Professor In-Chul Yeh
Laboratory of Chemical Physics
National Institutes of Health
Bethesda, MD

Wednesday, February 9, 2005
4:00 pm (CT)
464 Loomis

Abstract

Quantitative comparisons between theory and experiment of interesting biological phenomena are becoming increasingly feasible with recent advances in both computer simulations and measurements. In my talk, I will present results from extensive molecular dynamics simulations of fundamental biomolecular processes: peptide folding, polyelectrolyte electrophoresis, and transport of nucleic acids through membrane pores. I will compare results from simulations with those obtained by recent experiments on peptide loop-closure kinetics, capillary zone electrophoresis, and DNA translocation through alpha hemolysin protein pores. I found that calculated end-to-end contact formation rates of peptides are faster than those deduced from the experimental data because of the finite strength of contact quenchers used in the experiment. I also found that diffusion coefficients and electrophoretic mobilities of RNA in free solution satisfy a Nernst-Einstein relation in which the effective charge of RNA is reduced by the charge of transiently bound counterions. I observed sequence-dependent rates of translocation of RNA through carbon nanotube membranes. Long-time tails in the translocation kinetics were explained by a simple trap-diffusion model.