Related papers: Reliable computer simulation methods for electrost…
We present an efficient quantum algorithm for beyond-Born-Oppenheimer molecular energy computations. Our approach combines the quantum full configuration interaction method with the nuclear orbital plus molecular orbital (NOMO) method. We…
Fully computable a posteriori error estimates in the energy norm are given for singularly perturbed semilinear reaction-diffusion equations posed in polygonal domains. Linear finite elements are considered on anisotropic triangulations. To…
This work presents a finite element method for a modified Poisson-Nernst-Planck/Navier-Stokes (PNP/NS) model under the mechanical equilibrium, developed for compressible electrolytes. Another key contribution of this work is the reduction…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong…
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…
A nonlinear Poisson--Boltzmann equation with transmission boundary conditions at the interface between two materials is investigated. The model describes the electrostatic potential generated by a vector of ion concentrations in a periodic…
In this article we study adaptive finite element methods (AFEM) with inexact solvers for a class of semilinear elliptic interface problems. We are particularly interested in nonlinear problems with discontinuous diffusion coefficients, such…
This paper is concerned with the computable error estimates for the eigenvalue problem which is solved by the general conforming finite element methods on the general meshes. Based on the computable error estimate, we can give an…
We derive computable error estimates for finite element approximations of linear elliptic partial differential equations (PDE) with rough stochastic coefficients. In this setting, the exact solutions contain high frequency content that…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…
As the particle count escalates, the computational demands of diverse simulation algorithms surge, paralleled by a marked enhancement in accuracy. The question arises whether this heightened precision asymptotically dwindles towards zero or…
In simulating charged systems, it is often useful to treat some ionic components of the system at the mean-field level and solve the Poisson-Boltzmann (PB) equation to get their respective density profiles. The numerically intensive task of…
The paper is concerned with guaranteed a posteriori error estimates for a class of evolutionary problems related to poroelastic media governed by the quasi-static linear Biot equations. The system is decoupled employing the fixed-stress…
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…
In this paper, we propose a computable error estimate of the Gross-Pitaevskii equation for ground state solution of Bose-Einstein condensates by general conforming finite element methods on general meshes. Based on the proposed error…
This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular…