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: 7956292
• 负责人: BRUCE BOGHOSIAN
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956292
• 关键词: Affinity; Award; Benchmarking; Binding; Biological Models; Biomedical Research; Blood flow; Brain; Code; Communities; Computational algorithm; Computer Retrieval of Information on Scientific Projects Database; Drug resistance; Environment; Epidermal Growth Factor Receptor; Equation; Four-dimensional; Funding; Grant; HIV-1 protease; High Performance Computing; Institution; Kinetics; Liquid substance; Malignant Neoplasms; Methodology; Modeling; Mutation; Ocular orbit; Operative Surgical Procedures; Patients; Pharmaceutical Preparations; Polymers; Process; Property; Proteins; RNA-Directed DNA Polymerase; Research; Research Infrastructure; Research Personnel; Resources; Science; Source; Spices; Testing; United States National Institutes of Health; Work; base; clay; clinically relevant; cluster computing; computing resources; hemodynamics; inhibitor/antagonist; liquid crystal; molecular dynamics; nanocomposite; novel; response; self assembly; simulation

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.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 在本LRAC请求中，我们建议研究湍流，血流动力学，材料研究和生物分子科学方面的问题。在材料科学领域，我们计划定量研究具有巨大科学和技术相关性的液晶材料和粘土聚合物纳米复合材料的新兴特性。这项工作将用于非常大的系统模型，使用大量并行代码，迄今由于计算资源限制而无法进行。在生物分子科学领域，我们的项目与基于药物结合亲和力计算的生物学相关过程有关。在此处提出的项目中，我们建立在较早的工作中，在该工作中，我们已经开发并验证了新颖的计算算法和网格计算基础架构，从而可以通过分子动力学模拟访问物理时间表，到目前为止，这些模拟非常困难。我们将重点介绍该提案中的六个特定项目：（i）在Navier-Stokes方程中识别不稳定的周期性轨道（UPOS）：这项工作的目的是使用新颖的四维空间可行的可行方法来识别不稳定的周期轨道来表征湍流。 （ii）患者特异性的全脑血流模拟模拟：我们的目标是提供有效的计算环境，以通过在临床上相关的时间范围内提供有关患者特异性血液动力学的信息，以帮助介入神经放射科。 （iii）液晶材料的大规模晶格 - 玻璃体模拟：在此项目中，我们将使用我们的尝试和测试的动力学劳累螺栓手方法来研究三元两亲性混合物中立方液晶的流变响应和自组装动力学。 （iv）粘土聚合物纳米复合材料的材料特性：这项工作的目的是使用前所未有的模型尺寸使用分子动力学模拟来计算粘土聚合物纳米复合材料的批量材料特性。 （v）HIV-1蛋白酶和逆转录酶中的耐药性：这项工作的目的是阐明和预测患者特异性突变在HIV-1蛋白酶中的影响以及逆转录酶对药物结合亲密关系的影响。这项工作将使用NAMD构建在我们先前在Teragrid上开发的新型模拟方法上进行。 （vi）使用高性能计算分子动力学预测EGFR激酶结构域对药物抑制剂的亲和力：该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质，表皮生长因子受体（EGFR）对药物结合亲和力的影响。这项工作将使用NAMD和新型集合分子动力学模拟进行。我们使用可扩展的代码hypo4d，lelelb，lb3d，lammps和nAMD，这些代码已在先前在Teragrid上的工作中进行了广泛的基准测试和使用，尤其是在Ranger上，我们在该核心上实现了高达32768个核心的可伸缩性。 《止血管法》已用于在天才项目中进行模拟研究，我们在Teragrid'08获得了“变革型科学挑战”奖。我们还获得了Hypo4D和LB3D代码的5K俱乐部奖项。我们将使用NAMD进行分子动力学研究，该研究是一种广泛使用的社区代码，并以前已用于香料项目的获奖模拟。