Experimental dissolution of molybdenum-sulphides at low oxygen concentrations: A first-order approximation of late Archean atmospheric conditions

The abundance of atmospheric oxygen and its evolution through Earth's history is a highly debated topic. The earliest change of the Mo concentration and isotope composition of marine sediments are interpreted to be linked to the onset of the accumulation of free O2 in Earth's atmosphere. The O2 concentration needed to dissolve significant amounts of Mo in water is not yet quantified, however. We present laboratory experiments on pulverized and surface-cleaned molybdenite (MoS2) and a hydrothermal breccia enriched in Mo-bearing sulphides using a glove box setup. Duration of an experiment was 14 days, and first signs of oxidation and subsequent dissolution of Mo compounds start to occur above an atmospheric oxygen concentration of 72 ± 20 ppmv (i.e., 2.6 to 4.6 × 10−4 present atmospheric level (PAL)). This experimentally determined value coincides with published model calculations supporting atmospheric O2 concentrations between 1 × 10−5 to 3 × 10−4 PAL prior to the Great Oxidation Event and sets an upper limit to the molecular oxygen needed to trigger Mo accumulation and Mo isotope variations recorded in sediments. In combination with the published Mo isotope composition of the rock record, this result implies an atmospheric oxygen concentration prior to 2.76 Ga of below 72 ± 20 ppmv.

Benchmark problems for reactive transport modeling of the generation and attenuation of acid rock drainage

Acid rock drainage (ARD) is a problem of international relevance with substantial environmental and economic implications. Reactive transport modeling has proven a powerful tool for the process-based assessment of metal release and attenuation at ARD sites. Although a variety of models has been used to investigate ARD, a systematic model intercomparison has not been conducted to date. This contribution presents such a model intercomparison involving three synthetic benchmark problems designed to evaluate model results for the most relevant processes at ARD sites. The first benchmark (ARD-B1) focuses on the oxidation of sulfide minerals in an unsaturated tailing impoundment, affected by the ingress of atmospheric oxygen. ARD-B2 extends the first problem to include pH buffering by primary mineral dissolution and secondary mineral precipitation. The third problem (ARD-B3) in addition considers the kinetic and pH-dependent dissolution of silicate minerals under low pH conditions. The set of benchmarks was solved by four reactive transport codes, namely CrunchFlow, Flotran, HP1, and MIN3P. The results comparison focused on spatial profiles of dissolved concentrations, pH and pE, pore gas composition, and mineral assemblages. In addition, results of transient profiles for selected elements and cumulative mass loadings were considered in the intercomparison. Despite substantial differences in model formulations, very good agreement was obtained between the various codes. Residual deviations between the results are analyzed and discussed in terms of their implications for capturing system evolution and long-term mass loading predictions.

Implementation and evaluation of permeability-porosity and tortuosity-porosity relationships linked to mineral dissolution-precipitation

Changes of porosity, permeability, and tortuosity due to physical and geochemical processes are of vital importance for a variety of hydrogeological systems, including passive treatment facilities for contaminated groundwater, engineered barrier systems (EBS), and host rocks for high-level nuclear waste (HLW) repositories. Due to the nonlinear nature and chemical complexity of the problem, in most cases, it is impossible to verify reactive transport codes analytically, and code intercomparisons are the most suitable method to assess code capabilities and model performance. This paper summarizes model intercomparisons for six hypothetical scenarios with generally increasing geochemical or physical complexity using the reactive transport codes CrunchFlow, HP1, MIN3P, PFlotran, and TOUGHREACT. Benchmark problems include the enhancement of porosity and permeability through mineral dissolution, as well as near complete clogging due to localized mineral precipitation, leading to reduction of permeability and tortuosity. Processes considered in the benchmark simulations are advective-dispersive transport in saturated media, kinetically controlled mineral dissolution-precipitation, and aqueous complexation. Porosity changes are induced by mineral dissolution-precipitation reactions, and the Carman-Kozeny relationship is used to describe changes in permeability as a function of porosity. Archie’s law is used to update the tortuosity and the pore diffusion coefficient as a function of porosity. Results demonstrate that, generally, good agreement is reached amongst the computer models despite significant differences in model formulations. Some differences are observed, in particular for the more complex scenarios involving clogging; however, these differences do not affect the interpretation of system behavior and evolution.

Kinetic simulation of neutral∕ionized gas and electrically charged dust in the coma of comet 67P∕Churyumov-Gerasimenko

The cometary coma is a unique phenomenon in the solar system being a planetary atmosphere influenced by little or no gravity. As a comet approaches the sun, the water vapor with some fraction of other gases sublimate, generating a cloud of gas, ice and other refractory materials (rocky and organic dust) ejected from the surface of the nucleus. Sublimating gas molecules undergo frequent collisions and photochemical processes in the near‐nucleus region. Owing to its negligible gravity, comets produce a large and highly variable extensive dusty coma with a size much larger than the characteristic size of the cometary nucleus. The Rosetta spacecraft is en route to comet 67P/Churyumov‐Gerasimenko for a rendezvous, landing, and extensive orbital phase beginning in 2014. Both, interpretation of measurements and safety consideration of the spacecraft require modeling of the comet’s dusty gas environment. In this work we present results of a numerical study of multispecies gaseous and electrically charged dust environment of comet Chyuryumov‐Gerasimenko. Both, gas and dust phases of the coma are simulated kinetically. Photolytic reactions are taken into account. Parameters of the ambient plasma as well as the distribution of electric/magnetic fields are obtained from an MHD simulation [1] of the coma connected to the solar wind. Trajectories of ions and electrically charged dust grains are simulated by accounting for the Lorentz force and the nucleus gravity.

Comparison of 3D kinetic and hydrodynamic models to ROSINA-COPS measurements of the neutral coma of 67P/Churyumov-Gerasimenko

67P/Churyumov-Gerasimenko (67P) is a Jupiter-family comet and the object of investigation of the European Space Agency mission Rosetta. This report presents the first full 3D simulation results of 67P’s neutral gas coma. In this study we include results from a direct simulation Monte Carlo method, a hydrodynamic code, and a purely geometric calculation which computes the total illuminated surface area on the nucleus. All models include the triangulated 3D shape model of 67P as well as realistic illumination and shadowing conditions. The basic concept is the assumption that these illumination conditions on the nucleus are the main driver for the gas activity of the comet. As a consequence, the total production rate of 67P varies as a function of solar insolation. The best agreement between the model and the data is achieved when gas fluxes on the night side are in the range of 7% to 10% of the maximum flux, accounting for contributions from the most volatile components. To validate the output of our numerical simulations we compare the results of all three models to in situ gas number density measurements from the ROSINA COPS instrument. We are able to reproduce the overall features of these local neutral number density measurements of ROSINA COPS for the time period between early August 2014 and January 1 2015 with all three models. Some details in the measurements are not reproduced and warrant further investigation and refinement of the models. However, the overall assumption that illumination conditions on the nucleus are at least an important driver of the gas activity is validated by the models. According to our simulation results we find the total production rate of 67P to be constant between August and November 2014 with a value of about 1 × 10²⁶ molecules s⁻¹.

Redox front geochemistry and weathering: theory with application to the Osamu Utsumi uranium mine, Poços de Caldas, Brazil

Numerical calculations describing weathering of the Poços de Caldas alkaline complex (Minas Gerais, Brazil) by infiltrating groundwater are carried out for time spans up to two million years in the absence of pyrite, and up to 500,000 years with pyrite present. Deposition of uranium resulting from infiltration of oxygenated, uranium bearing groundwater through the hydrothermally altered phonolitic host rock at the Osamu Utsumi uranium mine is also included in the latter calculation. The calculations are based on the quasi-stationary state approximation to mass conservation equations for pure advective transport. This approximation enables the prediction of solute concentrations, mineral abundances and porosity as functions of time and distance over geologic time spans. Mineral reactions are described by kinetic rate laws for both precipitation and dissolution. Homogeneous equilibrium is assumed to be maintained within the aqueous phase. No other constraints are imposed on the calculations other than the initial composition of the unaltered host rock and the composition of the inlet fluid, taken as rainwater modified by percolation through a soil zone. The results are in qualitative agreement with field observations at the Osamu Utsumi uranium mine. They predict a lateritic cover followed by a highly porous saprolitic zone, a zone of oxidized rock with pyrite replaced by iron-hydroxide, a sharp redox front at which uranium is deposited, and the reduced unweathered host rock. Uranium is deposited in a narrow zone located on the reduced side of the redox front in association with pyrite, in agreement with field observations. The calculations predict the formation of a broad dissolution front of primary kaolinite that penetrates deep into the host rock accompanied by the precipitation of secondary illite. Secondary kaolinite occurs in a saprolitic zone near the surface and in the vicinity of the redox front. Gibbsite forms a bi-modal distribution consisting of a maximum near the surface followed by a thin tongue extending downward into the weathered profile in agreement with field observations. The results are found to be insensitive to the kinetic rate constants used to describe mineral reactions.

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

Optimized on-line enantioselective capillary electrophoretic method for kinetic and inhibition studies of drug metabolism mediated by cytochrome P450 enzymes.

Pharmacokinetic and pharmacodynamic properties of a chiral drug can significantly differ between application of the racemate and single enantiomers. During drug development, the characteristics of candidate compounds have to be assessed prior to clinical testing. Since biotransformation significantly influences drug actions in an organism, metabolism studies represent a crucial part of such tests. Hence, an optimized and economical capillary electrophoretic method for on-line studies of the enantioselective drug metabolism mediated by cytochrome P450 enzymes was developed. It comprises a diffusion-based procedure, which enables mixing of the enzyme with virtually any compound inside the nanoliter-scale capillary reactor and without the need of additional optimization of mixing conditions. For CYP3A4, ketamine as probe substrate and highly sulfated γ-cyclodextrin as chiral selector, improved separation conditions for ketamine and norketamine enantiomers compared to a previously published electrophoretically mediated microanalysis method were elucidated. The new approach was thoroughly validated for the CYP3A4-mediated N-demethylation pathway of ketamine and applied to the determination of its kinetic parameters and the inhibition characteristics in presence of ketoconazole and dexmedetomidine. The determined parameters were found to be comparable to literature data obtained with different techniques. The presented method constitutes a miniaturized and cost-effective tool, which should be suitable for the assessment of the stereoselective aspects of kinetic and inhibition studies of cytochrome P450-mediated metabolic steps within early stages of the development of a new drug.

New fully kinetic model for the study of electric potential, plasma, and dust above lunar landscapes

We have developed a new fully kinetic electrostatic simulation, HYBes, to study how the lunar landscape affects the electric potential and plasma distributions near the surface and the properties of lifted dust. The model embodies new techniques that can be used in various types of physical environments and situations. We demonstrate the applicability of the new model in a situation involving three charged particle species, which are solar wind electrons and protons, and lunar photoelectrons. Properties of dust are studied with test particle simulations by using the electric fields derived from the HYBes model. Simulations show the high importance of the plasma and the electric potential near the surface. For comparison, the electric potential gradients near the landscapes with feature sizes of the order of the Debye length are much larger than those near a flat surface at different solar zenith angles. Furthermore, dust test particle simulations indicate that the landscape relief influences the dust location over the surface. The study suggests that the local landscape has to be taken into account when the distributions of plasma and dust above lunar surface are studied. The HYBes model can be applied not only at the Moon but also on a wide range of airless planetary objects such as Mercury, other planetary moons, asteroids, and nonactive comets.

A probabilistic assessment of calcium carbonate export and dissolution in the modern ocean

The marine cycle of calcium carbonate (CaCO3) is an important element of the carbon cycle and co-governs the distribution of carbon and alkalinity within the ocean. However, CaCO3 export fluxes and mechanisms governing CaCO3 dissolution are highly uncertain. We present an observationally constrained, probabilistic assessment of the global and regional CaCO3 budgets. Parameters governing pelagic CaCO3 export fluxes and dissolution rates are sampled using a Monte Carlo scheme to construct a 1000-member ensemble with the Bern3D ocean model. Ensemble results are constrained by comparing simulated and observation-based fields of excess dissolved calcium carbonate (TA*). The minerals calcite and aragonite are modelled explicitly and ocean–sediment fluxes are considered. For local dissolution rates, either a strong or a weak dependency on CaCO3 saturation is assumed. In addition, there is the option to have saturation-independent dissolution above the saturation horizon. The median (and 68 % confidence interval) of the constrained model ensemble for global biogenic CaCO3 export is 0.90 (0.72–1.05) Gt C yr−1, that is within the lower half of previously published estimates (0.4–1.8 Gt C yr−1). The spatial pattern of CaCO3 export is broadly consistent with earlier assessments. Export is large in the Southern Ocean, the tropical Indo–Pacific, the northern Pacific and relatively small in the Atlantic. The constrained results are robust across a range of diapycnal mixing coefficients and, thus, ocean circulation strengths. Modelled ocean circulation and transport timescales for the different set-ups were further evaluated with CFC11 and radiocarbon observations. Parameters and mechanisms governing dissolution are hardly constrained by either the TA* data or the current compilation of CaCO3 flux measurements such that model realisations with and without saturation-dependent dissolution achieve skill. We suggest applying saturation-independent dissolution rates in Earth system models to minimise computational costs.