Molecular Dynamics

By Timothy O’Sullivan, The University of Melbourne

Most of us are familiar with the concept of Atoms, the idea that everything around us and inside us is made up of these very tiny building blocks. To know how the world truly works and why certain physical phenomenon occur the way they do, one must understand the motion of this unseen world. The fields of statistical and fluid mechanics have made attempt to show us how the world works, and for the most part these mathematical tools have served their purpose extremely well, but every now and then, these tools will return no or preposterous information. This is because these tools do not account for the atomic behaviour on the correct scales.

This motivates a technique that does give the correct treatment of systems at these tiny scales. Thankfully, I was able to study such a technique over the summer, due to a fantastic opportunity given by AMSI and supervision from Naida Lacevic and John Sader.

The technique in question is Molecular Dynamics (MD). Like the magnets we are all familiar with, atoms can attract and repel each other. If you know how atoms push and pull on each other, you can find their acceleration, which can then be used to solve for position. Now if you have a box full of atoms, and you know where every particle will be at every point in time (which is what MD tells us), you know everything there is to know about that system. To apply MD means, in simple terms, to take a box of atoms, quantify their interactions and then solve Newton’s equations with a little bit of calculus. Through this simple process, we can gain a very reasonable view into this microscopic world, shedding light on systems that were once untouchable by other, classical mathematical techniques.

This simple idea can then be applied to a variety of systems, both for one’s own curiosity and to illuminate further oddities that other mathematics alludes to. One is only limited by computing power (which is growing every day) and their imagination.


Timothy O’Sullivan was one of the recipients of a 2015/16 AMSI Vacation Research Scholarship.

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