A parallel Voronoi-based approach for mesoscale simulations of cell aggregate electropermeabilization
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Publication:2214528
finite volume methodmathematical biologylevel-set methodVoronoi meshelectropermeabilizationquad/oc-tree grids
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)
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 with more than well-resolved cells with a heterogeneous mix of morphologies that are randomly distributed throughout a spheroid region.
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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
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- A Voronoi interface approach to cell aggregate electropermeabilization
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