How internal friction affects polymer dynamics

Imagine that you are waiting underneath an umbrella at an uncovered bus-stop on a stormy, rainy evening. As the bus rolls into position, you try to fold the umbrella before boarding. The wind and rain make it difficult to do so, and you can feel the driver staring at you impatiently. As the wind slows down a jot, you realize that your umbrella is rusty, making the task of folding it even more difficult. You finally manage to fold the umbrella, amid the increasing number of cold stares from the bus, and slump gratefully in the seat closest to the entrance.

Such a resistance to folding is experienced by all protein molecules which have to fold correctly into their correct 3-D shape, starting from their respective 1-D structures.

When protein molecules are synthesized by RNA, they are simply a linear sequence of amino acid building blocks. In order to perform the function for which they were synthesized, the protein molecule needs to ‘fold’ or reorient itself into the requisite three-dimensional shape. An excellent discussion on the structure of proteins can be found here.

Proteins not only experience an external resistance to folding from the solvent they are present in (water, mostly), they also experience an ‘internal’ resistance to folding (like the rust in the umbrella). This ‘internal friction’ in polymer molecules is a key focus of my PhD research. [Protein folding, taken in its entirety, is a much larger question, and I do not work on the protein-folding problem.] The biological consequences of internal friction, especially in connection with the protein-folding problem, has begun to receive a lot of academic attention recently.

Now, proteins are just a type of polymer: long chain molecules that are composed of several repeating units. At a fine enough level of detail, the chemistry of these building blocks will begin to matter: there is a significant difference between the bond that joins a carbon atom to a hydrogen atom, and a nitrogen-hydrogen bond.

My research training involves the use of statistical mechanical principles, and a tool called Brownian Dynamics (BD) simulations, wherein polymer molecules are modeled as beads connected by springs, without going into the finer chemical details of the molecule. Such a calculated and deliberate neglect of detail prevents us from answering certain questions about the polymer molecules (“what should be the shape of the drug molecule that binds specifically to site #27 of the molecule?”) but offers payback in terms of insight about specific universal properties of polymers. These universal properties could be