Core--Computer and instrumentation

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The proposed program project will exam structure-function relationships in model high density lipoprotein particles (HDLs) in a series of computer simulations which will need state -of- the- art computer hardware. The foundation for this work is a set of molecular dynamics (MD) simulations that were carried out on model membranes. Basic protocols and the parameters appropriate for lipid MD simulations have been established. More recently, MD simulations on model HDL particles have begun. The impact of computer hardware on these simulations is apparent. It is stated that simulation on these models requires four months on their in-house hardware, a four processor SGI Origin system. A larger simulation has been carried out on a dedicated 32 processor Beowulf cluster at the University of Illinois. They propose to carry out simulations on several belt models, including those described above and other mutations. These are to be done for HDL particles containing a variety of lipids (DMPC, DPPC, POPC). Several control simulations will also be done, both on belt models and on competing picket fence models. They estimate that these initial simulations would require 1-2 years of CPU time on the proposed 64 processor Beowulf cluster. A wide variety of structural problems on other lipoprotein particles would consume the cluster for the remainder of the proposed grant period. Instrumentation for the Program Project is centralized in this Core.