相关论文: A Cartesian FMM-accelerated Galerkin boundary inte…
In this paper, we present a GPU-accelerated direct-sum 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…
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…
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…
The Poisson-Boltzmann equation offers an efficient way to study electrostatics in molecular settings. Its numerical solution with the boundary element method is widely used, as the complicated molecular surface is accurately represented by…
We introduce a fast Fourier spectral method for the multi-species Boltzmann collision operator. The method retains the riveting properties of the single-species fast spectral method (Gamba et al. SIAM J. Sci. Comput., 39 pp. B658--B674…
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…
Implicit-solvent models are widely used to study the electrostatics in dissolved biomolecules, which are parameterized using force fields. Standard force fields treat the charge distribution with point charges, however, other force fields…
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 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 high-order hybridizable discontinuous Galerkin (HDG) method combining with an implicit iterative scheme is used to find the steady-state solution of the Boltzmann equation with full collision integral on two-dimensional triangular…
We present a spectral Petrov-Galerkin method for the Boltzmann collision operator. We expand the density distribution $f$ to high order orthogonal polynomials multiplied by a Maxwellian. By that choice, we can approximate on the whole…
Numerical approximation of the Boltzmann equation presents a challenging problem due to its high-dimensional, nonlinear, and nonlocal collision operator. Among the deterministic methods, the Fourier-Galerkin spectral method stands out for…
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 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…
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.…
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…
In this paper we perform, by means of Discontinuous Galerkin (DG) Finite Element Method (FEM) based numerical solvers for Boltzmann-Poisson (BP) semiclassical models of hot electronic transport in semiconductors, a numerical study of…
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 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…
In this paper we deal with the extension of the Fast Kinetic Scheme (FKS) [J. Comput. Phys., Vol. 255, 2013, pp 680-698] originally constructed for solving the BGK equation, to the more challenging case of the Boltzmann equation. The scheme…