Related papers: PB-AM: An Open-Source, Fully Analytical Linear Poi…
The Poisson-Boltzmann (PB) equation provides a mean-field theory of electrolyte solutions at interfaces and in confinement, describing how ions reorganize close to charged surfaces to form the so-called electrical double layer (EDL), with…
Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics which has been applied to numerous problems of physical chemistry and biophysics. Its essential limitations are the neglect of correlation effects and of…
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…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
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…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
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…
We present an analytical many-body formalism for systems of spherical particles carrying arbitrary free charge distributions and interacting in a polarizable electrolyte solution, that we model within the linearized Poisson--Boltzmann…
We derive the partial differential equation (PDE) to which the pseudo-potential lattice Boltzmann method (P-LBM) converges under diffusive scaling, providing a rigorous basis for its consistency analysis. By establishing a direct link…
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…
In this paper, we propose a fast multipole method (FMM) for 3-D linearized Poisson-Boltzmann (PB) equation in layered media. The main framework of the algorithm is analogous to the FMM for Helmholtz and Laplace equation in layered media…
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…
We present BO-PBK (BO-Product-Bi-Kappa), a new solver for kinetic dispersion relations of obliquely propagating waves in magnetized plasmas with complex velocity distributions. It reformulates the linearized Vlasov-Maxwell system into a…
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
We study the geometric particle-in-cell methods for an electrostatic hybrid plasma model. In this model, ions are described by the fully kinetic equations, electron density is determined by the Boltzmann relation, and space-charge effects…
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…
In this paper, a domain decomposition method for the Poisson-Boltzmann (PB) solvation model that is widely used in computational chemistry is proposed. This method, called ddLPB for short, solves the linear Poisson-Boltzmann (LPB) equation…
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…
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.…
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…