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.

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。 在这个LRAC的要求，我们建议调查湍流，血液动力学，材料研究和生物分子科学的问题。在材料科学领域，我们计划定量研究液晶材料和粘土-聚合物纳米复合材料的涌现特性，这具有巨大的科学和技术相关性。这项工作将进行非常大的系统模型，使用大规模并行代码，迄今为止不可能由于计算资源的限制。在生物分子科学领域，我们的项目关注基于药物结合亲和力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。我们将集中在六个具体的项目在这个建议：（一）确定不稳定的周期轨道（UPO）的Navier-Stokes方程：这项工作的目标是确定不稳定的周期轨道的湍流特性使用一种新的四维时空并行的方法。(ii)患者特定的全脑血流模拟：我们在这个项目中的目标是提供一个有效的计算环境，以协助介入神经放射科医生在神经血管手术中提供有关患者特定的血流动力学在临床相关的时间范围内的信息。(iii)液晶材料的大规模格子玻尔兹曼模拟：在这个项目中，我们将使用我们久经考验的动力学格子玻尔兹曼方法研究三元两亲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计算粘土-聚合物纳米复合材料的体材料特性。(v)HIV-1蛋白酶和逆转录酶的耐药性：这项工作的目的是阐明和预测HIV-1蛋白酶和逆转录酶的患者特异性突变对药物结合亲和力的影响。这项工作将进行使用NAMD建立在我们以前的TeraGrid工作中开发的新的模拟方法。(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：这项工作的目的是阐明和预测癌症特异性蛋白表皮生长因子受体（EGFR）中患者特异性突变对药物结合亲和力的影响。这项工作将进行NAMD和新的合奏分子动力学模拟。我们使用可扩展代码HYPO 4D，HemeLB，LB 3D，LAMMPS和NAMD，这些代码已经在我们以前的TeraGrid工作中进行了广泛的基准测试和使用，特别是在Ranger上，我们已经实现了高达32768个核心的可扩展性。HemeLB代码已被用于在GENIUS项目中进行模拟研究，为此，我们在TeraGrid'08上获得了“转型科学挑战”奖。我们还获得了HYPO 4D和LB 3D代码的5 K俱乐部奖。我们将使用NAMD进行分子动力学研究，这是一种广泛使用的社区代码，以前曾用于SPICE项目的获奖模拟。