Research was begun in two areas of membrane simulations. In the first, the stability of """"""""water wires"""""""" in the lipid bilayer was investigated by carrying out a series of molecular dynamics (MD) simulations starting with an intact (model built) wire traversing the bilayer. The wires, which are held together by hydrogen bonds were shown to be relatively stable in the highly hydrophobic environment of the membrane interior; i.e., individual configurations remained intact for close to 100 ps. This result supports a model of water mediated proton conduction across membranes. Simulations were also carried out on water wires in a water/octane/water """"""""sandwich"""""""". The decay of the water wires showed qualitative differences with the decay in the lipid bilayer, highlighting the limitations in this popular membrane model system. A method for simulating lipid bilayers in P21 periodic boundary conditions was developed. With these boundary conditions a lipid traverses to the opposite leaflet when leaving the primary simulation cell. This allows the membrane to adjust to changes in surface area as would be expected when binding a peptide, and represents a signficant advance in our ability to simulate complex membranes. Simulations of pure octyl glucoside (OG) micelles and OG/peptide complexes continued. The most significant result was that a solution of 27 lipids aggregated into a micelle during a 4 ns simulation. This indicates that a wide variety of systems and behavior can finally be studied with MD simulation.
