LATTICE BOLTZMANN AND MOLECULAR DYNAMICS STUDIES IN MATERIALS AND BIOMOLECULAR

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 在这项补充请求中，我们建议延长我们在MRAC分配(DMR070014N和DMR070013N)范围内进行的调查。我们将重点关注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-玻尔兹曼介观模拟来研究剪切诱导的海绵相与片层和多层泡囊相之间的转变。这项工作是从我们目前对两亲混合物立方和非立方中间相之间流变转变的模拟研究继续进行的。在材料科学领域，我们还将以前所未有的规模扩展我们对粘土-聚合物纳米复合材料的全原子分子动力学研究。我们现在将对粘土-聚合物纳米复合材料进行显式边缘的原子分子动力学模拟，复制实验系统并计算其特征材料性质。在生物分子科学领域，我们使用先进的网格中间件功能在HIV-1蛋白酶与药物底物结合的分子动力学模拟方面取得了重大进展，我们现在建议将这项工作扩展到各种蛋白酶和相关的与耐药性相关的突变，并对HIV-1逆转录酶进行类似的研究。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蛋白酶中翻盖的门控机制的动力学。该项目将利用网格中间件，提供TeraGrid资源的自动联合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.