Ab initio calculations of the Fe(II) and Fe(III) isotopic effects in citrates,nicotianamine, and phytosiderophore,and new Fe isotopic measurements in higher plants

Iron is one of the most abundant transition metal in higher plants and variations in its isotopic compositions can be used to trace its utilization. In order to better understand the effect of plant-induced isotopic fractionation on the global Fe cycling, we have estimated by quantum chemical calculations the magnitude of the isotopic fractionation between different Fe species relevant to the transport and storage of Fe in higher plants: Fe(II)-citrate, Fe(III)-citrate, Fe(II)-nicotianamine, and Fe(III)-phytosiderophore. The ab initio calculations show firstly, that Fe(II)-nicotianamine is ～3‰ (⁵⁶Fe/⁵⁴Fe) isotopically lighter than Fe(III)-phytosiderophore; secondly, even in the absence of redox changes of Fe, change in the speciation alone can create up to ～1.5‰ isotopic fractionation. For example, Fe(III)-phytosiderophore is up to 1.5‰ heavier than Fe(III)-citrate₂ and Fe(II)-nicotianamine is up to 1‰ heavier than Fe(II)-citrate. In addition, in order to better understand the Fe isotopic fractionation between different plant components, we have analyzed the iron isotopic composition of different organs (roots, seeds, germinated seeds, leaves and stems) from six species of higher plants: the dicot lentil (Lens culinaris), and the graminaceous monocots Virginia wild rye (Elymus virginicus), Johnsongrass (Sorghum halepense), Kentucky bluegrass (Poa pratensis), river oat (Uniola latifolia), and Indian goosegrass (Eleusine indica). The calculations may explain that the roots of strategy-II plants (Fe(III)-phytosiderophore) are isotopically heavier (by about 1‰ for the δ⁵⁶Fe) than the upper parts of the plants (Fe transported as Fe(III)-citrate in the xylem or Fe(II)-nicotianamine in the phloem). In addition, we suggest that the isotopic variations observed between younger and older leaves could be explained by mixing of Fe received from the xylem and the phloem.     

Modulation of soil moisture–precipitation interactions over France by large scale circulation

How soil moisture affects precipitation is an important question—with far reaching consequences, from weather prediction to centennial climate change—, albeit a poorly understood one. In this paper, an analysis of soil moisture–precipitation interactions over France based on observations is presented. A first objective of this paper is to investigate how large scale circulation modulates soil moisture–precipitation interactions, thanks to a weather regime approach. A second objective is to study the influence of soil moisture not only on precipitation but also on the difference between precipitation and evapotranspiration. Indeed, to have a total positive soil moisture–precipitation feedback, the potential decrease in precipitation associated with drier soils should be larger than the decrease in evapotranspiration that drier soils may also cause. A potential limited impact of soil moisture on precipitation is found for some weather regimes, but its sign depends on large scale circulation. Indeed, antecedent dry soil conditions tend to lead to smaller precipitation for the negative phase of the North Atlantic Oscillation (NAO) regime but to larger precipitation for the Atlantic Low regime. This differential response of precipitation to soil moisture anomalies depending on large scale circulation is traced back to different responses of atmospheric stability. For all circulation regimes, dry soils tend to increase the lifted condensation level, which is unfavorable to precipitation. But for the negative phase of the NAO, low soil moisture tends to lead to an increase of atmospheric stability while it tends to lead to a decrease of stability for Atlantic Low. Even if the impact of soil moisture anomalies varies depending on large scale circulation (it is larger for Atlantic low and the positive phase of the NAO), dry soils always lead to a decrease in evapotranspiration. As the absolute effect of antecedent soil moisture on evapotranspiration is always much larger than its effects on precipitation, for all circulation regimes dry soil anomalies subsequently lead to positive precipitation minus evapotranspiration anomalies i.e. the total soil moisture feedback is found to be negative. This negative feedback is stronger for the Atlantic Low and the positive phase of the NAO regimes.     

Earth system curator: metadata infrastructure for climate modeling

The Earth System Curator is a National Science Foundation sponsored project developing a metadata formalism for describing the digital resources used in climate simulations. The primary motivating observation of the project is that a simulation/model’s source code plus the configuration parameters required for a model run are a compact representation of the dataset generated when the model is executed. The end goal of the project is a convergence of models and data where both resources are accessed uniformly from a single registry. In this paper we review the current metadata landscape of the climate modeling community, present our work on developing a metadata formalism for describing climate models, and reflect on technical challenges we have faced that require new research in the area of Earth Science Informatics.     

Petroleum and aqueous inclusions from deeply buried reservoirs: Experimental simulations and consequences for overpressure estimates

Synthetic hydrocarbon and aqueous inclusions have been created in the laboratory batch reactors in order to mimic inclusion formation or re-equilibration in deeply buried reservoirs. Inclusions were synthesized in quartz and calcite using pure water and Mexican dead oil, or n-tetradecane (C₁₄H₃₀), at a temperature and pressure of 150 °C and 1 kbar. One-phase hydrocarbon inclusions are frequently observed at standard laboratory conditions leading to homogenization temperatures between 0 and 60 °C. UV epifluorescence of Mexican oil inclusions is not uniform; blue and green-yellow colored inclusions coexist; however, no clear evidence of variations in fluid chemistry were observed. Homogenization temperatures were recorded and the maxima of T_h plotted on histograms are in good agreement with expected T_h in a range of 6 °C. Broad histograms were reconstructed showing non-symmetrical T_h distributions over a 20 °C temperature range centered on the expected T_h. This histogram broadening is due to the fragility of the fluid inclusions that were created by re-filling of pre-existing microcavities. Such T_h histograms are similar to T_h histograms recorded on natural samples from deeply buried carbonate reservoirs. T_h values lower than those expected were measured for hydrocarbon inclusions in quartz and calcite, and for aqueous inclusions in calcite. However, the results confirm the ability of fluid inclusions containing two immiscible fluids to lead to PT reconstructions, even in overpressured environments.     

Strain response and re-equilibration of CH4-rich synthetic aqueous fluid inclusions in calcite during pressure drops

Aqueous fluids in sedimentary basins often contain dissolved methane, particularly in petroleum environments. PVTX (Pressure-Volume-Temperature-Composition) reconstructions performed using fluid inclusion data are largely based on the assumption that inclusions do not change from the time of trapping until the present. Many authors, however, consider that fluid inclusions can re-equilibrate, particularly in fragile minerals like calcite. In order to understand this re-equilibration phenomenon in the metamorphic domain, previous experiments have been performed under high PT conditions, but few have been performed at low to medium PT conditions such as those associated with sedimentary burial diagenesis, and no previous studies have examined CH₄-bearing aqueous inclusions in calcite.An experimental study of the preservation/modification of CH₄-rich synthetic fluid inclusions in calcite during isothermal decompression was conducted. An autoclave was used for accurate PTX control allowing equilibrium between liquid and vapour in the CH₄-H₂O system. PTX conditions were maintained at four stages of decreasing pressure, with each stage held for 7 days to simulate an isothermal pressure drop. In order of decreasing pressure, the pressure-temperature conditions monitored were 276 ± 10 bar at 180 ± 7 °C, 176 ± 10 bar at 180 ± 7 °C, 76 ± 10 bar at 180 ± 7 °C and 10 ± 3 bar at 180 ± 15 °C. At the end of the experiment, the calcite was recovered and analyzed by microthermometry and Raman microspectroscopy for PTX reconstruction. A careful procedure was adopted to limit re-equilibration of inclusions during analytical procedures. Four types of inclusion shapes and four types of strain patterns were differentiated. Classification of the petrographic strain patterns was carried out. These strain patterns were associated with inclusion stretching and/or leakage regarding CH₄, T_h and P_h compared to experimental conditions. Factors controlling the preservation or acquisition of strain patterns included the initial shape and size of the inclusion, and the pressure differential (ΔP) between the confining pressure (P_cf) and the internal pressure (P_i) within the inclusion. Most fluid inclusions seemed to be trapped during the first 7 days of the experiment, although few (4%) of these preserved the initial PT conditions of 276 ± 10 bar, whereas 8% preserved the second and third run of PT conditions. Overall, the majority of inclusions (88%) did not reflect accurately the PTX trapping conditions. A petrographic guide to the inclusions is presented here that allows strain identification for PVT reconstructions. Re-equilibration patterns and evidence for preferential methane leakage from aqueous inclusions in calcite are important findings revealed by this study, and may be useful for the reconstruction of post-trapping events in investigations of natural samples, and in other experiments using synthetic inclusions in calcite.     

A vibrational study of phase transitions among the GeO2 polymorphs

Infrared and Raman spectra of the quartz, rutile and amorphous forms of GeO₂ have been recorded under pressure and/or temperature, in order to study the crystalline to crystalline — or amorphous — transformations of this compound in the solid state. X-ray diffraction data shown that crystalline quartz-GeO₂ subjected to high pressure amorphizes. Infrared data are consistent with a gradual amorphisation of this compound at static pressures between 6 to 12 GPa at 300 K. With increasing pressure, the Ge-O distance appears to remain constant and amorphization is associated with a progressive change in the coordination of germanium atoms from fourfold to sixfold. This apparent change in coordination is not quenchable at room pressure. On decompression, the Ge in the amorphous form returns to tetrahedral coordination. The anharmonic parameters for the Raman modes of the quartz and rutile forms of GeO₂, have also been estimated from pressure and temperature shifts. These data have been used to calculate heat capacities and entropies of the two polymorphs at different pressures, with the Kieffer vibrational model. The calculated heat capacities at room pressure are within 1% of the experimental values between 20 and 1500 K. The calculated entropies are used to estimate the phase boundary in the (P, T) plane. The slope of the curve at room pressure (17 bar/K) is in good agreement with experimental values.     

Modelling in-situ upgrading of heavy oil using operator splitting method

The in-situ upgrading (ISU) of bitumen and oil shale is a very challenging process to model numerically because of the large number of components that need to be modelled using a system of equations that are both highly non-linear and strongly coupled. Operator splitting methods are one way of potentially improving computational performance. Each numerical operator in a process is modelled separately, allowing the best solution method to be used for the given numerical operator. A significant drawback to the approach is that decoupling the governing equations introduces an additional source of numerical error, known as the splitting error. The best splitting method for modelling a given process minimises the splitting error whilst improving computational performance compared to a fully implicit approach. Although operator splitting has been widely used for the modelling of reactive-transport problems, it has not yet been applied to the modelling of ISU. One reason is that it is not clear which operator splitting technique to use. Numerous such techniques are described in the literature and each leads to a different splitting error. While this error has been extensively analysed for linear operators for a wide range of methods, the results cannot be extended to general non-linear systems. It is therefore not clear which of these techniques is most appropriate for the modelling of ISU. In this paper, we investigate the application of various operator splitting techniques to the modelling of the ISU of bitumen and oil shale. The techniques were tested on a simplified model of the physical system in which a solid or heavy liquid component is decomposed by pyrolysis into lighter liquid and gas components. The operator splitting techniques examined include the sequential split operator (SSO), the Strang-Marchuk split operator (SMSO) and the iterative split operator (ISO). They were evaluated on various test cases by considering the evolution of the discretization error as a function of the time-step size compared with the results obtained from a fully implicit simulation. We observed that the error was least for a splitting scheme where the thermal conduction was performed first, followed by the chemical reaction step and finally the heat and mass convection operator (SSO-CKA). This method was then applied to a more realistic model of the ISU of bitumen with multiple components, and we were able to obtain a speed-up of between 3 and 5.