相关论文: Poisson-Boltzmann based machine learning (PBML) mo…
The Poisson-Boltzmann equation is a widely used model to study the electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
The convergence of statistical learning and molecular physics is transforming our approach to modeling biomolecular systems. Physics-informed machine learning (PIML) offers a systematic framework that integrates data-driven inference with…
We develop a double mean-field theory for charged macrogels immersed in electrolyte solutions in the spirit of the cell model approach. We first demonstrate that the equilibrium sampling of a single explicit coarse-grained charged polymer…
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…
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,…
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…
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 Poisson-Boltzmann equation (PBE) is a relevant partial differential equation commonly used in biophysical applications to estimate the electrostatic energy of biomolecular systems immersed in electrolytic solutions. A conventional mean…
The molecular electrostatic potential (MEP) is a key quantity for describing and predicting intermolecular and ion-molecule interactions. Here, we assess the ability of machine-learning (ML) models to infer the MEP, based on the equivariant…
The Boltzmann equation, a fundamental equation in kinetic theory, serves as a bridge between microscopic particle dynamics and macroscopic continuum mechanics. However, deriving closed macroscopic moment systems from the Boltzmann equation…
This paper analyzes various schemes for the Euler-Poisson-Boltzmann (EPB) model of plasma physics. This model consists of the pressureless gas dynamics equations coupled with the Poisson equation and where the Boltzmann relation relates the…
Within the Poisson-Boltzmann (PB) framework useful for a wealth of charged soft matter problems, we work out the Coulombic grand potential of a long cylindrical charged polyion in a binary electrolyte solution of arbitrary valency and for…
A Poisson-Boltzmann approach is used to determine the double-layer integral and differential capacitances in a finite-length situation for an electrolytic cell. By means of simple analytical calculations, it is shown how these quantities…
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…
We present two successive mean-field approximations for describing the mechanical properties and the swelling equilibrium of polyelectrolyte gels in contact with a salt solution. The first mean-field approximation reduces the many-chain…
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…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
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…
We propose a Poisson-Bikerman (PBik) formula for calculating the differential capacitance (DC) of electrical double layers (EDLs) in aqueous electrolytes or ionic liquids. The PBik theory is a generalization of the classical…