LATTICE BOLTZMANN AND MOLECULAR DYNAMICS STUDIES IN MATERIALS AND BIOMOLECULAR

材料和生物分子中的格子玻尔兹曼和分子动力学研究

• 批准号: 7723231
• 负责人: BRUCE BOGHOSIAN
• 金额: $ 0.05万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723231
• 关键词: Affinity; Binding; Characteristics; Computer Retrieval of Information on Scientific Projects Database; Endopeptidases; Funding; Grant; HIV-1 Reverse Transcriptase; HIV-1 protease; Institution; Investigation; Modeling; Mutation; Peptide Hydrolases; Pharmaceutical Preparations; Phase; Polymers; Porifera; Property; Research; Research Personnel; Resistance; Resources; Science; Site; Source; Surgical Flaps; System; United States National Institutes of Health; Vesicle; Work; clay; molecular dynamics; nanocomposite; simulation; size

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.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 在此补充请求中，我们建议扩大在 MRAC 分配（DMR070014N 和 DMR070013N）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，我们将扩展晶格玻尔兹曼介观模拟，以研究海绵相与层状和多层囊泡相之间剪切诱导的转变。这项工作是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的继续。在材料科学领域，我们还将扩展对前所未有尺寸的大规模模型的粘土聚合物纳米复合材料的全原子分子动力学研究。我们现在将对具有明确边缘的粘土聚合物纳米复合材料进行原子分子动力学模拟，复制实验系统并计算其材料特性。在生物分子科学领域，我们利用先进的网格中间件功能，在 HIV-1 蛋白酶与药物底物的结合亲和力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赋予耐药性的突变，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，利用复制品交换分子动力学来阐明 HIV-1 蛋白酶中襟翼的门控机制的动力学。该项目将利用网格中间件来自动共同分配 TeraGrid 资源并启动跨站点模拟。