Principal Investigator

S   Kuyucak Theoretical Physics, RSPhysSE, ANU

Project Title

Density Functional and Ab Initio (Car-Parrinello) MD Studies of Ion Channels

Brief Description for General Publications

Ion channels play an essential role in normal functioning of cells, and understanding their operation is a fundamental problem in biophysics and neurology. A variety of approaches from continuum theories to Brownian dynamics, molecular dynamics (MD) and ab initio MD can be employed for this purpose. The phenomenological approaches in this hierarchy have to be justified by the ab initio methods. The aim of this project is to present such a test for the force fields used in classical MD simulations using the the gramicidin and KcsA potassium channels whose molecular structures are known to a high precision. Recent calculations of the potential of mean force of potassium ions in the gramicidin channel have revealed problems with the nonpolarizable force fields. The proposed resarch will clarify the source of this discrepancy and help to design better force fields for use in ion channel simulations.