Related papers: Reduced basis method for the nonlinear Poisson-Bol…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong…
In this paper, we apply the range-separated (RS) tensor format [6] for the construction of new regularization scheme for the Poisson-Boltzmann equation (PBE) describing the electrostatic potential in biomolecules. In our approach, we use…
In numerical simulations of many charged systems at the micro/nano scale, a common theme is the repeated solution of the Poisson-Boltzmann equation. This task proves challenging, if not entirely infeasible, largely due to the nonlinearity…
The nonlinear Poisson-Boltzmann equation (NPBE) is an elliptic partial differential equation used in applications such as protein interactions and biophysical chemistry (among many others). It describes the nonlinear electrostatic potential…
We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a…
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…
In this paper, we propose a certified reduced basis (RB) method for quasilinear elliptic problems together with its application to nonlinear magnetostatics equations, where the later model permanent magnet synchronous motors (PMSM). The…
We consider a class of nonlinear elliptic problems associated with models in biophysics, which are described by the Poisson-Boltzmann equation (PBE). We prove mathematical correctness of the problem, study a suitable class of…
The Poisson-Boltzmann equation (PBE) models the electrostatic interactions of charged bodies such as molecules and proteins in an electrolyte solvent. The PBE is a challenging equation to solve numerically due to the presence of…
Physics-informed neural networks (PINN) is a machine learning (ML)-based method to solve partial differential equations that has gained great popularity due to the fast development of ML libraries in the last few years. The…
The Poisson-Boltzmann equation is widely used to model molecular electrostatics; however, it is usually solved in linearised form because the sinh nonlinearity is challenging, limiting its applicability in highly charged systems such as…
The electrostatic potential in the neighborhood of a biomolecule can be computed thanks to the non-linear divergence-form elliptic Poisson-Boltzmann PDE. Dedicated Monte-Carlo methods have been developed to solve its linearized version (see…
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…
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…
The task of repeatedly solving parametrized partial differential equations (pPDEs) in, e.g. optimization or interactive applications, makes it imperative to design highly efficient and equally accurate surrogate models. The reduced basis…
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 (PBE) is a relevant partial differential equation commonly used in biophysical applications to estimate the electrostatic energy of biomolecular systems immersed in electrolytic solutions. A conventional mean…
The Reduced Basis Method (RBM) is a rigorous model reduction approach for solving parametrized partial differential equations. It identifies a low-dimensional subspace for approximation of the parametric solution manifold that is embedded…
The radiative transfer equation (RTE) is a fundamental mathematical model to describe physical phenomena involving the propagation of radiation and its interactions with the host medium. Deterministic methods can produce accurate solutions…