Seminars People Information Computing Research
Structure and Dynamics of DNA
P.I.s: Thomas Bishop (Environmental Health Sciences),Ricardo Cortez (Mathematics), Oleksandr Zhmudsky (CCS).
This project combines mathematical techniques with molecular biology to investigate the way in which DNA folds and twists under the influence of various types of forces to produce a hierarchy of structures. These eventually enable DNA to be neatly compacted into the nucleus. No consistent theory has been developed to describe how this folding of DNA affects a hierarchy of time, energy and length scales that enable molecular interactions at the atomic level to be integrated into a coherent mechanism that orchestrates large-scale biological processes such as the cell cycle. The goal of the project is not only to describe a final state in the hierarchy but to model the transformation from an initial configuration to the final one. Computationally, this is done by dividing the DNA into small segments and deriving a complex set of differential equations that describes the motion of one segment relative to neighboring ones. The computations are done in mathematically convenient coordinates, which must be converted to position coordinates for visualization. The entire response of DNA to different stimuli can then be analyzed. The final states are very complex structures that require imaging techniques such as slicing, shading and projecting (onto planes) in order to understand the configurations and the way they affect the energy of the system.
The result will be a powerful tool that scientists will be able to use to formulate and test hypotheses, and to construct, analyze and visualize the dynamics of DNA in a variety of cellular mechanisms.

The investigators leading this project are Dr. Thomas Bishop (Environmental Health Sciences), Dr.Ricardo Cortez (Mathematics) and postdoctoral researcher Dr. Oleksandr Zhmudsky. Dr. Bishop's expertise is in protein-DNA interactions and he is one of the investigators who have developed the elastic rod model for DNA, which is at the core of the project. Dr. Cortez is an expert in computational methods for differential equations and oversees the numerical aspects of the project. Dr. Zhmudsky has extensive experience in mathematical physics, scientific computation and the elastic rod model developed by Dr. Bishop from previous collaborations.

Tulane Tulane University
201 Lindy Boggs Center
Computational Science
6823 St. Charles Ave.
New Orleans, LA 70118
(504)862-8391 ccs@tulane.edu