Molecular Dynamics Exercise

  1. Click on MD Applet and read the text marked "The physics" below the applet. Question: how many atoms are there in the initial simulation?
  2. Once you click the Start button, what phase is this ensemble of atoms in, gas, liquid, solid? Defend your answer.
  3. Now start clicking the Slower button - this lowers the average kinetic energy == temperature. Does the phase change? If so, to what and at what temperature?
  4. Once the temperature is low enough so that there are usually no gas-phase atoms, what is the state of the material? Describe the motion of the atoms near the core. Describe the motion of the atoms on the surface. What is this temperature?
  5. Click the browser's refresh button (or F5 on your keyboard) to reload the applet. Repeat the simulation, but after clicking Start, click the Make bonds button. This adds significant bond energy, so the temperatures will not correspond with 2-4, above. Click Slower repeatedly until T ~0.25. Note the ordered arrangement of the atoms; this is the crystal structure. Note too, that there are defects in this structure. Now, try raising the temperature to ~.75 and then clicking Freeze a few times ... note the number of defects. Finally, raise the temperature to ~.75 again, but this time lower the temperature with Slower, but only click it once every few seconds. This allows the atoms to randomly arrange themselves into the lowest state prior to being cooled again. Are there more, fewer, or the same number of defects? The first process is called quenching - sudden cooling - plunging a hot iron bar in cold oil or water. The second is annealing - repeating a reheating and slow cooling cycle, with a bit more cooling than reheating each time. Can you create a crystal with no defects?
  6. Click on the Presets button and select "Atmosphere." First increase the number of atoms to ~600 and heat the atoms up so that they are flying all over the box. At what temperature does this occur? Now, slowly decrease the temperature - by clicking the Slower button. What happens near the bottom at T~0.45? Why at the bottom?
  7. Run the preset "Hot and Cold" or "Friction" or "Molecule Zoo." Explain what you think it demonstrates. Be specific and complete.
    8. Describe any two of the following phenomena in terms of the atomic theory:
  8. Boiling of a liquid.
  9. Surface tension in a liquid.
  10. The fact that when a gas is compressed by a piston, it gets hotter.