G. Andrés Cisneros, Professor
Department of Chemistry
Wayne State University   

"Insights on liquid systems and DNA repair from computational simulations"

Two topics related to development and application of computational simulations will be presented. We have developed a novel force field that combines terms from two advanced potentials. The Coulomb and exchange repulsion are calculated using fitted electronic densities based on a force field developed by us called Gaussian Electrostatic Model (GEM). These terms are coupled to the polarization, van der Waals and bonded terms from AMOEBA. The required electronic integrals are calculated by means of reciprocal space methods to in-crease computational speed. We will present the details of our method, which we term GEM*, its implementation and performance for molecular dynamics simulations and it re-cent application to liquid water simulations as well as the development of AMOEBA for ionic liquids. The second topic involves the use of simulations to investigate DNA repair enzymes. Replication and repair of DNA are critical processes. Errors in either of these transactions can result in mutations, some of which can lead to disease or even death. Results will be presented on simulations of the rate limiting step of the reaction catalyzed by E. coli AlkB. AlkB is a DNA repair enzyme that catalyzes the oxidative de-alkylation of DNA by means of a non-herme iron using α-keto glutarate and O₂ as co-factors.