Wednesday, October 9, 2013

Chemistry prize!

Congratulations to Karplus, Levitt and Warshel on the 2013 Chemistry Nobel. These three made important strides in integrating the two sides of computational modeling. Computational chemists use two different methods to simulate molecules and make predictions about their structures and properties. Molecular mechanics, MM, uses classical physics and treats atoms as balls and springs. This does not give very exact answers, but these calculations are very fast and can be used for large systems (e.g. proteins). Quantum mechanics, QM, treats electrons individually. This gives very exact answers, but molecules that have only ten or twenty atoms can sometimes take many hours to complete, so things like proteins would take lifetimes to calculate. QM/MM is the solution. Karplus, Levitt and Warshel worked out ways to integrate the two methods so that large systems could be broken into parts, with part treated with MM and the other part treated with QM. This allows you to take some big system, like an enzyme, and very quickly solve the structure of the larger part with MM, but closely model reactions in the active site using QM.

To make an analogy, let's look at DUPLO and System LEGO. DUPLO are the larger blocks built for young children (my almost-2-year-old loves to chew on these). System bricks are what you probably think of as LEGO. You may not have realized it, but these two types of pieces can be combined:

Some LEGO builders use this trick when making large creations. DUPLO bricks are larger, and can quickly build up big mountains or whatever, but System bricks can be used to make the final result much more detailed. Here we see this principle in a WIP of a train display.

Now, this isn't so hard, since DUPLO and System bricks are both by LEGO, and they designed these to integrate. But QM/MM is a different matter. The theories underlying them are completely unrelated, and the real difficulty that faced Karplus, Levitt and Warshel (and others) and the reason they were recognized by the Nobel committee, was how to develop tools that connected them together in a meaningful way. A couple of years ago, Golan Levin and Shawn Sims came up with a series of connection pieces that can link LEGO, Lincoln Logs, TinkerToys, and other building toys. They don't sell them, but they made the designs available so you can make your own with a 3D printer.

With these you can link up previously-unconnected constructions. It's QM/MM for the building toy world! Hmm, is their a Nobel for toys?

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