Related papers: Solution decomposition for the nonlinear Poisson-B…
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
The classical Poisson-Boltzmann (PB) theory of electrolytes assumes a dilute solution of point charges with mean-field electrostatic forces. Even for very dilute solutions, however, it predicts absurdly large ion concentrations (exceeding…
Pressure Poisson equation (PPE) reformulations of the incompressible Navier-Stokes equations (NSE) replace the incompressibility constraint by a Poisson equation for the pressure and a suitable choice of boundary conditions. This yields a…
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet for fluid problems it only achieves first-order spatial accuracy near embedded boundaries for the velocity field and…
The interaction of particles in an electrolytic medium can be calculated by solving the Poisson equation inside the solutes and the linearized Poisson--Boltzmann equation in the solvent, with suitable boundary conditions at the interfaces.…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
We perform a linearization of the Poisson-Boltzmann (PB) density functional for spherical Wigner-Seitz cells that yields Debye-H\"uckel-like equations agreeing asymptotically with the PB results in the weak-coupling (high-temperature)…
We present a new solver for coupled nonlinear elliptic partial differential equations (PDEs). The solver is based on pseudo-spectral collocation with domain decomposition and can handle one- to three-dimensional problems. It has three…
This work unifies pseudo-time and inexact regularization techniques for nonmonotone classes of partial differential equations, into a regularized pseudo-time framework. Convergence of the residual at the predicted rate is investigated…
Consider the Boltzmann equation in a general non-convex domain with the diffuse boundary condition. We establish optimal BV estimates for such solutions. Our method consists of a new $W^{1,1}-$trace estimate for the diffuse boundary…
A three-dimensional (3D) Poisson solver with longitudinal periodic and transverse open boundary conditions can have important applications in beam physics of particle accelerators. In this paper, we present a fast efficient method to solve…
We study a system of interacting diffusions that models chemotaxis of biological cells or microorganisms (referred to as particles) in a chemical field that is dynamically modified through the collective contributions from the particles.…
This work is concerned with the quantification of the epistemic uncertainties induced the discretization of partial differential equations. Following the paradigm of probabilistic numerics, we quantify this uncertainty probabilistically.…
High-dimensional partial-differential equations (PDEs) arise in a number of fields of science and engineering, where they are used to describe the evolution of joint probability functions. Their examples include the Boltzmann and…
We introduce and analyse a continuum model for an interacting particle system of Vicsek type. The model is given by a non-linear kinetic partial differential equation (PDE) describing the time-evolution of the density $f_t$, in the single…
Reciprocal space methods for solving Poisson's equation for finite charge distributions are investigated. Improvements to previous proposals are presented, and their performance is compared in the context of a real-space density functional…
Realistic nucleon-nucleon (NN) potentials are generally not in separable form, but there is a way to convert them into separable potentials, called the generalized separable expansion (GSE). When the separable potential is substituted into…
The Poisson-Nernst-Planck (PNP) diffusional model for the immittance or impedance spectroscopy response of an electrolytic cell in a finite-length situation is extended to a general framework. In this new formalism, the bulk behavior of the…
Robust physics discovery is of great interest for many scientific and engineering fields. Inspired by the principle that a representative model is the one simplest possible, a new model selection criteria considering both model's Parsimony…
Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is…