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A widely used electrostatics model in the biomolecular modeling community, the nonlinear Poisson-Boltzmann equation, along with its finite element approximation, are analyzed in this paper. A regularized Poisson-Boltzmann equation is…
The interaction between charged bodies in an ionic solution is a general problem in colloid physics and becomes a central topic in the study of biological systems where the electrostatic interaction between proteins, nucleic acids,…
Mobile charge in an electrolytic solution can in principle be represented as the divergence of ionic polarization. After adding explicit solvent polarization a finite volume of electrolyte can then be treated as a composite non-uniform…
We study the Stokes--Poisson--Boltzmann equations with Dirichlet and Navier boundary conditions. The system consists of the incompressible Stokes equations coupled with a nonlinear Poisson--Boltzmann equation through electrostatic forcing…
The energy functional, the governing partial differential equation(s) (PDE), and the boundary conditions need to be consistent with each other in a modeling system. In electrolyte solution study, people usually use a free energy form of an…
In preparation to the exascale era, an alternative approach to calculate the electrostatic forces in Particle Mesh (PM) methods is proposed. While the traditional techniques are based on the calculation of the electrostatic potential by…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…
In this paper, we solve the linearized Poisson-Boltzmann equation, used to model the electric potential of macromolecules in a solvent. We derive a corrected trapezoidal rule with improved accuracy for a boundary integral formulation of the…
To accurately model the electron density and polarization, a polarizable multipole (PM) model using the AMOEBA force field has been introduced \cite{Ren:2003, Shi:2013} recently. In the AMOEBA force field, the traditional point atomic…
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, $\Delta…
This paper presents a grid-free simulation algorithm for the fully three-dimensional Vlasov--Poisson system for collisionless electron plasmas. We employ a standard particle method for the numerical approximation of the distribution…
We present a method that gives highly accurate electrostatic potentials for systems where we have periodic boundary conditions in two spatial directions but free boundary conditions in the third direction. These boundary conditions are…
A finite element methodology for large classes of variational boundary value problems is defined which involves discretizing two linear operators: (1) the differential operator defining the spatial boundary value problem; and (2) a Riesz…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
A unified framework to derive discrete time-marching schemes for coupling of immersed solid and elastic objects to the lattice Boltzmann method is presented. Based on operator splitting for the discrete Boltzmann equation, second-order…
The paper is concerned with the development of efficient and accurate solution procedures for the isogeometric boundary element method (BEM) when applied to problems that contain inclusions that have elastic properties different to the…
Recently proposed formulation of the Boundary Element Method for adhesive contacts has been generalized for contacts of functionally graded materials with and without adhesion. First, proceeding from the fundamental solution for single…
We present an efficient and accurate immersed boundary (IB) finite element (FE) solver for numerically solving incompressible Navier--Stokes equations. Particular emphasis is given to internal flows with complex geometries (blood flow in…
We present a fully analytical integration of the Maxwell stress tensor and derive exact relations for interparticle forces in systems of multiple dielectric spheres immersed in a polarizable ionic solvent, within the framework of the…
Poisson-Boltzmann theory is the cornerstone for soft matter electrostatics. We provide novel exact analytical solutions to this non-linear mean-field approach, for the diffuse layer of ions in the vicinity of a planar or a cylindrical…