Related papers: Mass-Zero constrained molecular dynamics for elect…
This review discusses progress in efficient solvers which have as their foundation a representation in real space, either through finite-difference or finite-element formulations. The relationship of real-space approaches to linear-scaling…
In several domains of physics, including first principle simulations and classical models for polarizable systems, the minimization of an energy function with respect to a set of auxiliary variables must be performed to define the dynamics…
We evaluate an efficient overset grid method for two-dimensional and three-dimensional particulate flows for small numbers of particles at finite Reynolds number. The rigid particles are discretised using moving overset grids overlaid on a…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
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…
The solution of the Poisson equation is a ubiquitous problem in computational astrophysics. Most notably, the treatment of self-gravitating flows involves the Poisson equation for the gravitational field. In hydrodynamics codes using…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
A grid-based real-space implementation of the Projector Augmented Wave (PAW) method of P. E. Blochl [Phys. Rev. B 50, 17953 (1994)] for Density Functional Theory (DFT) calculations is presented. The use of uniform 3D real-space grids for…
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 consider the problem of efficiently solving large-scale linear least squares problems that have one or more linear constraints that must be satisfied exactly. Whilst some classical approaches are theoretically well founded, they can face…
A new particle-based sampling and approximate inference method, based on electrostatics and Newton mechanics principles, is introduced with theoretical ground, algorithm design and experimental validation. This method simulates an…
Density functional theory (DFT) has emerged as one of the most versatile and lucrative approaches in electronic structure calculations of many-electron systems in past four decades. Here we give an account of the development of a…
We describe a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods provide effective convergence acceleration and preconditioning on all…
We present a numerical method for simulating rarefied gases that interact with moving boundaries and rigid bodies. The gas is described by the BGK equation in Lagrangian form and solved using an Arbitrary Lagrangian-Eulerian method, in…
We present a direct Poisson solver for massively parallel simulations on three-dimensional Cartesian grids with non-uniform spacing. The method uses a tensor-based formulation in which the operator is diagonalized numerically along two…
This paper presents a grid-free simulation algorithm for the fully three-dimensional Vlasov--Poisson system for collisionless electron plasmas. We employ a standard particle method for the numerical approximation of the distribution…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
Aligning theoretical atomistic structural models of materials with available experimental data presents a significant challenge for disordered systems. The configurational space to navigate is vast, and faithful realizations require large…
Simulating Markovian open quantum systems in the semiclassical regime poses a grand challenge for computational physics, as the highly oscillatory nature of the dynamics imposes prohibitive resolution requirements on traditional grid-based…