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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… (More)

The Poisson-Boltzmann equation is an important tool in modeling solvent in biomolecular systems. In this article, we focus on numerical approximations to the electrostatic potential expressed in the regularized linear Poisson-Boltzmann equation. We expose the flux directly through a first-order system form of the equation. Using this formulation, we propose… (More)

- Jehanzeb Hameed Chaudhry, Jeffrey Comer, Aleksei Aksimentiev, Luke N Olson, Bo Li, J H Chaudhry +1 other
- 2013

The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular, near highly charged surfaces. A modified form of the Poisson-Nernst-Planck equations accounts for steric effects and… (More)

The finite element methodology has become a standard framework for approximating the solution to the Poisson-Boltzmann equation in many biological applications. In this article, we examine the numerical efficacy of least-squares finite element methods for the linearized form of the equations. In particular, we highlight the utility of a first-order form,… (More)

- Jehanzeb Hameed Chaudhry, Stephen D Bond, Luke N Olson, J H Chaudhry, Sdbond@sandia Gov, S D Bond +1 other
- 2011

The finite element methodology has become a standard framework for approximating the solution to the Poisson–Boltzmann equation in many biological applications. In this article, we examine the numerical efficacy of least-squares finite element methods for the linearized form of the equations. In particular, we highlight the utility of a first-order form,… (More)

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