Search

This paper provides a new open-source software, named BioReactPy, for simulation of microbial-mediated coupled processes of flow and reactive transport in porous media. The software is based on the micro-continuum approach, and geochemistry is handled in a fully coupled manner with biomass-nutrient growth treated with Monod equation in a single integrated framework, without dependencies on third party packages. The distinguishing features of the software, its design principles, and formulation of multiphysics problems and discretizations are discussed. Validation of the Python implementation using several established benchmarks for flow, reactive transport, and biomass growth is presented. The flexibility of the framework is then illustrated by simulations of highly non-linearly coupled flow and microbial reactive transport at conditions relevant to carbon mineralization for CO2 storage. All results can be reproduced by openly available simulation scripts., This project has received funding from the European Union’s Horizon 2021 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101063414 – CO2FOREARM., Peer Reviewed, Postprint (published version)

Biologically mediated degradation of organic compounds in porous media is a complex mathematical problem, described by a non-linear differential equation. The organic compound gets in contact with the biomass, and an enzyme-catalysed reaction takes place. The net result is that part of the parent compound degrades into some daughter product, while some of the organic carbon is used for microbial growth. The rate of biomass growth in the presence of a limiting nutrient supply is usually modelled with the experimentally derived Monod equation, i.e., it is proportional to the actual existing biomass multiplied by a factor that is non-linear in terms of available organic matter. This non-linearity in the degradation equation implies a strong difficulty in directly implementing a numerical solution within a fully Lagrangian framework, and thus, numerical solutions have traditionally been sought in either an Eulerian, or else an Eulerian–Lagrangian framework. Here we pursue a fully Lagrangian solution to the problem. First, the Monod empirical equation is formulated as the outcome of a two-step reaction; while the approach is less general than other derivations existing in the literature based on a full understanding of the thermodynamics of the process, it allows two things: 1) providing some physical meaning to the actual parameters in the Monod equation, and more interestingly, 2) formulating a methodology for the solution of the degradation equation incorporating Monod kinetics by means of a particle tracking formulation. For the latter purpose, both reactants and biomass are represented by particles, and their location at any given time is represented by a kernel that accounts for the uncertainty in the actual physical location. By solving the reaction equation in a kernel framework, we can reproduce the Monod kinetics and, as a particular result in the case no biomass growth is allowed, the Michaelis–Menten kinetics. The methodology proposed is then successfully app, This work was partially supported by the Spanish Ministry of Economy and Competitiveness, project MONOPOLIOS (RTI 2018–101990-B-I00, MINECO/FEDER); and by the Catalan Agency for Management of University and Research Grants through FI 2017 (EMC/2199/2017). M. D. acknowledges the support of the Grant CEX2018-000797-S funded by MCIN/AEI/10.13039/501100011033., Peer Reviewed, Postprint (author's final draft)

The version of record is available online at: http://dx.doi.org/10.1007/s00285-021-01699-8, Cells and tissues exhibit sustained oscillatory deformations during remodelling, migration or embryogenesis. Although it has been shown that these oscillations correlate with intracellular biochemical signalling, the role of these oscillations is as yet unclear, and whether they may trigger drastic cell reorganisation events or instabilities remains unknown. Here, we present a rheological model that incorporates elastic, viscous and frictional components, and that is able to generate oscillatory response through a delay adaptive process of the rest-length. We analyse its stability as a function of the model parameters and deduce analytical bounds of the stable domain. While increasing values of the delay and remodelling rate render the model unstable, we also show that increasing friction with the substrate destabilises the oscillatory response. This fact was unexpected and still needs to be verified experimentally. Furthermore, we numerically verify that the extension of the model with non-linear deformation measures is able to generate sustained oscillations converging towards a limit cycle. We interpret this sustained regime in terms of non-linear time varying stiffness parameters that alternate between stable and unstable regions of the linear model. We also note that this limit cycle is not present in the linear model. We study the phase diagram and the bifurcations of the non-linear model, based on our conclusions on the linear one. Such dynamic analysis of the delay visco-elastic model in the presence of friction is absent in the literature for both linear and non-linear rheologies. Our work also shows how increasing values of some parameters such as delay and friction decrease its stability, while other parameters such as stiffness stabilise the oscillatory response., JJM and MD have been financially supported by the Spanish Ministry of Science, Innovation and Universities (MICINN) with grant DPI2016-74929-R and by the local government Generalitat de Catalunya with grant 2017 SGR 1278., Peer Reviewed, Postprint (author's final draft)

Many epithelial developmental processes like cell migration and spreading, cell sorting, or T1 transitions can be described as planar deformations. As such, they can be studied using two-dimensional tools and vertex models that can properly predict collective dynamics. However, many other epithelial shape changes are characterized by out-of-plane mechanics and three-dimensional effects, such as bending, cell extrusion, delamination, or invagination. Furthermore, during planar cell dynamics or tissue repair in monolayers, spatial intercalation between the apical and basal sides has even been detected. Motivated by this lack of symmetry with respect to the midsurface, we here present a 3D hybrid model that allows us to model differential contractility at the apical, basal or lateral sides. We use the model to study the effects on wound closure of solely apical or lateral contractile contributions and show that an apical purse-string can be sufficient for full closure when it is accompanied by volume preservation., Peer Reviewed, Postprint (published version)

Recent microscopic techniques allow scientists to describe the kinematics of a single bological cell or cell aggregates with high accuracy. However, the analysis of the forces that cell ls activate on the environment under different conditions remains elusive and not well understood. This work aims to develop and apply inverse analysis to compute the tractions that a cell monolayer exerts on a gel substrate from a sequence of displacement maps.