The purpose of this project is to implement and to further develop the methods of molecular dynamics, stochastic dynamics, Monte Carlo, hydrodynamics and computer graphics to investigate the solution structures of peptides, proteins, nucleic acids and lipid bilayers. The project thus involves questions of both methodology and modeling. This past year the methodological part of the research principally involved: (i) statistical analysis of the accuracy of order parameters and diffusion constants computed from dynamics simulations; (ii) statistical analysis of concerted dihedral transitions in polymers, with application to """"""""kink"""""""" motions in membrane chains; (iii) an exhaustive comparison of Monte Carlo and dynamics algorithms for conformational searching using the bistable oscillator as a paradigm; (iv) an analysis of systematic bias in rates calculated from short trajectories. Simulations pertaining more to modeling included: (i) MD simulations of the series butane, octane, dodecane, hexadecane, and eicosane, with extensive analysis of the viscosity dependence of translational and rotational diffusion, and isomerization; (ii) MD simulation of a fluid phase dipalmitoyl phosphatidylcholine lipid bilayer in water, including an analysis showing that on the 100 ps timescale there is effectively no difference in the reorientational dynamics of the carbons in the membrane interior and in pure hexadecane. The result strongly implies that the apparently high viscosity of the membrane is more closely related to molecular interactions on the surface rather than in the interior.
