Related papers: Fast Solution of the Linearized Poisson-Boltzmann …
The Reduced Basis Method (RBM) is a model reduction technique used to solve parametric PDEs that relies upon a basis set of solutions to the PDE at specific parameter values. To generate this reduced basis, the set of a small number of…
This paper presents a numerical method for variable coefficient elliptic PDEs with mostly smooth solutions on two dimensional domains. The PDE is discretized via a multi-domain spectral collocation method of high local order (order 30 and…
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…
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…
Efficient and stable solution of partial differential equations (PDEs) is central to scientific and engineering applications, yet existing numerical solvers rely heavily on matrix based discretizations, while learning based methods require…
Partial differential equations (PDEs) are widely used for modeling various physical phenomena. These equations often depend on certain parameters, necessitating either the identification of optimal parameters or the solution of the…
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…
The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to…
The reduced basis method is a powerful model reduction technique designed to speed up the computation of multiple numerical solutions of parametrized partial differential equations. We consider a quantity of interest, which is a linear…
This paper is interested in developing reduced order models (ROMs) for repeated simulation of fractional elliptic partial differential equations (PDEs) for multiple values of the parameters (e.g., diffusion coefficients or fractional…
In this paper, we present a parallel higher-order boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…
This work proposes a fast iterative method for local steric Poisson--Boltzmann (PB) theories, in which the electrostatic potential is governed by the Poisson's equation and ionic concentrations satisfy equilibrium conditions. To present the…
One of the major challenges of coupled problems is to manage nonconforming meshes at the interface between two models and/or domains, due to different numerical schemes or domains discretizations employed. Moreover, very often complex…
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…
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…
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 present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities.…
The onerous task of repeatedly resolving certain parametrized partial differential equations (pPDEs) in, e.g. the optimization context, makes it imperative to design vastly more efficient numerical solvers without sacrificing any accuracy.…
We prove the existence and uniqueness of the complexified Nonlinear Poisson-Boltzmann Equation (nPBE) in a bounded domain in $\mathbb{R}^3$. The nPBE is a model equation in nonlinear electrostatics. The standard convex optimization argument…
High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on…