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We study the boundary layer solution to singular perturbation problems involving Poisson-Boltzmann (PB) type equations with a small parameter $\epsilon$ in general bounded smooth domains (including multiply connected domains) under the…
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…
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…
We present a new multi-fluid, multi-temperature plasma solver with adaptive Cartesian mesh (ACM) based on a full-Newton (non-linear, implicit) scheme for collisional low-temperature plasma. The particle transport is described using the…
We propose a field-theoretical approach based on the thermodynamic perturbation theory and within it derive a grand thermodynamic potential of the inhomogeneous ionic fluid as a functional of electrostatic potential for an arbitrary…
The Poisson-Boltzmann equation (PBE) is a fundamental implicit solvent continuum model for calculating the electrostatic potential of large ionic solvated biomolecules. However, its numerical solution encounters severe challenges arising…
The classical problem of two uniformly charged infinite planes in electrochemical equilibrium with an infinite monovalent salt reservoir is solved exactly at the mean-field nonlinear Poisson-Boltzmann (PB) level, including an explicit…
The Vlasov-Poisson system for ions is a kinetic equation for dilute, unmagnetised plasma. It describes the evolution of the ions in a plasma under the assumption that the electrons are thermalized. Consequently, the Poisson coupling for the…
We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA and other polarizable QM/MM methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced…
Recently we have developed a robust, basis-space implementation of the iterated stockholder atoms (BS-ISA) approach for defining atoms in a molecule. This approach has been shown to yield rapidly convergent distributed multipole expansions…
A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is…
This paper provides a rigorous analysis of boundary element methods for the magnetic field integral equation on Lipschitz polyhedra. The magnetic field integral equation is widely used in practical applications to model electromagnetic…
Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting growing attention in biophysics. Meanwhile, leveraging the efficiency of…
In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the…
A one-dimensional harmonic oscillator in a box is used to introduce the oblique-basis concept. The method is extended to the nuclear shell model by combining traditional spherical states, which yield a diagonal representation of the usual…
A novel electromagnetic particle-in-cell algorithm has been developed for fully kinetic plasma simulations on unstructured (irregular) meshes in complex body-of-revolution geometries. The algorithm, implemented in the BORPIC++ code,…
The standard Poisson-Boltzmann model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult…
This article describes Monte-Carlo algorithms for charged systems using constrained updates for the electric field. The method is generalized to treat inhomogeneous dielectric media, electrolytes via the Poisson-Boltzmann equation and…
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…
The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge-charge interactions in solution may become…