Pulling on a Molecule

Now, suppose you grab the black dots as if they were handles.

To begin, you hold the ends at a certain distance and allow the molecule to relax. The molecule still moves around as it feels frequent collisions from water molecules. However, you remain peaceful and allow the molecule to reach an equilibrium with the surrounding water. This is why we color the molecule green.

Suddenly, you get restless and yank on the RNA molecule, making its end-to-end distance much greater.

Since this perturbation disturbs the molecule from its initial equilibrium, we now color the RNA red.

One of the miracles of modern physics is that one can be all powerful and perform this experiment. Since the mid 1990's, the field of "single molecule spectroscopy" has blossomed to give us insights into the laws of physics. In particular, scientists have made the following observations. During most instances of this pulling experiment, the total entropy of the molecule and surrounding water increases. This entropy increase is proportional to the heat transferred from the molecule to the water. However, sometimes, by chance, the total entropy decreases!!! This violates our cherished Second Law of Thermodynamics. If you're going to remember anything from this site, it should be this: a very, very small pot can unbreak. What is going on???