Related papers: Molecular Dynamics Simulations of Active Matter us…

We use molecular dynamics simulations to study the evaporation of particle-laden droplets on a heated surface. The droplets are composed of a Lennard-Jones fluid containing rigid particles which are spherical sections of an atomic lattice,…

FMs, particularly LLMs, are increasingly used to support various software engineering activities (e.g., coding and testing). Their applications in the software engineering of CPSs are also growing. However, research in this area remains…

Cancer is a complex disease that is characterized by uncontrolled growth and division of cells. It involves a complex interplay between genetic and environmental factors that lead to the initiation and progression of tumors. Recent advances…

To fill the gap between accurate (and expensive) ab initio calculations and efficient atomistic simulations based on empirical interatomic potentials, a new class of descriptions of atomic interactions has emerged and been widely applied;…

All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…

We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…

Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…

Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…

We implement two recently developed fast Coulomb solvers, HSMA3D [J. Chem. Phys. 149 (8) (2018) 084111] and HSMA2D [J. Chem. Phys. 152 (13) (2020) 134109], into a new user package HSMA for molecular dynamics simulation engine LAMMPS. The…

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…

Laminate mechanisms are a reliable concept in producing lowcost robots for educational and commercial purposes. These mechanisms are produced using low-cost manufacturing techniques which have improved significantly during recent years and…

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond…

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…

Linear multistep methods (LMMs) are popular time discretization techniques for the numerical solution of differential equations. Traditionally they are applied to solve for the state given the dynamics (the forward problem), but here we…

Large language models have increasingly been proposed as a powerful replacement for classical agent-based models (ABMs) to simulate social dynamics. By using LLMs as a proxy for human behavior, the hope of this new approach is to be able to…

Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…

We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…

We examine the issue of assessing the efficiency of components of a parallel program at the example of the MD package LAMMPS. In particular, we look at how LAMMPS deals with the issue and explain why the approach adopted might lead to…

As data science and machine learning methods are taking on an increasingly important role in the materials research community, there is a need for the development of machine learning software tools that are easy to use (even for nonexperts…