Microbial Alkalinity Production and Silicate Alteration in Methane Charged Marine Sediments: Implications for Porewater Chemistry and Diagenetic Carbonate Formation

A numerical reaction-transport model was developed to simulate the effects of microbial activity and mineral reactions on the composition of porewater in a 230-m-thick Pleistocene interval drilled in the Peru-Chile Trench (Ocean Drilling Program, Site 1230). This site has porewater profiles similar to those along many continental margins, where intense methanogenesis occurs and alkalinity surpasses 100 mmol/L. Simulations show that microbial sulphate reduction, anaerobic oxidation of methane, and ammonium release from organic matter degradation only account for parts of total alkalinity, and excess CO2 produced during methanogenesis leads to acidification of porewater. Additional alkalinity is produced by slow alteration of primary aluminosilicate minerals to kaolinite and SiO2. Overall, alkalinity production in the methanogenic zone is sufficient to prevent dissolution of carbonate minerals; indeed, it contributes to the formation of cemented carbonate layers at a supersaturation front near the sulphate-methane transition zone. Within the methanogenic zone, carbonate formation is largely inhibited by cation diffusion but occurs rapidly if cations are transported into the zone via fluid conduits, such as faults. The simulation presented here provides fundamental insight into the diagenetic effects of the deep biosphere and may also be applicable for the long-term prediction of the stability and safety of deep CO2 storage reservoirs.

A Finite Element Mesh Regrouping Strategy-Based Hybrid Light Transport Model for Enhancing the Efficiency and Accuracy of XLCT

X-ray luminescence computed tomography (XLCT) is an emerging hybrid imaging modality in optical molecular imaging, which has attracted more attention and has been widely studied. In XLCT, the accuracy and operational efficiency of an optical transmission model play a decisive role in the rapid and accurate reconstruction of light sources. For simulation of optical transmission characteristics in XLCT, considering the limitations of the diffusion equation (DE) and the time and memory costs of simplified spherical harmonic approximation equation (SPN), a hybrid light transport model needs to be built. DE and SPN models are first-order and higher-order approximations of RTE, respectively. Due to the discontinuity of the regions using the DE and SPN models and the inconsistencies of the system matrix dimensions constructed by the two models in the solving process, the system matrix construction of a hybrid light transmission model is a problem to be solved. We provided a new finite element mesh regrouping strategy-based hybrid light transport model for XLCT. Firstly, based on the finite element mesh regrouping strategy, two separate meshes can be obtained. Thus, for DE and SPN models, the system matrixes and source weight matrixes can be calculated separately in two respective mesh systems. Meanwhile, some parallel computation strategy can be combined with finite element mesh regrouping strategy to further save the system matrix calculation time. Then, the two system matrixes with different dimensions were coupled though repeated nodes were processed according to the hybrid boundary conditions, the two meshes were combined into a regrouping mesh, and the hybrid optical transmission model was established. In addition, the proposed method can reduce the computational memory consumption than the previously proposed hybrid light transport model achieving good balance between computational accuracy and efficiency. The forward numerical simulation results showed that the proposed method had better transmission accuracy and achieved a balance between efficiency and accuracy. The reverse simulation results showed that the proposed method had superior location accuracy, morphological recovery capability, and image contrast capability in source reconstruction. In-vivo experiments verified the practicability and effectiveness of the proposed method.

Influence of innovative hydrogen multi strut injector with different spacing on cavity-based scramjet combustor

In this study, the flow dynamics with finite volume approach on commercial software Ansys-Fluent 20.0 to solve the compressible two-dimensional fluid flow with Reynolds Average Navier Stokes equation (RANS) equation by considering the density-based solver with Shaer stress transport model (SST) k- ω turbulent model. The species transport model with volumetric reaction and finite rate/eddy dissipation turbulence chemistry interaction is adopted to study the combustion phenomena. Additionally, the effect of spacing between the struts on the flow characters and performance of the combustor is studied by increasing the spacing of struts from 1 mm to 4 mm for each increment of 1 mm. It is found that the multi strut improves the mixing and combustion efficiency compared with that of the single strut owing to the formation of a significant separation layer, resulting in multiple shocks, vortices, and a larger recirculation zone. However, when the spacing of struts is increased further, the performance of the combustor is found to be deteriorating owing to the formation of larger separation layers. The recirculation zone is significant when the strut spacing is minimal and shrinks and restricts itself within the cavity when spacing is increased. So, for better performance of combustor, multi strut with minimum spacing is preferable.

Single-particle fluorescence tracking combined with TrackMate assay reveals highly heterogeneous and discontinuous lysosomal transport in freely orientated axons

Axonal transport plays a significant role in the establishment of neuronal polarity, axon growth, and synapse formation during neuronal development. The axon of a naturally growing neuron is a highly complex and multifurcated structure with a large number of bends and branches. Nowadays, the study of dynamic axonal transport in morphologically complex neurons is greatly limited by the technological barrier. Here, a sparse gene transfection strategy was developed to locate fluorescent mCherry in the lysosome of primary neurons, thus enabling us to track the lysosome-based axonal transport with a single-particle resolution. Thereby, several axonal transport models were observed, including forward or backward transport model, stop-and-go model, repeated back-and-forth transport model, and cross-branch transport model. Then, the accurate single-particle velocity quantification by TrackMate revealed a highly heterogeneous and discontinuous transportation process of lysosome-based axonal transport in freely orientated axons. And, multiple physical factors, such as the axonal structure and the size of particles, were disclosed to affect the velocity of particle transporting in freely orientated axons. The combined single-particle fluorescence tracking and TrackMate assay can be served as a facile tool for evaluating axonal transport in neuronal development and axonal transport-related diseases.

Development of aerosol optical properties for improving the MESSy photolysis module in the GEM-MACH v2.4 air quality model and application for calculating photolysis rates in a biomass burning plume

The photolysis module in Environment and Climate Change Canada's online chemical transport model GEM-MACH (GEM: Global Environmental Multi-scale – MACH: Modelling Air quality and Chemistry) was improved to make use of the online size and composition-resolved representation of atmospheric aerosols and relative humidity in GEM-MACH, to account for aerosol attenuation of radiation in the photolysis calculation. We coupled both the GEM-MACH aerosol module and the MESSy-JVAL (Modular Earth Submodel System) photolysis module, through the use of the online aerosol modeled data and a new Mie lookup table for the model-generated extinction efficiency, absorption and scattering cross sections of each aerosol type. The new algorithm applies a lensing correction factor to the black carbon absorption efficiency (core-shell parameterization) and calculates the scattering and absorption optical depth and asymmetry factor of black carbon, sea salt, dust and other internally mixed components. We carried out a series of simulations with the improved version of MESSy-JVAL and wildfire emission inputs from the Canadian Forest Fire Emissions Prediction System (CFFEPS) for 2 months, compared the model aerosol optical depth (AOD) output to the previous version of MESSy-JVAL, satellite data, ground-based measurements and reanalysis products, and evaluated the effects of AOD calculations and the interactive aerosol feedback on the performance of the GEM-MACH model. The comparison of the improved version of MESSy-JVAL with the previous version showed significant improvements in the model performance with the implementation of the new photolysis module and with adopting the online interactive aerosol concentrations in GEM-MACH. Incorporating these changes to the model resulted in an increase in the correlation coefficient from 0.17 to 0.37 between the GEM-MACH model AOD 1-month hourly output and AERONET (Aerosol Robotic Network) measurements across all the North American sites. Comparisons of the updated model AOD with AERONET measurements for selected Canadian urban and industrial sites, specifically, showed better correlation coefficients for urban AERONET sites and for stations located further south in the domain for both simulation periods (June and January 2018). The predicted monthly averaged AOD using the improved photolysis module followed the spatial patterns of MERRA-2 reanalysis (Modern-Era Retrospective analysis for Research and Applications – version 2), with an overall underprediction of AOD over the common domain for both seasons. Our study also suggests that the domain-wide impacts of direct and indirect effect aerosol feedbacks on the photolysis rates from meteorological changes are considerably greater (3 to 4 times) than the direct aerosol optical effect on the photolysis rate calculations.

Hemispheric asymmetries in recent changes of the stratospheric circulation

Despite the expected opposite effects of ozone recovery, the stratospheric Brewer-Dobson circulation (BDC) has been found to weaken in the Northern hemisphere (NH) relative to the Southern hemisphere (SH) in recent decades, inducing substantial effects on chemical composition. We investigate hemispheric asymmetries in BDC changes since about 2000 in simulations with the transport model CLaMS driven with different reanalyses (ERA5, ERA-Interim, JRA-55, MERRA-2) and contrast those to a suite of free-running climate model simulations. We find that age of air increases robustly in the NH stratosphere relative to the SH in all reanalyses considered. Related nitrous oxide changes agree well between reanalysis-driven simulations and satellite measurements, providing observational evidence for the hemispheric asymmetry in BDC changes. Residual circulation metrics further show that the composition changes are caused by structural BDC changes related to an upward shift and strengthening of the deep BDC branch, resulting in longer transit times, and a downward shift and weakening shallow branch in the NH relative to the SH. All reanalyses agree on this mechanism. Although climate model simulations show that ozone recovery will lead to overall reduced circulation and age of air trends, the hemispherically asymmetric signal in circulation trends is small compared to internal variability. Therefore, the observed circulation trends over the recent past are not in contradiction to expectations from climate models. Furthermore, the hemispheric asymmetry in BDC trends imprints on the composition of the lower stratosphere and the signal might propagate into the troposphere, potentially affecting composition down to the surface.

Modelling SO₂ conversion into sulphates in the mid-troposphere with a 3D chemistry-transport model: the case of Mount Etna's eruption on April 12, 2012

Volcanic activity is an important source of atmospheric sulphur dioxide (SO2), which, after conversion into sulphuric acid, induces impacts on, among others, rain acidity, human health, meteorology and the radiative balance of the atmosphere. This work focuses on the conversion of SO2 into sulphates (, S(+VI)) in the mid-tropospheric volcanic plume emitted by the explosive eruption of Mount Etna (Italy) on Apr. 12, 2012, using the CHIMERE chemistry-transport model. Since volcanic plume location and composition depend on several often poorly constrained parameters, using a chemistry-transport model allows us to study the sensitivity of SO2 oxidation to multiple aspects such as volcanic water emissions, transition metal emissions, plume diffusion and plume altitude. Our results show that in the mid-troposphere, two pathways contribute to sulphate production, the oxidation of SO2 by OH in the gaseous phase (70 %), and the aqueous oxidation by O2 catalyzed by Mn2+ and Fe3+ ions (25 %). The oxidation in aqueous phase is the faster process, but in the mid-troposphere, liquid water is scarce, therefore the relative share of gaseous oxidation can be important. After one day in the mid-troposphere, about 0.5 % of the volcanic SO2 was converted to sulphates through the gaseous process. Because of the nonlinear dependency of the kinetics in the aqueous phase to the amount of volcanic water emitted and on the availability of transition metals in the aqueous phase, several experiments have been designed to determine the prominence of different parameters. Our simulations show that during the short time that liquid water remains in the plume, around 0.4 % of sulphates manage to quickly enter the liquid phase. Sensitivity tests regarding the advection scheme have shown that this scheme must be chosen wisely, as dispersion will impact both oxidation pathways explained above.

Numerical Simulation Study of Proppant Transport in Cross Fractures

Hydraulic fracturing technology is an important means to stimulate unconventional reservoirs, and the placement morphology of proppant in cross fractures is a key factor affecting the effect of hydraulic fracturing. It is very important to study the proppant transport law in cross fractures. In order to study the proppant transportation law in cross fractures, based on the CFD-DEM method, a proppant transport model in cross fractures was established. From the two aspects of the flow field in the fractures and the morphology of the proppant dune, the influence of the natural fracture approach angle, the fracturing fluid viscosity and injection rate on the proppant transport is studied. Based on the principle of hydropower similarity, the conductivity of proppant dune under different conditions is quantitatively studied. The results show that the natural fracture approach angle affects the distribution of proppant and fracturing fluid in natural fractures, and further affects the proppant placement morphology in hydraulic fractures and natural fractures. When the fracturing fluid viscosity is low and the displacement is small, the proppant forms a "high and narrow" dune at the entrance of the fracture. With the increase of the fracturing fluid viscosity and injection rate, the proppant settles to form a "short and wide" placement morphology. Compared with the natural fracture approach angle, the fracturing fluid viscosity and injection rate have a more significant impact on the conductivity of proppant dune. This paper investigated the proppant transportation in cross fractures, and quantitatively analyzes the conductivity of proppant dunes with different placement morphology. The results of this study can provide theoretical guidance for the design of hydraulic fracturing.

Implementing the Water, HEat and Transport model in GEOframe (WHETGEO-1D v.1.0): algorithms, informatics, design patterns, open science features, and 1D deployment

This paper presents WHETGEO and its 1D deployment: a new physically based model simulating the water and energy budgets in a soil column. The purpose of this contribution is twofold. First, we discuss the mathematical and numerical issues involved in solving the Richardson–Richards equation, conventionally known as the Richards equation, and the heat equation in heterogeneous soils. In particular, for the Richardson–Richards equation (R2) we take advantage of the nested Newton–Casulli–Zanolli (NCZ) algorithm that ensures the convergence of the numerical solution in any condition. Second, starting from numerical and modelling needs, we present the design of software that is intended to be the first building block of a new customizable land-surface model that is integrated with process-based hydrology. WHETGEO is developed as an open-source code, adopting the object-oriented paradigm and a generic programming approach in order to improve its usability and expandability. WHETGEO is fully integrated into the GEOframe/OMS3 system, allowing the use of the many ancillary tools it provides. Finally, the paper presents the 1D deployment of WHETGEO, WHETGEO-1D, which has been tested against the available analytical solutions presented in the Appendix.