LATTICE BOLTZMANN AND MOLECULAR DYNAMICS STUDIES IN MATERIALS AND BIOMOLECULAR

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 在本补充申请中，我们建议扩展我们在MRAC分配范围内进行的研究（DMR 070014 N和DMR 070013 N）。我们将专注于材料和生物分子科学领域的四个项目。在材料科学领域，我们将扩展我们的格子玻尔兹曼介观尺度模拟研究剪切诱导的海绵相和层状和多层囊泡相之间的转变。这项工作继续从我们目前的两亲性混合物的立方和非立方中间相之间的流变学转变的模拟研究。在材料科学领域，我们还将扩展我们的全原子分子动力学研究的粘土聚合物纳米复合材料的大规模模型在前所未有的大小。我们现在将进行原子分子动力学模拟的粘土聚合物纳米复合材料与明确的边缘复制实验系统，并计算其特征材料的性能。在生物分子科学领域，我们已经取得了显着的成功，在我们的分子动力学模拟的结合亲和力的HIV-1蛋白酶的药物基板使用先进的网格中间件的能力，我们现在建议将这项工作扩展到各种蛋白酶和相关的耐药突变，并进行类似的研究HIV-1逆转录酶。我们还提出了一个项目，利用复制交换分子动力学来阐明HIV-1蛋白酶的皮瓣门控机制的动力学。该项目将利用网格中间件，提供TeraGrid资源的自动协同分配和跨站点模拟的启动。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In this supplemental request, we propose to extend our investigations carried out within the MRAC allocation(DMR070014N and DMR070013N). We shall focus on four projects in the materials and biomolecular sciences domain. In the materials science domain we will extend our lattice-Boltzmann mesoscale simulations to study shear-induced transitions between the sponge phase and the lamellar and multi-lamellar vesicle phase. This work continues from our current simulation studies of the rheological transitions between cubic and non-cubic mesophases of amphiphilic mixtures. In the materials science domain, we will also extend our fully-atomistic molecular dynamics studies of clay-polymer nanocomposites of large-scale models at unprecedented sizes. We will now carry out atomistic molecular dynamics simulations of clay-polymer nanocomposites with explicit edges which replicate the experimental system and calculate their characteristic material properties. In the biomolecular sciences domain, we have made significant progess in our molecular dynamics simulations of the binding affinities of HIV-1 proteases to drug substrates using advanced grid middleware capabilities, We now propose to extend this work to a variety of proteases and associated resistance-conferring mutations and to carry out analogous studies for the HIV-1 reverse transcriptases. We are also proposing a project which utilizes replica exchange molecular dynamics to elucidate the dynamics of the gating mechanism of the flaps in HIV-1 protease. This project will utilize grid middleware that provides automatic co-allocation of TeraGrid resources and launching of cross-site simulations.