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.
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