Related papers: Reduced basis method for the nonlinear Poisson-Bol…
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 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…
Semi-linear elliptic Partial Differential Equations (PDEs) such as the non-linear Poisson Boltzmann Equation (nPBE) is highly relevant for non-linear electrostatics in computational biology and chemistry. It is of particular importance for…
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…
In recent years, reduced basis methods (RBMs) have been adapted to the many-body eigenvalue problem and they have been used, largely in nuclear physics, as fast emulators able to bypass expensive direct computations while still providing…
The Poisson-Boltzmann (PB) model is a widely used implicit solvent model in protein simulations. Although variants, such as the size modified PB and nonlocal modified PB models, have been developed to account for ionic size effects and…
This work investigates a two-stage method for constructing projection-based reduced-order models (ROMs) of parameterized partial differential equations (PDEs). Based on established tensorial ROM methodology, the proposed approach reduces…
The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an…
In this paper, reduced-order models (ROMs) are constructed for the Ablowitz-Ladik equation (ALE), an integrable semi-discretization of the nonlinear Schr\"odinger equation (NLSE) with and without damping. Both ALEs are non-canonical…
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…
We present a class of reduced basis (RB) methods for the iterative solution of parametrized symmetric positive-definite (SPD) linear systems. The essential ingredients are a Galerkin projection of the underlying parametrized system onto a…
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.…
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 need for multiple interactive, real-time simulations using different parameter values has driven the design of fast numerical algorithms with certifiable accuracies. The reduced basis method (RBM) presents itself as such an option. RBM…
In this manuscript, we introduce the tensor-train reduced basis method, a novel projection-based reduced-order model designed for the efficient solution of parameterized partial differential equations. While reduced-order models are widely…
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…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
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…
We consider the problem of empirical Bayes estimation for (multivariate) Poisson means. Existing solutions that have been shown theoretically optimal for minimizing the regret (excess risk over the Bayesian oracle that knows the prior) have…