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。 我们建议研究材料和生物分子科学中的问题。在材料科学领域，我们计划通过用非常大的系统模型进行模拟，使用大规模并行代码来定量研究复杂材料的涌现特性，由于计算资源的限制，到目前为止这是不可能的。这样的大规模模拟使我们能够计算材料的性质，这是较小模型的模拟所不能获得的，并可以定量地评估有限尺寸效应的作用。在生物分子科学领域，我们的项目关注于了解基于自由能计算的生物相关过程。在这里提出的项目中，我们建立在早期工作的基础上，我们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访问物理时间尺度，这到目前为止很难实现。我们将集中在四个具体的科学研究领域-i)液晶材料的大规模格子Boltzmann模拟II)粘土-聚合物纳米复合材料的材料特性III)HIV-1蛋白酶的抗药性和iv)通过α-溶血素蛋白纳米孔的核酸易位。在项目(I)中，我们的目标是研究油/水表面活性剂体系的介观立方相的流变性和形态性质。特别是，我们计划研究缺陷对自组装回旋体中间相流变性的影响。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执行分子动力学模拟，以便直接从这些模拟中观察到的紧急起伏运动中计算材料的性质，包括弯曲模数、杨氏模数和泊松比。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。计算酶-抑制剂(药物)和酶-底物复合体中的差异动力学和结合亲和力的差异将使人们能够对HIV蛋白酶耐药性的基础做出越来越准确的推断。在项目(IV)中，我们的目标是计算DNA沿埋在脂膜双层中的跨膜蛋白质孔的垂直轴的转位过程的自由能分布。我们使用可伸缩代码LB3D、LAMMPS和NAMD，这些代码已经过广泛的基准测试，并在我们之前的TeraGrid工作中使用。LB3D和NAMD代码已经用于我们获奖的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)，它提供对包括TeraGrid在内的分布式计算资源的简单、统一的访问。AHE已被证明是一个强大的工具；它目前正被科学家用来管理他们在TeraGrid上的模拟和工作流程。如果与TeraGrid上的漫游访问结合使用，可以进一步利用AHE功能。在这项提案中，在第一节中，我们介绍了首席调查员和联合调查员的概要以及我们希望调查的主要研究主题。在本提案的下一部分中，我们将介绍我们研究的背景，并使用TeraGrid资源提供以前研究的详细信息。然后，我们简要描述AHE以及它如何使科学家能够利用网格资源。在这项提案的倒数第二部分中，我们描述了我们希望利用这一MRAC分配执行的科学问题和模拟的细节。在本提案的最后一节中，我们提供了此MRAC提案所请求的TeraGrid资源的摘要。

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.