Related papers: An implicit boundary integral method for computing…
In this paper, we develop a domain decomposition method for the nonlinear Poisson-Boltzmann equation based on a solvent-excluded surface widely used in computational chemistry. The model relies on a nonlinear equation defined in…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution…
We present an extension to the Poisson-Boltzmann model where the dipolar features of solvent molecules are taken explicitly into account. The formulation is derived at mean-field level and can be extended to any order in a systematic…
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory…
This work proposes a fast iterative method for local steric Poisson--Boltzmann (PB) theories, in which the electrostatic potential is governed by the Poisson's equation and ionic concentrations satisfy equilibrium conditions. To present the…
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…
A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104},…
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…
Several different approaches are proposed for solving fully implicit discretizations of a simplified Boltzmann-Poisson system with a linear relaxation-type collision kernel. This system models the evolution of free electrons in…
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In this paper, we introduce a new high-order…
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 present a GPU-accelerated direct-sum 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…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
The multipole-expansion (MPE) model is an implicit solvation model used to efficiently incorporate solvent effects in quantum chemistry. Even within the recent direct approach, the multipole basis used in MPE to express the dielectric…
We introduce a method-of-lines formulation of the closest point method, a numerical technique for solving partial differential equations (PDEs) defined on surfaces. This is an embedding method, which uses an implicit representation of the…
This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the units typically used to contour/visualize isopotential…
Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large…
In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic…