相关论文: A Nonlocal size modified Poisson-Boltzmann Model a…

We present a soft-potential-enhanced Poisson-Boltzmann (SPB) theory to efficiently capture ion distributions and electrostatic potential around rodlike charged macromolecules. The SPB model is calibrated with a coarse-grained particle-based…

In this work, we introduce an inverse averaging finite element method (IAFEM) for solving the size-modified Poisson-Nernst-Planck (SMPNP) equations. Comparing with the classical Poisson-Nernst-Planck (PNP) equations, the SMPNP equations add…

In computational biochemistry and biophysics, understanding the role of electrostatic interactions is crucial for elucidating the structure, dynamics, and function of biomolecules. The Poisson-Boltzmann (PB) equation is a foundational tool…

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…

This work investigates the convergence of a domain decomposition method for the Poisson-Boltzmann model that can be formulated as an interior-exterior transmission problem. To study its convergence, we introduce an interior-exterior…

We consider in this paper random batch interacting particle methods for solving the Poisson-Nernst-Planck (PNP) equations, and thus the Poisson-Boltzmann (PB) equation as the equilibrium, in the external unbounded domain. To justify the…

We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent generalizing the point-like Dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (J. Phys. Chem 100, 2612 (1996)) and…

Biomolecular electrostatics is key in protein function and the chemical processes affecting it. Implicit-solvent models via the Poisson-Boltzmann (PB) equation provide insights with less computational cost than atomistic models, making…

The non-linear Poisson-Boltzmann equation for a circular, uniformly charged platelet, confined together with co- and counter-ions to a cylindrical cell, is solved semi-analytically by transforming it into an integral equation and solving…

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…

Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…

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…

In numerical simulations of many charged systems at the micro/nano scale, a common theme is the repeated solution of the Poisson-Boltzmann equation. This task proves challenging, if not entirely infeasible, largely due to the nonlinearity…

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities.…

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 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.…

Physics-informed neural networks (PINN) is a machine learning (ML)-based method to solve partial differential equations that has gained great popularity due to the fast development of ML libraries in the last few years. The…

We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters…

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…

We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as…