Monday, February 23rd, 2004
2:30pm - 3:30pm, in Science 2-065

Ethan Bolker

UMass Boston

A too simple model for protein folding

Abstract: Supercomputers and computer grids are regularly employed attempting to decide how a sequence of amino acids will fold into a three dimensional configuration. In this talk we'll examine a very simple analogue for that impossible problem in biochemistry. We model amino acids as disks (or balls) each of which wants (or does not want) to be exposed to water. Polypeptides are sequences of amino acids which we try to arrange on a grid in the plane (or in space) in an attempt to give each acid the environment it wants. The model is too simple to help biochemists, but complex enough to be useful in the teaching of biology and to suggest interesting problems in combinatorics and algorithm development. Undergraduates (math, bio, cs) welcome.