Biological membranes can be viewed in their natural disordered state solely through computer simulations. The necessary large scale simulations, as illustrated here, have become feasible through the rapid advancement of hardware and software. A single layer of lipids grafted chemically to the surface of silicates (lower left in figure) contains about 11,000 atoms and barely can be modeled today with conventional hardware and software tools such as XPLOR. Using novel algorithms, a complete lipid bilayer with 27,000 atoms (upper left) was modeled on a 60 processor machine built in-house and required two years of runtime (1990-1992). More recently, advances in algorithm and processor technology have allowed the simulation of a 32,800-atom membrane (upper right) that was run on a workstation cluster in two months. This latter membrane model is a prerequisite to modeling the complex of one of its monolayers with the protein phospholipase A2 (lower right). These advances allow research today to contribute to the design of drugs that need to pass through membranes effectively. Proteins functioning in membranes or transporting bilayers of lipids through the bloodstream can soon be described in simulations involving 100,000 atoms. This latest accompishment is from the Resource for Concurrent Biological Computing at the Beckman Institute, University of Illinois, with support from the National center for Research Resources at NIH.
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