Related papers: HSMA: An O(N) electrostatics package implemented i…

This article presents the parallel implementation of the coupled harmonic oscillator. From the analytical solution of the coupled harmonic oscillator, the design parameters are obtained. After that, a numerical integration of the system…

Constant potential methods (CPM) enable computationally efficient simulations of the solid-liquid interface at conducting electrodes in molecular dynamics (MD). They have been successfully used, for example, to realistically model the…

We present a numerical framework for the simulation of collisional plasma dynamics, based on a coupling between Direct Simulation Monte Carlo (DSMC) and Particle-in-Cell (PIC) methods for the Vlasov-Maxwell-Landau system. The approach…

Many natural phenomena involve processes that happen simultaneously at different characteristic length- and timescales. Typically, the region where the process of interest happens is affected by fluctuations in its surroundings. Modeling…

We present a new algorithm which is named the Dynamical Functional Particle Method, DFPM. It is based on the idea of formulating a finite dimensional damped dynamical system whose stationary points are the solution to the original…

We propose a local, O(N) molecular dynamics algorithm for the simulation of charged systems. The long ranged Coulomb potential is generated by a propagating electric field that obeys modified Maxwell equations. On coupling the…

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…

An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…

Machine-learned interatomic potentials can offer near first-principles accuracy but are computationally expensive, limiting their application to large-scale molecular dynamics simulations. Inspired by quantum mechanics/molecular mechanics…

With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…

This paper proposes SMADMM, a single-loop Stochastic Momentum Alternating Direction Method of Multipliers for solving a class of nonconvex and nonsmooth composite optimization problems. SMADMM achieves the optimal oracle complexity of…

We propose a novel deterministic particle method to numerically approximate the Landau equation for plasmas. Based on a new variational formulation in terms of gradient flows of the Landau equation, we regularize the collision operator to…

A new class of parallel algorithms is introduced that can achieve a complexity of O(n^3/2) with respect to the interprocessor communication, in the exact computation of systems with pairwise mutual interactions of all elements. Hitherto,…

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…

The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…

In this manuscript, we undertake an examination of a classical plasma deployed on two finite co-planar surfaces: a circular region $\Omega_{in}$ into an annular region $\Omega_{out}$ with a gap in between. It is studied both from the point…

Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…

We introduce the cosmological HYPER code based on an innovative hydro-particle-mesh (HPM) algorithm for efficient and rapid simulations of gas and dark matter. For the HPM algorithm, we update the approach of Gnedin & Hui (1998) to expand…

We present an efficient linear-scaling algorithm for evaluating the analytical force and stress contributions derived from the exact-exchange energy, a key component in hybrid functional calculations. The algorithm, working equally well for…

Scientific applications that involve simulation ensembles can be accelerated greatly by using experiment design methods to select the best simulations to perform. Methods that use machine learning (ML) to create proxy models of simulations…