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This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
The family of generalized Pseudo-Spectral Time Domain (including the Pseudo-Spectral Analytical Time Domain) Particle-in-Cell algorithms offers substantial versatility for simulating particle beams and plasmas, and well written codes using…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Particle in Cell (PIC) simulations have become a vital tool for the investigation of kinetic processes in plasma physics. Many of the systems investigated with PIC simulations contain particles with relativistic velocities. The correct…
This work introduces CLIP, a CUDA-accelerated phase-field lattice Boltzmann framework for simulating immiscible two-phase flows with high density and viscosity ratios in both two- and three-dimensional domains. By leveraging GPU…
Reduced-order particle-in-cell (PIC) scheme is a novel modeling approach that enables computationally efficient electrostatic kinetic simulations of plasma. In our previous publications, we demonstrated the potentials of a preliminary…
Achieving large-scale kinetic modelling is a crucial task for the development and optimization of modern plasma devices. With the trend of decreasing pressure in applications such as plasma etching, kinetic simulations are necessary to…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
A new Particle-in-Cell (PIC) method, that conserves energy exactly, is presented. The particle equations of motion and the Maxwell's equations are differenced implicitly in time by the midpoint rule and solved concurrently by a…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
In this work, we develop an accelerated sharp-interface method based on (Hu et al., JCP, 2006) and (Luo et al., JCP, 2015) for multiphase flows simulations. Traditional multiphase simulation methods use the minimum time step of all fluids…
In recent years, the increasing interest in Stochastic model predictive control (SMPC) schemes has highlighted the limitation arising from their inherent computational demand, which has restricted their applicability to slow-dynamics and…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
We propose a spectral Particle-In-Cell (PIC) algorithm that is based on the combination of a Hankel transform and a Fourier transform. For physical problems that have close-to-cylindrical symmetry, this algorithm can be much faster than…
Conventional explicit electromagnetic particle-in-cell (PIC) algorithms do not conserve discrete energy exactly. Time-centered fully implicit PIC algorithms can conserve discrete energy exactly, but may introduce large dispersion errors in…
We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, $\rho_{e}$, is comparable to or less than the Debye length, $\lambda_{De}$, and…