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Register a new userAccurate numerical simulation of electrodiffusion and water movement in brain tissue
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Added by
Ada Johanne Ellingsrud
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Mathematical modelling of ionic electrodiffusion and water movement is emerging as a powerful avenue of investigation to provide new physiological insight into brain homeostasis. However, in order to provide solid answers and resolve controversies, the accuracy of the predictions is essential. Ionic electrodiffusion models typically comprise non-trivial systems of non-linear and highly coupled partial and ordinary differential equations that govern phenomena on disparate time scales. Here, we study numerical challenges related to approximating these systems. We consider a homogenized model for electrodiffusion and osmosis in brain tissue and present and evaluate different associated finite element-based splitting schemes in terms of their numerical properties, including accuracy, convergence, and computational efficiency for both idealized scenarios and for the physiologically relevant setting of cortical spreading depression (CSD). We find that the schemes display optimal convergence rates in space for problems with smooth manufactured solutions. However, the physiological CSD setting is challenging: we find that the accurate computation of CSD wave characteristics (wave speed and wave width) requires a very fine spatial and fine temporal resolution.
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Overland flow on agricultural fields may have some undesirable effects such as soil erosion, flood and pollutant transport. To better understand this phenomenon and limit its consequences, we developed a code using state-of-the-art numerical methods: FullSWOF (Full Shallow Water equations for Overland Flow), an object oriented code written in C++. It has been made open-source and can be downloaded from http://www.univ-orleans.fr/mapmo/soft/FullSWOF/. The model is based on the classical system of Shallow Water (SW) (or Saint-Venant system). Numerical difficulties come from the numerous dry/wet transitions and the highly-variable topography encountered inside a field. It includes runon and rainfall inputs, infiltration (modified Green-Ampt equation), friction (Darcy-Weisbach and Manning formulas). First we present the numerical method for the resolution of the Shallow Water equations integrated in FullSWOF_2D (the two-dimension version). This method is based on hydrostatic reconstruction scheme, coupled with a semi-implicit friction term treatment. FullSWOF_2D has been previously validated using analytical solutions from the SWASHES library (Shallow Water Analytic Solutions for Hydraulic and Environmental Studies). Finally, FullSWOF_2D is run on a real topography measured on a runoff plot located in Thies (Senegal). Simulation results are compared with measured data. This experimental benchmark demonstrate the capabilities of FullSWOF to simulate adequately overland flow. FullSWOF could also be used for other environmental issues, such as river floods and dam-breaks.
We are interested in simulating blood flow in arteries with a one dimensional model. Thanks to recent developments in the analysis of hyperbolic system of conservation laws (in the Saint-Venant/ shallow water equations context) we will perform a simple finite volume scheme. We focus on conservation properties of this scheme which were not previously considered. To emphasize the necessity of this scheme, we present how a too simple numerical scheme may induce spurious flows when the basic static shape of the radius changes. On contrary, the proposed scheme is well-balanced: it preserves equilibria of Q = 0. Then examples of analytical or linearized solutions with and without viscous damping are presented to validate the calculations. The influence of abrupt change of basic radius is emphasized in the case of an aneurism.
In this paper, two finite difference numerical schemes are proposed and analyzed for the droplet liquid film model, with a singular Leonard-Jones energy potential involved. Both first and second order accurate temporal algorithms are considered. In the first order scheme, the convex potential and the surface diffusion terms are implicitly, while the concave potential term is updated explicitly. Furthermore, we provide a theoretical justification that this numerical algorithm has a unique solution, such that the positivity is always preserved for the phase variable at a point-wise level, so that a singularity is avoided in the scheme. In fact, the singular nature of the Leonard-Jones potential term around the value of 0 prevents the numerical solution reaching such singular value, so that the positivity structure is always preserved. Moreover, an unconditional energy stability of the numerical scheme is derived, without any restriction for the time step size. In the second order numerical scheme, the BDF temporal stencil is applied, and an alternate convex-concave decomposition is derived, so that the concave part corresponds to a quadratic energy. In turn, the combined Leonard-Jones potential term is treated implicitly, and the concave part the is approximated by a second order Adams-Bashforth explicit extrapolation, and an artificial Douglas-Dupont regularization term is added to ensure the energy stability. The unique solvability and the positivity-preserving property for the second order scheme could be similarly established. In addition, optimal rate convergence analysis is provided for both the first and second order accurate schemes. A few numerical simulation results are also presented, which demonstrate the robustness of the numerical schemes.
We show that for the simulation of crack propagation in quasi-brittle, two-dimensional solids, very good results can be obtained with an embedded strong discontinuity quadrilateral finite element that has incompatible modes. Even more importantly, we demonstrate that these results can be obtained without using a crack tracking algorithm. Therefore, the simulation of crack patterns with several cracks, including branching, becomes possible. The avoidance of a tracking algorithm is mainly enabled by the application of a novel, local (Gauss-point based) criterion for crack nucleation, which determines the time of embedding the localisation line as well as its position and orientation. We treat the crack evolution in terms of a thermodynamical framework, with softening variables describing internal dissipative mechanisms of material degradation. As presented by numerical examples, many elements in the mesh may develop a crack, but only some of them actually open and/or slide, dissipate fracture energy, and eventually form the crack pattern. The novel approach has been implemented for statics and dynamics, and the results of computed difficult examples (including Kalthoffs test) illustrate its very satisfying performance. It effectively overcomes unfavourable restrictions of the standard embedded strong discontinuity formulations, namely the simulation of the propagation of a single crack only. Moreover, it is computationally fast and straightforward to implement. Our numerical solutions match the results of experimental tests and previously reported numerical results in terms of crack pattern, dissipated fracture energy, and load-displacement curve.
In this work, we introduce a novel computational framework that we developed to use numerical simulations to investigate the complexity of brain tissue at a microscopic level with a detail never realised before. Directly inspired by the advances in computational neuroscience for modelling brain cells, we propose a generative model that enables us to simulate molecular diffusion within realistic digitalised brain cells, such as neurons and glia, in a completely controlled and flexible fashion. We validate our new approach by showing an excellent match between the morphology and simulated DW-MR signal of the generated digital model of brain cells and those of digital reconstruction of real brain cells from available open-access databases. We demonstrate the versatility and potentiality of the framework by showing a select set of examples of relevance for the DW-MR community. Further development is ongoing, which will support even more realistic conditions like dense packing of numerous 3D complex cell structures and varying cell surface permeability.
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