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Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
We solve Poisson's equation using new multigrid algorithms that converge rapidly. The novel feature of the 2D and 3D algorithms are the use of extra diagonal grids in the multigrid hierarchy for a much richer and effective communication…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…
Potential flow has many applications, including the modelling of unsteady flows in aerodynamics. For these models to work efficiently, it is best to avoid Biot-Savart interactions. This work presents a grid-based treatment of potential…
A new penalty-free neural network method, PFNN-2, is presented for solving partial differential equations, which is a subsequent improvement of our previously proposed PFNN method [1]. PFNN-2 inherits all advantages of PFNN in handling the…
The Fast Multipole Method (FMM) for the Poisson equation is extended to the case of non-axisymmetric problems in an axisymmetric domain, described by cylindrical coordinates. The method is based on a Fourier decomposition of the source into…
This paper presents a "two-dimensional Fourier Continuation" method (2D-FC) for construction of bi-periodic extensions of smooth non-periodic functions defined over general two-dimensional smooth domains. The approach can be directly…
In multi-phase fluid flow, fluid-structure interaction, and other applications, partial differential equations (PDEs) often arise with discontinuous coefficients and singular sources (e.g., Dirac delta functions). These complexities arise…
We consider the isoparametric finite element method (FEM) for the Poisson equation in a smooth domain with the homogeneous Dirichlet boundary condition. Because the boundary is curved, standard triangulated meshes do not exactly fit it.…
Multigrid solvers are among the most efficient methods for solving the Poisson equation, which is ubiquitous in computational physics. For example, in the context of incompressible flows, it is typically the costliest operation. The present…
A fast algorithm (linear in the degrees of freedom) for the solution of linear variable-coefficient rational-order fractional integral and differential equations is described. The approach is related to the ultraspherical method for…
This paper is concerned with finite element methods for Poisson's equation with rough boundary data. Conventional methods require that the boundary data $g$ of the problem belongs to $H^{1/2} (\partial \Omega)$. However, in many…
We design a Quasi-Polynomial time deterministic approximation algorithm for computing the integral of a multi-dimensional separable function, supported by some underlying hyper-graph structure, appropriately defined. Equivalently, our…
We propose a flat nonlinear placement algorithm FFTPL using fast Fourier transform for density equalization. The placement instance is modeled as an electrostatic system with the analogy of density cost to the potential energy. A…
Ab initio calculations are fundamentally bottlenecked for large systems by the steep computational scaling of solving self-consistent field (SCF) equations. While machine learning offers potential accelerations, existing methods often…
This paper proposes and analyzes a novel efficient high-order finite volume method for the ideal magnetohydrodynamics (MHD). As a distinctive feature, the method simultaneously preserves a discretely divergence-free (DDF) constraint on the…
In recent work, Li et al.\ (Comm.\ Math.\ Sci., 7:81-107, 2009) developed a diffuse-domain method (DDM) for solving partial differential equations in complex, dynamic geometries with Dirichlet, Neumann, and Robin boundary conditions. The…
We describe a quantum algorithm for preparing states that encode solutions of non-homogeneous linear partial differential equations. The algorithm is a continuous-variable version of matrix inversion: it efficiently inverts differential…
In this paper, we propose a novel multiscale model reduction strategy tailored to address the Poisson equation within heterogeneous perforated domains. The numerical simulation of this intricate problem is impeded by its multiscale…
We present a method to extend the finite element library FEniCS to solve problems with domains in dimensions above three by constructing tensor product finite elements. This methodology only requires that the high dimensional domain is…