COMPUTER MODELING AND OTHER THEORETICAL STUDIES OF BIOPOLYMERS

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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) refinement of the recently developed distribution based Monte Carlo sampling procedure to more accurately describe the conformation of lipid headgroups and all-atom systems; (ii) extensive molecular dynamics (MD) of water, butane and octane to test a variety of force fields, and preliminary simulation of the octane-water interface; (iii) development of a simple hydrodynamic method to calculate diffusion tensors of proteins and DNA by considering only C-alpha carbons and phosphorus atoms, respectively; (iv) Brownian dynamics simulations of a bistable oscillator in order to determine the positional time correlation function and thereby evaluate the importance of memory function corrections to the Optimized Rouse-Zimm Approximation. Simulations pertaining more to modeling included: (i) MD of a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer in gel phase where, in agreement with experiment, the system maintained a 30 degree chain tilt and showed disorder in the terminal methyl region; (ii) Langevin dynamics of the disaccharide cellobiose which have enabled the decomposition of motional contributions to the NOE build-up curves; (iii) MD of a DNA 12-mer including water and ions in order to determine the fluid phase, with particular attention being paid to convergence of the deuterium order parameters and the interplay of hydration level and surface area.