Molecular dynamics simulations

I use molecular dynamics to study huge molecules like proteins, the molecular machinery cells use to accomplish almost necessary to sustain life. The information encoded in your genes is the sequence of amino acids which make up all the proteins in your body. My goal is to use information about a proteins chemical composition and its structure and determine its function; molecular dynamics gives us a way to ‘watch the movie’ of the protein going about its job.

A similar algorithm to MD is used to study the motions of stars and galaxies, since both molecular and galactic motion are dominated by a 1/r law, either Newton’s Law of gravity m1m2 / r or Coulomb’s Law q1q2 / r. This means that often a majority of the world’s supercomputer time is spent on MD and similar calculations.

If you want to get an idea about how MD works, you can play with this free, online interactive MD simulator, or you can fall down the MD Wikipedia rabbit hole.