Core--Computer and instrumentation

建议的程序项目将检查模型高密度的结构-功能关系 脂蛋白颗粒（HDL）在一系列的计算机模拟，这将需要最先进的 计算机硬件这项工作的基础是一套分子动力学（MD） 在模型膜上进行的模拟。基本协议和参数 适合于脂质MD模拟已经建立。最近，MD模拟 模型HDL颗粒已经开始。计算机硬件对这些模拟的影响是 很明显据称，这些模型的模拟需要四个月的内部时间 硬件，四处理器SGI Origin系统。一个更大的模拟已经在一个 专门的32处理器Beowulf集群在伊利诺伊大学。他们建议执行 在几个带模型上的模拟，包括上述的和其他的变化。 这些将对含有各种脂质（DMPC、DPPC、POPC）的HDL颗粒进行。 几个控制模拟也将完成，无论是在带模型和竞争纠察 围栏模型 他们估计，这些初始模拟将需要1-2年的CPU时间， 64处理器Beowulf集群。其他脂蛋白颗粒的各种各样的结构问题将在拟议的资助期的剩余时间内消耗集群。计划项目的仪器集中在此核心中。

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.