Physics Colloquium - Friday, Dec. 7th, 2007, 4:00 P.M.

E300 Math/Science Center; Refreshments at 3:30 P.M. in Room E200

David Swigon
Department of Mathematics
University of Pittsburgh

Mesoscale modeling of DNA elasticity and DNA-protein assemblies

Advances in the theory of the elastic rod model for DNA enhanced our understanding of a wide range of phenomena associated with biological manipulation and storage of DNA. Most recently, the development of a base-pair level model for DNA made it possible to incorporate the effects of nucleotide sequence and the negative charge of DNA in new mesoscale models of complex DNA-protein assemblies, which yielded insights into the role of DNA deformability in gene regulation. This talk will give an overview of resent research of the speaker and his collaborators on the above topics, in particular, methods for solving equilibrium equations of the elastic rod model for DNA in cases when self-contact is present, determining the likely configurational states and their free energy, and the importance of sequence dependent DNA elasticity in modeling of looped DNA-protein assemblies. Emphasis will be on models of Lac repressor-mediated DNA loop, which are supported by available data and yield experimentally verifiable conclusions about the influence of DNA deformability on the mechanism of gene regulation. Students and non-specialists are welcome.