Generalized Born studies of ABC DNA sequences

Saturday, May 7, 2005 - 1:30pm - 2:15pm
EE/CS 3-180
David Case (Scripps Research Institute)
It is often useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. The generalized Born model is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids.

I will describe two applications of this methodology to the study of DNA duplex oligomers taken from the ABC sequence set. The first uses molecular dynamics simulations to look at mean structures, fluctuations and conformational transitions, with an eye towards explicit solvent simulations already carried out. The second application uses normal mode analysis (as a function of sequence length) to analyze low frequency distortion modes, and to prepare for a parameterization of a low-resolution model that could be used for much large pieces of DNA.