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

浸入边界 (IB) 方法既是解决流固耦合问题的数学公式，也是一种数值方法，处理弹性结构浸入粘性不可压缩流体中的具体情况。 IB 方法被引入来描述心脏瓣膜的流体动力学，但该方法也已应用于生物和非生物流体动力学的广泛问题。 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，并在较高的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 IB 方法的自适应版本，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内存并行实现。 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，从而建立一个研究人员社区，他们采用通用软件基础设施进行生物流体模型开发和模拟。 该项目旨在通过以下方式大幅增强 IBAMR：(1) 开发和实施隐式 IB 方案，该方案将允许有效使用大型数值时间步长； (2) 开发和实施基本 IB 方法的扩展，包括 IB 方法的新的可变粘度版本，以及用于布朗运动很重要的微米级和纳米级问题的现有随机版本； (3) 优化 IBAMR，使其与现代以及预计未来的高性能计算系统一起使用，该系统由通过高速网络互连的多核计算节点组成； (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，特别是计算经验有限的学生和研究人员。从 DNA 的扭动和卷曲，到纤毛和鞭毛的跳动和泵动，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无处不在。 该项目旨在显着增强首席研究员开发的 IBAMR 软件。 IBAMR 是一个用于执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 已在多个独立研究项目中得到积极使用，这些项目旨在模拟心血管动力学的不同方面，例如血小板聚集以及天然和人工心脏瓣膜的流体动力学。 此类模拟最终有望提高治疗心血管疾病的设备和程序的功效。 该软件还被用于研究生物流体力学其他问题的项目中，包括昆虫飞行、水生运动和浮游植物动力学。 通过增强 IBAMR，该项目还将显着增强这些研究小组和其他研究小组构建详细生物流体模型的能力，而无需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。 该项目将极大地增强IBAMR软件，扩大其可应用的问题范围，并改进软件内实施的方法以及实施的效率。 该项目的工作将极大地扩展学生和研究人员的社区，他们能够使用 IBAMR 来模拟生物流体-结构相互作用，部分是通过实施图形软件工具来构建 IB 模型和运行 IB 模拟。

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.