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.
