Exploration of a Model of Two Atoms

In this section, you will explore a model (we describe what we mean by models in detail in Ch. 2) of the interactions between two atoms. You'll be able to drag one atom around and see how the other atom reacts. The core method underlaying this model is a simulation technique known as molecular dynamics. You will learn the basics of how this technique works later. For now, before we delve into why atoms interact in the way they do, our goal is to gain some intuition on how atoms interact and bond.

If you want to learn more about the approach of developing intuition through exploration before getting into more formal approaches (i.e. mathematical derivations), you can read this short article on the learning cycle.

Two-atom Molecular Dynamics Model

In NetLogo model 3.3.1, we model two atoms, one represented by a yellow circle, the other by a one blue one. Press the setup button and then go to run the model. The two atoms will appear to move (or not) based on their initial relative positions. Note that the simulation is a so-called "wrapped" world, where if one atom leaves one side of the simulation it appears on the other side of the world (you'll see this happen). This also means that if (for example) one atom is near the top of the world and the other is near the bottom, the distance between the two is actually through the world boundary. Play around with the model... you'll see what we mean.

While the model is running (go is pressed), you can click anywhere in the black square and the closest atom will move to where you clicked. Click and drag the atoms to see how they interact and answer the questions below. If you'd like to trace the atom's paths, activate the trace-yellow? and/or trace-blue? options. Then, complete the three questions in Exercise 3.3.1.

Exercise 3.3.1: Observations of Interatomic Interactions
Not Currently Assigned

Take about 5-10 minutes on this problem.

  1. What happens when the atoms are placed far apart (greater than 10 atomic radii, 10$r_0$, where $r_0$ is half the diameter of the atom) and are initially not moving?

  2. What happens when the atoms are a small distance apart - perhaps closer than $3 r_0$ apart - and not moving initially? (Here, just press go and move one atom toward the other until you perceive appreciable motion)

  3. What happens when the atoms are very close together, that is, the edges of the atoms are nearly touching? (Here, just press go and try to push the two atoms together.)