# Etomica Modules

This page provides access to a suite of instructional modules based in molecular simulation. Their purpose is to foster molecular understanding of phenomena and processes commonly taught in standard science and engineering courses. They are interactive, graphically oriented, and quantitative (i.e., they provide real data for the models being simulated). Instructions, examples, and homework problems are provided as part of most modules; these resources may be accessed from the corresponding links in the Index of Molecular Simulation Modules, below.

The modules differ in the level of understanding needed to fully appreciate them, covering a range of topics across high-school, undergraduate, and graduate levels. However, they are all easy to run and control, and anyone with an interest in physics and chemistry should be able to learn from them.

This is a project of CACHE. Funding for this development has been provided by the National Science Foundation, Grants DUE-9752243 and DUE-0618521.

### Download Instructionsâ€‹

The modules are distributed together as a single self-contained application that allows selecting and launching individual modules. Note that this distribution does not require Java to be installed on your system!

You can download the latest build from GitHub here and run the application from the zip archive. On MacOS and Windows your system may need to be configured to allow running unsigned applications.

### Index of Molecular Simulation Modulesâ€‹

Simple reaction equlibrium involving two atomic species and the three dimeric molecules they can form. Atoms move about via 2-D molecular dynamics, and can "react" to form dimers. Dynamic equilibria is demonstrated through constant recombining of atoms, and equilibria can be quantified and analyzed with thermodynamic reaction equilibria models.

Molecular dynamics of a 2-dimensional mono-atomic Lennard-Jones system. The Lennard-Jones model is a simple but widely-used approximation for the way atoms interact. Elementary molecular features of this model's dynamical and structural behavior are calculated in this simulation. More appropriate for a graduate-level student.

Model of two fundamental polymerization reaction types: stepwise growth and chain addition. The difference between the reaction mechanisms can be visualized, the resulting products of each can be observed, and calculations of molecular weights, molecular weight distributions, and kinetics can be conducted.

An integrated tutorial on pressure, temperature, density, and model equations through the piston/cylinder module combined with 2D and 3D simulations using periodic boundary conditions. The simulations are based on the square well potential, which characterizes the fundamental repulsions and attractions in a discontinuous but simple manner.

Dual Control Volume Grand-Canonical Molecular Dynamics (DCVGCMD) simulation, in which a long simulation volume is subject to grand-canonical Monte Carlo at opposite ends, with molecular dynamics in between. The MC simulations establish a chemical-potential gradient, and the resulting diffusion process can be used to measure the diffusion coefficient.

Demonstrates the independent collective motions that can be used to describe the dynamics of a system of one-dimensional coupled harmonic oscillators.