A parallel Voronoi-based approach for mesoscale simulations of cell aggregate electropermeabilization

DOI10.1016/J.JCP.2018.12.009zbMATH Open1451.76078arXiv1802.01781OpenAlexW2787582410WikidataQ128642475 ScholiaQ128642475MaRDI QIDQ2214528FDOQ2214528

Authors: Pouria A. Mistani, Arthur Guittet, Clair Poignard, Frédéric Gibou 

Publication date: 9 December 2020

Published in: Journal of Computational Physics (Search for Journal in Brave)

Abstract: We introduce a numerical framework that enables unprecedented direct numerical studies of the electropermeabilization effects of a cell aggregate at the meso-scale. Our simulations qualitatively replicate the shadowing effect observed in experiments and reproduce the time evolution of the impedance of the cell sample in agreement with the trends observed in experiments. This approach sets the scene for performing homogenization studies for understanding the effect of tissue environment on the efficiency of electropermeabilization. We employ a forest of Octree grids along with a Voronoi mesh in a parallel environment that exhibits excellent scalability. We exploit the electric interactions between the cells through a nonlinear phenomenological model that is generalized to account for the permeability of the cell membranes. We use the Voronoi Interface Method (VIM) to accurately capture the sharp jump in the electric potential on the cell boundaries. The case study simulation covers a volume of $(1mm{)}^3$ with more than $27,000$ well-resolved cells with a heterogeneous mix of morphologies that are randomly distributed throughout a spheroid region.

Full work available at URL: https://arxiv.org/abs/1802.01781

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zbMATH Keywords

finite volume methodmathematical biologylevel-set methodVoronoi meshelectropermeabilizationquad/oc-tree grids

Mathematics Subject Classification ID

Finite volume methods for initial value and initial-boundary value problems involving PDEs (65M08) Mesh generation, refinement, and adaptive methods for the numerical solution of initial value and initial-boundary value problems involving PDEs (65M50) Physiological flows (76Z05) Cell biology (92C37) Finite volume methods applied to problems in fluid mechanics (76M12)

Cites Work

• p4est: scalable algorithms for parallel adaptive mesh refinement on forests of octrees
• Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations
• An improved low-discrepancy sequence for multidimensional quasi-Monte Carlo integration
• On the efficiency of certain quasi-random sequences of points in evaluating multi-dimensional integrals
• Quad trees: A data structure for retrieval by composite keys
• A second order accurate level set method on non-graded adaptive Cartesian grids
• A non-oscillatory Eulerian approach to interfaces in multimaterial flows (the ghost fluid method)
• Convergence of the ghost fluid method for elliptic equations with interfaces
• A boundary condition capturing method for multiphase incompressible flow.
• Less is different: emergence and reduction reconciled
• Geometric integration over irregular domains with application to level-set methods
• Emergence, reduction and supervenience: a varied landscape
• Tree methods for moving interfaces
• An adaptive discretization of incompressible flow using a multitude of moving Cartesian grids
• Local level set method in high dimension and codimension
• Relating theories via renormalization
• Conducting and permeable states of cell membrane submitted to high voltage pulses: mathematical and numerical studies validated by the experiments
• A review of level-set methods and some recent applications
• Solving elliptic problems with discontinuities on irregular domains -- the Voronoi interface method
• A Voronoi interface approach to cell aggregate electropermeabilization
• Parallel level-set methods on adaptive tree-based grids

Cited In (8)

• A non-parametric gradient-based shape optimization approach for solving inverse problems in directed self-assembly of block copolymers
• JAX-DIPS: neural bootstrapping of finite discretization methods and application to elliptic problems with discontinuities
• Efficient calculation of fully resolved electrostatics around large biomolecules
• A finite volume method to solve the Poisson equation with jump conditions and surface charges: application to electroporation
• Cell electropermeabilization modeling via multiple traces formulation and time semi-implicit multistep coupling
• Solving inverse-PDE problems with physics-aware neural networks
• Solving elliptic interface problems with jump conditions on Cartesian grids
• A Voronoi interface approach to cell aggregate electropermeabilization

Uses Software

• p4est
• Voro++

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