P3D-BRNS v1.0.0: a three-dimensional, multiphase, multicomponent, pore-scale reactive transport modelling package for simulating biogeochemical processes in subsurface environments

The porous microenvironment of soil offers various environmental functions which are governed by physical and reactive processes. Understanding reactive transport processes in porous media is essential for many natural systems (soils, aquifers, aquatic sediments or subsurface reservoirs) or technological processes (water treatment or ceramic and fuel cell technologies). In particular, in the vadose zone of the terrestrial subsurface the spatially and temporally varying saturation of the aqueous and the gas phase leads to systems that involve complex flow and transport processes as well as reactive transformations of chemical compounds in the porous material. To describe these interacting processes and their dynamics at the pore scale requires a well-suited modelling framework accounting for the proper description of all relevant processes at a high spatial resolution. Here we present P3D-BRNS as a new open-source modelling toolbox harnessing the core libraries of OpenFOAM and coupled externally to the Biogeochemical Reaction Network Simulator (BRNS). The native OpenFOAM volume-of-fluid solver is extended to have an improved representation of the fluid–fluid interface. The solvers are further developed to couple the reaction module which can be tailored for a specific reactive transport simulation. P3D-RBNS is benchmarked against three different flow and reactive transport processes: (1) fluid–fluid configuration in a capillary corner, (2) mass transfer across the fluid–fluid interface and (3) microbial growth with a high degree of accuracy. Our model allows for simulation of the spatio-temporal distribution of all biochemical species in the porous structure (obtained from μ-CT images), for conditions that are commonly found in the laboratory and environmental systems. With our coupled computational model, we provide a reliable and efficient tool for simulating multiphase, reactive transport in porous media.</p

Predictive Task Monitoring for Business Processes

Information sources providing real-time status of physical objects have drastically increased in recent times. So far, research in business process monitoring has mainly focused on checking the completion of tasks. However, the availability of real-time information allows for a more detailed tracking of individual business tasks. This paper describes a framework for controlling the safe execution of tasks and signalling possible misbehaviours at runtime. It outlines a real use case on smart logistics and the preliminary results of its application.European Union FP7/2007-2013 / 318275 (GET Service

Anthropogenic perturbation of the carbon fluxes from land to ocean

A substantial amount of the atmospheric carbon taken up on land through photosynthesis and chemical weathering is transported laterally along the aquatic continuum from upland terrestrial ecosystems to the ocean. So far, global carbon budget estimates have implicitly assumed that the transformation and lateral transport of carbon along this aquatic continuum has remained unchanged since pre-industrial times. A synthesis of published work reveals the magnitude of present-day lateral carbon fluxes from land to ocean, and the extent to which human activities have altered these fluxes. We show that anthropogenic perturbation may have increased the flux of carbon to inland waters by as much as 1.0 Pg C yr-1 since pre-industrial times, mainly owing to enhanced carbon export from soils. Most of this additional carbon input to upstream rivers is either emitted back to the atmosphere as carbon dioxide (~0.4 Pg C yr-1) or sequestered in sediments (~0.5 Pg C yr-1) along the continuum of freshwater bodies, estuaries and coastal waters, leaving only a perturbation carbon input of ~0.1 Pg C yr-1 to the open ocean. According to our analysis, terrestrial ecosystems store ~0.9 Pg C yr-1 at present, which is in agreement with results from forest inventories but significantly differs from the figure of 1.5 Pg C yr-1 previously estimated when ignoring changes in lateral carbon fluxes. We suggest that carbon fluxes along the land–ocean aquatic continuum need to be included in global carbon dioxide budgets.Peer reviewe

Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: Theoretical analysis and reactive transport simulations

At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways

Introduction of a new platform for parameter estimation of kinetically complex environmental systems.

A modeling framework (ReKinSim - Reaction Kinetics Simulator) is introduced, within which biogeochemical reactions in environmental systems can be described and inversely fitted to experimental data. Three key features of this simulation environment are: (1) a generic mathematical tool for solving sets of unlimited, arbitrary, non-linear ordinary differential equations; (2) no limitation to the number or type of reactions or other influential dynamics (e.g., isotope fractionation or small-scale mass-transfer limitations); (3) an easy to use and flexible module for nonlinear data-fitting. It allows users to easily define any kinetic model by a set of biogeochemical reactions relevant to the experimental application and to obtain the values of the kinetic parameters by fitting of the model to data. By allowing users to include the environmentally related processes and solving them along with the chemical kinetics, ReKinSim helps the user to elucidate the extent that these processes are controlled by factors other than kinetics. The novelty of the presented program primary lays in its unique combination of flexibility, computational efficiency and user-friendliness. ReKinSim&#39;s usability is showcased by four case studies of varying complexity, and compared against a set of currently available modeling tools

Modeling population patterns of chemotactic bacteria in homogeneous porous media

The spatio-temporal distribution of subsurface microorganisms determines their efficiency in providing essential ecosystem services such as the degradation of organic matter, the remineralization of carbon and nitrogen, or the remediation of anthropogenic contaminants. Populations of motile, chemotactic bacteria have been shown to be capable of pattern formation even in the absence of environmental heterogeneities. Focusing on the water saturated domain of the subsurface (e.g., aquatic sediments, porous aquifers), we analyze this innate capability of bacterial populations in an idealized model of a homogeneous, saturated porous medium. Considering a linear array of connected, identical microhabitats populated by motile, chemotactic bacterial cells, we identify prerequisites for pattern formation, analyze types of patterns, and assess their impact on substrate utilization. In our model, substrate supplied to the microhabitats facilitates bacterial growth, and microbial cells can migrate between neighboring microhabitats due to (i) random motility, (ii) chemotaxis towards substrate, and (iii) self-attraction. A precondition for inhomogeneous population patterns is analytically derived, stating that patterns are possible if the self-attraction exceeds a threshold defined by the random motility and the steady state population density in the microhabitats. An individual-based implementation of the model shows that static and dynamic population patterns can unfold. Degradation efficiency is highest for homogeneous bacterial distributions and decreases as pattern formation commences. If during biostimulation efforts the carrying capacity of the microhabitats is successively increased, simulation results show that degradation efficiency can unexpectedly decrease when the pattern formation threshold is crossed

How the chemotactic characteristics of bacteria can determine their population patterns

Spatial distribution of soil microorganisms is relevant for the functioning and performance of many ecosystem processes such as nutrient cycling or biodegradation of organic matters and contaminants. Beside the multitude of abiotic environmental factors controlling the distribution of microorganisms in soil systems, many microbial species exhibit chemotactic behavior by directing their movement along concentration gradients of nutrients or of chemoattractants produced by cells of their own kind. This chemotactic ability has been shown to promote the formation of complex distribution patterns even in the absence of environmental heterogeneities. Microbial population patterns in heterogeneous soil systems might be, hence, the result of the interplay between the heterogeneous environmental conditions and the microorganisms' intrinsic pattern formation capabilities.In this modeling study, we combined an individual-based modeling approach with a reactive pore-network model to investigate the formation of bacterial patterns in homogeneous and heterogeneous porous media. We investigated the influence of different bacterial chemotactic sensitivities (toward both substrate and bacteria) on bacterial distribution patterns. The emerging population patterns were classified with the support of a geostatistical approach, and the required conditions for the formation of any specific pattern were analyzed.Results showed that the chemotactic behavior of the bacteria leads to non-trivial population patterns even in the absence of environmental heterogeneities. The presence of structural pore scale heterogeneities had also an impact on bacterial distributions. For a range of chemotactic sensitivities, microorganisms tend to migrate preferably from larger pores toward smaller pores and the resulting distribution patterns thus resembled the heterogeneity of the pore space. The results clearly indicated that in a porous medium like soil the distribution of bacteria may not only be related to the external constraints but also to the chemotactic behavior of the bacterial cells