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We develop a package of numerical simulations implemented in MATLAB to solve complex many-body quantum systems. We focus on widely used examples that include the calculation of the magnetization dynamics for the closed and open Ising model,…
In this work, algorithms for the parallel computation of three-body interactions in molecular dynamics are developed. While traversals for the computation of pair interactions are readily available in the literature, here, such traversals…
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…
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…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
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…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
This paper invites the reader to experiment with an easy-to-use MATLAB implementation of Metropolis integrators for Molecular Dynamics (MD) simulation. These integrators are analysis-based, in the sense that they can rigorously simulate…
We present a fully covariant transport framework for Molecular Dynamics that enables a consistent description of the evolution of relativistic N-body systems. For the first time, we derive relativistic equations of motion incorporating both…
Matrix mechanics is an important component of an undergraduate education in quantum mechanics. In this paper we present several examples of the use of matrix mechanics to solve for a number of three dimensional problems involving central…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
During the last decade we have witnessed an impressive development in so-called interpreted languages and computational environments such as Maple, Mathematica, IDL, Matlab etc. Problems which until recently were typically solved on…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Understanding the many-body dynamics of isolated quantum systems is one of the central challenges in modern physics. To this end, the direct experimental realization of strongly correlated quantum systems allows one to gain insights into…
A novel mixed quantum-classical approach to simulating nonadiabatic dynamics of molecules at metal surfaces is presented. The method combines the numerically exact hierarchical equations of motion approach for the quantum electronic degrees…
Fundamental understanding of interatomic forces in molecules must emerge from quantum mechanics, yet widely used empirical force fields rely on simplified mechanistic approximations that often fail to capture the complexity of many-body…
Microscopic stress fields are widely used in molecular simulations to understand mechanical behavior. Recently, decomposition methods of multibody forces to central force pairs between the interacting particles have been proposed. Here, we…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Electronic friction and Langevin dynamics is a popular mixed quantum-classical method for simulating the nonadiabatic dynamics of molecules interacting with metal surfaces, as it can be computationally more efficient than fully quantum…
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…