Course Description

Scientists use computers to study all kinds of physical and biological systems. In computational biophysics, we will learn how to use computers to model a few simple, but important biological processes. After learning the basics of programming using the python language, we will use that knowledge to model:

1) How the genetic code of DNA is translated into proteins. From a DNA sequence, we will discover how cells use the code to create proteins and other bio-molecules. Then we will "reverse engineer" the code to find what DNA sequences could produce a given protein. Finally, we will create some special string processing programs to find the frequency of certain "words" in the genetic code- a tool biologists use to isolate where in the bacteria genome the copying (replication) of DNA starts. Along the way, we will learn many biological and physics concepts.

2) How biological molecules migrate and make their way through the crowded, chaotic environment inside a living cell. Will they find each other rapidly enough if they simply randomly bump around inside the cell until they happen upon each other? Or do molecules need to be guided in some way to their destinations?

We will develop some answers to this question by writing programs which simulate the random walks that molecules take inside cells. After putting together initial programs we will be able to do "numerical experiments" to generate data telling us, for example, whether molecules find each other more rapidly in long narrow cells or in more roundish environments. Alternately we can see how the size and shape of a molecule itself affect things.

Instructors: Rajiv Singh, Dave Cone TA: Michael Flynn