LATTICE-BOLTZMANN STUDIES OF TURBULENCE, BLOOD FLOW AND LIQUID CRYSTALS, AND MO

湍流、血流和液晶以及 MO 的格子-玻尔兹曼研究

• 批准号: 8171742
• 负责人: BRUCE BOGHOSIAN
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8171742
• 关键词: LATTICE; BOLTZMANN; STUDIES; TURBULENCE; BLOOD

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 LRAC request, we propose to investigate problems in turbulence, haemodynamics, materials research and the biomolecular science. In the materials science domain, we plan to quantitatively study the emergent properties of liquid crystalline materials and of clay-polymer nanocomposites which have immense scientific and technological relevance. This work will be carried for very large system models, using massively parallel codes, hitherto not possible due to computational resource limitations. In the biomolecular sciences domain, our projects are concerned with understanding biologically relevant processes based on drug binding affinity 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 six specific projects in this proposal: (i) Identification of Unstable Periodic Orbits (UPOs) in the Navier-Stokes equations: The objective of this work is to identify Unstable Periodic Orbits for the characterisation of turbulent flows using a novel four- dimensional spacetime parallelisable approach. (ii) Patient-specific whole brain blood flow simulations: Our objective in this project is to provide an efficient computational environment to assist interventional neuroradiologists in neurovascular surgery by providing information on patient-specific haemodynamics within clinically relevant timeframes. (iii) Large-scale lattice-Boltzmann simulations of liquid crystalline materials: In this project we will study the rheological response and self-assembly dynamics of cubic liquid crystals in ternary amphiphilic mixtures using our tried and tested kinetic lattice-Boltzmann approach. (iv) Materials properties of clay-polymer nanocomposites: The objective of this work is to calculate the bulk materials properties of clay-polymer nanocomposites using molecular dynamics simulations using unprecedented model sizes. (v) Drug resistance in HIV-1 proteases and reverse transcriptases: The objective of this work is to elucidate and predict the effect of patient-specific mutations in HIV-1 Proteases and Reverse Transcriptases on drug-binding affinities. This work will be carried using NAMD building on novel simulation methodologies developed in our previous work on the TeraGrid. (vi) Predicting affinity of EGFR kinase domain for drug inhibitors using high performance computing molecular dynamics: The objective this work is to elucidate and predict the effect of patient-specific mutations in the cancer-specific protein, epidermal growth factor receptor (EGFR) on drug-binding affinities. This work will be carried using NAMD and novel ensemble molecular dynamics simulations. We use scalable codes HYPO4D, HemeLB, LB3D, LAMMPS and NAMD which have been extensively benchmarked and used in our previous work on the TeraGrid, particularly on Ranger, where we have achieved scalability on up to 32768 cores. The HemeLB code has been used to conduct simulation studies within the GENIUS project for which we received the "Transformational Science Challenge" award at TeraGrid'08. We have also received 5K Club awards for the HYPO4D and LB3D codes. We will use NAMD for our molecular dynamics studies which is a widely used community-code and has been previously used in award winning simulations of the SPICE project.

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 LRAC 请求中，我们建议调查湍流问题， 血液动力学、材料研究和生物分子科学。在材料上 科学领域，我们计划定量研究液体的涌现性质 结晶材料和粘土聚合物纳米复合材料具有巨大的 科学和技术相关性。这项工作将针对非常大的系统进行 使用大规模并行代码的模型，由于计算的原因迄今为止是不可能的 资源限制。在生物分子科学领域，我们的项目涉及 基于药物结合亲和力了解生物学相关过程 计算。在这里提出的项目中，我们以早期工作为基础 开发并验证了新颖的计算算法和网格计算 基础设施，允许通过分子动力学访问物理时间尺度 模拟，迄今为止很难实现。我们要重点抓好六方面工作 本提案中的具体项目： (i) 不稳定周期轨道（UPO）的识别 在纳维-斯托克斯方程中：这项工作的目的是确定不稳定 使用新颖的四周期轨道来表征湍流 维度时空可并行方法。 (ii) 患者特异性全脑血 流动模拟：我们在这个项目中的目标是提供有效的计算 协助介入神经放射科医生进行神经血管手术的环境 提供临床相关的患者特异性血流动力学信息 时间范围。 (iii) 液晶的大规模晶格玻尔兹曼模拟 材料：在这个项目中，我们将研究流变响应和自组装 使用我们的尝试和方法，研究了三元两亲混合物中立方液晶的动力学 测试了动力学格子玻尔兹曼方法。 (iv) 粘土聚合物的材料特性 纳米复合材料：这项工作的目的是计算散装材料 使用分子动力学模拟研究粘土-聚合物纳米复合材料的性能 使用前所未有的模型尺寸。 (v) HIV-1蛋白酶的耐药性和 逆转录酶：这项工作的目的是阐明和预测 HIV-1 蛋白酶和逆转录酶中患者特异性突变的影响 药物结合亲和力。这项工作将使用基于小说的 NAMD 进行 我们之前在 TeraGrid 上的工作中开发了仿真方法。 (六) 使用高性能预测 EGFR 激酶结构域对药物抑制剂的亲和力 计算分子动力学：这项工作的目的是阐明和预测 患者特异性突变对癌症特异性蛋白、表皮生长的影响 因子受体（EGFR）对药物结合亲和力的影响。这项工作将使用 NAMD 进行 和新颖的系综分子动力学模拟。我们使用可扩展代码HYPO4D， HemeLB、LB3D、LAMMPS 和 NAMD 已经过广泛的基准测试和 在我们之前关于 TeraGrid 的工作中使用过，特别是在 Ranger 上，我们有 实现了多达 32768 个内核的可扩展性。 HemeLB 代码已用于 在 GENIUS 项目中进行模拟研究，我们为此获得了 TeraGrid'08 的“变革性科学挑战”奖。我们还收到了 HYPO4D 和 LB3D 代码获得 5K 俱乐部奖项。我们将使用 NAMD 作为我们的分子 动力学研究是一种广泛使用的社区代码，之前已被 用于 SPICE 项目的获奖模拟。