Related papers: An introduction to classical molecular dynamics si…
We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
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…
Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…
An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally…
Selected results of a classical simulation of N bodies in strong interaction are presented. The static properties of such classical systems are qualitatively similar to the known properties of atomic nuclei. The simulations of collisions…
Establishing the existence of periodic orbits is one of the crucial and most intricate topics in the study of dynamical systems, and over the years, many methods have been developed to this end. On the other hand, finding closed orbits in…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We present quantum algorithms for simulating the dynamics of a broad class of classical oscillator systems containing $2^n$ coupled oscillators (Eg: $2^n$ masses coupled by springs), including those with time-dependent forces, time-varying…
Generic open quantum systems are notoriously difficult to simulate unless one looks at specific regimes. In contrast, classical dissipative systems can often be effectively described by stochastic processes, which are generally less…
We present a detailed account of the technical aspects of stochastic quantum molecular dynamics, an approach introduced recently by the authors [H. Appel and M. Di Ventra, Phys. Rev. B 80 212303 (2009)] to describe coupled electron-ion…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
We outline an unified introduction to the evolution equations of classical and quantum systems intended for a high school students audience. The attempt consists in circumventing the lack of mathematical knowledge with the use of simplified…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…