SI2-SSI: Collaborative Research: Scalable Infrastructure for Enabling Multiscale and Multiphysics Applications in Fluid Dynamics, Solid Mechanics, and Fluid-Structure Interaction

SI2-SSI：协作研究：可扩展基础设施，支持流体动力学、固体力学和流固耦合中的多尺度和多物理场应用

• 批准号: 1450327
• 负责人: Boyce Griffith
• 金额: $ 92.44万
• 依托单位: University of North Carolina at Chapel Hill
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1450327&HistoricalAwards=false
• 关键词: SI2; SSI; Collaborative; Research; Scalable

Many biological and biomedical systems involve the interaction of a flexible structure and a fluid. These systems range from the writhing and coiling of DNA, to the beating and pumping of cilia and flagella, to the flow of blood in the body, to the locomotion of fish, insects, and birds. This project aims to develop advanced software infrastructure for performing dynamic computer simulations of such biological and biomedical systems. To facilitate the deployment of this software in a range of scientific and engineering applications, this project will develop new software capabilities in concert with new computer models that use the software. Specific application domains to be advanced in this project include models of aquatic locomotion that can be used to understand the neural control of movement and ultimately to develop new treatments for neurological pathologies such as spinal cord injuries, and models that simulate the interaction between the electrophysiology of the heart and the contractions of the heart that pump blood throughout the body, which could lead to improved approaches to treating heart disease. The software to be developed within the project is freely available online and is used by a number of independent research groups in a variety of scientific and engineering domains. It is being actively used in projects that model different aspects of cardiovascular dynamics, such as platelet aggregation and the dynamics of natural and prosthetic heart valves, and in projects that study other biological problems, including cancer dynamics, insect flight, aquatic locomotion, and the dynamics of phytoplankton. The software is also being applied to non-biological problems, including nanoscale models of colloidal suspensions and models of active particles. The improved methods and software to be developed in this project will thereby have a broad and sustained impact on a large number of ongoing research efforts in the biological and biomedical sciences and other scientific and engineering disciplines.The immersed boundary (IB) method is a broadly applicable framework for modeling and simulating fluid-structure interaction (FSI). The IB method was introduced to model the fluid dynamics of heart valves, and subsequent development initially focused on simulating cardiac fluid dynamics. This methodology is broadly useful, however, and has been applied to a variety of problems in which a fluid flow interacts with immersed structures, including elastic bodies, bodies with known or prescribed deformational kinematics, and rigid bodies. Extensions of the IB method have also been developed to model electrophysiological systems and systems with chemically active structures. To improve the efficiency of the IB method, the PI has developed adaptive versions of the IB method that employ structured adaptive mesh refinement (AMR) to deploy high spatial resolution only where needed. These methods have been implemented within the IBAMR software framework, which provides parallel implementations of the IB method and its extensions that leverage high-quality computational libraries including SAMRAI, PETSc, and libMesh. This project will further extend the IBAMR software by implementing modeling and discretization technologies required by the research applications of current and prospective users of the software, by developing improved solver infrastructure facilitated by the implementation of native support for structured AMR discretizations in the PETSc library, and by integrating with existing high-quality software tools for model development, deployment, and analysis. IBAMR is freely distributed online and is used within a number of independent research groups both to the further development of the IB method and also to its application to simulate diverse problems in fluid dynamics and FSI. By enhancing IBAMR, this project will also enhance the ability of these and other researchers to construct detailed models without requiring those researchers to develop the significant software infrastructure needed to perform such simulations. This project will also develop general-purpose support for AMR discretizations in PETSc, a software library with thousands of active users, ~400 downloads per month, and numerous applications. The work of this project will help to grow the IBAMR user community of students and researchers by developing UI tools for building models, running simulations, and analyzing results. Students will be actively engaged in all aspects of the project, including code, method, and model development.

许多生物和生物医学系统涉及柔性结构和流体的相互作用。这些系统包括DNA的扭动和盘绕，纤毛和鞭毛的跳动和泵送，体内血液的流动，鱼类，昆虫和鸟类的运动。该项目旨在开发先进的软件基础设施，用于对此类生物和生物医学系统进行动态计算机模拟。为了促进在一系列科学和工程应用中部署这一软件，该项目将开发新的软件功能，以配合使用该软件的新计算机模型。在这个项目中要推进的具体应用领域包括水生运动模型，可用于理解运动的神经控制，并最终开发神经病理学（如脊髓损伤）的新治疗方法，以及模拟心脏电生理学和心脏收缩之间相互作用的模型，心脏收缩将血液泵入全身，这可能会改善治疗心脏病的方法。在该项目内开发的软件可在网上免费获得，并由许多科学和工程领域的独立研究小组使用。它正被积极用于模拟心血管动力学不同方面的项目，如血小板聚集和天然和人工心脏瓣膜的动力学，以及研究其他生物学问题的项目，包括癌症动力学，昆虫飞行，水生运动和浮游植物动力学。该软件也被应用于非生物问题，包括胶体悬浮液的纳米级模型和活性颗粒模型。在这个项目中开发的改进的方法和软件，从而将有一个广泛的和持续的影响，大量的正在进行的研究工作，在生物和生物医学科学和其他科学和工程disciplines.The沉浸边界（IB）方法是一个广泛适用的框架，建模和模拟流体-结构相互作用（FSI）。IB方法被引入来模拟心脏瓣膜的流体动力学，随后的开发最初集中在模拟心脏流体动力学。然而，这种方法是广泛有用的，并且已经应用于流体流与浸没结构相互作用的各种问题，包括弹性体、具有已知或规定的变形运动学的体和刚体。IB方法的扩展也被开发用于模拟电生理系统和具有化学活性结构的系统。为了提高IB方法的效率，PI开发了IB方法的自适应版本，该版本采用结构化自适应网格细化（AMR），仅在需要的地方部署高空间分辨率。这些方法已经在IBAMR软件框架内实现，该框架提供了IB方法及其扩展的并行实现，这些扩展利用了高质量的计算库，包括SAMRAI，PETSc和libMesh。该项目将进一步扩展IBAMR软件，通过实施该软件当前和潜在用户的研究应用所需的建模和离散化技术，通过开发改进的求解器基础设施，通过在PETSc库中实施对结构化AMR离散化的本地支持，以及通过与现有的高质量软件工具集成进行模型开发，部署和分析。IBAMR在网上免费发布，并在许多独立的研究小组中使用，以进一步开发IB方法，并将其应用于模拟流体动力学和FSI中的各种问题。通过增强IBAMR，该项目还将提高这些研究人员和其他研究人员构建详细模型的能力，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。该项目还将开发对PETSc中AMR离散化的通用支持，PETSc是一个拥有数千名活跃用户的软件库，每月约400次下载，以及众多应用程序。该项目的工作将有助于通过开发用于构建模型，运行模拟和分析结果的UI工具来发展IBAMR用户社区的学生和研究人员。学生将积极参与项目的各个方面，包括代码，方法和模型开发。

项目成果

An immersed interface-lattice Boltzmann method for fluid-structure interaction

• DOI: 10.1016/j.jcp.2020.109807
• 发表时间: 2020-03
• 期刊: ArXiv
• 作者: J. Qin;E. M. Kolahdouz;Boyce E. Griffith

The smooth forcing extension method: A high-order technique for solving elliptic equations on complex domains

平滑力扩展法：求解复杂域上椭圆方程的高阶技术

• DOI: 10.1016/j.jcp.2021.110390
• 发表时间: 2021
• 期刊: Journal of Computational Physics
• 影响因子: 4.1
• 作者: Qadeer, Saad;Griffith, Boyce E.
• 通讯作者: Griffith, Boyce E.

A sharp interface Lagrangian-Eulerian method for rigid-body fluid-structure interaction

• DOI: 10.1016/j.jcp.2021.110442
• 发表时间: 2020-03
• 期刊: Journal of computational physics
• 影响因子: 4.1
• 作者: E. M. Kolahdouz;A. Bhalla;L. Scotten;B. Craven;Boyce E. Griffith

A one-sided direct forcing immersed boundary method using moving least squares

• DOI: 10.1016/j.jcp.2021.110359
• 发表时间: 2021-04
• 期刊: J. Comput. Phys.
• 作者: Rahul Bale;A. Bhalla;Boyce E. Griffith;M. Tsubokura

Transition in swimming direction in a model self-propelled inertial swimmer

• DOI: 10.1103/physrevfluids.4.021101
• 发表时间: 2018-01
• 期刊: Physical Review Fluids
• 影响因子: 2.7
• 作者: Thomas Dombrowski;Shannon K. Jones;G. Katsikis;A. Bhalla;Boyce E. Griffith;D. Klotsa