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: 7601494
• 负责人: BRUCE BOGHOSIAN
• 金额: $ 0.07万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601494
• 关键词: Affinity; Area; Award; Benchmarking; Binding; Biological Models; Code; Complex; Computational algorithm; Computer Retrieval of Information on Scientific Projects Database; DNA; Decompression Sickness; Defect; Drug resistance; Endopeptidases; Environment; Free Energy; Funding; Grant; HIV Protease; HIV-1 protease; Hemolysin; Institution; Integral Membrane Protein; Lipid Bilayers; Liquid substance; Modeling; Motion; Mutation; Nucleic Acids; Oils; Peptide Hydrolases; Pharmaceutical Preparations; Phase; Polymers; Pore Proteins; Principal Investigator; Process; Property; Protease Inhibitor; Proteins; Research; Research Infrastructure; Research Personnel; Resources; Role; Science; Scientist; Source; Spices; System; United States National Institutes of Health; Water; Work; base; clay; cluster computing; large scale simulation; molecular dynamics; nanocomposite; novel; simulation; size; surfactant; tool

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. We propose to investigate problems in materials and biomolecular sciences. In the materials science domain, we plan to quantitatively study the emergent properties of complex materials by performing simulations with very large system models, using massively parallel codes, hitherto not possible due to computational resource limitations. Such large scale simulations allow us to calculate materials properties which are not accessible with simulations of smaller models and to quantitatively assess the role of finite size effects. In the biomolecular sciences domain, our projects are concerned with understanding biologically relevant processes based on free energy calculations. In the projects proposed here, we build on earlier work where we have developed and validated novel computational algorithms and grid computing infrastructure, allowing access to physical timescales via molecular dynamics simulations, which have so far been very difficult to achieve. We shall focus on projects on four specific scientific research areas - i) Large-scale lattice-Boltzmann simulations of liquid crystalline materials ii) Material properties of clay-polymer nanocomposites iii) Drug resistance in HIV-1 proteases and iv) Nucleic acid translocation through alpha-hemolysin protein nanopores. In project (i), our objective is to investigate the rheological and morphological properties of mesoscopic cubic phases of oil/water surfactant systems. In particular, we plan to examine the effect of defects on the rheological properties of self-assembled gyroid mesophases. In project (ii), we propose to calculate the materials properties of clay-polymer nanocomposite systems. We will use physically realistic-sized models and perform molecular dynamics simulations in order to calculate material properties, including the bending modulus, Young.s modulus and Poisson.s ratio, directly from emergent undulating motions observed in these simulations. The objective of the work in project (iii), is to study the effect of pairwise complementary mutations on HIV-1 protease activity and drug resistance. Calculation of differential dynamics and differences in binding affinities in protease-inhibitor(drug) and protease-substrate complexes will allow increasingly accurate inferences to be made about the basis of HIV protease drug resistance. In project (iv), our objective is to compute the free energy profile of the translocation process of DNA along the vertical axis of a transmembrane protein pore buried in a lipid membrane bilayer. We use scalable codes LB3D, LAMMPS and NAMD which have been extensively benchmarked and used in our previous work on the TeraGrid. The codes LB3D and NAMD have been used in our award winning simulations of the TeraGyroid and SPICE projects. We intend to use grid middleware, called the Application Hosting Environment (AHE), which provides easy, uniform access to distributed computational resources, including the TeraGrid. The AHE has proved to be a powerful tool; it is currently being used by scientists to manage their simulations and workflows on the TeraGrid. AHE capabilities can be further exploited if used in conjunction with roaming access on the TeraGrid. In this proposal, in the first section, we present a precis for the Principal Investigator and for the Co-Investigators as well as the main research topics we wish to investigate. In the next section of this proposal, we describe the background for our research and provide details of previous research using TeraGrid resources. We then briefly describe AHE and how it enables scientists to utilize grid resources. In the penultimate section of this proposal we described the specifics of the scientific issues and simulations that we wish to perform with this MRAC allocation. In the final section of this proposal, we provide a summary of the TeraGrid resources requested in this MRAC proposal.

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。 我们打算研究材料和生物分子科学中的问题。在材料科学领域，我们计划通过使用大规模并行代码对非常大的系统模型进行模拟来定量研究复杂材料的涌现特性，由于计算资源的限制，迄今为止这是不可能的。这种大规模的模拟，使我们能够计算材料的性能，这是不可访问的模拟较小的模型，并定量评估有限尺寸效应的作用。在生物分子科学领域，我们的项目关注基于自由能计算的生物相关过程。在这里提出的项目中，我们建立在早期的工作，我们已经开发和验证了新的计算算法和网格计算基础设施，允许通过分子动力学模拟，这是迄今为止非常难以实现的物理时标。我们将专注于四个特定科学研究领域的项目- i）液晶材料的大规模格子玻尔兹曼模拟ii）粘土-聚合物纳米复合材料的材料特性iii）HIV-1蛋白酶的耐药性和iv）通过α-溶血素蛋白纳米孔的核酸移位。在项目（i）中，我们的目标是研究油/水表面活性剂体系介观立方相的流变学和形态学性质。特别是，我们计划检查的自组装螺旋状中间相的流变性能的缺陷的影响。在项目（ii）中，我们建议计算粘土-聚合物纳米复合体系的材料性质。我们将使用物理上真实大小的模型，并进行分子动力学模拟，以计算材料特性，包括弯曲模量，杨氏模量和泊松比，直接从这些模拟中观察到的起伏运动。项目（iii）的工作目标是研究成对互补突变对HIV-1蛋白酶活性和耐药性的影响。计算微分动力学和蛋白酶抑制剂（药物）和蛋白酶底物复合物的结合亲和力的差异，将允许越来越准确的推断，以作出有关的基础上，艾滋病毒蛋白酶耐药性。在项目（iv）中，我们的目标是计算DNA沿着包埋在脂膜双层中的跨膜蛋白孔的垂直轴移位过程的自由能分布。我们使用可扩展的代码LB 3D，LAMMPS和NAMD已被广泛的基准测试，并在我们以前的工作中使用的TeraGrid。代码LB 3D和NAMD已被用于我们获奖的TeraGyroid和SPICE项目的模拟。我们打算使用网格中间件，称为应用托管环境（AHE），它提供了对分布式计算资源（包括TeraGrid）的简单、统一的访问。AHE已被证明是一个强大的工具;科学家目前正在使用它来管理TeraGrid上的模拟和工作流程。如果与TeraGrid上的漫游访问结合使用，则可以进一步利用AHE功能。在本提案的第一部分，我们为主要研究者和合作研究者以及我们希望研究的主要研究主题提供了一份摘要。在本提案的下一节中，我们将描述我们研究的背景，并提供以前使用TeraGrid资源的研究的详细信息。然后，我们简要介绍AHE以及它如何使科学家利用网格资源。在本提案的倒数第二节中，我们描述了我们希望使用此MRAC分配执行的科学问题和模拟的具体情况。在本提案的最后一节中，我们提供了本MRAC提案中请求的TeraGrid资源的摘要。