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.
As featured in NCSA's Access Summer 2010
As featured in Nucleic Acids Research Webserver Edition 2010
As featured by Faculty of 1000 Biology: A Must Read
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.
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.