Related papers: The Multiple Time-Stepping Method for 3-Body Inter…

Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materials science and computational chemistry. We present…

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…

We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…

Simulations of colloidal suspensions consisting of mesoscopic particles and smaller species such as ions or depletants are computationally challenging as different length and time scales are involved. Here, we introduce a machine learning…

Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…

A fully parallel version of the contact dynamics (CD) method is presented in this paper. For large enough systems, 100% efficiency has been demonstrated for up to 256 processors using a hierarchical domain decomposition with dynamic load…

Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…

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…

Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…

Collision detection plays a key role in the simulation of interacting rigid bodies. However, owing to its computational complexity current methods typically prioritize either maximizing processing speed or fidelity to real-world behaviors.…

We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…

We present a distilled multi-time-step (DMTS) strategy to accelerate molecular dynamics simulations using foundation neural network models. DMTS uses a dual-level neural network where the target accurate potential is coupled to a simpler…

All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…

The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…

We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU…

Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…

Direct $N$-body simulations of a large number of particles, especially in the study of planetesimal dynamics and planet formation, have been computationally challenging even with modern machines. This work presents the combination of fully…

Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…