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This article discusses the co-evolution of soil structure and function during the process of soil formation. It emphasizes the importance of understanding the relationship between soil architecture and its functions, such as water retention, nutrient supply, and habitat provision. The authors propose hypotheses on the formation, stability, and functions of microaggregates and present a research program that includes observational, experimental, and theoretical studies. The article also highlights the role of organic matter, clay-sized minerals, microbial activity, and earthworm mucus in promoting soil aggregation and nutrient storage. It discusses the use of modeling, data analysis, and multi-omics approaches in soil science research, as well as the impact of climate and land-use changes on soil structure and function. The document concludes by calling for the development of comprehensible algorithms based on physical, chemical, biological, and ecological concepts to inform soil science research. [Extracted from the article]

We present a mathematical model for the full drying process of a single protein formulation droplet taking into account the convective impact arising from its levitation by a standing ultrasound wave. Using the finite element method allows us to compute the evaporation rate directly from the fully resolved heat and mass transfer within and around the levitated droplet. We apply our model to simulate the drying kinetics of pure water and aqueous phosphoglycerate kinase (PGK) droplets under various levitation and drying conditions. Empirical data from the literature are used to validate and discuss our numerical results. The acoustic streaming turns out to accelerate not only the first but also the second drying stage. Moreover, the dehydration of the protein molecules is found to be primarily responsible for their enzymatic inactivation throughout the drying process. [ABSTRACT FROM AUTHOR]

Structural changes of the pore space and clogging phenomena are inherent to many porous media applications. However, related analytical investigations remain challenging due to potentially vanishing coefficients in the respective systems of partial differential equations. In this research, we apply an appropriate scaling of the unknowns and work with porosity-weighted function spaces. This enables us to prove existence, uniqueness and non-negativity of weak solutions to a combined flow and transport problem with vanishing, but prescribed porosity field, permeability and diffusion. [ABSTRACT FROM AUTHOR]

Mineral dissolution and precipitation alter a porous medium's structure and its bulk properties. Due to the medium's heterogeneity and lack in dynamic pore-scale measurements, there has been an increasing interest in comprehensive models accessing such phenomena on the macroscale without disregarding available pore-scale information. Such micro-macro models may be derived from detailed pore-scale models applying upscaling techniques and comprise several levels of couplings. Our model consists of transport equations at the scale of the porous medium (macroscale) while taking the processes of convection and diffusion into account. They include averaged time- and space-dependent coefficient functions which are in turn explicitly computed by means of auxiliary cell problems (microscale). Structural changes due to dissolution and precipitation reactions result in a time- and space-dependent domain on which cell problems are defined. The interface between the mineral and the fluid, and consequently the explicit geometric structure, is characterized by means of a level set. Here, information from the transport equations' solutions is taken into account (micro-macroscale). A numerical scheme is introduced which enables evaluating such complex settings. For the level-set equation, an upwind scheme by Rouy and Tourin is applied. An extended finite element method is used for the evaluation of the cell problems while the transport equations are solved applying mixed finite elements. Ultimately, we investigate the potentially degenerating bulk properties of the medium such as porosity and effective diffusion. Moreover, we apply our approach to the dissolution of an array of calcite grains in the micro-macro context and validate our numerical scheme. [ABSTRACT FROM AUTHOR]

Two-scale models pose a promising approach in simulating reactive flow and transport in evolving porous media. Classically, homogenised flow and transport equations are solved on the macroscopic scale, while effective parameters are obtained from auxiliary cell problems on possibly evolving reference geometries (micro-scale). Despite their perspective success in rendering lab/field-scale simulations computationally feasible, analytic results regarding the arising two-scale bilaterally coupled system often restrict to simplified models. In this paper, we first derive smooth dependence results concerning the partial coupling from the underlying geometry to macroscopic quantities. Therefore, alterations of the representative fluid domain are described by smooth paths of diffeomorphisms. Exploiting the gained regularity of the effective space- and time-dependent macroscopic coefficients, we present local-in-time existence results for strong solutions to the partially coupled micro-macro system using fixed-point arguments. What is more, we extend our results to the bilaterally coupled diffusive transport model including a level-set description of the evolving geometry. [ABSTRACT FROM AUTHOR]

Background: Carbon storage and turnover in soils depend on the interplay of soil architecture, microbial activities, and soil organic matter (SOM) dynamics. For a fundamental understanding of the mechanisms that drive these processes, not only the exploitation of advanced experimental techniques down to the nanoscale is necessary but also spatially explicit and dynamic image‐based modeling at the pore scale. Aim: We present a modeling approach that is capable of transferring microscale information into macroscale simulations at the profile scale. This enables the prediction of future developments of carbon fluxes and the impact of changes in the environmental conditions linking scales. Method: We consider a mathematical model for CO2 transport across soil profiles (macroscale), which is informed by a pore‐scale (microscale) model for C turnover. It allows for the dynamic, self‐organized re‐arrangement of solid building units, aggregates and particulate organic matter (POM) based on surface interactions, realized by a cellular automaton method, and explicitly takes spatial effects on POM turnover such as occlusion into account. We further include the macroscopic environmental conditions water saturation, POM content, and oxygen concentration. Results: The coupled simulations of macroscopic transport and pore‐scale carbon and aggregate turnover reveal the complex, nonlinear interplay of the underlying processes. Limitations by diffusive transport, oxygen availability, texture‐dependent occlusion and turnover of OM drive CO2 production and carbon storage. Conclusions: This emphasizes the need for such micro–macro models exchanging information on different scales to investigate and quantify the effects of structural changes, variations in environmental conditions, or degradation processes on carbon turnover. [ABSTRACT FROM AUTHOR]

Reactive flow and transport in porous media is topic of intense research since decades. Since dispersion is one of the key parameters in solute transport, its accurate modeling is essential to avoid wrong predictions of flow and transport behavior. In this research, we investigate novel effective dispersion models for reactive transport of electrically charged chemical species in a thin, potentially evolving strip taking into account Taylor–Aris and electroosmotic‐induced dispersion as well as their cross‐coupling effects. We prove positivity of the dispersion coefficient and the existence and uniqueness of strong solutions in the fixed geometry setting. Moreover, we numerically investigate scenarios for both the fixed and evolving geometry situation. The simulation results illustrate the possibility of separating charged species, such that the findings of this study can lead to a better understanding of mixing and separation processes of charged solutes and an improved prediction of breakthrough curves. Finally, we study the limits of vanishing channel width, precipitation layer thickness, and molecular diffusion. We show convergence of the solutions to the corresponding limit cases such as a hyperbolic model or the fixed geometry case. From these results, we can rate the impact of distinct dispersion mechanisms and evaluate the necessity of a detailed modeling for different parameter regimes. [ABSTRACT FROM AUTHOR]

Upscaling transport in porous media including both biomass development and simultaneous structural changes in the solid matrix is extremely challenging. This is because both affect the medium’s porosity as well as mass transport parameters and flow paths. We address this challenge by means of a multiscale model. At the pore scale, the local discontinuous Galerkin (LDG) method is used to solve differential equations describing particularly the bacteria’s and the nutrient’s development. Likewise, a sticky agent tightening together solid or bio cells is considered. This is combined with a cellular automaton method (CAM) capturing structural changes of the underlying computational domain stemming from biomass development and solid restructuring. Findings from standard homogenization theory are applied to determine the medium’s characteristic time- and space-dependent properties. Investigating these results enhances our understanding of the strong interplay between a medium’s functional properties and its geometric structure. Finally, integrating such properties as model parameters into models defined on a larger scale enables reflecting the impact of pore scale processes on the larger scale. [ABSTRACT FROM AUTHOR]

The objective of this research is to investigate the upscaling of flow and transport models including both an evolving solid-liquid interface and a quite general potentially even oscillating interaction potential. Starting from a comprehensive pore-scale model, formal, two-scale, asymptotic expansion in a level set framework is applied. In doing so, the interplay between flow, transport, interaction potential, and evolving geometry becomes evident. As a result of an averaging procedure, a fully coupled micro-macro model is established with new main variables. Moreover, time- and space-dependent coefficient functions are explicitly characterized by means of supplementary, fully coupled cell problems. The theoretical results obtained are complemented by the numerical computations of a heterogeneous multiscale scenario with a focus on the development of anisotropic transport. Because of the general framework considered in this research, numerous application are expected, such as in biology or colloidal dynamics. [ABSTRACT FROM AUTHOR]

This paper deals with the analytical investigations of a nonstationary Darcy-Nernst-Planck-Poisson-type system which is a mathematical model describing electrolyte solutions. For this nonlinear fully coupled system of partial differential equations we proof existence and uniqueness of global weak solutions. Furthermore, we establish physical properties for the number densities such as nonnegativity and boundedness in L∞((0, T) × Ω) (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [ABSTRACT FROM AUTHOR]

We consider charged transport within a porous medium, which at the pore scale can be described by the non-stationary Stokes-Nernst-Planck-Poisson (SNPP) system. We state three different homogenization results using the method of two-scale convergence. In addition to the averaged macroscopic equations, auxiliary cell problems are solved in order to provide closed-form expressions for effective coefficients. Our aim is to study numerically the convergence of the models for vanishing microstructure, i. e., the behavior for $$\varepsilon \rightarrow 0$$ , where $$\varepsilon $$ is the characteristic ratio between pore diameter and size of the porous medium. To this end, we propose a numerical scheme capable of solving the fully coupled microscopic SNPP system and also the corresponding averaged systems. The discretization is performed fully implicitly in time using mixed finite elements in two space dimensions. The averaged models are evaluated using simulation results and their approximation errors in terms of $$\varepsilon $$ are estimated numerically. [ABSTRACT FROM AUTHOR]

Microaggregates are the fundamental building blocks of soils and thus important for their structure, properties, and functions. Although there has been much research investigating the dynamics, stability, and structure of soil microaggregates, there is still a substantial lack in quantifying the relationships between the major driving forces. The major driving forces are known to be soil fauna, microorganisms, roots, inorganics, and physical processes. Mathematically based modeling can facilitate the understanding of self-organization, formation, build-up, composition, properties and stability of microaggregates, provided that these major driving forces are taken into account. We assess the complex coupling of biological, chemical and physical processes with the help of a mechanistic modeling approach in order to create a process-based tool to studythe interplay of relevant mechanisms in silico and consequently gain a model-based understanding of the microaggregate dynamics in soils. In our framework, dynamic wetting (fluid) and non-wetting (gas) phases are included, in which the diffusion of mobile bacteria, possibly transforming into immobile biomass, sticky agent (EPS), nutrients, and ions are prescribed by means of partial differential equations. In particular a kinetic Langmuir isotherm for heterogeneous surface reactions and a Henry condition for the transfer from/into the gas phase are applied. The model further includes the development of the biomass phase and structural changes in the solid phase originating from stabilizing sticky agents or electrostatic attraction/repulsion. Arbitrary shapes for the potentially charged solid building units (e.g., spherical, needle-like, or platy particles), and also their compositions are incorporated into the model. The interplay between and within the different phases results in a structural self-organization of the respective phases which defines the time-dependent composition of the computational domain. It is realized in a cellular automaton framework while the partial differential equations are discretized by a fully implicit local discontinuous Galerkin method. The operational, comprehensive model allows to study structure formation as a function of the size and shape of the solid particles. Moreover, the effect of attraction and repulsion by chargesis thoroughly discussed. Another main objective of this research is to examine the strong interplay between functional properties and geometric structure. To that end standard homogenization results are used to compute the soil's characteristic properties such as porosity or effective diffusion tensors for the resulting complex and time-dependent geometries. [ABSTRACT FROM AUTHOR]

Mineral dissolution and precipitation alter a porous medium's structure and its bulk properties. Due to the medium's heterogeneity and lacks in dynamic pore-scale measurements, there has been an increasing interest in comprehensive models accessing such phenomena on the macroscale without disregarding available pore-scale (micro-scale) information. Such micro-macro models may be derived from detailed pore-scale models applying upscaling techniques and comprise several levels of couplings. Our model consists of transport equations for dissolved chemical species at the scale of the porous medium (macro scale) while taking the processes of convection and diffusion into account. They include averaged time- and space-dependent coefficient functions such as porosity and the effective, potentially anisotropic diffusion tensor. These coefficient functions are in turn explicitly computed by means of auxiliary cell problems (micro scale). Structural changes due to mineral dissolution and precipitation reactions result in a time- and space dependent domain on which cell problems are defined. We characterize the interface between the mineral and the fluid and consequently the explicit geometric structure by means of a level-set. Its evolution depends on the transport equations' solutions, i.e. the chemical species' concentrations (micro-macro scale). A numerical scheme is introduced which enables evaluating such complex micro-macro settings. For the level-set equation an upwind scheme by Rouy and Tourin is applied. An eXtended Finite Element Method is used for the evaluation of the cell problems while the transport equations are solved applying Mixed Finite Elements. Ultimately, we investigate the potentially degenerating bulk properties of the medium such as porosity and effective diffusion. Moreover, we apply our approach to the dissolution of an array of calcite grains in the micro-macro context and validate our numerical scheme. [ABSTRACT FROM AUTHOR]

An accurate quantitative description of the permeability and diffusion coefficient in a porous medium is essential for predictive transport modeling. Well-established relations such as the Kozeny-Carman equation and relations proposed by Buckingham, Penman, or Millington-Quirk, relate the scalar permeability and diffusion coefficient to the porous medium's porosity, respectively. To capture the porous medium's structure in more detail, further models include fitting parameters, geometric, or shape factors. Some models additionally account for the tortuosity, e.g. via Archie's law. A validation of such models has been carried out mainly via experiments relating the proposed description to a specific class of porous media (by means of parameter fitting).Contrary to these approaches, upscaling methods directly enable calculating the full, potentially anisotropic permeability and effective diffusion tensor without any fitting parameters. As input only the geometric information in terms of a representative elementary volume is needed. To compute the permeability and diffusion-porosity relations, supplementary cell problems must be solved numerically for this volume and their (flux) solutions must be integrated. We apply this approach to provide easy to use quantitative relations that are based on representative single grain, platy, blocky, prismatic soil structures, porous networks, or random porous media. As a discretization method we use the Discontinuous Galerkin method on structured grids. To make the relations explicit, interpolation of the obtained data is used.We furthermore compare the relations obtained with the well-established relations mentioned above and also with the well-known Voigt-Reiss or Hashin-Shtrikman bounds. We discuss the ranges of validity and comment on the role of tortuosity - porosity relations. [ABSTRACT FROM AUTHOR]

The functions of soils are intimately linked to their three‐dimensional pore space and the associated biogeochemical interfaces, mirrored in the complex structure that developed during pedogenesis. Under stress overload, soil disintegrates into smaller compound structures, conventionally named aggregates. Microaggregates (<250 µm) are recognized as the most stable soil structural units. They are built of mineral, organic, and biotic materials, provide habitats for a vast diversity of microorganisms, and are closely involved in the cycling of matter and energy. However, exploring the architecture of soil microaggregates and their linkage to soil functions remains a challenging but demanding scientific endeavor. With the advent of complementary spectromicroscopic and tomographic techniques, we can now assess and visualize the size, composition, and porosity of microaggregates and the spatial arrangement of their interior building units. Their combinations with advanced experimental pedology, multi‐isotope labeling experiments, and computational approaches pave the way to investigate microaggregate turnover and stability, explore their role in element cycling, and unravel the intricate linkage between structure and function. However, spectromicroscopic techniques operate at different scales and resolutions, and have specific requirements for sample preparation and microaggregate isolation; hence, special attention must be paid to both the separation of microaggregates in a reproducible manner and the synopsis of the geography of information that originates from the diverse complementary instrumental techniques. The latter calls for further development of strategies for synlocation and synscaling beyond the present state of correlative analysis. Here, we present examples of recent scientific progress and review both options and challenges of the joint application of cutting‐edge techniques to achieve a sophisticated picture of the properties and functions of soil microaggregates. [ABSTRACT FROM AUTHOR]

The structure of soil aggregates plays an important role for the turnover of particulate organic matter (POM) and vice versa. Analytical approaches usually do not disentangle the continuous re‐organization of soil aggregates, caught between disintegration and assemblage. This led to a lack of understanding of the mechanistic relationship between aggregation and organic matter dynamics in soils. In this study, we took advantage of a process‐based mechanistic model that describes the interaction between the dynamic (re‐)arrangement of soil aggregates, based on dynamic image analysis data of wet‐sieved aggregates, to analyze the turnover of POM, and simultaneous soil surface interactions in a spatially and temporally explicit way. Our novel modeling approach enabled us to unravel the temporal development of aggregate sizes, organic carbon (OC) turnover of POM, and surface coverage as affected by soil texture, POM input, and POM decomposition rate comparing a low and high clay soil (18% and 33% clay content). Our results reveal the importance of the dynamic re‐arrangement of soil structure on POM‐related turnover of OC in soils. Firstly, aggregation was largely determined by the POM input fostering aggregates through additional gluing joints outweighing soil texture at lower decomposition rate, whereas at higher decomposition rate, soil texture had a higher influence leading to larger aggregates in the high clay soil. Secondly, the POM storage increased with clay content, showing that surface interactions may delay the turnover of OC into CO2. Thirdly, we observed a structural priming effect in which the increased input of POM induced increased structural re‐arrangement stimulating the mineralization of old POM. This work highlights that the dynamic re‐arrangement of soil aggregates has important implications for OC turnover and is driven by underlying surface interactions where temporary gluing spots stabilize larger aggregates. [ABSTRACT FROM AUTHOR]

We investigate reactive flow and transport in evolving porous media. Solute species that are transported within the fluid phase are taking part in mineral precipitation and dissolution reactions for two competing mineral phases. The evolution of the three phases is not known a-priori but depends on the concentration of the dissolved solute species. To model the coupled behavior, phase-field and level-set models are formulated. These formulations are compared in three increasingly challenging setups including significant mineral overgrowth. Simulation outcomes are examined with respect to mineral volumes and surface areas as well as derived effective quantities such as diffusion and permeability tensors. In doing so, we extend the results of current benchmarks for mineral dissolution/precipitation at the pore-scale to the multiphasic solid case. Both approaches are found to be able to simulate the evolution of the three-phase system, but the phase-field model is influenced by curvature-driven motion. [ABSTRACT FROM AUTHOR]

• We model soil microbial dynamics by a cellular automaton and differential equations. • Simulations are based on CT-scans of microaggregates and realistic parameter values. • Scenarios in silico allowed investigations at scales still inaccessibe ex-situ. • Connectivity, not supply controls microbial degradation at the microaggregate scale. • We contribute to the understanding of metabolic factors driving the Birch effect. Microaggregates are hot spots of microbial activity at a scale that frequently poses a severe experimental challenge or defies a direct observation. Mathematical models that combine the mechanisms of spatially resolved organic matter transport with the processes of organic matter turnover can facilitate the understanding of soil microbial dynamics and the function of soils at these scales. In this study, we investigate microbial population dynamics and the turnover of particulate organic matter (POM) in soil microaggregates. CT images of microaggregates obtained from samples of natural soils serve as basis for selecting the simulation domain. For different levels of water saturation, the fluid (liquid and gas) distribution within the pore space is calculated according to a morphological model. We consider bacteria and POM, which are heterogeneously distributed within the liquid phase. Dissolved organic carbon (DOC) is released by hydrolyzing POM, assuming a reaction following first-order kinetics. DOC spreads by diffusion and can subsequently be consumed by bacteria and turned into CO 2. The growth of bacteria is realized by a cellular automaton framework (CAM) and based on Michaelis–Menten kinetics due to the uptake of DOC. Our simulations show that the heterogeneous distribution of substrate and bacteria results in an overall biodegradation kinetics and CO 2 output that strongly depends on the microaggregate scale (<250μm). Only very specific cases can be distinguished globally, e.g., when the substrates are isolated from bacteria due to a disconnected liquid phase. Locally, however, heterogeneities in substrate distribution impact the development of bacteria populations, e.g., a smaller geodesic distance of bacteria to the substrate promotes bacterial growth locally. [ABSTRACT FROM AUTHOR]

Abstract: All soils harbor microaggregates, i.e., compound soil structures smaller than 250 µm. These microaggregates are composed of diverse mineral, organic and biotic materials that are bound together during pedogenesis by various physical, chemical and biological processes. Consequently, microaggregates can withstand strong mechanical and physicochemical stresses and survive slaking in water, allowing them to persist in soils for several decades. Together with the physiochemical heterogeneity of their surfaces, the three‐dimensional structure of microaggregates provides a large variety of ecological niches that contribute to the vast biological diversity found in soils. As reported for larger aggregate units, microaggregates are composed of smaller building units that become more complex with increasing size. In this context, organo‐mineral associations can be considered structural units of soil aggregates and as nanoparticulate fractions of the microaggregates themselves. The mineral phases considered to be the most important as microaggregate forming materials are the clay minerals and Fe‐ and Al‐(hydr)oxides. Within microaggregates, minerals are bound together primarily by physicochemical and chemical interactions involving cementing and gluing agents. The former comprise, among others, carbonates and the short‐range ordered phases of Fe, Mn, and Al. The latter comprise organic materials of diverse origin and probably involve macromolecules and macromolecular mixtures. Work on microaggregate structure and development has largely focused on organic matter stability and turnover. However, little is known concerning the role microaggregates play in the fate of elements like Si, Fe, Al, P, and S. More recently, the role of microaggregates in the formation of microhabitats and the biogeography and diversity of microbial communities has been investigated. Little is known regarding how microaggregates and their properties change in time, which strongly limits our understanding of micro‐scale soil structure dynamics. Similarly, only limited information is available on the mechanical stability of microaggregates, while essentially nothing is known about the flow and transport of fluids and solutes within the micro‐ and nanoporous microaggregate systems. Any quantitative approaches being developed for the modeling of formation, structure and properties of microaggregates are, therefore, in their infancy. We respond to the growing awareness of the importance of microaggregates for the structure, properties and functions of soils by reviewing what is currently known about the formation, composition and turnover of microaggregates. We aim to provide a better understanding of their role in soil function, and to present the major unknowns in current microaggregate research. We propose a harmonized concept for aggregates in soils that explicitly considers the structure and build‐up of microaggregates and the role of organo‐mineral associations. We call for experiments, studies and modeling endeavors that will link information on aggregate forming materials with their functional properties across a range of scales in order to better understand microaggregate formation and turnover. Finally, we hope to inspire a novel cohort of soil scientists that they might focus their research on improving our understanding of the role of microaggregates within the system of aggregates and so help to develop a unified and quantitative concept of aggregation processes in soils. [ABSTRACT FROM AUTHOR]

In recent years, convolutional neural networks (CNNs) have experienced an increasing interest in their ability to perform a fast approximation of effective hydrodynamic parameters in porous media research and applications. This paper presents a novel methodology for permeability prediction from micro-CT scans of geological rock samples. The training data set for CNNs dedicated to permeability prediction consists of permeability labels that are typically generated by classical lattice Boltzmann methods (LBM) that simulate the flow through the pore space of the segmented image data. We instead perform direct numerical simulation (DNS) by solving the stationary Stokes equation in an efficient and distributed-parallel manner. As such, we circumvent the convergence issues of LBM that frequently are observed on complex pore geometries, and therefore, improve the generality and accuracy of our training data set. Using the DNS-computed permeabilities, a physics-informed CNN (PhyCNN) is trained by additionally providing a tailored characteristic quantity of the pore space. More precisely, by exploiting the connection to flow problems on a graph representation of the pore space, additional information about confined structures is provided to the network in terms of the maximum flow value, which is the key innovative component of our workflow. The robustness of this approach is reflected by very high prediction accuracy, which is observed for a variety of sandstone samples from archetypal rock formations. [ABSTRACT FROM AUTHOR]

Clay minerals and Fe- and Al-oxyhydroxides are considered as the most important materials for the formation of microaggregate building units in soils. The mode of aggregation and the resulting structure and stability are largely determined by their size, aspect ratio (AR), differences in surface charge (SC), and mixing ratio. Here, the impact of these parameters on the formation of microaggregate building units (BUs) was elucidated with a mechanistic model, i.e. using a twophase cellular automaton method, in which prototypes of illite and goethite were implemented. The simulations allowed assessing the formation of particle arrangements during aggregation, moreover building unit diameters, and the number of discrete particles. The contact area between particles was evaluated as a quantitative measure for stability. Homoaggregation of illite under the sole influence of attracting van der Waals forces enabling face-to-face as well as edge-to-face contacts, resulted in compact structures with a small mean diameter and specific surface area. In contrast, electrostatic attraction between negatively charged faces and positively charged edges favored formation of larger card-house structures, where low contact areas indicated the low stability of the resulting BUs. At constant AR, homoaggregation of illite of different particle size led to BUs of different stability, more precisely smaller particle sizes led to more stable BUs. Variation of the AR of illite, while keeping the particle size constant, revealed that most stable BUs arose from illite with smallest AR. Shielding of coarse goethite particles due to attachment of fine illite with negatively charged edges increased the number of discrete fine illite particles not aggregated. Aggregation of illite with positively charged edges was in fundamental difference to results from simulations with negative edges because of electrostatic attraction between illite particles. The simulation setting, without using fitting parameters resulted in an appropriate approximation of laboratory findings. The simulation clearly facilitated the understanding of microaggregate building unit formation and stability by illuminating turnover dynamics and provision of quantitative data. Unlabelled Image • Aggregation of illite and goethite was determined by a mechanistic model in 2D. • Particle shape, surface charge and mixing ratio impact the mode of aggregation. • Simulations give temporally resolved insights into aggregate structures and stability. • Simulation results match laboratory findings well without using fitting parameters. [ABSTRACT FROM AUTHOR]