Tom Bishop's Theoretical Molecular Biology Lab

Dr. Bishop's research interests are in the area of theoretical and computational molecular biology, with a particular emphasis in molecular modeling and molecular dynamics simulations of proteins and DNA. The current focus is developing a multiscale model of DNA, nucleosomes and chromatin.

Structure and Dynamics of DNA, Nucleosomes and Chromatin.

The structure and dynamics of DNA and chromatin are being modeled by a combination of molecular dynamics and mathematical modeling techniques. The goal of this research is to develop an understanding of how local events, such as DNA binding, affect the global structure and dynamics of DNA and chromatin. For this purpose, all atom molecular dynamics simulations are used to model DNA and protein-DNA interactions in solution. The results are analyzed to characterize the effects of the protein on the conformation and dynamics of the DNA, including DNA bending, twisting, and stretching. This information is then included in a model of DNA based on the theory of elastic rods that predicts how local distortions of DNA alter the structure and dynamics of DNA and chromatin on longer length scales. The elastic rod model being developed thus provides a rigorous mathematical basis for analyzing how protein-DNA interactions and DNA sequence specific properties orchestrate cellular processes such as gene regulation.

Methods:
This research requires classical mechanics, mathematical and numerical analysis, numerical integration, computer programming, molecular modeling and visualization techniques, as well as, an understanding of the structure and function of DNA and chromatin.