Back when I was writing my Master’s thesis I developed molecular dynamics simulations. These simulations have fascinated me ever since.
Molecular dynamics is used to understand material properties and cellular processes by simulating the interaction between the individual atoms. You can for instance study crystallization in a material that is rapidly cooled.
In the below simulation, you can drag the slider to adjust the target temperature. By increasing the temperature the motion of the atoms will be faster and more chaotic. Reducing the temperature will make the atoms start to form crystal structures.
Each sphere represents an atom and each line represents a bond. The color in this simulations only depicts the current position of the atom. It was added simply to make them easier to distinguish, since having a single color makes it hard to see which atoms are in front of one another.
The atoms in this simulation are quite simple. In other words the forces acting between them are very simplified. The force is modeled after the Lennard-Jones potential, which is suitable for simulating atoms in noble gases such as Helium, Neon, and Argon. It is a two-body force, meaning that it models only interactions between pairs of atoms. In more complex interactions, such as between oxygen and hydrogen in water, three-body potentials are necessary.
I might return to more complex potentials in a later post.