Interactive Molecular Dynamics Simulations in AIMS

By Charles Xie

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Molecular dynamics empowers scientists and engineers to design and perform computational experiments to test hypotheses about the microscopic world. Making molecular dynamics visual and interactive on the Web can make this powerful tool more accessible to a larger audience, such as researchers who are not savvy in using computational tools and students who struggle with abstruse science concepts. Equipping AIMS with interactive molecular dynamics is an important goal of its development as AIMS views data and computation as two complementary engines that drive scientific discovery in the contemporary era.

You can play with a simple molecular dynamics simulation with some inert gas atoms below to experience and appreciate the power of computation in the browser. This simulation is simple because inert gas atoms only interact with one another through the van der Waals interaction, which is typically modeled as the Lennard-Jones potential.

Live model above (view in full screen) — Chrome or Edge recommended

What can you observe from this simulation? The following provides a list of interesting things.

Thermal Motion

Molecules are in constant random thermal motion. On average, heavy molecules move more slowly than light molecules. It is evident in the above simulation that the helium atoms (the smallest ones) move much faster than the larger ones. However, the average momenta of different types of molecules in the mix are not that different, as you can see from the momentum vectors shown in the simulation. This is because momentum is the product of mass and velocity (p=mv).

Conservation of Energy

You can notice from the graph that the total energy, which is the sum of the kinetic energy and the potential energy of the atoms, remains approximately the same during the simulation — while the kinetic energy and the potential energy exhibit fluctuations that increase when the molecules move faster. This is because these atoms are isolated in a box without exchanging energy with the environment. According to the Law of Conservation of Energy, the total energy should not change no matter how many times the atoms collide with one another inside the box. The conservation of total energy can also be used to validate the simulation.

Phase Change

Despite the simplicity, this simulation demonstrates how profound concepts such as phase change can be vividly brought to your screen. You can use the buttons on the Control Panel at the bottom of the 3D window to heat or cool the atoms and observe how they crystallize into a solid, condense into a liquid, or boil into a vapor as energy is subtracted from or added to them.

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