The above web app simulates the dynamics of simple atoms and molecules in a two-dimensional universe and is the creation of D.V. Schroeder. This article describes the computation technique. See his web page for more details.
Many phenomena can be reproduced using this simulation. To understand how crystalline defects are formed during solidification, press the "restart" button (top right) many times. Each run is a numerical simulation of solidification. (The atoms follow their equations of motion, due to interatomic potentials; I just added some dissipation by hand.) You will see that the atoms order perfectly into hexagonal arrays sometimes, but not most of the time. Here you see crystalline defects forming. See if you can identify point, line, and plane defects. (For the line and plane defects, imagine that the 2D arrangements extend out of the plane).
"If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or the atomic fact, or whatever you wish to call it) that all things are made of atoms—little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another. In that one sentence, you will see, there is an enormous amount of information about the world, if just a little imagination and thinking are applied."