SUPERCOMPUTING STUDIES OF BIOMEMBRANES

Although computer simulation of biological molecules has seen widespre ad growth and is widely accepted as an important biochemical tool, it is hampered by limited computing resources. Biomolecular systems, by n ecessity, contain a large number of interaction sites, In many cases, these sites interact over quite large distances. Further, the time sca les of biological interest are long, which requires that simulations o f dynamical properties at the atomic level must be lengthy to adequate ly probe these motions. We address these issues through discussions of atomic-level molecular dynamics simulations of biological lipid bilay er membranes, which are key constructs in biochemistry. These simulati ons reproduce many experimental observables and provide a degree of re solution currently unavailable experimentally. The lengths of these si mulations, the longest of which was 2 nanoseconds, were sufficient to effectively sample many of the motions governing the behavior of biome mbranes. Examples are given showing the importance of long-range inter actions. The number of interaction sites required by these simulations is discussed, particularly the need for explicit representation of so lvent molecules.