Numerical complete solution for random genetic drift by energetic variational approach

DOI10.1051/M2AN/2018058MaRDI QIDQ5230145zbMATH OpenOpenAlexWikidataFDO

Authors Chenghua Duan, Chun Liu, C. Wang, Xingye Yue

Publication date 20 August 2019

Published in ESAIM: Mathematical Modelling and Numerical Analysis (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1803.09436

zbMATH Keywords

convex splitting schemeDirac delta singularityenergetic variational approachfixation phenomenonrandom genetic driftWright-Fisher model

Mathematics Subject Classification ID

Degenerate parabolic equations (35K65) PDEs in connection with biology, chemistry and other natural sciences (35Q92) Numerical methods for partial differential equations, initial value and time-dependent initial-boundary value problems (65M99) Genetics and epigenetics (92D10)

Abstract: In this paper, we focus on numerical solutions for random genetic drift problem, which is governed by a degenerated convection-dominated parabolic equation. Due to the fixation phenomenon of genes, Dirac delta singularities will develop at boundary points as time evolves. Based on an energetic variational approach (EnVarA), a balance between the maximal dissipation principle (MDP) and least action principle (LAP), we obtain the trajectory equation. In turn, a numerical scheme is proposed using a convex splitting technique, with the unique solvability (on a convex set) and the energy decay property (in time) justified at a theoretical level. Numerical examples are presented for cases of pure drift and drift with semi-selection. The remarkable advantage of this method is its ability to catch the Dirac delta singularity close to machine precision over any equidistant grid.

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Cited in

(14)

• A positive and energy stable numerical scheme for the Poisson-Nernst-Planck-Cahn-Hilliard equations with steric interactions
• Numerical methods for porous medium equation by an energetic variational approach
• Behavior of different numerical schemes for random genetic drift
• Neutral competition in a deterministically changing environment: revisiting continuum approaches
• An optimal mass transport method for random genetic drift
• Structure-preserving numerical methods for nonlinear Fokker-Planck equations with nonlocal interactions by an energetic variational approach
• Numerical method for multi-alleles genetic drift problem
• EnVarA-FEM for the flux-limited porous medium equation
• Hidden Dissipation and Convexity for Kimura Equations
• Convergence analysis of structure‐preserving numerical methods for nonlinear Fokker–Planck equations with nonlocal interactions
• On a continuum model for random genetic drift: a dynamic boundary condition approach
• Integral formulation of the Kimura equation for random genetic drift
• A structure-preserving numerical method for a radially symmetric solution of porous medium equation
• On Lagrangian schemes for porous medium type generalized diffusion equations: a discrete energetic variational approach

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