The purpose of this project is to implement and to further develop the methods of molecular dynamics, stochastic dynamics, energy minimization, hydrodynamics and computer graphics to investigate the solution structures of peptides, proteins, nucleic acids and the liquid crystal state of the lipid bilayer. The project thus involves questions of both methodology and modeling. This past year the methodological part of the research principally involved: (i) an extension of our analysis of Langevin dynamics algorithms for calculating statistical errors in dynamics averages; (ii) a detailed analysis of methods for calculating rate constants from simulations; (iii) a comparison of the barrier crossing dynamics of glycol in water as simulated by Langevin and molecular dynamics. Calculations on lipid bilayers primarily concerned the development of a mean field technique for carrying out stochastic simulations on a boundary layer of lipids.
