Thermodynamics (and it's "older brother" statistical mechanics -- but I'll refer to both as Thermodynamics) plays a very important role in what we do. I thought I'd talk a little about it. Thermodynamics plays a major role in several aspects of work. What thermodynamics helps us answer is what the eventual probability of finding various states would be in equilibrium (i.e. if we wait long enough for everything to settle down). For example, what is the probability of finding the folded state?
First, let me talk a bit about how to think of this concept of probability. One way to think of this is in terms of ensembles -- if there's a 70% chance of finding the native state, that means that if we ran 100 simulations and looked at them to see which ones folded, 70 of them would have folded. We can also think of this in terms of time -- if there's a 70% chance of finding the native state, that means that if we look at a single protein, 70% of the time we'll see it in the folded state. Either way works and often we use these two ideas interchangeably.
WIth knowing about thermodynamics, we can develop and apply new tricks which let us run our calculations much more efficiently. In particular, sometimes the probabilities we're looking for is 1 in a million. In cases like that, it's not efficient at all to run millions of simulations to look for a few rare cases. Instead, with a knowledge of thermodynamics, we have methods that allow one to use many fewer simulations and still find these rare events.
I teach Thermodynamics to juniors at Stanford in the fall and Statistical Mechanics to graduate students in the Spring. The nature of the course is the basis behind the research that we do.
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