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Lennard-Jones System The Lennard-Jones system is still the most popular model for researchers in statistic mechanics and materials simulations. The user can investigate gas, liquid, and solid, and if careful enough, observe gas/liquid/solid interphase transitions, by playing with such a simple system.

Pattern Formation These patterns were actually created from a low-density Lennard-Jones system. The temperature was set zero at initial time. A green line was drawn between any pair of atoms with an interatomic distance less than a certain length. I believe that behind these patterns there could be profound math and physics. (For example, some patterns could hibernate for a long time, big changes onset suddenly.) What's more, every time the user changes the size of the atoms, or rezero the temperature at an arbitary time in the middle of the simulation, the result will be completely different. (Note that at some point the mirror symmetry of the evolution was broken because of the numerical error of the integrator has reached such a level that symmetry breaking became visible. Symmetry is a very sensitive property of the system. Once it is broken, it can never be recovered. And no matter how small the numerical error is, it will sooner or later break the symmetry, considering the fact that a numerical error is unlikely a symmetrical one. Although the symmetry breaking in the time evolution may not be good, it is after all a nice test ---at least it shows to people that running our molecular dynamics is a high performance integrator.)

Osmosis In the above screenshots, the sigma's are chosen such that the membrane is semipermeable. For simplicity, it was assumed that the left compartment was filled with pure solvent atoms (completely hypotonic) and the right compartment was filled with pure solute (completey hypertonic). Of course, the user can change the concentrations of both compartments by moving the atoms from one side to the other, or deleting and adding, with the use of the model editor. By changing the radii of the atoms, the user can also change the permeability and investigate the change of osmostic pressure with respect to that. The membrane model is based on Computer simulation of the classic experiment on osmosis and osmotic pressure, S. Murad and J. G. Powles, Journal of Chemical Physics, 99, 7271, 1993. (These authors reported that the model could replicate Pfeffer's experiment on osmosis in semipermeable membranes in 1877 and numerically prove the van't Hoff equation for osmotic pressure over a wide range of concentrations.)

Diffusion into Vacuum This simulation may describe gas molecules leaking through the wall of a container. By changing the temperature, the user can feel that the leakage rate increases. By changing the thickness of the wall, i.e. the number of atomic layers, the leakage rate will decrease.

Explosion Doesn't this process look like explosion? Explosion starts with huge chemical energy turning into kinetic energy. Here the initial great kinetic energy was created by the release of high repulsion energy.

Condensation, adsorption and evaporation Let's imagine we have a vapor in a container with a cold substrate (here 'cold' means strongly restrained, as they are restrained, the velocities are smaller). First randomly scatter the small atoms in the empty part of the container, cool down the system, the user sees that the atoms aggregate to clusters. Playing with the temperature slider, the user changes the dynamical behavior. For instance, after the majority of the atoms have been adsorped to the substrate, the user can raise the temperature to see how evoporation happens.

Phase separation This shows how the left structure, a uniformly distributed mixture, can be 'cooked into' the right one, a few separate islands of atoms. Repulsive cross interactions (customizable) between the two species were introduced to keep them apart from each other. Because different types of atoms 'hate' each other, atoms of the same type tend to form blocks.

Lattice Mismatch This picture shows the boundaries between three grains of different atoms and different structures (hexgonal and square). Pay attention to the lattice mismatching across the boundaries.

Charged Systems If you add six A atoms and six B atoms and give the A atoms positive charges, the B atoms negative charges, and start running the simulation, you will see this dozen of atoms immediately conform to a ring, given appropriate atomic radii for the two species. This was also observed with the Interactive Physics. In most cases, charged Lennard-Jones particles prefer rectangular arrangement, as is shown on the right. (With only the Lennard-Jones potentials, atoms form hexagonal lattice.) By playing with this example, the user can understand why ionic crystals have much higher melting points than crystals formed by only the Van der Waals potentials, e.g. salt does not melt at high temperature whereas the inert gas elements form crystals at very low temperature.

Polymerization This is an example to show how different a physical force the electrostatic potential is from the Lennard-Jones potential. It shows that the Coulombic interactions play an important role in polymerization, which is an important reaction in life science. This series of pictures show that, with a highly idealized model, how long chain polymers could form from small organic molecules (something that the theories about the origin of life assume).

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