相关论文: Argon Simulations with EM3, a New Modular Molecula…

Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…

Molecular dynamics (MD) simulations are essential for studying complex molecular systems, but their high computational cost limits scalability. Coarse-grained (CG) models reduce this cost by simplifying the system, yet traditional…

We present, in a unifying way, the main components of three asynchronous event-driven algorithms for simulating physical systems of interacting particles. The first example, hard-particle molecular dynamics, is well-known. We also present a…

Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due…

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…

We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…

Machine-learned force fields have generated significant interest in recent years as a tool for molecular dynamics (MD) simulations, with the aim of developing accurate and efficient models that can replace classical interatomic potentials.…

The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally…

We develop a new Lagrangian material particle -- dynamical domain decomposition method (MPD^3) for large scale parallel molecular dynamics (MD) simulation of nonstationary heterogeneous systems on a heterogeneous computing net. MPD^3 is…

Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…

Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…

Extensively exploring protein conformational landscapes remains a major challenge in computational biology due to the high computational cost involved in dynamic physics-based simulations. In this work, we propose a novel pipeline, MoDyGAN,…

Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…

We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…

We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…

Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…

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,…

This paper discusses the latest generation of the MONARC (MOdels of Networked Analysis at Regional Centers) simulation framework, as a design and modelling tool for large scale distributed systems applied to HEP experiments. A…

Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…

We present our ongoing work aimed at accelerating a particle-resolved direct numerical simulation model designed to study aerosol-cloud-turbulence interactions. The dynamical model consists of two main components - a set of fluid dynamics…