Tag Archives: Erik Lindahl

Course Review: Biophysical Chemistry

Biology? Physics? Chemistry? Despite of its intimidating name, the course biophysical chemistry is one of the most inspiring one I have ever had, and is regarded as the most popular course by two branches of our students. Eager to know what it is?

All you need is Boltzmann

The core concept of the whole course is the Boltzmann distribution, which tells us how likely a state is according to its energy.

  The simplest form of Boltzmann Equation

Hmm….how can we link this awkward mathematical expression to biology? Think of this example: inside a protein, atoms are connected with bonds. Some of these bonds are very strong; the others are weaker. Besides bonds, they can also interact with the surrounding molecules, such as water or its ligand/receptor. Imagine that we know the magnitude of all these bonds and interactions, and the temperature is also given. The question is, can we predict what will happen next? Will the protein unfold spontaneously? If yes, how long will the process take? If no, will the protein binds to other molecules, and how long can this binding sustain?

The answer is, yes AND no. Boltzmann distribution says, it is all PROBABILITY that matters.

Expanding the same concept from a single protein to the entire world of biochemistry,  biophysical chemistry digs into the universal physical laws under the complex reactions and ever-changing states, acting as a key to unmask them, and make prediction about the future. It is not difficult to imagine how understanding of biophysical chemistry is essential to pharmaceutical applications, such as study of protein-protein docking and ligand screening in early drug development.

Structure of the course

The course was divided into two parts: three hours lecture in the morning and four hours of computer lab, which is a extension of the content in lecture.  In order to pass the course, you need to get a “Pass” grade in all the 8 computer lab assignments (Only Pass/Fail for these assignments). The course is graded as A (highest) to F (fail), which is 100% dependent of the four-hour final exam.

After spending the first lecture reviewing the properties of common biological molecules and interactions, we were introduced the Boltzmann distribution at the first lecture. In the computer lab on the same day, we quickly had a feeling of the effect of sampling on this distribution by trying the simulation by ourselves on computer:

Taking more “steps”, closer the results of simulation to prediction

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