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The modified Poisson-Boltzmann (MPB) equations are often used to describe equilibrium particle distribution of ionic systems. In this paper, we propose a fast algorithm to solve MPB equations with the self Green's function as the self…
Developing accurate solvers for the Poisson Boltzmann (PB) model is the first step to make the PB model suitable for implicit solvent simulation. Reducing the grid size influence on the performance of the solver benefits to increasing the…
A Green's function based solver for the modified Bessel equation has been developed with the primary motivation of solving the Poisson equation in cylindrical geometries. The method is implemented using a Discrete Hankel Transform and a…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
The Poisson-Boltzmann (PB) theory is widely used to depict ionic systems. As a mean-field theory, the PB theory neglects the correlation effect in the ionic atmosphere and leads to deviations from experimental results as the concentration…
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…
The electrostatic potential in the neighborhood of a biomolecule can be computed thanks to the non-linear divergence-form elliptic Poisson-Boltzmann PDE. Dedicated Monte-Carlo methods have been developed to solve its linearized version (see…
The Linearized Poisson--Boltzmann (LPB) equation is a popular and widely accepted model for accounting solvent effects in computational (bio-) chemistry. In the present article we derive the analytical forces of the…
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an…
In this paper, we present a parallel higher-order boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
This article presents a high-order accurate numerical method for the evaluation of singular volume integral operators, with attention focused on operators associated with the Poisson and Helmholtz equations in two dimensions. Following the…
The development of numerical methods capable of simulating realistic materials with strongly correlated electrons, with controllable errors, is a central challenge in quantum many-body physics. Here we describe how a hybrid between…
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…
Green's function plays a significant role in both theoretical analysis and numerical computing of partial differential equations (PDEs). However, in most cases, Green's function is difficult to compute. The troubles arise in the following…
In this work, we present an algorithm for the diagonalization of the Integration-by-Parts (IBP) equations. Diagonalized IBP equations are indispensable for reducing loop integrals with high numerator powers to master integrals and for…
A new fast multipole formulation for solving elliptic difference equations on unbounded domains and its parallel implementation are presented. These difference equations can arise directly in the description of physical systems, e.g.…
A linear algebraic method named the shifted conjugate-orthogonal-conjugate-gradient method is introduced for large-scale electronic structure calculation. The method gives an iterative solver algorithm of the Green's function and the…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
A new approximation method for inverting the Poisson's equation is presented for a continuously distributed and finite-sized source in an unbound domain. The advantage of this image multipole method arises from its ability to place the…