Related papers: Hierarchical Interpolative Factorization for Self …
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 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 magnon Hedin's equations are derived via the Schwinger functional derivative technique, and the resulting self-consistent Green's function method is used to calculate ground state spin patterns and magnetic structure factors for…
We present a data-driven approach to mathematically model physical systems whose governing partial differential equations are unknown, by learning their associated Green's function. The subject systems are observed by collecting…
Previous work in the literature has studied gravitational radiation in black-hole collisions at the speed of light. In particular, it had been proved that the perturbative field equations may all be reduced to equations in only two…
We have developed efficient numerical algorithms for solving 3D steady-state Poisson-Nernst-Planck (PNP) equations with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are…
We present an accurate and efficient method to calculate the gravitational potential of an isolated system in three-dimensional Cartesian and cylindrical coordinates subject to vacuum (open) boundary conditions. Our method consists of two…
In this manuscript, we develop an efficient algorithm to evaluate the azimuthal Fourier components of the Green's function for the Helmholtz equation in cylindrical coordinates. A computationally efficient algorithm for this modal Green's…
This paper presents a general high-order kernel regularization technique applicable to all four integral operators of Calder\'on calculus associated with linear elliptic PDEs in two and three spatial dimensions. Like previous density…
We present a fast algorithm that constructs a data-sparse approximation of matrices arising in the context of integral equation methods for elliptic partial differential equations. The new algorithm uses Green's representation formula in…
In this paper a method is presented for evaluating the convolution of the Green's function for the Laplace operator with a specified function $\rho(\vec x)$ at all grid points in a rectangular domain $\Omega \subset {\mathrm R}^{d}$ ($d =…
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…
In this article, we develop goal-oriented error indicators to drive adaptive refinement algorithms for the Poisson-Boltzmann equation. Empirical results for the solvation free energy linear functional demonstrate that goal-oriented…
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 popular, stable, robust and computationally inexpensive cubic spline interpolation algorithm is adopted and used for finite temperature Green's function calculations of realistic systems. We demonstrate that with appropriate…
We use a diagrammatic hopping expansion to calculate finite-temperature Green functions of the Bose-Hubbard model which describes bosons in an optical lattice. This technique allows for a summation of subsets of diagrams, so the divergence…
In this paper we propose new algorithm to reduce autocorrelation in Markov chain Monte-Carlo algorithms for euclidean field theories on the lattice. Our proposing algorithm is the Hybrid Monte-Carlo algorithm (HMC) with restricted Boltzmann…
A numerical method is developed for calculating the real time Green's functions of very large sparse Hamiltonian matrices, which exploits the numerical solution of the inhomogeneous time-dependent Schroedinger equation. The method has a…
The ion distribution around charged colloids in solution has been investigated intensely during the last decade. However, few theoretical approaches have included the influence of variation in the dielectric permittivity within the system,…
In this paper, we develop fast multipole methods for 3D Helmholtz kernel in layered media. Two algorithms based on different forms of Taylor expansion of layered media Green's function are developed. A key component of the first algorithm…