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: 1450339
• 负责人: Matthew Knepley
• 金额: $ 26.27万
• 依托单位: University of Chicago
• 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 2016-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1450339&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。这些系统的范围从DNA的扭动和盘绕，到纤毛和鞭毛的跳动和泵动，到体内血液的流动，到鱼、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。为了促进该软件在一系列科学和工程应用中的部署，该项目将开发新的软件功能，与使用该软件的新计算机模型相结合。该项目要推进的具体应用领域包括水中运动模型，可用于理解运动的神经控制，并最终开发针对脊髓损伤等神经病理学的新治疗方法，以及模拟神经电生理学之间相互作用的模型。心脏和将血液泵送到全身的心脏收缩，这可能会导致治疗心脏病的方法得到改进。该项目中要开发的软件可在线免费获取，并由多个科学和工程领域的许多独立研究小组使用。它被积极用于模拟心血管动力学不同方面的项目，例如血小板聚集以及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的动态。该软件还应用于非生物问题，包括胶体悬浮液的纳米级模型和活性颗粒模型。因此，该项目中要开发的改进方法和软件将对生物和生物医学科学以及其他科学和工程学科中正在进行的大量研究工作产生广泛和持续的影响。浸入边界（IB）方法是一种广泛的方法用于建模和模拟流固耦合 (FSI) 的适用框架。 IB方法被引入来模拟心脏瓣膜的流体动力学，随后的发展最初集中在模拟心脏流体动力学。然而，这种方法具有广泛的用途，并且已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物体以及刚体。 IB 方法的扩展也已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，该方法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。这些方法已在 IBAMR 软件框架内实现，该框架提供 IB 方法及其扩展的并行实现，利用高质量计算库（包括 SAMRAI、PETSc 和 libMesh）。该项目将通过实施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，通过在 PETSc 库中实现对结构化 AMR 离散化的本机支持来开发改进的求解器基础设施，从而进一步扩展 IBAMR 软件，以及通过与现有的高质量软件工具集成来进行模型开发、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，该项目还将增强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、每月约 400 次下载和众多应用程序的软件库。该项目的工作将通过开发用于构建模型、运行模拟和分析结果的 UI 工具，帮助扩大由学生和研究人员组成的 IBAMR 用户社区。学生将积极参与该项目的各个方面，包括代码、方法和模型开发。