Understanding Molecular Simulation
Understanding Molecular Simulation
Introduction to Numerical Continuation Methods
Introduction to Numerical Continuation Methods
Variational Analysis in Sobolev and BV Spaces: Applications to PDEs and Optimization (Mps-Siam Series on Optimization 6)
The Finite Element Approximation of the Nonlinear Poisson-Boltzmann Equation
SIAM Journal on Numerical Analysis
Goal-Oriented Adaptivity and Multilevel Preconditioning for the Poisson-Boltzmann Equation
Journal of Scientific Computing
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The inclusion of steric effects is important when determining the electrostatic potential near a solute surface. We consider a modified form of the Poisson-Boltzmann equation, often called the Poisson-Bikerman equation, in order to model these effects. The modifications lead to bounded ionic concentration profiles and are consistent with the Poisson-Boltzmann equation in the limit of zero-size ions. Moreover, the modified equation fits well into existing finite element frameworks for the Poisson-Boltzmann equation. In this paper, we advocate a wider use of the modified equation and establish well-posedness of the weak problem along with convergence of an associated finite element formulation. We also examine several practical considerations such as conditioning of the linearized form of the nonlinear modified Poisson-Boltzmann equation, implications in numerical evaluation of the modified form, and utility of the modified equation in the context of the classical Poisson-Boltzmann equation.