Related papers: Fast Solution of the Linearized Poisson-Boltzmann …
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…
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 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…
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…
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…
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In this paper, we introduce a new high-order…
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…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
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…
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…
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…
Fractional Laplace equations are becoming important tools for mathematical modeling and prediction. Recent years have shown much progress in developing accurate and robust algorithms to numerically solve such problems, yet most solvers for…
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…
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 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 this paper, a nonsmooth semilinear parabolic partial differential equation (PDE) is considered. For a reduced basis (RB) approach, a space-time formulation is used to develop a certified a-posteriori error estimator. This error estimator…
This paper presents a systematic methodology for the discretization and reduction of a class of one-dimensional Partial Differential Equations (PDEs) with inputs and outputs collocated at the spatial boundaries. The class of system that we…
Scientific and engineering problems often involve parametric partial differential equations (PDEs), such as uncertainty quantification, optimizations, and inverse problems. However, solving these PDEs repeatedly can be prohibitively…
We present a reduced basis (RB) method for parametrized linear elliptic partial differential equations (PDEs) in a least-squares finite element framework. A rigorous and reliable error estimate is developed, and is shown to bound the error…
Traditional reduced order modeling techniques such as the reduced basis (RB) method (relying, e.g., on proper orthogonal decomposition (POD)) suffer from severe limitations when dealing with nonlinear time-dependent parametrized PDEs,…