Energy and implicit discretization of the Fokker-Planck and Keller-Segel type equations

DOI10.3934/NHM.2019002zbMATH Open1423.35177arXiv1803.10629OpenAlexW2794730880WikidataQ96790744 ScholiaQ96790744MaRDI QIDQ2328339FDOQ2328339

Authors: Yanyan Li 

Publication date: 10 October 2019

Published in: Networks and Heterogeneous Media (Search for Journal in Brave)

Abstract: The parabolic-elliptic Keller-Segel equation with sensitivity saturation, because of its pattern formation ability, is a challenge for numerical simulations. We provide two finite-volume schemes whose goals are to preserve, at the discrete level, the fundamental properties of the solutions, namely energy dissipation, steady states, positivity and conservation of total mass. These requirements happen to be critical when it comes to distinguishing between discrete steady states, Turing unstable transient states, numerical artifacts or approximate steady states as obtained by a simple upwind approach. These schemes are obtained either by following closely the gradient flow structure or by a proper exponential rewriting inspired by the Scharfetter-Gummel discretization. An interesting feature is that upwind is also necessary for all the expected properties to be preserved at the semi-discrete level. These schemes are extended to the fully discrete level and this leads us to tune precisely the terms according to explicit or implicit discretizations. Using some appropriate monotony properties (reminiscent of the maximum principle), we prove well-posedness for the scheme as well as all the other requirements. Numerical implementations and simulations illustrate the respective advantages of the three methods we compare.

Full work available at URL: https://arxiv.org/abs/1803.10629

Recommendations

• Unconditionally bound preserving and energy dissipative schemes for a class of Keller-Segel equations
• An unconditionally energy stable and positive upwind DG scheme for the Keller-Segel model
• Finite volume methods for a Keller-Segel system: discrete energy, error estimates and numerical blow-up analysis
• Conservative numerical schemes for the Keller-Segel system and numerical results
• Bound/positivity preserving and energy stable scalar auxiliary variable schemes for dissipative systems: applications to Keller-Segel and Poisson-Nernst-Planck equations

zbMATH Keywords

finite volume methodgradient flowKeller-Segel systemmathematical biologynumerical methodsenergy dissipationScharfetter-Gummel methodupwind schemes

Mathematics Subject Classification ID

Nonlinear parabolic equations (35K55) Fokker-Planck equations (35Q84) PDEs in connection with biology, chemistry and other natural sciences (35Q92) Finite volume methods for initial value and initial-boundary value problems involving PDEs (65M08) Cell movement (chemotaxis, etc.) (92C17) Numerical solution of discretized equations for initial value and initial-boundary value problems involving PDEs (65M22)

Cites Work

• Mathematical biology. Vol. 1: An introduction.
• Transport equations in biology.
• Two-dimensional Keller-Segel model: Optimal critical mass and qualitative properties of the solutions
• Blow-up in multidimensional aggregation equations with mildly singular interaction kernels
• Convergence of the Mass-Transport Steepest Descent Scheme for the Subcritical Patlak–Keller–Segel Model
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Initiation of slime mold aggregation viewed as an instability
• A user's guide to PDE models for chemotaxis
• Metastability in chemotaxis models
• Finite volume methods
• A finite-volume method for nonlinear nonlocal equations with a gradient flow structure
• Notes on finite difference schemes to a parabolic-elliptic system modelling chemotaxis
• A finite volume scheme for nonlinear degenerate parabolic equations
• A continuum approach to modelling cell-cell adhesion
• A class of asymptotic-preserving schemes for the Fokker-Planck-Landau equation
• Global existence for chemotaxis with finite sampling radius
• Quasilinear non-uniformly parabolic-elliptic system modelling chemotaxis with volume filling effect. Existence and uniqueness of global-in-time solutions
• Zoology of a nonlocal cross-diffusion model for two species
• Positivity-preserving and asymptotic preserving method for 2D Keller-Segal equations
• Particle interactions mediated by dynamical networks: assessment of macroscopic descriptions
• Stationary solutions of Keller-Segel-type crowd motion and herding models: multiplicity and dynamical stability
• A hybrid mass transport finite element method for Keller-Segel type systems

Cited In (20)

• Some examples of kinetic schemes whose diffusion limit is Il'in's exponential-fitting
• A nonnegativity preserving scheme for the relaxed Cahn-Hilliard equation with single-well potential and degenerate mobility
• Positivity-preserving and asymptotic preserving method for 2D Keller-Segal equations
• Effect of a membrane on diffusion-driven Turing instability
• Finite difference approximation with ADI scheme for two-dimensional Keller-Segel equations
• Treatment-induced shrinking of tumour aggregates: a nonlinear volume-filling chemotactic approach
• A convergent entropy diminishing finite volume scheme for a cross-diffusion system
• Unconditionally bound preserving and energy dissipative schemes for a class of Keller-Segel equations
• Aggregation-diffusion equations: dynamics, asymptotics, and singular limits
• A variational finite volume scheme for Wasserstein gradient flows
• Bound-Preserving Finite-Volume Schemes for Systems of Continuity Equations with Saturation
• Lagrangian schemes for Wasserstein gradient flows
• Bound/positivity preserving and energy stable scalar auxiliary variable schemes for dissipative systems: applications to Keller-Segel and Poisson-Nernst-Planck equations
• An asymptotic preserving scheme for a tumor growth model of porous medium type
• Diffusive limit of a two-dimensional well-balanced approximation to a kinetic model of chemotaxis
• A general cell-fluid Navier-Stokes model with inclusion of chemotaxis
• A unified structure preserving scheme for a multispecies model with a gradient flow structure and nonlocal interactions via singular kernels
• Bound/positivity preserving SAV schemes for the Patlak-Keller-Segel-Navier-Stokes system
• Numerical study of Bose-Einstein condensation in the Kaniadakis-Quarati model for bosons
• A coupled 3D-1D multiscale Keller-Segel model of chemotaxis and its application to cancer invasion

This page was built for publication: Energy and implicit discretization of the Fokker-Planck and Keller-Segel type equations

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2328339)