×

A finite volume method to solve the Poisson equation with jump conditions and surface charges: application to electroporation. (English) Zbl 07842850

Summary: Efficient numerical schemes for solving the Poisson equation with jump conditions are of great interest for a variety of problems, including the modeling of electroporation phenomena and filamentary discharges. In this paper, we propose a modification to a finite volume scheme, namely the discrete dual finite volume method, in order to account for jump conditions with surface charges, i.e. with a source term. Our numerical tests demonstrate second-order convergence even with highly distorted meshes. We then apply the proposed method to model electroporation phenomena in biological cells by proposing a model that considers the thickness of the cell membrane as a separate domain, which differs from the literature. We show the advantages of the proposed method in this context through numerical experiments.

MSC:

65Nxx Numerical methods for partial differential equations, boundary value problems
65Mxx Numerical methods for partial differential equations, initial value and time-dependent initial-boundary value problems
35Jxx Elliptic equations and elliptic systems

Software:

BoomerAMG; hypre
Full Text: DOI

References:

[1] Boyer, F.; Hubert, F., Finite volume method for 2D linear and nonlinear elliptic problems with discontinuities, SIAM J. Numer. Anal., 46, 6, 3032-3070, 2008 · Zbl 1180.35533
[2] Egan, R.; Gibou, F., xGFM: recovering convergence of fluxes in the ghost fluid method, J. Comput. Phys., 409, Article 109351 pp., 2020 · Zbl 1435.76050
[3] Pancheshnyi, S.; Nudnova, M.; Starikovskii, A., Development of a cathode-directed streamer discharge in air at different pressures: experiment and comparison with direct numerical simulation, Phys. Rev. E, 71, 1, Article 016407 pp., 2005
[4] Bessieres, D.; Paillol, J.; Bourdon, A.; Ségur, P.; Marode, E., A new one-dimensional moving mesh method applied to the simulation of streamer discharges, J. Phys. D, Appl. Phys., 40, 21, 6559, 2007
[5] Jánskỳ, J.; Pasko, V. P., Modeling of streamer ignition and propagation in the system of two approaching hydrometeors, J. Geophys. Res., Atmos., 125, 6, Article e2019JD031337 pp., 2020
[6] Pasko, V.; Jansky, J., Monte Carlo modeling of photoionization in air with application to lightning initiation in low thundercloud fields, (AGU Fall Meeting Abstracts, vol. 2021, 2021), pp. AE23A-07
[7] Weaver, J. C., Electroporation Theory, Electroporation Protocols for Microorganisms, 1-26, 1995
[8] Babaeva, N. Y.; Kushner, M. J., Intracellular electric fields produced by dielectric barrier discharge treatment of skin, J. Phys. D, Appl. Phys., 43, 18, Article 185206 pp., 2010
[9] Leguebe, M.; Silve, A.; Mir, L. M.; Poignard, C., Conducting and permeable states of cell membrane submitted to high voltage pulses: mathematical and numerical studies validated by the experiments, J. Theor. Biol., 360, 83-94, 2014 · Zbl 1343.92037
[10] Guittet, A.; Poignard, C.; Gibou, F., A Voronoi interface approach to cell aggregate electropermeabilization, J. Comput. Phys., 332, 143-159, 2017 · Zbl 1378.92015
[11] Kantar, E.; Mauseth, F.; Ildstad, E.; Hvidsten, S., Interfacial breakdown between dielectric surfaces determined by gas discharge, (2017 IEEE Conference on Electrical Insulation and Dielectric Phenomenon (CEIDP), 2017, IEEE), 556-559
[12] Kantar, E.; Hvidsten, S., A deterministic breakdown model for dielectric interfaces subjected to tangential electric field, J. Phys. D, Appl. Phys., 54, 29, Article 295503 pp., 2021
[13] Poignard, C.; Silve, A., Différence de potentiel induite par un champ electrique sur la membrane d’une cellule biologique, Revue 3EI, 75, 11-20, 2014
[14] Guo, F.; Qian, K.; Zhang, L.; Liu, X.; Peng, H., Multiphysics modelling of electroporation under uni- or bipolar nanosecond pulse sequences, Bioelectrochemistry, 141, Article 107878 pp., 2021
[15] Leguèbe, M.; Poignard, C.; Weynans, L., A second-order cartesian method for the simulation of electropermeabilization cell models, J. Comput. Phys., 292, 114-140, 2015 · Zbl 1349.78093
[16] Zienkiewicz, O. C.; Morice, P., The Finite Element Method in Engineering Science, vol. 1977, 1971, McGraw-Hill: McGraw-Hill London · Zbl 0237.73071
[17] Kwak, D. Y.; Lee, S.; Hyon, Y., A new finite element for interface problems having Robin type jump, Int. J. Numer. Anal. Model., 14, 4-5, 532-549, 2017 · Zbl 1429.65277
[18] Eymard, R.; Gallouët, T.; Herbin, R., Finite volume methods, Handb. Numer. Anal., 7, 713-1018, 2000 · Zbl 0981.65095
[19] Coudiere, Y.; Pierre, C.; Rousseau, O.; Turpault, R., A 2D/3D discrete duality finite volume scheme. Application to ECG simulation, Int. J. Finite Vol., 6, 1, 1-24, 2008 · Zbl 1490.65238
[20] Droniou, J., Finite volume schemes for diffusion equations: introduction to and review of modern methods, Math. Models Methods Appl. Sci., 24, 08, 1575-1619, 2014 · Zbl 1291.65319
[21] Yuan, G.; Sheng, Z., Analysis of accuracy of a finite volume scheme for diffusion equations on distorted meshes, J. Comput. Phys., 224, 2, 1170-1189, 2007 · Zbl 1119.65084
[22] Guittet, A.; Lepilliez, M.; Tanguy, S.; Gibou, F., Solving elliptic problems with discontinuities on irregular domains-the Voronoi interface method, J. Comput. Phys., 298, 747-765, 2015 · Zbl 1349.65579
[23] Bochkov, D.; Gibou, F., Solving Poisson-type equations with Robin boundary conditions on piecewise smooth interfaces, J. Comput. Phys., 376, 1156-1198, 2019 · Zbl 1416.65409
[24] Hermeline, F., A finite volume method for the approximation of diffusion operators on distorted meshes, J. Comput. Phys., 160, 2, 481-499, 2000 · Zbl 0949.65101
[25] Krell, S., Stabilized DDFV schemes for Stokes problem with variable viscosity on general 2D meshes, Numer. Methods Partial Differ. Equ., 27, 6, 1666-1706, 2011, publisher: John Wiley & Sons, Ltd. · Zbl 1426.76389
[26] Hermeline, F., Approximation of diffusion operators with discontinuous tensor coefficients on distorted meshes, Comput. Methods Appl. Mech. Eng., 192, 16-18, 1939-1959, 2003 · Zbl 1037.65118
[27] Coudiere, Y.; Hubert, F.; Manzini, G., A CeVeFE DDFV scheme for discontinuous anisotropic permeability tensors, (Finite Volumes for Complex Applications VI Problems & Perspectives, 2011, Springer), 283-291 · Zbl 1246.76075
[28] Fries, T.-P.; Belytschko, T., The extended/generalized finite element method: an overview of the method and its applications, Int. J. Numer. Methods Eng., 84, 3, 253-304, 2010 · Zbl 1202.74169
[29] Gracie, R.; Wang, H.; Belytschko, T., Blending in the extended finite element method by discontinuous Galerkin and assumed strain methods, Int. J. Numer. Methods Eng., 74, 11, 1645-1669, 2008 · Zbl 1195.74175
[30] Dolbow, J.; Harari, I., An efficient finite element method for embedded interface problems, Int. J. Numer. Methods Eng., 78, 2, 229-252, 2009 · Zbl 1183.76803
[31] Bochkov, D.; Gibou, F., Solving elliptic interface problems with jump conditions on Cartesian grids, J. Comput. Phys., 407, Article 109269 pp., 2020 · Zbl 1537.65190
[32] Hyman, J. M.; Li, S.; Knupp, P.; Shashkov, M., An algorithm for aligning a quadrilateral grid with internal boundaries, J. Comput. Phys., 163, 1, 133-149, 2000 · Zbl 0963.65121
[33] Coudière, Y.; Pierre, C.; Turpault, R., A 2d/3d finite volume method used to solve the bidomain equations of electrocardiology, (Algorithmy 2009, 2009), 1-10 · Zbl 1170.92330
[34] Blanc, X.; Hermeline, F.; Labourasse, E.; Patela, J., Monotonic diamond and DDFV type finite-volume schemes for 2D elliptic problems, 2023 · Zbl 1519.65047
[35] Barrett, J. W.; Elliott, C. M., Finite element approximation of the Dirichlet problem using the boundary penalty method, Numer. Math., 49, 4, 343-366, 1986 · Zbl 0614.65116
[36] Maury, B., Numerical analysis of a finite element/volume penalty method, SIAM J. Numer. Anal., 47, 2, 1126-1148, 2009 · Zbl 1191.65157
[37] Pierre, C., Modélisation et simulation de l’activité électrique du coeur dans le thorax, analyse numérique et méthodes de volumes finis, 2005, Université de Nantes, Ph.D. thesis
[38] Henson, V. E.; Yang, U. M., BoomerAMG: a parallel algebraic multigrid solver and preconditioner, Developments and Trends in Iterative Methods for Large Systems of Equations - in memorium Rudiger Weiss. Developments and Trends in Iterative Methods for Large Systems of Equations - in memorium Rudiger Weiss, Appl. Numer. Math., 41, 1, 155-177, 2002 · Zbl 0995.65128
[39] Falgout, R. D.; Jones, J. E.; Yang, U. M., The design and implementation of hypre, a library of parallel high performance preconditioners, (Bruaset, A. M.; Tveito, A., Numerical Solution of Partial Differential Equations on Parallel Computers, 2006, Springer Berlin Heidelberg: Springer Berlin Heidelberg Berlin, Heidelberg), 267-294 · Zbl 1097.65059
[40] Hyman, J.; Shashkov, M.; Steinberg, S., The numerical solution of diffusion problems in strongly heterogeneous non-isotropic materials, J. Comput. Phys., 132, 1, 130-148, 1997 · Zbl 0881.65093
[41] Lohr, F.; Lo, D. Y.; Zaharoff, D. A.; Hu, K.; Zhang, X.; Li, Y.; Zhao, Y.; Dewhirst, M. W.; Yuan, F.; Li, C.-Y., Effective tumor therapy with plasmid-encoded cytokines combined with in vivo electroporation, Cancer Res., 61, 8, 3281-3284, 2001
[42] Gothelf, A.; Mir, L. M.; Gehl, J., Electrochemotherapy: results of cancer treatment using enhanced delivery of bleomycin by electroporation, Cancer Treat. Rev., 29, 5, 371-387, 2003
[43] Potter, H., Electroporation in biology: methods, applications, and instrumentation, Anal. Biochem., 174, 2, 361-373, 1988
[44] Andre, F.; Mir, L., DNA electrotransfer: its principles and an updated review of its therapeutic applications, Gene Ther., 11, 1, S33-S42, 2004
[45] Daud, A. I.; DeConti, R. C.; Andrews, S.; Urbas, P.; Riker, A. I.; Sondak, V. K.; Munster, P. N.; Sullivan, D. M.; Ugen, K. E.; Messina, J. L., Phase I trial of interleukin-12 plasmid electroporation in patients with metastatic melanoma, J. Clin. Oncol., 26, 36, 5896, 2008
[46] Zeira, M.; Tosi, P.-F.; Mouneimne, Y.; Lazarte, J.; Sneed, L.; Volsky, D. J.; Nicolau, C., Full-length CD4 electroinserted in the erythrocyte membrane as a long-lived inhibitor of infection by human immunodeficiency virus, Proc. Natl. Acad. Sci., 88, 10, 4409-4413, 1991
[47] Vernier, P. T.; Sun, Y.; Marcu, L.; Salemi, S.; Craft, C. M.; Gundersen, M. A., Calcium bursts induced by nanosecond electric pulses, Biochem. Biophys. Res. Commun., 310, 2, 286-295, 2003
[48] Smith, K. C.; Weaver, J. C., Active mechanisms are needed to describe cell responses to submicrosecond, megavolt-per-meter pulses: cell models for ultrashort pulses, Biophys. J., 95, 4, 1547-1563, 2008
[49] Teissie, J., Electropermeabilization of the cell membrane, Electroporation Protocols, 25-46, 2014
[50] Gowrishankar, T. R.; Esser, A. T.; Vasilkoski, Z.; Smith, K. C.; Weaver, J. C., Microdosimetry for conventional and supra-electroporation in cells with organelles, Biochem. Biophys. Res. Commun., 341, 4, 1266-1276, 2006
[51] Kotnik, T.; Miklavčič, D., Analytical description of transmembrane voltage induced by electric fields on spheroidal cells, Biophys. J., 79, 2, 670-679, 2000
[52] Hu, Q.; Joshi, R., Transmembrane voltage analyses in spheroidal cells in response to an intense ultrashort electrical pulse, Phys. Rev. E, 79, 1, Article 011901 pp., 2009
[53] Kavian, O.; Leguèbe, M.; Poignard, C.; Weynans, L., “Classical” electropermeabilization modeling at the cell scale, J. Math. Biol., 68, 235-265, 2014 · Zbl 1300.92023
[54] Deka, B.; Roy, P., Weak Galerkin finite element methods for electric interface model with nonhomogeneous jump conditions, Numer. Methods Partial Differ. Equ., 36, 4, 734-755, 2020 · Zbl 07771412
[55] Salimi, E.; Thomson, D. J.; Bridges, G. E., Membrane dielectric dispersion in nanosecond pulsed electroporation of biological cells, IEEE Trans. Dielectr. Electr. Insul., 20, 4, 1256-1265, 2013
[56] Guo, F.; Zhang, L.; Liu, X., Nonlinear dispersive cell model for microdosimetry of nanosecond pulsed electric fields, Sci. Rep., 10, 1, 1-11, 2020
[57] Ghosh, D.; Saluja, N. K.; Singh, T. G., A FEM study of molecular transport through a single nanopore in a spherical cell, Biointerface Res. Appl. Chem., 12, 3, 2958-2969, 2022
[58] Mescia, L.; Chiapperino, M. A.; Bia, P.; Gielis, J.; Caratelli, D., Modeling of electroporation induced by pulsed electric fields in irregularly shaped cells, IEEE Trans. Biomed. Eng., 65, 2, 414-423, 2017
[59] Mescia, L.; Chiapperino, M.; Bia, P.; Lamacchia, C.; Gielis, J.; Caratelli, D., Relevance of the cell membrane modelling for accurate analysis of the pulsed electric field-induced electroporation, (2019 PhotonIcs & Electromagnetics Research Symposium-Spring (PIERS-Spring), 2019, IEEE), 2985-2991
[60] Chiapperino, M. A.; Bia, P.; Caratelli, D.; Gielis, J.; Mescia, L.; Dermol-Černe, J.; Miklavčič, D., Nonlinear dispersive model of electroporation for irregular nucleated cells, Bioelectromagnetics, 40, 5, 331-342, 2019
[61] Kotnik, T.; Miklavčič, D., Theoretical evaluation of voltage inducement on internal membranes of biological cells exposed to electric fields, Biophys. J., 90, 2, 480-491, 2006
[62] Vasilkoski, Z.; Esser, A. T.; Gowrishankar, T.; Weaver, J. C., Membrane electroporation: the absolute rate equation and nanosecond time scale pore creation, Phys. Rev. E, 74, 2, Article 021904 pp., 2006
[63] Yao, C.; Mi, Y.; Li, C.; Hu, X.; Chen, X.; Sun, C., Study of transmembrane potentials on cellular inner and outer membrane—frequency response model and its filter characteristic simulation, IEEE Trans. Biomed. Eng., 55, 7, 1792-1799, 2008
[64] Merla, C.; Denzi, A.; Paffi, A.; Casciola, M.; d’Inzeo, G.; Apollonio, F.; Liberti, M., Novel passive element circuits for microdosimetry of nanosecond pulsed electric fields, IEEE Trans. Biomed. Eng., 59, 8, 2302-2311, 2012
[65] Vu, T. D.T.; Kohler, S.; Merla, C.; Arnaud-Cormos, D.; Leveque, P., FDTD-based microdosimetry for high-intensity nanosecond pulsed electric fields (nsPEFs) application, (2012 IEEE/MTT-S International Microwave Symposium Digest, 2012, IEEE), 1-3
[66] Salimi, E.; Bridges, G.; Thomson, D., The effect of dielectric relaxation in nanosecond pulse electroporation of biological cells, (2010 14th International Symposium on Antenna Technology and Applied Electromagnetics & the American Electromagnetics Conference, 2010, IEEE), 1-4
[67] Vu, T. D.T., Contribution à la modélisation du comportement électromagnétique de milieux biologiques exposés à des impulsions de champ électrique nanosecondes, 2012, Ph.D. thesis, Limoges
[68] Böttcher, C.; Van Belle, O.; Bordewijk, P.; Rip, A.; Yue, D. D., Theory of electric polarization, J. Electrochem. Soc., 121, 6, 211C, 1974
[69] Gabriel, S.; Lau, R.; Gabriel, C., The dielectric properties of biological tissues: III. Parametric models for the dielectric spectrum of tissues, Phys. Med. Biol., 41, 11, 2271, 1996
[70] Guo, F.; Qian, K.; Deng, H.; Li, X., Multiphysics analysis of nsPEF induced electrodeformation in a dispersive cell model, Appl. Phys. Lett., 118, 8, 2021
[71] Ding, L.; Fang, Z.; Moser, M. A.; Zhang, W.; Zhang, B., A single-cell electroporation model for quantitatively estimating the pore area ratio by high-frequency irreversible electroporation, Appl. Sci., 13, 3, 1808, 2023
[72] Neu, J. C.; Krassowska, W., Asymptotic model of electroporation, Phys. Rev. E, 59, 3, 3471, 1999
[73] Pucihar, G.; Miklavcic, D.; Kotnik, T., A time-dependent numerical model of transmembrane voltage inducement and electroporation of irregularly shaped cells, IEEE Trans. Biomed. Eng., 56, 5, 1491-1501, 2009
[74] Joshi, R. P.; Hu, Q.; Schoenbach, K. H., Modeling studies of cell response to ultrashort, high-intensity electric fields-implications for intracellular manipulation, IEEE Trans. Plasma Sci., 32, 4, 1677-1686, 2004
[75] Guo, F.; Qian, K.; Zhang, L.; Deng, H.; Li, X.; Zhou, J.; Wang, J., Anisotropic conductivity for single-cell electroporation simulation with tangentially dispersive membrane, Electrochim. Acta, 385, Article 138426 pp., 2021
[76] Kumar, M.; Kumar, S.; Chakrabartty, S.; Poulose, A.; Mostafa, H.; Goyal, B., Dispersive modeling of normal and cancerous cervical cell responses to nanosecond electric fields in reversible electroporation using a drift-step rectifier diode generator, Micromachines, 14, 12, 2136, 2023
[77] Guo, F.; Nie, X.; Hong, J.; Zhang, Y.; Sun, J.; Zhang, Y., Influence of Joule heating during single-cell electroporation simulation under IRE and H-FIRE pulses, Mater. Today Commun., 36, Article 106853 pp., 2023
[78] Kumar, M.; Mishra, A., Multiphysics analysis of reversible electroporation and electrodeformation of cervical cells using a nanosecond pulse generator, IEEE Trans. Plasma Sci., 51, 2, 534-543, 2023
[79] Mistani, P.; Guittet, A.; Poignard, C.; Gibou, F., A parallel Voronoi-based approach for mesoscale simulations of cell aggregate electropermeabilization, J. Comput. Phys., 380, 48-64, 2019 · Zbl 1451.76078
[80] Poignard, C., A few advances in biological modeling and asymptotic analysis, 2014, Universite de Bordeaux, Ph.D. thesis
[81] Calhoun, D. A.; Helzel, C., A finite volume method for solving parabolic equations on logically cartesian curved surface meshes, SIAM J. Sci. Comput., 31, 6, 4066-4099, 2010 · Zbl 1208.65136
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.