or interface) is formulated in terms of the displacements (u) and the fluid pressure (p) at the nodes. After assembly, a particular expression of the traditional ‘u–p’ system of coupled equations is obtained, which is highly non‐linear due to the strong dependence between the permeability and the aperture of discontinuities. The formulation is valid for both pre‐existing and developing discontinuities by using the appropriate constitutive model that relates effective stresses to relative displacements in the interface. The system of coupled equations is solved following two different numerical approaches: staggered and fully coupled. In the latter, the Newton–Raphson method is used, and it is shown that the Jacobian matrix becomes non‐symmetric due to the dependence of the discontinuity permeability on the aperture. In the part II companion paper (Int. J. Numer. Anal. Meth. Geomech. 2008; DOI: 10.1002/nag.730 ), the formulation proposed is verified and illustrated with some application examples. Copyright © 2008 John Wiley & Sons, Ltd.     

SPH-DEM coupling method based on GPU and its application to the landslide tsunami. Part I: method and validation

Landslide-induced tsunami is a complex fluid–solid coupling process that plays a crucial role in the study of a disaster chain. To simulate the coupling behaviors between the fluid and solid, a graphics processing unit-based coupled smoothed particle hydrodynamics (SPH)-discrete element method (DEM) code is developed. A series of numerical tests, which are based on the laboratory test by Koshizuka et al. (Particle method for calculating splashing of incompressible viscous fluid, 1995) and Kleefsman et al. (J Comput Phys 206:363–393, 2005), are carried out to study the influence of the parameters, and to verify the accuracy of the developed SPH code. To ensure accurate results of the SPH simulation, the values for the diffusion term, particle resolution (1/25 characteristic length), and smoothing length (1.2 times of particle interval) are suggested. The ratio of the SPH particle size and the DEM particle’s diameter influences the accuracy of the coupling simulation between solid particles and water. For the coupling simulation of a single particle or a loose particle assembly (not contact each other) with fluid, this ratio should be smaller than 1/20; for a dense particle assembly, a ratio of smaller than 1/6 will be good.

     

A numerical simulation of residual circulation in Tampa Bay. Part I: Low-frequency temporal variations

The residual (time-average) salinity and circulation in a numerical ocean model of the Tampa Bay estuary are shown to experience significant temporal variation under realistic forcing conditions. A version of the Estuarine Coastal Ocean Model developed for Tampa Bay with 70 by 100 horizontal grid points and 11 sigma levels is examined for the years 2001–2003. Model output variables are averaged over the entire time of the simulation to generate long-term residual fields. The residual axial current is found to be dominated by the buoyancy-driven baroclinic circulation with an outflow (southwestward) at the surface and to the sides of the shipping channel, and an inflow (northeastward) usually occurring subsurface within or above the shipping channel. Averages over 30 d are used to examine variations in the residual fields. During the simulation the average surface salinity near the head of Tampa Bay varies with the freshwater inflow, from 12‰ to 33%. At the bay mouth salinity varies from 30%. to 36%.. A localized measure of the baroclinic circulation in the shipping channel indicates the residual circulation can vary strongly, attaining a magnitude triple the long-term mean value. The baroclinic circulation can be disrupted, going to near zero or even reversing, when the buoyancy-driven flow is weak and the surface winds are to the northeast. Three time periods, representing different environmental conditions, are chosen to examine these results in detail. A scaling argument indicates the relative strength of buoyancy versus wind as ΔρgH²(LC _Dω²)⁻¹, where δρ is head-to-mouth density difference across the bay,g is gravitational acceleration,H is depth,L is bay length,C _D is the surface wind drag coefficient, andw is wind speed. Tampa Bay is usually in the buoyancy dominated regime. The importance of winds in the weak-buoyancy case is demonstrated in an additional simulation without wind stress.     

The Use of Lagrange Diagrams in Precise Initiation Blasting. Part I: Two Interacting Blastholes

Using the concept of Lagrange diagrams this contribution details the calculation of the delay time between blastholes in a row and rows of blastholes with respect to precise initiation timing within the new advanced blasting technology which is based on the use of electronic detonators. After introducing the representations of stress waves and cracks, this contribution focuses on the role of stress wave interaction in optimal fragmentation in surface blasting and bench blasting. Part I of the paper considers two interacting blast-holes, Part II will be devoted to three or more out of plane interacting blastholes, whereas Part III will treat the interaction with a free face such as encountered in bench blasting. A few simplifying assumptions have been made in this paper with respect to the rock mass as well as the mechanical treatment. The essential assumptions include that the rock mass is treated as a continuum with finite tensile and compressive strength and the effects of structural geology are not taken into account. In addition, the analysis in Part I is simplified by two 'educational' assumption, that all waves are plane (i.e., one-dimensional) waves and three-dimensional effects of finite size blastholes and charges are not taken into account. This contribution will also show that knowledge in wave propagation and fracture mechanics is essential for the successful application of the new blasting technique in industry. In particular, the delay time, the wave speeds in the rock mass, the shape of the wave pulse and the acoustic impedance mismatch (not considered in this paper) have become decisive parameters in advanced blasting. Utilizing the wave speed and wave shapes of detonations, large scale tests in various countries (Australia, Chile, etc.) have shown that optimal delay timing requires shorter delay times in conjunction with allowing for a wider drilling pattern and the use of a grossly reduced amount of explosives , i.e., a lower powder factor. This seemingly contradictory arrangement is fully justified by using scientific principles in blasting, and converting blasting from an art to a scientific discipline .     

The development of acidic groundwaters in coal-bearing strata: Part I. Rare earth element fingerprinting

This study examines the rare earth element (REE) pattern of acidic mine discharges in the Durham basin (NE England) as a means of fingerprinting their sources and understanding the water-rock interactions Although whole rock compositions proved to be unhelpful, mimicking acid mine water generation in a series of selective leachates of the coal and coal-bearing strata gave REE patterns similar to those measured in the emergent waters. REE ratios and anomalies were used as indicators of specific interactions in the development of acidic groundwater. The implications of the findings for the classification and evolution of acid mine discharges are discussed.     

Dynamic simulation of littoral zone habitats in lower Chesapeake Bay. I. Ecosystem characterization related to model development

The fringing environments of lower Chesapeake Bay include sandy shoals, seagrass meadows, intertidal mud flats, and marshes. A characterization of a fringing ecosystem was conducted to provide initialization and calibration data for the development of a simulation model. The model simulates primary production and material exchange in the littoral zone of lower Chesapeake Bay. Carbon (C) and nitrogen (N) properties of water and sediments from sand, seagrass, intertidal silt-mud, and intertidal marsh habitats of the Goodwin Islands (located within the Chesapeake Bay National Estuarine Research Reserve in Virginia, CBNERR-VA) were determined seasonally. Spatial and temporal differences in sediment microalgal biomass among the habitats were assessed along with annual variations in the distribution and abundance ofZostera marina L. andSpartina alterniflora Loisel. Phytoplankton biomass displayed some seasonality related to riverine discharge, but sediment microalgal biomass did not vary spatially or seasonally. Macrophytes in both subtidal and intertidal habitats exhibited seasonal biomass patterns that were consistent with other Atlantic estuarine ecosystems. Marsh sediment organic carbon and inorganic nitrogen differed significantly from that of the sand, seagrass, and silt habitats. The only biogeochemical variable that exhibited seasonality was low marsh NH₄ ⁺. The subtidal sediments were consistent temporally in their carbon and nitrogen content despite seasonal changes in seagrass abundance. Eelgrass has a comparatively low C:N ratio and is a potential N sink for the ecosystem. Changes in the composition or size of the vegetated habitats could have a dramatic influence over resource partitioning within the ecosystem. A spatial database (or geographic information system, GIS) of the Goodwin Islands site has been initiated to track long-term spatial habitat features and integrate model output and field data. This ecosystem characterization was conducted as part of efforts to link field data, geographic information, and the dynamic simulation of multiple habitats. The goal of these efforts is to examine ecological structure, function, and change in fringing environments of lower Chesapeake Bay.     

Towards a Higher Comparability of Geothermometric Data obtained by Raman Spectroscopy of Carbonaceous Material. Part I: Evaluation of Biasing Factors

Raman spectroscopy of carbonaceous material (RSCM) is frequently used to determine metamorphic peak temperatures from the structural order of carbonaceous material enclosed in metasediments. This method provides a quick, robust and relatively cheap geothermometer. However, the comparability of the RSCM parameter is low as there are at least three major sources of biasing factors. These sources are the spectral curve‐fitting procedure, the sample characteristics itself and the experimental design including the used Raman system. To assess the impacts of the biasing factors on RSCM, a series of experiments was performed. The experiments showed that curve‐fitting is strongly influenced by individual operator‐bias and the degrees of freedom in the model, implying the need for a standardised curve‐fitting procedure. Due to the diversity of components (optics, light detection device, gratings, etc.) and their combinations within the Raman systems, different Raman instruments generally give differing results. Consequently, to estimate comparable metamorphic temperatures from RSCM data, every Raman instrument needs its own calibration. This demands a reference material series that covers the entire temperature calibration range. Although sample heterogeneity will still induce some variation, a reference material series combined with standardised curve‐fitting procedures will significantly increase the overall comparability of RSCM data from different laboratories.