Related papers: PB-AM: An Open-Source, Fully Analytical Linear Poi…
We investigate the global well-posedness of the ionic Vlasov-Poisson-Boltzmann system which models the evolution of dilute collisional ions. This system distinguishes the electronic Vlasov-Poisson-Boltzmann system via an additional…
We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer [EPL 111, 28002 (2015)]. We formulate a modified Poisson-Boltzmann theory,…
We develop an algorithm for bosonic path integral molecular dynamics (PIMD) simulations with periodic boundary conditions (PBC) that scales quadratically with the number of particles. Path integral methods are a powerful tool to simulate…
A hybrid lattice Boltzmann method (LBM) for binary mixtures based on the free-energy approach is proposed. Non-ideal terms of the pressure tensor are included as a body force in the LBM kinetic equations, used to simulate the continuity and…
The linear Boltzmann model for proton beams is a six-dimensional partial differential equation (PDE). We propose a deterministic solver for the linear Boltzmann model based on scattering decomposition and depth-splitting methods. The main…
Despite recent numerical evidence, one of the fundamental theoretical mysteries of polaritonic chemistry is how and if collective strong coupling can induce local changes of the electronic structure to modify chemical properties. Here we…
When ions are crowded, the effect of steric repulsion between ions (which can produce oscillations in charge density profiles) becomes significant and the conventional Poisson-Boltzmann (PB) equation should be modified. Several modified PB…
A boson sampler implements a restricted model of quantum computing. It is defined by the ability to sample from the distribution resulting from the interference of identical bosons propagating according to programmable, non-interacting…
In simulating charged systems, it is often useful to treat some ionic components of the system at the mean-field level and solve the Poisson-Boltzmann (PB) equation to get their respective density profiles. The numerically intensive task of…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
In this paper we present a model based on dynamics of the electrons in the plasma using a simplified Boltzmann equation coupled with a Poisson equation. The motivation arose to simulate active plasma resonance spectroscopy which is used for…
Millimeter wave (mmWave) signals are useful for simultaneous localization and mapping (SLAM), due to their inherent geometric connection to the propagation environment and the propagation channel. To solve the SLAM problem, existing…
In this work a dynamical system approach is taken to systematically investigate the one-dimensional classical Poisson-Boltzmann (PB) equation with various boundary conditions. This framework, particularly, the phase space portrait, has a…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
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 paper, we solve the linearized Poisson-Boltzmann equation, used to model the electric potential of macromolecules in a solvent. We derive a corrected trapezoidal rule with improved accuracy for a boundary integral formulation of the…
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, $\Delta…
We present an exact many-body framework for electrostatic interactions among $N$ arbitrarily charged spheres in an electrolyte, modeled by the linearized Poisson--Boltzmann equation. Building on a spectral analysis of nonstandard…
This paper presents an improved immersed moving boundary model (IBM) for solving complex fluid-particle interactions in a coupled lattice Boltzmann method (LBM) and an adhesive discrete element method (DEM), using the "partially saturated…
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…