How Computer Science Will Revolutionize Biochemistry
TJ Brunette
University of Massachusetts Amherst
October 26, 2006
12:50 pm - 1:50pm
NWSE 222
Abstract
The cell is a machine with many parts. Full understanding of how these parts interact will help cure diseases faster, design drugs without side-effects and enable us to create cells with desired functions. However to get to that level of proficiency numerous advances must take place.

Biochemistry has always been limited by the tools that are available to study the phenomena. For example a cell could not be studied until a microscope was powerful enough to investigate the components. The human genome project could not be completed until DNA could be sequenced quickly. But a major revolution is about to happen. In the post human genome era all information necessary to fully understand the cell is already known. This means you no longer need a cell in order to study it. As computer scientists it is now our job to create the tools of the future so we can study phenomena that are impossible to study today.

Proteins are the main building blocks for the cell. Through interactions with other proteins and changes in shape they control almost all cellular processes. Unfortunately with the present tools they are very difficult to study. A biochemist might spend years determining the shape and function of a single protein. One of the best computational technique to study a protein is called molecular dynamics. Molecular dynamics tries to determine the internal movements in a protein based on forces acting within it. However molecular dynamics is very slow and incapable of simulating long trajectories of motion. As computer scientists we can break down this problem and create better tools.

This work was done in collaboration with Oliver Brock and Filip Jagodzinski at UMass Amherst.

Lunch will be provided in Steinmetz 209 at noon.