SI2-SSE: Parallel and Adaptive Simulation Infrastructure for Biological Fluid-Structure Interaction

SI2-SSE：生物流固耦合的并行自适应仿真基础设施

• 批准号: 1047734
• 负责人: Boyce Griffith
• 金额: $ 50万
• 依托单位: New York University Medical Center
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2014-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1047734&HistoricalAwards=false
• 关键词: SI2; SSE; Parallel; Adaptive; Simulation

The immersed boundary (IB) method is both a mathematical formulation and a numerical approach to problems of fluid-structure interaction, treating the specific case in which an elastic structure is immersed in a viscous incompressible fluid. The IB method was introduced to describe the fluid dynamics of heart valves, but this methodology has also been applied to a wide range of problems in biological and non-biological fluid dynamics. The IB method typically requires high spatial resolution to resolve the viscous boundary layers at fluid-structure interfaces and, at higher Reynolds numbers, to resolve vortices shed from such interfaces. To improve the efficiency of the IB method, the principal investigator has developed an adaptive version of the IB method that employs block-structured adaptive mesh refinement (AMR) to deploy high spatial resolution only where it is needed. IBAMR software is a distributed-memory parallel implementation of this adaptive scheme. The key goal of this project is to make IBAMR the unifying software framework for users of the IB method, thereby establishing a community of researchers who employ a common software infrastructure for biofluids model development and simulation. The project aims to enhance IBAMR substantially by (1) developing and implementing implicit IB schemes that will allow for the efficient use of large numerical timesteps; (2) developing and implementing extensions of the basic IB methodology, including a new variable-viscosity version of the IB method, and an existing stochastic version for microscale and nanoscale problems in which Brownian motion is important; (3) optimizing IBAMR for use with modern as well as projected-future high performance computing systems comprised of multi-core compute nodes interconnected by a high-speed network; and (4) developing front-end tools for model construction, validation, and execution, thereby facilitating the adoption and use of IBAMR, especially by students and researchers with limited computational experience.From the writhing and coiling of DNA, to the beating and pumping motions of cilia and flagella, to the flow of blood in the heart and throughout the circulation, coupled fluid-structure systems are ubiquitous in biology and physiology. This project aims to enhance significantly the IBAMR software developed by the principal investigator. IBAMR is a framework for performing computer simulations of biological fluid mechanics, and this project seeks to establish IBAMR as a unifying software infrastructure that will serve as a common "language" for developing and exchanging such models. IBAMR is already being actively used within several independent research projects that aim to model different aspects of cardiovascular dynamics, such as platelet aggregation and the fluid dynamics of natural and prosthetic heart valves. Such simulations promise ultimately to improve the efficacy of devices and procedures for treating cardiovascular disease. This software also is being used within projects that study other problems in biofluid mechanics, including insect flight, aquatic locomotion, and the dynamics of phytoplankton. By enhancing IBAMR, this project will also enhance significantly the ability of these and other research groups to construct detailed biofluids models without requiring those researchers to develop the significant software infrastructure needed to perform such simulations. This project will enhance the IBAMR software substantially, extending the range of problems to which it may be applied, and improving the methods implemented within the software as well as the efficiency of the implementation. The work of this project will extend greatly the community of students and researchers who are able to use IBAMR to model biological fluid-structure interaction, in part by implementing graphical software tools for building IB models and running IB simulations.

浸没边界（IB）方法是流体-结构相互作用问题的数学公式和数值方法，处理弹性结构浸没在粘性不可压缩流体中的特定情况。 IB方法被引入来描述心脏瓣膜的流体动力学，但是这种方法也被应用于生物和非生物流体动力学中的广泛问题。 IB方法通常需要高空间分辨率来解析流体-结构界面处的粘性边界层，并且在较高雷诺数下，解析从此类界面脱落的涡流。 为了提高IB方法的效率，主要研究者开发了一种自适应版本的IB方法，该方法采用块结构自适应网格细化（AMR），仅在需要的地方部署高空间分辨率。 IBAMR软件是这种自适应方案的分布式存储器并行实现。 该项目的主要目标是使IBAMR成为IB方法用户的统一软件框架，从而建立一个采用通用软件基础设施进行生物流体模型开发和模拟的研究人员社区。 该项目旨在通过以下方式大大增强IBAMR：（1）开发和实施隐式IB方案，以便有效地使用大数值时间步长;（2）开发和实施基本IB方法的扩展，包括IB方法的新变粘度版本，以及布朗运动重要的微尺度和纳米尺度问题的现有随机版本;（3）优化IBAMR以用于现代以及预计未来的高性能计算系统，该高性能计算系统包括通过高速网络互连的多核计算节点;以及（4）开发用于模型构建、验证和执行的前端工具，从而促进IBAMR的采用和使用，尤其是那些计算经验有限的学生和研究人员。从DNA的扭动和盘绕，到纤毛和鞭毛的跳动和泵送运动，再到心脏和整个循环中的血液流动，耦合的流体-结构系统在生物学和生理学中普遍存在。 该项目旨在大大增强首席研究员开发的IBAMR软件。 IBAMR是一个用于进行生物流体力学计算机模拟的框架，该项目旨在将IBAMR建立为一个统一的软件基础设施，作为开发和交换此类模型的通用“语言”。 IBAMR已经被积极用于几个独立的研究项目，旨在模拟心血管动力学的不同方面，如血小板聚集和天然和人工心脏瓣膜的流体动力学。 这种模拟最终有望提高治疗心血管疾病的设备和程序的功效。 该软件也被用于研究生物流体力学的其他问题，包括昆虫飞行，水生运动和浮游植物动力学。 通过增强IBAMR，该项目还将显著提高这些和其他研究小组构建详细生物流体模型的能力，而不需要这些研究人员开发执行此类模拟所需的重要软件基础设施。 该项目将大大增强IBAMR软件，扩大其可能适用的问题范围，并改进软件内实施的方法以及实施的效率。 该项目的工作将大大扩展能够使用IBAMR来模拟生物流体-结构相互作用的学生和研究人员的社区，部分是通过实施用于构建IB模型和运行IB模拟的图形软件工具。